Query psy15118
Match_columns 132
No_of_seqs 120 out of 619
Neff 5.5
Searched_HMMs 46136
Date Fri Aug 16 21:02:56 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15118.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15118hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00018 histone H3; Provision 100.0 2.6E-51 5.5E-56 305.4 9.8 123 1-123 1-123 (136)
2 PLN00121 histone H3; Provision 100.0 4.7E-51 1E-55 304.0 10.4 122 1-122 1-122 (136)
3 PLN00161 histone H3; Provision 100.0 6.8E-50 1.5E-54 296.9 9.3 115 1-122 1-116 (135)
4 KOG1745|consensus 100.0 2.7E-46 5.8E-51 277.9 8.3 122 1-122 1-123 (137)
5 smart00428 H3 Histone H3. 100.0 2.6E-42 5.7E-47 247.6 8.0 88 35-122 2-91 (105)
6 PLN00160 histone H3; Provision 100.0 2.4E-42 5.2E-47 244.6 6.6 86 42-127 1-89 (97)
7 COG2036 HHT1 Histones H3 and H 99.8 1.8E-21 4E-26 136.6 6.2 78 44-126 1-78 (91)
8 PF00125 Histone: Core histone 99.7 9.5E-17 2.1E-21 106.7 5.3 67 59-125 2-68 (75)
9 cd07981 TAF12 TATA Binding Pro 98.8 1.2E-08 2.6E-13 68.4 5.8 52 73-124 8-59 (72)
10 PTZ00463 histone H2B; Provisio 98.5 7.8E-07 1.7E-11 65.1 7.4 59 64-122 26-84 (117)
11 PLN00158 histone H2B; Provisio 98.4 1E-06 2.3E-11 64.4 6.3 59 64-122 25-83 (116)
12 smart00427 H2B Histone H2B. 98.3 2.5E-06 5.4E-11 59.9 6.0 56 67-122 2-57 (89)
13 cd00076 H4 Histone H4, one of 98.0 1.1E-05 2.4E-10 56.0 4.5 60 62-126 13-72 (85)
14 smart00417 H4 Histone H4. 97.9 1.6E-05 3.5E-10 54.0 4.7 60 62-126 13-72 (74)
15 smart00803 TAF TATA box bindin 97.9 3.1E-05 6.7E-10 51.1 4.8 59 62-125 2-60 (65)
16 PLN00035 histone H4; Provision 97.9 2.6E-05 5.6E-10 56.1 4.6 59 63-126 30-88 (103)
17 PTZ00015 histone H4; Provision 97.8 2.9E-05 6.3E-10 55.7 4.8 61 62-127 30-90 (102)
18 KOG1744|consensus 97.8 3.4E-05 7.5E-10 57.3 4.7 62 63-124 34-95 (127)
19 PF00808 CBFD_NFYB_HMF: Histon 97.7 0.00011 2.3E-09 47.6 5.7 54 72-125 8-61 (65)
20 cd07979 TAF9 TATA Binding Prot 97.4 0.00041 8.8E-09 50.6 5.1 61 68-129 3-63 (117)
21 PF15630 CENP-S: Kinetochore c 97.3 0.00057 1.2E-08 46.6 5.2 61 65-125 4-66 (76)
22 KOG0870|consensus 97.2 0.00048 1.1E-08 53.3 3.9 65 60-126 8-72 (172)
23 PF15511 CENP-T: Centromere ki 97.0 0.0016 3.4E-08 56.4 5.8 53 70-122 355-412 (414)
24 smart00576 BTP Bromodomain tra 96.4 0.0091 2E-07 40.1 5.1 44 83-126 22-65 (77)
25 PF03847 TFIID_20kDa: Transcri 96.4 0.011 2.4E-07 39.4 5.4 53 73-125 6-58 (68)
26 PF02969 TAF: TATA box binding 95.9 0.028 6.1E-07 37.3 5.3 53 71-124 8-60 (66)
27 PF02291 TFIID-31kDa: Transcri 95.6 0.022 4.8E-07 42.3 4.6 61 69-130 15-75 (129)
28 KOG1142|consensus 94.9 0.068 1.5E-06 44.0 5.7 68 54-125 146-213 (258)
29 cd08050 TAF6 TATA Binding Prot 93.7 0.14 3.1E-06 43.1 5.3 51 71-122 4-54 (343)
30 KOG3467|consensus 91.6 0.29 6.3E-06 34.6 3.7 44 83-126 45-88 (103)
31 cd00074 H2A Histone 2A; H2A is 89.8 0.39 8.4E-06 35.1 3.2 64 60-127 18-81 (115)
32 PF07524 Bromo_TP: Bromodomain 88.0 1.1 2.3E-05 29.7 4.1 46 81-126 19-65 (77)
33 KOG3334|consensus 86.2 1.8 4E-05 33.0 5.0 59 69-128 16-74 (148)
34 cd08045 TAF4 TATA Binding Prot 85.7 2 4.4E-05 33.7 5.2 55 61-116 43-97 (212)
35 PF05236 TAF4: Transcription i 83.6 1.1 2.4E-05 36.3 3.0 58 60-118 41-98 (264)
36 KOG0871|consensus 83.4 2.2 4.7E-05 32.8 4.2 61 59-122 9-69 (156)
37 KOG0869|consensus 76.5 4.4 9.5E-05 31.4 4.0 68 62-132 32-99 (168)
38 PF02269 TFIID-18kDa: Transcri 74.8 3.9 8.4E-05 28.4 3.1 59 68-126 3-61 (93)
39 COG5150 Class 2 transcription 74.3 5.9 0.00013 29.9 4.1 61 59-122 8-68 (148)
40 KOG1658|consensus 63.8 7.2 0.00016 30.2 2.7 67 63-131 57-124 (162)
41 KOG2389|consensus 59.9 12 0.00027 32.2 3.7 48 83-130 45-92 (353)
42 PF10911 DUF2717: Protein of u 58.1 16 0.00035 25.0 3.4 60 49-111 2-64 (77)
43 KOG2549|consensus 56.8 23 0.00051 32.4 5.1 42 82-123 26-67 (576)
44 PF13581 HATPase_c_2: Histidin 51.8 41 0.0009 23.0 4.8 45 69-113 8-52 (125)
45 COG5248 TAF19 Transcription in 40.0 1.1E+02 0.0024 22.5 5.5 52 68-119 11-62 (126)
46 PRK14562 haloacid dehalogenase 38.8 22 0.00047 28.0 1.8 49 80-129 70-118 (204)
47 TIGR01924 rsbW_low_gc serine-p 38.6 62 0.0013 23.9 4.2 47 64-110 14-60 (159)
48 KOG1657|consensus 36.9 50 0.0011 26.8 3.7 65 57-122 66-130 (236)
49 cd07978 TAF13 The TATA Binding 34.1 1.6E+02 0.0035 20.4 5.9 52 68-119 4-56 (92)
50 PF09123 DUF1931: Domain of un 32.3 1.2E+02 0.0025 23.0 4.7 53 68-125 1-53 (138)
51 PF04604 L_biotic_typeA: Type- 30.9 43 0.00093 21.2 1.9 20 88-107 7-26 (51)
52 PF10083 DUF2321: Uncharacteri 28.5 56 0.0012 25.2 2.6 22 77-98 72-93 (158)
53 PRK04069 serine-protein kinase 27.2 1.3E+02 0.0029 22.0 4.4 47 64-110 14-60 (161)
54 PF07278 DUF1441: Protein of u 26.8 2.2E+02 0.0048 21.7 5.5 64 48-111 75-149 (152)
55 PHA02604 rI.-1 hypothetical pr 26.3 1.3E+02 0.0028 22.4 4.1 44 67-113 82-125 (126)
56 PF07105 DUF1367: Protein of u 25.7 1.2E+02 0.0025 24.3 3.9 16 91-106 91-106 (196)
57 COG2178 Predicted RNA-binding 25.0 78 0.0017 25.4 2.9 56 47-102 24-91 (204)
58 COG5304 Uncharacterized protei 24.6 51 0.0011 23.3 1.6 17 63-79 72-88 (92)
59 KOG4336|consensus 24.4 1.3E+02 0.0028 25.8 4.2 44 85-128 23-66 (323)
60 PF03172 Sp100: Sp100 domain; 24.0 1.1E+02 0.0024 22.0 3.2 48 53-113 40-87 (103)
61 KOG1969|consensus 22.8 1.8E+02 0.004 28.1 5.2 72 45-118 449-521 (877)
62 COG5094 TAF9 Transcription ini 22.5 1.8E+02 0.0038 22.0 4.2 37 85-121 32-68 (145)
63 PRK08487 DNA polymerase III su 22.2 1.9E+02 0.0041 23.8 4.8 60 70-129 139-199 (328)
64 COG5208 HAP5 CCAAT-binding fac 21.3 1.2E+02 0.0027 25.0 3.4 76 45-122 80-165 (286)
65 PRK06585 holA DNA polymerase I 20.0 1.5E+02 0.0033 24.1 3.8 50 81-130 158-210 (343)
No 1
>PTZ00018 histone H3; Provisional
Probab=100.00 E-value=2.6e-51 Score=305.38 Aligned_cols=123 Identities=91% Similarity=1.254 Sum_probs=117.6
Q ss_pred CCCccccccccCCCCCCcchhhhhhhccCCCCCCCCCCCcccCCCchhhHHHhhhhcccchhccccchhHHHHHHHhhhc
Q psy15118 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK 80 (132)
Q Consensus 1 MARtK~~a~k~~g~kaprk~~a~k~~~k~~~~~~~~kk~~r~rpg~~al~EIr~~Qkst~llI~k~pF~rlVreI~~~~~ 80 (132)
|||||+++++++|+++|+++.++++..++.+..++.++++||+||+++|+|||+||+||+|||||+||+||||||++++.
T Consensus 1 MaRtk~~~~k~~~~~~prk~~~~~~~~~~~~~~~~~~~~~r~rpGt~aLrEIr~yQkst~lLI~k~pF~RLVREI~~~~~ 80 (136)
T PTZ00018 1 MARTKQTARKSTGGKAPRKQLASKAARKSAPVTGGIKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK 80 (136)
T ss_pred CCCCCcCccCCCCCCCCcccccccccccCCCCCCCCCCCcccCCchhHHHHHHHHcccchhccccccHHHHHHHHHHHcC
Confidence 99999999999999999999988877777777778899999999999999999999999999999999999999999999
Q ss_pred ccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeeeh
Q psy15118 81 TDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASLV 123 (132)
Q Consensus 81 ~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~~ 123 (132)
.++|||++||+|||||+|+|||+||||+|+||+||||||||..
T Consensus 81 ~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~k 123 (136)
T PTZ00018 81 TDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPK 123 (136)
T ss_pred CcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchh
Confidence 9999999999999999999999999999999999999999983
No 2
>PLN00121 histone H3; Provisional
Probab=100.00 E-value=4.7e-51 Score=303.98 Aligned_cols=122 Identities=93% Similarity=1.273 Sum_probs=117.6
Q ss_pred CCCccccccccCCCCCCcchhhhhhhccCCCCCCCCCCCcccCCCchhhHHHhhhhcccchhccccchhHHHHHHHhhhc
Q psy15118 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK 80 (132)
Q Consensus 1 MARtK~~a~k~~g~kaprk~~a~k~~~k~~~~~~~~kk~~r~rpg~~al~EIr~~Qkst~llI~k~pF~rlVreI~~~~~ 80 (132)
|||||+++++++|+++|+++.++++..++.+..++.++++||+||+++|+|||+||+||++||||+||+||||||++++.
T Consensus 1 MaRtk~~~~k~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~r~rpGt~aLrEIr~yQkst~lLI~k~pF~RLVREI~~~~~ 80 (136)
T PLN00121 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFK 80 (136)
T ss_pred CCCCCcCccCCCCCCCCcccccccccccCCCCCCCCCCCcccCchhHHHHHHHHhccccccccccccHHHHHHHHHHHhC
Confidence 99999999999999999999988887777777788899999999999999999999999999999999999999999999
Q ss_pred ccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeee
Q psy15118 81 TDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASL 122 (132)
Q Consensus 81 ~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~ 122 (132)
+++|||++||+|||||+|+|||+||||+|+||+|+||||||.
T Consensus 81 ~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~ 122 (136)
T PLN00121 81 TDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMP 122 (136)
T ss_pred ccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecch
Confidence 999999999999999999999999999999999999999998
No 3
>PLN00161 histone H3; Provisional
Probab=100.00 E-value=6.8e-50 Score=296.92 Aligned_cols=115 Identities=59% Similarity=0.875 Sum_probs=106.4
Q ss_pred CCCccccccccCCCCCCcchhhhhhhccCCCCCCCCCCCcccCCCchhhHHHhhhhcccchhccccchhHHHHHHHhhhc
Q psy15118 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK 80 (132)
Q Consensus 1 MARtK~~a~k~~g~kaprk~~a~k~~~k~~~~~~~~kk~~r~rpg~~al~EIr~~Qkst~llI~k~pF~rlVreI~~~~~ 80 (132)
||||||+ +++++|+.|++....+ ...++.++++||+||+++|+|||+||+||++||||+||+||||||++++.
T Consensus 1 mar~k~~-~~~~~~~~~~~~~~~~------~~~~~~kk~~r~rpGtvaLrEIR~yQkst~lLIpklPF~RLVREI~~~~~ 73 (135)
T PLN00161 1 MARRLQG-KRFRKGKKPQKEASGV------TRQELDKKPHRYRPGTVALREIRKYQKSTELLIRKLPFARLVREISNEML 73 (135)
T ss_pred CCccccc-ccccCCCCCcccCCCC------CCCCCCCCCccCCCcchHHHHHHHHccccccccccccHHHHHHHHHHhcC
Confidence 9999999 7788999898887653 13456789999999999999999999999999999999999999999996
Q ss_pred -ccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeee
Q psy15118 81 -TDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASL 122 (132)
Q Consensus 81 -~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~ 122 (132)
.++|||++||+|||||+|+|||+||||+|+||+||||||||.
T Consensus 74 ~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~ 116 (135)
T PLN00161 74 REPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMP 116 (135)
T ss_pred CCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccch
Confidence 589999999999999999999999999999999999999998
No 4
>KOG1745|consensus
Probab=100.00 E-value=2.7e-46 Score=277.94 Aligned_cols=122 Identities=89% Similarity=1.222 Sum_probs=115.4
Q ss_pred CCCccccccccCCCCCCcchhhhhhhccCC-CCCCCCCCCcccCCCchhhHHHhhhhcccchhccccchhHHHHHHHhhh
Q psy15118 1 MARTKQTARKSTGGKAPRKQLATKAARKSA-PATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDF 79 (132)
Q Consensus 1 MARtK~~a~k~~g~kaprk~~a~k~~~k~~-~~~~~~kk~~r~rpg~~al~EIr~~Qkst~llI~k~pF~rlVreI~~~~ 79 (132)
|+|++++++++.++++|++..+.+...+++ +..+...++++|+||+++++|||+||++|||||+|+||+||||||.++|
T Consensus 1 m~r~~~t~~k~~~~~~~r~~~a~~~~~~~~~~~~~~~~k~~r~rpg~~al~eirkyQkstdLlI~K~PFqRlvrei~q~f 80 (137)
T KOG1745|consen 1 MARTKQTARKSTGGKAPRKQLAGKAARKSAAPRTGRVKKPHRYRPGTVALREIRKYQKSTDLLIRKLPFQRLVREIAQDF 80 (137)
T ss_pred CCCCCcccccccCCCCCccccccccccccccccccccCccccccCchHHHHHHHHHHhhhHHHhhcCcHHHHhHHHHhcc
Confidence 899999999999999999999988877663 3455668899999999999999999999999999999999999999999
Q ss_pred cccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeee
Q psy15118 80 KTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASL 122 (132)
Q Consensus 80 ~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~ 122 (132)
.+|+|||+.||.|||||+|+|||+||||+|+||+||||||||-
T Consensus 81 ~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimp 123 (137)
T KOG1745|consen 81 KTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMP 123 (137)
T ss_pred cccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecc
Confidence 9999999999999999999999999999999999999999997
No 5
>smart00428 H3 Histone H3.
Probab=100.00 E-value=2.6e-42 Score=247.59 Aligned_cols=88 Identities=80% Similarity=1.112 Sum_probs=85.3
Q ss_pred CCCCCcccCCCchhhHHHhhhhcccchhccccchhHHHHHHHhhhcc--cccccHHHHHHHHHHHHHHHHHhhhhhhHhh
Q psy15118 35 GVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT--DLRFQSSAVMALQEASEAYLVGLFEDTNLCA 112 (132)
Q Consensus 35 ~~kk~~r~rpg~~al~EIr~~Qkst~llI~k~pF~rlVreI~~~~~~--~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a 112 (132)
+.++++||+||+++|+|||+||+||++||||+||+||||||++++.+ ++|||++|++||||++|+|||++|||||+||
T Consensus 2 ~~~~~~r~rpg~~aLrEIr~yQkst~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a 81 (105)
T smart00428 2 GKTKHRRYRPGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLA 81 (105)
T ss_pred CCCCCcCCCCcchHHHHHHHHccCcccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45788999999999999999999999999999999999999999976 9999999999999999999999999999999
Q ss_pred hccCcceeee
Q psy15118 113 IHAKRMIASL 122 (132)
Q Consensus 113 ~HakRvTi~~ 122 (132)
+|||||||+.
T Consensus 82 ~HAkRvTl~~ 91 (105)
T smart00428 82 IHAKRVTIMP 91 (105)
T ss_pred HHhCCccCcH
Confidence 9999999988
No 6
>PLN00160 histone H3; Provisional
Probab=100.00 E-value=2.4e-42 Score=244.61 Aligned_cols=86 Identities=60% Similarity=0.925 Sum_probs=81.1
Q ss_pred cCCCchhhHHHhhhhcccchhccccchhHHHHHHHhhhc-ccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCccee
Q psy15118 42 YRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK-TDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIA 120 (132)
Q Consensus 42 ~rpg~~al~EIr~~Qkst~llI~k~pF~rlVreI~~~~~-~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi 120 (132)
+|||+++|+|||+||+||++||||+||+||||||++++. +++|||++||+|||||+|+|||++|||+|+||+|||||||
T Consensus 1 ~rpGt~aLrEIR~yQkst~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl 80 (97)
T PLN00160 1 MRPGEKALKEIKMYQKSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTI 80 (97)
T ss_pred CCCccHHHHHHHHHccchhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhccccc
Confidence 689999999999999999999999999999999999985 5699999999999999999999999999999999999999
Q ss_pred ee--hhhcc
Q psy15118 121 SL--VSLVG 127 (132)
Q Consensus 121 ~~--~~~~~ 127 (132)
|. +.|+.
T Consensus 81 ~~kD~~L~~ 89 (97)
T PLN00160 81 MPKDMQLAR 89 (97)
T ss_pred chhhHHHHH
Confidence 98 44443
No 7
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.85 E-value=1.8e-21 Score=136.60 Aligned_cols=78 Identities=46% Similarity=0.655 Sum_probs=73.5
Q ss_pred CCchhhHHHhhhhcccchhccccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeeeh
Q psy15118 44 PGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASLV 123 (132)
Q Consensus 44 pg~~al~EIr~~Qkst~llI~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~~ 123 (132)
||...++|||+||++++++||++||.|++|+...+ ||+.+|+++||++.|.|++.++|+|+.||.|++|+||+..
T Consensus 1 ~~~~~~~~~r~~~~~~~~~Lp~apv~Ri~r~~~~~-----Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~ 75 (91)
T COG2036 1 PGAVGLKEIRRYQRSTDLLLPKAPVRRILRKAGAE-----RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAE 75 (91)
T ss_pred CCcchHHHHHhhhhhhhhhcCchHHHHHHHHHhHH-----HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHH
Confidence 57889999999999999999999999999999875 9999999999999999999999999999999999999985
Q ss_pred hhc
Q psy15118 124 SLV 126 (132)
Q Consensus 124 ~~~ 126 (132)
|..
T Consensus 76 DI~ 78 (91)
T COG2036 76 DIK 78 (91)
T ss_pred HHH
Confidence 543
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=99.67 E-value=9.5e-17 Score=106.71 Aligned_cols=67 Identities=39% Similarity=0.535 Sum_probs=62.9
Q ss_pred cchhccccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeeehhh
Q psy15118 59 TELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASLVSL 125 (132)
Q Consensus 59 t~llI~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~~~~ 125 (132)
++++||+.||.|+++||..++..+++|+.+|+.+||+++|+|++.+||+|+.||.|+||+||+..|.
T Consensus 2 ~~~~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI 68 (75)
T PF00125_consen 2 TRRLIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDI 68 (75)
T ss_dssp HSHSSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHH
T ss_pred cccccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHH
Confidence 5688999999999999999887779999999999999999999999999999999999999998554
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=98.81 E-value=1.2e-08 Score=68.40 Aligned_cols=52 Identities=15% Similarity=0.210 Sum_probs=45.8
Q ss_pred HHHHhhhcccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeeehh
Q psy15118 73 REIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASLVS 124 (132)
Q Consensus 73 reI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~~~ 124 (132)
.|++.++.+..+++++|.++||+.+|+|+..++++|..||.|++|.||+..|
T Consensus 8 ~~lv~~id~~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~D 59 (72)
T cd07981 8 QELLKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKD 59 (72)
T ss_pred HHHHHhhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHH
Confidence 3444555567999999999999999999999999999999999999998844
No 10
>PTZ00463 histone H2B; Provisional
Probab=98.46 E-value=7.8e-07 Score=65.09 Aligned_cols=59 Identities=7% Similarity=0.030 Sum_probs=56.9
Q ss_pred cccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeee
Q psy15118 64 RKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASL 122 (132)
Q Consensus 64 ~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~ 122 (132)
++.+|..||+.|+.++++|..++..||..|+....|++.++-.+|..++.+.+|-||+.
T Consensus 26 r~esy~~YI~KVLKqVhPd~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~Tlts 84 (117)
T PTZ00463 26 RYDSYGLYIFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSS 84 (117)
T ss_pred ccchHHHHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCH
Confidence 46779999999999999999999999999999999999999999999999999999987
No 11
>PLN00158 histone H2B; Provisional
Probab=98.38 E-value=1e-06 Score=64.41 Aligned_cols=59 Identities=8% Similarity=0.107 Sum_probs=57.3
Q ss_pred cccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeee
Q psy15118 64 RKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASL 122 (132)
Q Consensus 64 ~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~ 122 (132)
++.+|..||+.|+.++++|..++..||..|.....|++.++-.+|..++.+.+|-||+.
T Consensus 25 r~esy~~YI~kVLKQVhPd~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~Tlts 83 (116)
T PLN00158 25 KTETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTS 83 (116)
T ss_pred ccccHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCH
Confidence 57899999999999999999999999999999999999999999999999999999987
No 12
>smart00427 H2B Histone H2B.
Probab=98.27 E-value=2.5e-06 Score=59.88 Aligned_cols=56 Identities=11% Similarity=0.113 Sum_probs=54.6
Q ss_pred chhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeee
Q psy15118 67 PFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASL 122 (132)
Q Consensus 67 pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~ 122 (132)
+|..||+.|+.++++|..++..||..|...+.|++.++-.+|..++.+.||-||+.
T Consensus 2 sy~~Yi~kvLKqVhpd~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~Tlts 57 (89)
T smart00427 2 TYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSS 57 (89)
T ss_pred cHHHHHHHHHHHhCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCH
Confidence 68899999999999999999999999999999999999999999999999999987
No 13
>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=97.98 E-value=1.1e-05 Score=56.05 Aligned_cols=60 Identities=23% Similarity=0.268 Sum_probs=53.7
Q ss_pred hccccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeeehhhc
Q psy15118 62 LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASLVSLV 126 (132)
Q Consensus 62 lI~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~~~~~ 126 (132)
-||+.|..||+|.- .--|++.++.+.+.++.|.||..+..||..++-|++|-||+..|.+
T Consensus 13 gi~k~~I~RLarr~-----GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~ 72 (85)
T cd00076 13 GITKPAIRRLARRG-----GVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVV 72 (85)
T ss_pred cCCHHHHHHHHHHc-----CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHH
Confidence 38999999998643 4579999999999999999999999999999999999999986654
No 14
>smart00417 H4 Histone H4.
Probab=97.95 E-value=1.6e-05 Score=53.98 Aligned_cols=60 Identities=20% Similarity=0.230 Sum_probs=54.0
Q ss_pred hccccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeeehhhc
Q psy15118 62 LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASLVSLV 126 (132)
Q Consensus 62 lI~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~~~~~ 126 (132)
-||+.|..||+|. ..--|++.++.+.|.++.|.||..+..||..++-|++|-||+.+|.+
T Consensus 13 gI~k~~IrRLaRr-----~GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~ 72 (74)
T smart00417 13 GITKPAIRRLARR-----GGVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVV 72 (74)
T ss_pred CCCHHHHHHHHHH-----cCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHhe
Confidence 4899999999863 24579999999999999999999999999999999999999988765
No 15
>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=97.87 E-value=3.1e-05 Score=51.11 Aligned_cols=59 Identities=14% Similarity=0.128 Sum_probs=48.8
Q ss_pred hccccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeeehhh
Q psy15118 62 LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASLVSL 125 (132)
Q Consensus 62 lI~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~~~~ 125 (132)
.+|+.|..|+.+. . +--+++.+|...|.+..|.++-.+.++|..++.|+||-||+..|.
T Consensus 2 ~~p~~~i~ria~~----~-Gi~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI 60 (65)
T smart00803 2 WLPKETIKDVAES----L-GIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDI 60 (65)
T ss_pred CCCHHHHHHHHHH----C-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHH
Confidence 3566666666543 3 334899999999999999999999999999999999999988553
No 16
>PLN00035 histone H4; Provisional
Probab=97.85 E-value=2.6e-05 Score=56.09 Aligned_cols=59 Identities=20% Similarity=0.230 Sum_probs=53.1
Q ss_pred ccccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeeehhhc
Q psy15118 63 IRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASLVSLV 126 (132)
Q Consensus 63 I~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~~~~~ 126 (132)
||+.|..||+|.- .--|++.+|.+.|.++.|.||..+..|+...+-|++|.||+..|.+
T Consensus 30 ipk~~IrRLARr~-----GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~ 88 (103)
T PLN00035 30 ITKPAIRRLARRG-----GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVV 88 (103)
T ss_pred CCHHHHHHHHHHc-----CcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHH
Confidence 8999999998643 3579999999999999999999999999999999999999986644
No 17
>PTZ00015 histone H4; Provisional
Probab=97.85 E-value=2.9e-05 Score=55.71 Aligned_cols=61 Identities=20% Similarity=0.184 Sum_probs=53.9
Q ss_pred hccccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeeehhhcc
Q psy15118 62 LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASLVSLVG 127 (132)
Q Consensus 62 lI~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~~~~~~ 127 (132)
-|++.|..||++.- .--|++.++.+.+.+..|.||..+..||..+|-|++|-||+..|.++
T Consensus 30 gI~k~~IrRLarr~-----GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~ 90 (102)
T PTZ00015 30 GITKGAIRRLARRG-----GVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVY 90 (102)
T ss_pred CCCHHHHHHHHHHc-----CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHH
Confidence 48999999998643 45799999999999999999999999999999999999999866543
No 18
>KOG1744|consensus
Probab=97.80 E-value=3.4e-05 Score=57.26 Aligned_cols=62 Identities=18% Similarity=0.162 Sum_probs=58.5
Q ss_pred ccccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeeehh
Q psy15118 63 IRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASLVS 124 (132)
Q Consensus 63 I~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~~~ 124 (132)
..+..|..+|+.++.++++|+.++..|+.+|+....+++.++..+|+++|.+.||-||.+..
T Consensus 34 ~~~e~~s~yv~kvlk~Vhpd~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSre 95 (127)
T KOG1744|consen 34 RRKESYSEYVYKVLKQVHPDLGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSRE 95 (127)
T ss_pred cccCceeeehhhhhhcccCCCCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHH
Confidence 57788999999999999999999999999999999999999999999999999999998843
No 19
>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=97.73 E-value=0.00011 Score=47.63 Aligned_cols=54 Identities=24% Similarity=0.281 Sum_probs=44.6
Q ss_pred HHHHHhhhcccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeeehhh
Q psy15118 72 VREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASLVSL 125 (132)
Q Consensus 72 VreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~~~~ 125 (132)
|+.|++...++.+++.+|..+|+.++|.|+..|-.+|+..+-+.+|-||+-.|+
T Consensus 8 vkri~k~~~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv 61 (65)
T PF00808_consen 8 VKRIMKSDPDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDV 61 (65)
T ss_dssp HHHHHHHTSTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHH
T ss_pred HHHHhccCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHH
Confidence 355555554567899999999999999999999999999999999999987554
No 20
>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=97.35 E-value=0.00041 Score=50.57 Aligned_cols=61 Identities=13% Similarity=0.172 Sum_probs=52.4
Q ss_pred hhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeeehhhcccc
Q psy15118 68 FQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASLVSLVGGA 129 (132)
Q Consensus 68 F~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~~~~~~~~ 129 (132)
..++|..|+.+. +..+++..+...|-|.++.|...+..||...|-||+|.||+.-|.-+.|
T Consensus 3 d~~~v~~iLk~~-Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi 63 (117)
T cd07979 3 DARVIAAILKSM-GITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAI 63 (117)
T ss_pred HHHHHHHHHHHC-CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHH
Confidence 357888888865 3469999999999999999999999999999999999999986655443
No 21
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=97.32 E-value=0.00057 Score=46.56 Aligned_cols=61 Identities=21% Similarity=0.191 Sum_probs=49.2
Q ss_pred ccchhHHHHHHHhhh--cccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeeehhh
Q psy15118 65 KLPFQRLVREIAQDF--KTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASLVSL 125 (132)
Q Consensus 65 k~pF~rlVreI~~~~--~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~~~~ 125 (132)
|..++.-|-+|+++. ..+..++++.+.+|-|.+=.++..+-.|--..|-||+|.||+.-|.
T Consensus 4 Kaal~~~v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV 66 (76)
T PF15630_consen 4 KAALWYTVGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDV 66 (76)
T ss_dssp HHHHHHHHHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHH
T ss_pred HHHHHHHHHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHH
Confidence 344556677777776 3678999999999999999999999999999999999999998443
No 22
>KOG0870|consensus
Probab=97.16 E-value=0.00048 Score=53.31 Aligned_cols=65 Identities=22% Similarity=0.279 Sum_probs=59.9
Q ss_pred chhccccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeeehhhc
Q psy15118 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASLVSLV 126 (132)
Q Consensus 60 ~llI~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~~~~~ 126 (132)
++.+|++-..|||+|++.+. +..++.+|+.||+.+|--|+.-|--.|+-.|.-.+|-||+.-|.+
T Consensus 8 dl~lP~AiI~rlvke~l~E~--~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl 72 (172)
T KOG0870|consen 8 DLNLPNAIITRLVKEVLPES--NVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVL 72 (172)
T ss_pred HhhccHHHHHHHHHHhCccc--cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHH
Confidence 58899999999999999877 789999999999999999999999999999999999999875543
No 23
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=96.98 E-value=0.0016 Score=56.40 Aligned_cols=53 Identities=28% Similarity=0.396 Sum_probs=40.5
Q ss_pred HHHHHHHhhh-----cccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeee
Q psy15118 70 RLVREIAQDF-----KTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASL 122 (132)
Q Consensus 70 rlVreI~~~~-----~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~ 122 (132)
-+|+.+++.| ....++..+||.+|..|+|-|+.+|-+|-...|-||+|.||.-
T Consensus 355 ~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIde 412 (414)
T PF15511_consen 355 GVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDE 412 (414)
T ss_dssp HHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-H
T ss_pred cHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCC
Confidence 3456665555 2568999999999999999999999999999999999999963
No 24
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=96.41 E-value=0.0091 Score=40.06 Aligned_cols=44 Identities=27% Similarity=0.245 Sum_probs=40.0
Q ss_pred ccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeeehhhc
Q psy15118 83 LRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASLVSLV 126 (132)
Q Consensus 83 ~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~~~~~ 126 (132)
-+.+++|++.|.+..|.|+..+-+.+...+-|+.|.+.+..|..
T Consensus 22 ~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~ 65 (77)
T smart00576 22 DSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVV 65 (77)
T ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHH
Confidence 38899999999999999999999999999999999998875543
No 25
>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=96.40 E-value=0.011 Score=39.37 Aligned_cols=53 Identities=11% Similarity=0.166 Sum_probs=40.2
Q ss_pred HHHHhhhcccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeeehhh
Q psy15118 73 REIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASLVSL 125 (132)
Q Consensus 73 reI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~~~~ 125 (132)
.|++.++.+...+.+++.++|.+.|++|+....+.|-.+|-|.+--||.+.|+
T Consensus 6 ~~Lv~~iDp~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv 58 (68)
T PF03847_consen 6 QELVKQIDPNEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDV 58 (68)
T ss_dssp HHHHHCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHH
T ss_pred HHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHH
Confidence 44555557899999999999999999999999999999999999999988443
No 26
>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=95.87 E-value=0.028 Score=37.31 Aligned_cols=53 Identities=23% Similarity=0.227 Sum_probs=40.5
Q ss_pred HHHHHHhhhcccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeeehh
Q psy15118 71 LVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASLVS 124 (132)
Q Consensus 71 lVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~~~ 124 (132)
-|+.|++.++- -..+.++...|-+-+|.-|-.+.++|..++.|+||-+|+.-|
T Consensus 8 svk~iAes~Gi-~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~D 60 (66)
T PF02969_consen 8 SVKDIAESLGI-SNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDD 60 (66)
T ss_dssp HHHHHHHHTT----B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHH
T ss_pred HHHHHHHHcCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHH
Confidence 35666665532 257899999999999999999999999999999999998743
No 27
>PF02291 TFIID-31kDa: Transcription initiation factor IID, 31kD subunit; InterPro: IPR003162 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription []. TAFII-31 protein is a transcriptional coactivator of the p53 protein [].; GO: 0006352 transcription initiation, DNA-dependent; PDB: 1TAF_A.
Probab=95.64 E-value=0.022 Score=42.35 Aligned_cols=61 Identities=20% Similarity=0.213 Sum_probs=47.9
Q ss_pred hHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeeehhhccccc
Q psy15118 69 QRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASLVSLVGGAS 130 (132)
Q Consensus 69 ~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~~~~~~~~~ 130 (132)
.++|..|+.+.+ -..+++..+..|-|.+-.|...+++||...+-||+|.+|..-|.-++|.
T Consensus 15 a~~i~~iL~~~G-v~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~ 75 (129)
T PF02291_consen 15 ARVIHLILKSMG-VTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQ 75 (129)
T ss_dssp HHHHHHHHHHTT----B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHH
T ss_pred HHHHHHHHHHcC-CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHH
Confidence 578888888764 2358999999999999999999999999999999999999866555543
No 28
>KOG1142|consensus
Probab=94.90 E-value=0.068 Score=44.04 Aligned_cols=68 Identities=13% Similarity=0.220 Sum_probs=58.6
Q ss_pred hhhcccchhccccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeeehhh
Q psy15118 54 RYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASLVSL 125 (132)
Q Consensus 54 ~~Qkst~llI~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~~~~ 125 (132)
.++-+++.++-|--..-||++| ..+..+..++-+.|.|.|++|+..+-.-+-.+|.|.|--||.+.|.
T Consensus 146 ~~~~~~~~il~k~kl~dLvqqI----d~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDI 213 (258)
T KOG1142|consen 146 QDEPGNNPILSKRKLDDLVQQI----DGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDI 213 (258)
T ss_pred cccCCCCccccccchhHHHHhh----cCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhhe
Confidence 5666777888877777777777 5678899999999999999999999999999999999999998553
No 29
>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=93.67 E-value=0.14 Score=43.12 Aligned_cols=51 Identities=18% Similarity=0.152 Sum_probs=44.9
Q ss_pred HHHHHHhhhcccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeee
Q psy15118 71 LVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASL 122 (132)
Q Consensus 71 lVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~ 122 (132)
-|+.|++..+ --+.+.+|..+|-+-+|.++-.+.++|..+|.|+||.||+.
T Consensus 4 ~i~~ia~~~G-i~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~ 54 (343)
T cd08050 4 SIKLIAESLG-IDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTT 54 (343)
T ss_pred HHHHHHHHcC-CCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCH
Confidence 4677777553 23899999999999999999999999999999999999987
No 30
>KOG3467|consensus
Probab=91.59 E-value=0.29 Score=34.63 Aligned_cols=44 Identities=18% Similarity=0.221 Sum_probs=37.5
Q ss_pred ccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeeehhhc
Q psy15118 83 LRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASLVSLV 126 (132)
Q Consensus 83 ~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~~~~~ 126 (132)
-|+..-..+-...++..||.+..-+|...+-||||.||+-|+.|
T Consensus 45 kRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv 88 (103)
T KOG3467|consen 45 KRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVV 88 (103)
T ss_pred chhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHH
Confidence 35556666777888999999999999999999999999998765
No 31
>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=89.83 E-value=0.39 Score=35.06 Aligned_cols=64 Identities=16% Similarity=0.013 Sum_probs=53.7
Q ss_pred chhccccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeeehhhcc
Q psy15118 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASLVSLVG 127 (132)
Q Consensus 60 ~llI~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~~~~~~ 127 (132)
.|.+|-.++.|+.++=. .-.|+..+|...|-..-|.+...++|-|...+.|+++.+|+-.++-+
T Consensus 18 gL~fPV~ri~R~Lk~~~----~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~l 81 (115)
T cd00074 18 GLQFPVGRIHRYLKKGR----YAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQL 81 (115)
T ss_pred CccCcHHHHHHHHHcCc----cccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHH
Confidence 48899999999986521 23799999999999999999999999999999999999997644433
No 32
>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=87.97 E-value=1.1 Score=29.68 Aligned_cols=46 Identities=24% Similarity=0.216 Sum_probs=40.2
Q ss_pred ccc-cccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeeehhhc
Q psy15118 81 TDL-RFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASLVSLV 126 (132)
Q Consensus 81 ~~~-r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~~~~~ 126 (132)
.+| ..++.||+.|-+.++.||..+...+...+-|+.|-..+.-|+.
T Consensus 19 ~GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~ 65 (77)
T PF07524_consen 19 AGFDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVE 65 (77)
T ss_pred cCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHH
Confidence 344 6889999999999999999999999999999999887775544
No 33
>KOG3334|consensus
Probab=86.21 E-value=1.8 Score=32.97 Aligned_cols=59 Identities=15% Similarity=0.248 Sum_probs=47.9
Q ss_pred hHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeeehhhccc
Q psy15118 69 QRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASLVSLVGG 128 (132)
Q Consensus 69 ~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~~~~~~~ 128 (132)
.+++--|+.+++ --.|.+..+.-|=|++=.|.+++++||...+-||++-||..-|..+.
T Consensus 16 a~~i~~iL~s~G-I~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA 74 (148)
T KOG3334|consen 16 ARVIASILKSLG-IQEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLA 74 (148)
T ss_pred HHHHHHHHHHcC-ccccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHH
Confidence 356666776653 23567889999999999999999999999999999999988655543
No 34
>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=85.72 E-value=2 Score=33.73 Aligned_cols=55 Identities=18% Similarity=0.217 Sum_probs=49.3
Q ss_pred hhccccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccC
Q psy15118 61 LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAK 116 (132)
Q Consensus 61 llI~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~Hak 116 (132)
.++...++...+..|+.+.+-. .++.+.+..|..|+|.+|-.|.++...++-|..
T Consensus 43 ~fl~~~~l~~~~~~i~~~~g~~-~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~ 97 (212)
T cd08045 43 SFLNPSPLAKKIRKIAKKHGLK-EVDEDVLDLISLALEERLRNLLEKLIEVSEHRV 97 (212)
T ss_pred hccCHHHHHHHHHHHHHHcCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 6788889999999999876533 889999999999999999999999999999973
No 35
>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=83.64 E-value=1.1 Score=36.27 Aligned_cols=58 Identities=21% Similarity=0.263 Sum_probs=38.7
Q ss_pred chhccccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcc
Q psy15118 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRM 118 (132)
Q Consensus 60 ~llI~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRv 118 (132)
.+++...+++..+.+|+..+. ...+..+.+..|-.|+|.+|-.|+|++..++.|....
T Consensus 41 ~~fL~~~~L~~~i~~i~~~~g-~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~ 98 (264)
T PF05236_consen 41 EPFLNPSPLQKRIQKIAKKHG-LKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDS 98 (264)
T ss_dssp ---S-HHHHHHHHHHHHHCTT---EE-TCHHHHHHHHHHHHHHHHHHHHH---------
T ss_pred ccccCHHHHHHHHHHHHHHcC-CcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence 357788889999999987654 5678999999999999999999999999999996544
No 36
>KOG0871|consensus
Probab=83.38 E-value=2.2 Score=32.79 Aligned_cols=61 Identities=13% Similarity=0.203 Sum_probs=54.1
Q ss_pred cchhccccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeee
Q psy15118 59 TELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASL 122 (132)
Q Consensus 59 t~llI~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~ 122 (132)
.++-+||+.....|.|++. .|+||..+|=+.+++.+=.|+--+=-.||..+---.+-||.-
T Consensus 9 de~sLPkAtv~KmIke~lP---~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~ 69 (156)
T KOG0871|consen 9 DELSLPKATVNKMIKEMLP---KDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAP 69 (156)
T ss_pred ccccCcHHHHHHHHHHhCC---cccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCH
Confidence 4577999999999999874 699999999999999999999999999999988888888854
No 37
>KOG0869|consensus
Probab=76.49 E-value=4.4 Score=31.45 Aligned_cols=68 Identities=13% Similarity=0.147 Sum_probs=51.6
Q ss_pred hccccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeeehhhcccccCC
Q psy15118 62 LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASLVSLVGGASAL 132 (132)
Q Consensus 62 lI~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~~~~~~~~~~~ 132 (132)
++|-+--.|+.+.++ ..+-.+..+|=+.+||.+-.|+-=+--+|+.-+.--||.||+--|++.-+++|
T Consensus 32 ~LPIANV~RIMK~~l---P~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tL 99 (168)
T KOG0869|consen 32 FLPIANVSRIMKKAL---PANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTL 99 (168)
T ss_pred hccHHHHHHHHHhcC---CcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHc
Confidence 345554455544443 46789999999999999999988888888877788899999988877655543
No 38
>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=74.81 E-value=3.9 Score=28.45 Aligned_cols=59 Identities=14% Similarity=0.197 Sum_probs=32.4
Q ss_pred hhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeeehhhc
Q psy15118 68 FQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASLVSLV 126 (132)
Q Consensus 68 F~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~~~~~ 126 (132)
|..=|+.++--|+..-.-..+....+.+..-.|++.+...|..+|.+..+-.|.+-|++
T Consensus 3 f~~eI~~mMy~fGD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~ 61 (93)
T PF02269_consen 3 FSKEIRQMMYGFGDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLL 61 (93)
T ss_dssp -CCCCHHHHHCTTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC----------------
T ss_pred hHHHHHHHHHHcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHH
Confidence 33345566666666677889999999999999999999999999999976666665543
No 39
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=74.31 E-value=5.9 Score=29.87 Aligned_cols=61 Identities=20% Similarity=0.201 Sum_probs=51.5
Q ss_pred cchhccccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeee
Q psy15118 59 TELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASL 122 (132)
Q Consensus 59 t~llI~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~ 122 (132)
.++.+||+--+..|-+|+. .|+-|+.+|-+.+++++=.|+--|=-.||..+-.-+..||.-
T Consensus 8 De~sLPKATVqKMvS~iLp---~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~ 68 (148)
T COG5150 8 DENSLPKATVQKMVSSILP---KDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAY 68 (148)
T ss_pred ccccCcHHHHHHHHHHhcc---ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccH
Confidence 4567899999999999875 789999999999999999999888888888776666666643
No 40
>KOG1658|consensus
Probab=63.79 E-value=7.2 Score=30.17 Aligned_cols=67 Identities=19% Similarity=0.298 Sum_probs=51.3
Q ss_pred ccccchhHHHHHHHhhhcccccccHH-HHHHHHHHHHHHHHHhhhhhhHhhhccCcceeeehhhcccccC
Q psy15118 63 IRKLPFQRLVREIAQDFKTDLRFQSS-AVMALQEASEAYLVGLFEDTNLCAIHAKRMIASLVSLVGGASA 131 (132)
Q Consensus 63 I~k~pF~rlVreI~~~~~~~~r~~~~-Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~~~~~~~~~~ 131 (132)
..++|.+|. ++|.. ..+|+++..+ |+.++-.++|.|+-.|=.+++.|+--.||+|++.++.=.-|++
T Consensus 57 l~rLpL~ri-k~vvk-l~pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai~~ 124 (162)
T KOG1658|consen 57 LSRLPLARI-KQVVK-LDPDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAIEA 124 (162)
T ss_pred hhhccHHHH-Hhhcc-CCcchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccccc
Confidence 356666653 44443 4578888765 5667889999999999999999999999999998766555543
No 41
>KOG2389|consensus
Probab=59.90 E-value=12 Score=32.20 Aligned_cols=48 Identities=21% Similarity=0.182 Sum_probs=43.3
Q ss_pred ccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeeehhhccccc
Q psy15118 83 LRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASLVSLVGGAS 130 (132)
Q Consensus 83 ~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~~~~~~~~~ 130 (132)
-.++..|++-|+-.+-.|+-+|-+.|...+-|+.|+--++-|-|++++
T Consensus 45 ~~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~ 92 (353)
T KOG2389|consen 45 SSTQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQ 92 (353)
T ss_pred cccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHH
Confidence 357788999999999999999999999999999999999988887654
No 42
>PF10911 DUF2717: Protein of unknown function (DUF2717); InterPro: IPR020121 The proteins in this entry are uncharacterised.
Probab=58.08 E-value=16 Score=25.03 Aligned_cols=60 Identities=25% Similarity=0.421 Sum_probs=46.0
Q ss_pred hHHHhhhhcccchhccccchhHHHHHHHhh-hcccccccHHHHHHHHH--HHHHHHHHhhhhhhHh
Q psy15118 49 LREIRRYQKSTELLIRKLPFQRLVREIAQD-FKTDLRFQSSAVMALQE--ASEAYLVGLFEDTNLC 111 (132)
Q Consensus 49 l~EIr~~Qkst~llI~k~pF~rlVreI~~~-~~~~~r~~~~Al~aLQe--aaE~~Lv~lfe~a~l~ 111 (132)
|++|.+|+...+ =||-.| |.+.|-++. |+.++-..+..+..|+. -+|+|+-++.+..+.|
T Consensus 2 L~~I~h~l~np~-DiP~ip--ra~aeyLqvrfN~~yl~~sG~i~~lr~~G~SE~~I~Gfl~Gl~~A 64 (77)
T PF10911_consen 2 LKPIQHLLDNPD-DIPDIP--RAAAEYLQVRFNAAYLMASGIISALRKQGWSESYILGFLAGLQYA 64 (77)
T ss_pred cchHHHHhcCCc-ccCCcc--HHHHHHHHHHhcHHHHHHhhhHHHHHHccccHHHHHHHHHHHHHH
Confidence 678999988763 355554 666676663 57788888888999875 5899999999998887
No 43
>KOG2549|consensus
Probab=56.75 E-value=23 Score=32.41 Aligned_cols=42 Identities=19% Similarity=0.234 Sum_probs=38.4
Q ss_pred cccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeeeh
Q psy15118 82 DLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASLV 123 (132)
Q Consensus 82 ~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~~ 123 (132)
--.++.+|..+|-+-+|.-+-.+.+|+..++.|+||-++++-
T Consensus 26 i~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~ 67 (576)
T KOG2549|consen 26 ITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVD 67 (576)
T ss_pred ccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHH
Confidence 346889999999999999999999999999999999999883
No 44
>PF13581 HATPase_c_2: Histidine kinase-like ATPase domain
Probab=51.78 E-value=41 Score=22.96 Aligned_cols=45 Identities=18% Similarity=0.097 Sum_probs=36.0
Q ss_pred hHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHhhhhhhHhhh
Q psy15118 69 QRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAI 113 (132)
Q Consensus 69 ~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~ 113 (132)
-+.+++.+..+.....|..+.+..+.-+++..+++.++.++...-
T Consensus 8 i~~~r~~~~~~~~~~~~~~~~~~~~~lav~E~~~Nav~H~~~~~~ 52 (125)
T PF13581_consen 8 IREARAFLREFLERLGLPEEDRDDLELAVSEALTNAVEHGYPGDP 52 (125)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHcCCCCC
Confidence 345666666665678999999999999999999999999887543
No 45
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=39.99 E-value=1.1e+02 Score=22.55 Aligned_cols=52 Identities=13% Similarity=0.130 Sum_probs=41.1
Q ss_pred hhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcce
Q psy15118 68 FQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMI 119 (132)
Q Consensus 68 F~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvT 119 (132)
|..=|..++--|+.+..--.+.+++|+|.+-+|++.+..+|-.+|--...+-
T Consensus 11 F~KDikslmYayGDvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq~rnK~k 62 (126)
T COG5248 11 FMKDIKSLMYAYGDVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQVRNKTK 62 (126)
T ss_pred HHHHHHHHHHHhCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHhcccch
Confidence 5556666676777777888899999999999999999998887776544443
No 46
>PRK14562 haloacid dehalogenase superfamily protein; Provisional
Probab=38.82 E-value=22 Score=28.02 Aligned_cols=49 Identities=22% Similarity=0.110 Sum_probs=30.0
Q ss_pred cccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeeehhhcccc
Q psy15118 80 KTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASLVSLVGGA 129 (132)
Q Consensus 80 ~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~~~~~~~~ 129 (132)
.++++|+...-.++||.+|++..-.|=..+.+..|-. +-|...+-++|+
T Consensus 70 ~~~~~y~~~~~~~lQEyvEA~~f~~~l~~~~l~s~ee-l~v~~~dYLlGl 118 (204)
T PRK14562 70 HPELYYAGYVGTALQEYVEALLVYSLLFENKIPSPEE-LGVPEAAYLLGL 118 (204)
T ss_pred CchhhhhhhcchHHHHHHHHHHHHHHHcCCCCCCHHH-cCCCHHHHHhHH
Confidence 3678888888889999999877665554333322211 223335555554
No 47
>TIGR01924 rsbW_low_gc serine-protein kinase RsbW. This model describes the anti-sigma B factor also known as serine-protein kinase RsbW. Sigma B controls the general stress regulon in B subtilis and is activated by cell stresses such as stationary phase and heat shock. RsbW binds to sigma B and prevents formation of the transcription complex at the promoter. RsbV (anti-anti-sigma factor) binds to RsbW to inhibit association with sigma B, however RsbW can phosphorylate RsbV, causing disassociation of the RsbV/RsbW complex. Low ATP level or environmental stress causes the dephosphorylation of RsbV.
Probab=38.57 E-value=62 Score=23.92 Aligned_cols=47 Identities=11% Similarity=0.090 Sum_probs=39.1
Q ss_pred cccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHhhhhhhH
Q psy15118 64 RKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNL 110 (132)
Q Consensus 64 ~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l 110 (132)
...-+-+.||..+..+.....|+.+.+..++-+++..+++.++.++.
T Consensus 14 a~~~~~~~vr~~~~~~a~~~g~~~~~~~~l~lav~Ea~~Nai~ha~~ 60 (159)
T TIGR01924 14 AKPEYVGLIRLTLSGIASRAGYTYDDIEDLKIAVSEACTNAVKHAYK 60 (159)
T ss_pred CcHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHhccC
Confidence 34556677888888887788999999999999999999999998863
No 48
>KOG1657|consensus
Probab=36.85 E-value=50 Score=26.85 Aligned_cols=65 Identities=15% Similarity=0.167 Sum_probs=52.4
Q ss_pred cccchhccccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeee
Q psy15118 57 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASL 122 (132)
Q Consensus 57 kst~llI~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~ 122 (132)
...++.+..+|..|+ +.|+..-..---++++|.-..-.|+|.|+..|=.-++.-+--++|-|+.-
T Consensus 66 ~~~d~~~~~lPlaRi-KkimK~dedv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~ 130 (236)
T KOG1657|consen 66 GQLDFKNHILPLARI-KKIMKSDEDVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQK 130 (236)
T ss_pred cccchhhccCcHhhc-cccccccccccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchH
Confidence 345788999999997 55655322223799999999999999999999999999888899998854
No 49
>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=34.06 E-value=1.6e+02 Score=20.37 Aligned_cols=52 Identities=15% Similarity=0.220 Sum_probs=39.4
Q ss_pred hhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHhhhhhhHhhh-ccCcce
Q psy15118 68 FQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAI-HAKRMI 119 (132)
Q Consensus 68 F~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~-HakRvT 119 (132)
|..=++.++--++..-.-..+....|.+.+=.|++.+.-.|..+|. ...|+.
T Consensus 4 f~~ei~~mmy~~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~~r~~k~~ 56 (92)
T cd07978 4 FTKEIRQMMYGFGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQRRRGKVK 56 (92)
T ss_pred cHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCC
Confidence 4444555555555555678899999999999999999999999998 455553
No 50
>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=32.25 E-value=1.2e+02 Score=23.04 Aligned_cols=53 Identities=23% Similarity=0.202 Sum_probs=39.5
Q ss_pred hhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeeehhh
Q psy15118 68 FQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASLVSL 125 (132)
Q Consensus 68 F~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~~~~ 125 (132)
|.++.|+-+ ++....+-+.-+-..+|.-|-.||+-++.-|-+..|-+|...+|
T Consensus 1 fe~lFR~aa-----~LdvdK~d~~r~~d~V~~Kl~DLl~va~~~Ak~ngRdvI~~~DL 53 (138)
T PF09123_consen 1 FERLFRKAA-----GLDVDKNDAKRYSDFVEKKLYDLLLVAQENAKANGRDVIEPRDL 53 (138)
T ss_dssp HHHHHHHHH-----S----HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS
T ss_pred ChHHHHHHh-----ccCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeeccccC
Confidence 556666554 46667788888999999999999999999999999999987554
No 51
>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=30.88 E-value=43 Score=21.23 Aligned_cols=20 Identities=30% Similarity=0.336 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHHHHHhhhh
Q psy15118 88 SAVMALQEASEAYLVGLFED 107 (132)
Q Consensus 88 ~Al~aLQeaaE~~Lv~lfe~ 107 (132)
+|+.+|||.+++-|.++...
T Consensus 7 ea~~~lqevs~eELd~ilGg 26 (51)
T PF04604_consen 7 EALNSLQEVSDEELDQILGG 26 (51)
T ss_pred HHHHHHHhcCHHHHHHHhCC
Confidence 89999999999999998865
No 52
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=28.55 E-value=56 Score=25.24 Aligned_cols=22 Identities=18% Similarity=0.199 Sum_probs=19.5
Q ss_pred hhhcccccccHHHHHHHHHHHH
Q psy15118 77 QDFKTDLRFQSSAVMALQEASE 98 (132)
Q Consensus 77 ~~~~~~~r~~~~Al~aLQeaaE 98 (132)
.++..+|-|+..+|++.+|.+|
T Consensus 72 ~~CGkpyPWt~~~L~aa~el~e 93 (158)
T PF10083_consen 72 HNCGKPYPWTENALEAANELIE 93 (158)
T ss_pred HhCCCCCchHHHHHHHHHHHHH
Confidence 4567899999999999999998
No 53
>PRK04069 serine-protein kinase RsbW; Provisional
Probab=27.24 E-value=1.3e+02 Score=22.04 Aligned_cols=47 Identities=9% Similarity=0.120 Sum_probs=37.7
Q ss_pred cccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHhhhhhhH
Q psy15118 64 RKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNL 110 (132)
Q Consensus 64 ~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l 110 (132)
...-+-+.||..+..+.....|+.+.+..|+-+++..+.+..+.++.
T Consensus 14 a~~~~~~~vr~~v~~~~~~~g~~~~~~~~l~lav~Ea~~Nai~Hg~~ 60 (161)
T PRK04069 14 AKAEYVSIIRLTLSGVANRMGFSYDDIEDMKIAVSEACTNAVQHAYK 60 (161)
T ss_pred CcHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHhccC
Confidence 34556788888888887888999999998988888888888887753
No 54
>PF07278 DUF1441: Protein of unknown function (DUF1441); InterPro: IPR009901 This entry is represented by Bacteriophage VT1-Sakai, H0025. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical Enterobacterial proteins of around 160 residues in length. The function of this family is unknown.
Probab=26.76 E-value=2.2e+02 Score=21.73 Aligned_cols=64 Identities=17% Similarity=0.193 Sum_probs=47.7
Q ss_pred hhHHHhhhhcccchhccccc----hhHHHHHHHhhh-------cccccccHHHHHHHHHHHHHHHHHhhhhhhHh
Q psy15118 48 ALREIRRYQKSTELLIRKLP----FQRLVREIAQDF-------KTDLRFQSSAVMALQEASEAYLVGLFEDTNLC 111 (132)
Q Consensus 48 al~EIr~~Qkst~llI~k~p----F~rlVreI~~~~-------~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~ 111 (132)
+-+|--+|++.+.-|||-.= |..+++-|.+.+ ..|..|+++++..+|.+.-+...+|-+...-+
T Consensus 75 sE~eRlk~e~e~g~Lipa~eV~~~~s~~~Kav~q~LetlPD~LERd~gL~p~~v~~vQ~~iD~lR~~l~~~i~~~ 149 (152)
T PF07278_consen 75 SENERLKFEKETGQLIPAEEVRREMSEMAKAVVQVLETLPDILERDAGLPPEQVARVQSVIDDLRDQLAERIQEA 149 (152)
T ss_pred HHHHHHHHHHHHcccCcHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34566678888889999764 455555555443 25799999999999999999998887765443
No 55
>PHA02604 rI.-1 hypothetical protein; Provisional
Probab=26.32 E-value=1.3e+02 Score=22.42 Aligned_cols=44 Identities=11% Similarity=0.052 Sum_probs=32.0
Q ss_pred chhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHhhhhhhHhhh
Q psy15118 67 PFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAI 113 (132)
Q Consensus 67 pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~ 113 (132)
.+..++.+|+++...-++ .....||.+.++++.-+..--+++++
T Consensus 82 d~~~~l~~~l~~a~~i~~---~l~s~L~N~~DdI~~~~~qt~YkLtL 125 (126)
T PHA02604 82 DTIAFLDELLQEAEEIYK---ELPSALQSTLDDITGLCYQTKYKLTL 125 (126)
T ss_pred CHHHHHHHHHHHHHHHHH---HhhHHHHHHHHHHHHHHHHHHHHHhc
Confidence 778888888887654333 44466999999998887776666653
No 56
>PF07105 DUF1367: Protein of unknown function (DUF1367); InterPro: IPR009797 This entry is represented by Bacteriophage VT2phi_272, P37. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several highly conserved, hypothetical bacterial and phage proteins of around 200 resides in length. The function of this family is unknown.
Probab=25.65 E-value=1.2e+02 Score=24.32 Aligned_cols=16 Identities=44% Similarity=0.567 Sum_probs=14.2
Q ss_pred HHHHHHHHHHHHHhhh
Q psy15118 91 MALQEASEAYLVGLFE 106 (132)
Q Consensus 91 ~aLQeaaE~~Lv~lfe 106 (132)
++||++++.||..+-+
T Consensus 91 ~~l~~~A~~yL~~va~ 106 (196)
T PF07105_consen 91 DALQEAADQYLAKVAK 106 (196)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 7899999999988765
No 57
>COG2178 Predicted RNA-binding protein of the translin family [Translation, ribosomal structure and biogenesis]
Probab=25.04 E-value=78 Score=25.43 Aligned_cols=56 Identities=29% Similarity=0.323 Sum_probs=39.1
Q ss_pred hhhHHHhhhhcccchhccccchhHH----------HHHHHhhh--cccccccHHHHHHHHHHHHHHHH
Q psy15118 47 VALREIRRYQKSTELLIRKLPFQRL----------VREIAQDF--KTDLRFQSSAVMALQEASEAYLV 102 (132)
Q Consensus 47 ~al~EIr~~Qkst~llI~k~pF~rl----------VreI~~~~--~~~~r~~~~Al~aLQeaaE~~Lv 102 (132)
...+||.++-+-.-.++.+-.|-.- |.++-..+ .+++-|+..+=.++||-+|+.+.
T Consensus 24 ~lsRei~r~s~~aI~~~H~~~~eeA~~~l~~a~~~v~~Lk~~l~~~pel~~ag~~~~a~QEyvEA~~l 91 (204)
T COG2178 24 KLSREIVRLSGEAIFLLHRGDFEEAEKKLKKASEAVEKLKRLLAGFPELYFAGFVTTALQEYVEATLL 91 (204)
T ss_pred HHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHhhcchHHHHHHHHHH
Confidence 3468888887777777888877543 22222222 26788888999999999998654
No 58
>COG5304 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.60 E-value=51 Score=23.29 Aligned_cols=17 Identities=35% Similarity=0.759 Sum_probs=14.6
Q ss_pred ccccchhHHHHHHHhhh
Q psy15118 63 IRKLPFQRLVREIAQDF 79 (132)
Q Consensus 63 I~k~pF~rlVreI~~~~ 79 (132)
-.-+|+|+|++||+...
T Consensus 72 a~GlpYQtyIreiLh~~ 88 (92)
T COG5304 72 AEGLPYQTYIREILHKY 88 (92)
T ss_pred hcCCcHHHHHHHHHHhh
Confidence 47799999999999865
No 59
>KOG4336|consensus
Probab=24.37 E-value=1.3e+02 Score=25.82 Aligned_cols=44 Identities=16% Similarity=0.093 Sum_probs=35.6
Q ss_pred ccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeeehhhccc
Q psy15118 85 FQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASLVSLVGG 128 (132)
Q Consensus 85 ~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~~~~~~~ 128 (132)
++..|++-|=++.-.|+-.+|+.+-..+-|++|.-.+.-|+.++
T Consensus 23 is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~ 66 (323)
T KOG4336|consen 23 ISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLT 66 (323)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHH
Confidence 55667777778888999999999999999999987777555543
No 60
>PF03172 Sp100: Sp100 domain; InterPro: IPR004865 The Sp100 and promyelocytic leukemia proteins (PML) are constituents of nuclear domains, known as nuclear dots (NDs or NBs - nuclear bodies or PML bodies), and are both covalently modified by the small ubiquitin-related protein SUMO-1. NBs play a role in autoimmunity, virus infections, and in the etiology of acute promyelocytic leukemia []. A functional nuclear localization signal and an NB-targeting region that coincides with an Sp100 homodimerization domain have been mapped. Sequences similar to the Sp100 homodimerization/ND-targeting region occur in several other proteins, which include the autoimmune regulator proteins (AIRE) and other numerous other transiently or permanently localised proteins. PML is expressed as a family of isoforms (PML I-VII) as a result of alternative splicing, most of which are found in the nucleus. Although there are many other functions of PML NBs in a wide range of cellular pathways, there is accumulating evidence that they represent preferential targets for viral infections and that PML plays a role in the mechanism of the antiviral action of interferon []. The Sp100 domain is usually found at the amino terminus of proteins that contain a SAND domain IPR000770 from INTERPRO. ; GO: 0005634 nucleus
Probab=24.01 E-value=1.1e+02 Score=22.02 Aligned_cols=48 Identities=27% Similarity=0.376 Sum_probs=34.4
Q ss_pred hhhhcccchhccccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHhhhhhhHhhh
Q psy15118 53 RRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAI 113 (132)
Q Consensus 53 r~~Qkst~llI~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~ 113 (132)
+.|+.+-+..--+.|-++.|+.|+..... ...-.+|..||.|.|+..+
T Consensus 40 ~~y~e~~e~crnlvpv~rvvY~vLs~Lek-------------~f~~~fl~~LFs~~nL~~Y 87 (103)
T PF03172_consen 40 QMYKESQEACRNLVPVQRVVYNVLSWLEK-------------TFIRSFLEALFSDYNLKEY 87 (103)
T ss_pred HHHHHHHHHHhccccHHHHHHHHHHHHHH-------------HhhHHHHHHHhhHHHHHHC
Confidence 34666555556778899999999876632 2345788889999988764
No 61
>KOG1969|consensus
Probab=22.77 E-value=1.8e+02 Score=28.06 Aligned_cols=72 Identities=21% Similarity=0.248 Sum_probs=52.8
Q ss_pred CchhhHHHhhhhcccchhccccchhHHHHHHHhhh-cccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcc
Q psy15118 45 GTVALREIRRYQKSTELLIRKLPFQRLVREIAQDF-KTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRM 118 (132)
Q Consensus 45 g~~al~EIr~~Qkst~llI~k~pF~rlVreI~~~~-~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRv 118 (132)
.+.+|+..|.|-.= ..++..+=.+||..+-.-| .++++..+.||.+|=|.++.=+-.-..--+.++.-++|.
T Consensus 449 YaPaLR~Lr~~A~i--i~f~~p~~s~Lv~RL~~IC~rE~mr~d~~aL~~L~el~~~DIRsCINtLQfLa~~~~r~ 521 (877)
T KOG1969|consen 449 YAPALRPLRPFAEI--IAFVPPSQSRLVERLNEICHRENMRADSKALNALCELTQNDIRSCINTLQFLASNVDRR 521 (877)
T ss_pred cchhhhhcccceEE--EEecCCChhHHHHHHHHHHhhhcCCCCHHHHHHHHHHhcchHHHHHHHHHHHHHhcccc
Confidence 77899999987542 4556666778885554445 478999999999999999876666666666666666664
No 62
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=22.51 E-value=1.8e+02 Score=21.99 Aligned_cols=37 Identities=22% Similarity=0.308 Sum_probs=29.8
Q ss_pred ccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceee
Q psy15118 85 FQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIAS 121 (132)
Q Consensus 85 ~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~ 121 (132)
+......-|-++|--|..+++|||...+-|+.|-.+.
T Consensus 32 ye~~VplQLl~FAhRYTq~vl~Dalvya~htgrg~~a 68 (145)
T COG5094 32 YEPKVPLQLLEFAHRYTQDVLEDALVYAKHTGRGHIA 68 (145)
T ss_pred hCccchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccC
Confidence 3445555677999999999999999999999876543
No 63
>PRK08487 DNA polymerase III subunit delta; Validated
Probab=22.25 E-value=1.9e+02 Score=23.77 Aligned_cols=60 Identities=10% Similarity=-0.025 Sum_probs=45.6
Q ss_pred HHHHHHHhhh-cccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhccCcceeeehhhcccc
Q psy15118 70 RLVREIAQDF-KTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRMIASLVSLVGGA 129 (132)
Q Consensus 70 rlVreI~~~~-~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~~~~~~~~ 129 (132)
.+.+=|.+.+ ..+..++.+|+..|-+.++.=|..+-.+-..++.+.+.+|...++.+.+.
T Consensus 139 ~l~~~i~~~~~~~g~~i~~~a~~~L~~~~g~dl~~l~~ELeKL~ly~~~It~edV~~~v~~ 199 (328)
T PRK08487 139 EALELLQERAKELGLDIDQNALNHLYFIHNEDLALAANELEKLAILNEPITLKDIQELVFG 199 (328)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHHhcCCCCHHHHHHHhcc
Confidence 3433343333 35788999999999999999888888888889999888888776665543
No 64
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=21.34 E-value=1.2e+02 Score=24.96 Aligned_cols=76 Identities=20% Similarity=0.291 Sum_probs=53.4
Q ss_pred CchhhHHHhhhhcccc---------hhccccchhHHHHHHHhhhcccc-cccHHHHHHHHHHHHHHHHHhhhhhhHhhhc
Q psy15118 45 GTVALREIRRYQKSTE---------LLIRKLPFQRLVREIAQDFKTDL-RFQSSAVMALQEASEAYLVGLFEDTNLCAIH 114 (132)
Q Consensus 45 g~~al~EIr~~Qkst~---------llI~k~pF~rlVreI~~~~~~~~-r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~H 114 (132)
|...-+-+|.||+..+ +-...+||.|. +.+++. .+|. =++++|=-..-.++|-|+..|---|-+.|-.
T Consensus 80 g~~~e~i~ryWq~ti~~~e~~~q~~~k~h~LPlARI-kkvMKt-dedVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~ 157 (286)
T COG5208 80 GLLDERISRYWQQTIKAAEEERQILLKDHNLPLARI-KKVMKT-DEDVKMISAEAPVLFAKITEIFIEELTMRAWINAEE 157 (286)
T ss_pred hhHHHHHHHHHHHHHHHHHHhHHHHHHhccCcHHHH-HHHHhc-ccchhheecccchHHHHHHHHHHHHHHHHHHHHHhH
Confidence 3344556788887532 22345899885 555542 2333 4677777778889999999998888888888
Q ss_pred cCcceeee
Q psy15118 115 AKRMIASL 122 (132)
Q Consensus 115 akRvTi~~ 122 (132)
+||-||.-
T Consensus 158 NkRRtLQk 165 (286)
T COG5208 158 NKRRTLQK 165 (286)
T ss_pred hhhhHHHH
Confidence 99998864
No 65
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=20.04 E-value=1.5e+02 Score=24.13 Aligned_cols=50 Identities=18% Similarity=0.085 Sum_probs=38.9
Q ss_pred ccccccHHHHHHHHHHHHHHHHHhhhhhhHhhhcc---Ccceeeehhhccccc
Q psy15118 81 TDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHA---KRMIASLVSLVGGAS 130 (132)
Q Consensus 81 ~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~Ha---kRvTi~~~~~~~~~~ 130 (132)
..+.++.+|++.|=+.++.=|..+-.+-..++.++ +.+|+..+..+.|.+
T Consensus 158 ~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~It~edV~~lv~~~ 210 (343)
T PRK06585 158 AGLRITPDARALLVALLGGDRLASRNEIEKLALYAHGKGEITLDDVRAVVGDA 210 (343)
T ss_pred CCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHhCCc
Confidence 57899999999999999987777777777777764 578887777666544
Done!