Query psy1398
Match_columns 102
No_of_seqs 114 out of 588
Neff 5.2
Searched_HMMs 46136
Date Fri Aug 16 16:29:56 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1398.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1398hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00160 histone H3; Provision 100.0 5.1E-47 1.1E-51 258.9 7.7 90 3-92 5-95 (97)
2 PLN00161 histone H3; Provision 100.0 3.9E-45 8.5E-50 261.7 7.7 90 3-92 39-129 (135)
3 smart00428 H3 Histone H3. 100.0 8.9E-45 1.9E-49 250.8 7.9 89 3-91 13-103 (105)
4 PTZ00018 histone H3; Provision 100.0 6.1E-45 1.3E-49 261.2 7.4 89 3-91 46-134 (136)
5 PLN00121 histone H3; Provision 100.0 8.1E-45 1.8E-49 260.5 7.4 89 3-91 46-134 (136)
6 KOG1745|consensus 100.0 7.9E-44 1.7E-48 255.4 4.1 89 3-91 47-135 (137)
7 COG2036 HHT1 Histones H3 and H 99.9 3.9E-28 8.4E-33 164.3 6.7 85 3-92 3-87 (91)
8 PF00125 Histone: Core histone 99.9 8E-22 1.7E-26 125.7 6.5 75 15-89 1-75 (75)
9 cd07981 TAF12 TATA Binding Pro 99.5 2.7E-13 5.8E-18 87.5 6.7 64 20-87 2-65 (72)
10 PLN00035 histone H4; Provision 99.4 1.7E-12 3.6E-17 89.8 5.9 67 20-91 30-96 (103)
11 cd00076 H4 Histone H4, one of 99.3 1.3E-12 2.9E-17 87.4 5.1 68 18-90 12-79 (85)
12 PTZ00015 histone H4; Provision 99.3 4.7E-12 1E-16 87.4 5.4 69 18-91 29-97 (102)
13 smart00803 TAF TATA box bindin 99.3 9.8E-12 2.1E-16 79.2 5.4 64 19-87 2-65 (65)
14 smart00417 H4 Histone H4. 99.2 1.4E-11 3.1E-16 80.6 3.7 62 18-84 12-73 (74)
15 PF00808 CBFD_NFYB_HMF: Histon 98.8 8.9E-09 1.9E-13 64.3 5.5 62 20-85 3-64 (65)
16 cd07979 TAF9 TATA Binding Prot 98.8 2E-08 4.3E-13 70.3 7.4 65 26-91 4-68 (117)
17 smart00576 BTP Bromodomain tra 98.5 3.4E-07 7.4E-12 59.3 6.2 51 38-88 20-70 (77)
18 PF15630 CENP-S: Kinetochore c 98.5 4.6E-07 9.9E-12 59.5 5.7 65 23-87 5-71 (76)
19 cd00074 H2A Histone 2A; H2A is 98.4 2.9E-07 6.3E-12 64.6 4.6 73 17-95 18-90 (115)
20 KOG0870|consensus 98.2 2E-06 4.4E-11 64.0 5.1 70 16-87 7-76 (172)
21 PF15511 CENP-T: Centromere ki 98.2 3.4E-06 7.3E-11 69.5 5.4 61 21-81 353-414 (414)
22 cd08050 TAF6 TATA Binding Prot 98.1 1E-05 2.2E-10 65.0 6.6 64 28-92 4-67 (343)
23 PF02969 TAF: TATA box binding 98.0 3.1E-05 6.7E-10 49.7 6.4 59 28-87 8-66 (66)
24 PF03847 TFIID_20kDa: Transcri 97.9 5.1E-05 1.1E-09 48.8 6.2 60 24-87 4-63 (68)
25 PF02291 TFIID-31kDa: Transcri 97.7 0.0002 4.3E-09 51.2 6.8 64 26-90 15-78 (129)
26 KOG1142|consensus 97.5 0.00017 3.7E-09 56.9 4.9 72 11-86 146-217 (258)
27 KOG3467|consensus 96.8 0.0041 8.9E-08 42.6 5.2 64 21-89 31-94 (103)
28 KOG0869|consensus 96.7 0.0035 7.6E-08 46.7 5.2 69 16-87 29-97 (168)
29 PF07524 Bromo_TP: Bromodomain 96.7 0.0062 1.4E-07 38.9 5.5 48 40-87 22-69 (77)
30 KOG3334|consensus 96.3 0.027 5.8E-07 41.3 7.2 65 27-92 17-81 (148)
31 smart00427 H2B Histone H2B. 95.9 0.065 1.4E-06 36.3 7.3 61 29-89 7-67 (89)
32 PLN00158 histone H2B; Provisio 95.7 0.074 1.6E-06 37.7 7.2 69 21-89 25-93 (116)
33 PLN00154 histone H2A; Provisio 95.6 0.028 6E-07 40.8 4.7 74 17-95 36-109 (136)
34 PTZ00463 histone H2B; Provisio 95.5 0.084 1.8E-06 37.5 7.0 68 22-89 27-94 (117)
35 smart00414 H2A Histone 2A. 95.5 0.018 3.9E-07 39.9 3.4 72 17-94 7-78 (106)
36 KOG0871|consensus 95.4 0.05 1.1E-06 40.2 5.6 69 15-86 8-76 (156)
37 PTZ00017 histone H2A; Provisio 95.2 0.023 5E-07 41.1 3.2 73 17-95 25-97 (134)
38 COG5262 HTA1 Histone H2A [Chro 95.1 0.037 8.1E-07 39.6 4.0 72 18-95 25-96 (132)
39 PLN00156 histone H2AX; Provisi 94.3 0.055 1.2E-06 39.4 3.4 73 17-95 27-99 (139)
40 PLN00157 histone H2A; Provisio 94.3 0.049 1.1E-06 39.3 3.1 73 17-95 24-96 (132)
41 PLN00153 histone H2A; Provisio 94.0 0.065 1.4E-06 38.5 3.3 73 17-95 22-94 (129)
42 KOG1756|consensus 94.0 0.079 1.7E-06 38.2 3.7 73 17-95 25-97 (131)
43 PF02269 TFIID-18kDa: Transcri 93.8 0.043 9.3E-07 36.8 1.9 59 29-87 7-65 (93)
44 PTZ00252 histone H2A; Provisio 93.0 0.15 3.1E-06 37.0 3.7 73 17-95 23-97 (134)
45 KOG2549|consensus 92.5 0.41 8.9E-06 41.7 6.4 53 38-90 25-77 (576)
46 COG5150 Class 2 transcription 91.9 0.57 1.2E-05 34.1 5.6 69 15-86 7-75 (148)
47 KOG1744|consensus 90.8 0.78 1.7E-05 33.0 5.3 64 28-91 42-105 (127)
48 COG5094 TAF9 Transcription ini 90.6 0.94 2E-05 32.9 5.6 60 27-87 18-80 (145)
49 cd07978 TAF13 The TATA Binding 87.9 3.9 8.4E-05 27.5 6.8 62 25-87 4-65 (92)
50 cd08045 TAF4 TATA Binding Prot 87.8 2 4.3E-05 32.3 5.9 56 17-73 42-97 (212)
51 PF05236 TAF4: Transcription i 87.0 1.1 2.4E-05 34.7 4.2 58 17-75 41-98 (264)
52 PF09123 DUF1931: Domain of un 85.6 2.2 4.7E-05 31.1 4.9 64 25-93 1-64 (138)
53 KOG2389|consensus 84.5 2.4 5.2E-05 35.1 5.2 50 38-87 43-92 (353)
54 KOG4336|consensus 84.3 2.4 5.2E-05 34.7 5.1 48 41-88 22-69 (323)
55 KOG1757|consensus 82.7 1.8 4E-05 30.9 3.4 70 23-94 31-100 (131)
56 COG5248 TAF19 Transcription in 77.7 14 0.0003 26.3 6.5 61 25-87 11-71 (126)
57 KOG3901|consensus 77.2 16 0.00034 25.7 6.6 64 21-87 7-70 (109)
58 COG5095 TAF6 Transcription ini 69.4 9.6 0.00021 31.9 4.6 62 27-89 9-70 (450)
59 COG1224 TIP49 DNA helicase TIP 67.9 12 0.00026 31.9 4.9 71 18-88 354-431 (450)
60 KOG1657|consensus 60.9 15 0.00033 28.6 4.1 72 14-86 66-137 (236)
61 PF10911 DUF2717: Protein of u 60.3 17 0.00036 24.1 3.6 60 6-68 2-64 (77)
62 KOG1658|consensus 57.1 8.5 0.00018 28.7 2.0 50 36-85 71-121 (162)
63 PF09415 CENP-X: CENP-S associ 57.0 17 0.00037 23.4 3.2 55 29-83 5-62 (72)
64 PF10788 DUF2603: Protein of u 54.5 8.5 0.00018 28.0 1.6 32 3-35 97-128 (137)
65 TIGR02902 spore_lonB ATP-depen 53.2 49 0.0011 28.2 6.2 50 38-87 279-330 (531)
66 COG5208 HAP5 CCAAT-binding fac 50.0 38 0.00082 27.0 4.7 68 23-92 110-178 (286)
67 TIGR00764 lon_rel lon-related 49.7 98 0.0021 27.0 7.6 64 26-89 315-391 (608)
68 KOG2680|consensus 47.1 66 0.0014 27.2 5.9 70 19-88 352-428 (454)
69 PRK07452 DNA polymerase III su 46.2 55 0.0012 25.3 5.1 59 26-86 136-196 (326)
70 cd08048 TAF11 TATA Binding Pro 42.4 98 0.0021 20.4 6.3 63 20-87 17-82 (85)
71 TIGR03015 pepcterm_ATPase puta 39.3 1.2E+02 0.0025 22.4 5.8 49 39-87 213-264 (269)
72 smart00350 MCM minichromosome 34.5 64 0.0014 27.2 4.1 32 61-92 476-507 (509)
73 PRK05907 hypothetical protein; 33.7 99 0.0021 24.6 4.9 66 20-85 131-199 (311)
74 PF13654 AAA_32: AAA domain; P 32.9 2.5E+02 0.0054 24.2 7.4 66 23-89 430-506 (509)
75 PF04914 DltD_C: DltD C-termin 32.5 33 0.00071 24.3 1.8 24 79-102 35-58 (130)
76 KOG1942|consensus 32.2 1.5E+02 0.0033 25.1 5.8 52 38-89 383-438 (456)
77 TIGR02030 BchI-ChlI magnesium 31.5 1.2E+02 0.0027 24.5 5.1 56 38-93 251-313 (337)
78 PF07962 Swi3: Replication For 29.9 23 0.00051 23.1 0.6 24 9-32 39-62 (83)
79 PF11823 DUF3343: Protein of u 29.4 51 0.0011 20.4 2.1 22 81-102 13-34 (73)
80 PF06709 DUF1196: Protein of u 29.2 36 0.00079 20.6 1.3 19 17-35 12-30 (51)
81 PRK14562 haloacid dehalogenase 27.1 89 0.0019 23.5 3.4 25 38-62 71-95 (204)
82 PRK05629 hypothetical protein; 26.0 1.8E+02 0.0039 22.6 5.1 59 26-85 129-188 (318)
83 COG2118 DNA-binding protein [G 25.0 1.6E+02 0.0035 20.9 4.1 32 50-89 68-99 (116)
84 PRK08487 DNA polymerase III su 24.6 2.1E+02 0.0046 22.4 5.3 47 38-86 151-197 (328)
85 PF06075 DUF936: Plant protein 24.2 1.5E+02 0.0033 26.1 4.7 41 25-68 325-367 (579)
86 COG5624 TAF61 Transcription in 23.0 19 0.0004 31.0 -1.0 71 21-98 385-455 (505)
87 PRK00411 cdc6 cell division co 22.6 3.8E+02 0.0082 21.0 7.1 48 41-88 228-281 (394)
88 PRK07914 hypothetical protein; 20.8 2.1E+02 0.0045 22.3 4.5 59 26-85 131-190 (320)
89 PF08369 PCP_red: Proto-chloro 20.6 1.4E+02 0.003 17.3 2.7 18 68-85 27-44 (45)
90 PF08145 BOP1NT: BOP1NT (NUC16 20.3 34 0.00074 27.3 0.0 44 43-91 21-66 (260)
91 PRK13877 conjugal transfer rel 20.2 1.7E+02 0.0036 20.4 3.5 52 39-91 14-67 (114)
92 cd00913 PCD_DCoH_subfamily_a P 20.2 55 0.0012 20.6 1.0 14 77-90 62-75 (76)
93 CHL00081 chlI Mg-protoporyphyr 20.2 2.8E+02 0.0062 22.7 5.3 57 38-94 264-327 (350)
No 1
>PLN00160 histone H3; Provisional
Probab=100.00 E-value=5.1e-47 Score=258.90 Aligned_cols=90 Identities=59% Similarity=0.826 Sum_probs=87.1
Q ss_pred chhhhhhhcccccchhhcccchHHHHHHHHHhhcc-cccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCccc
Q psy1398 3 WVARERFQKPMKSTELLIRKLPFQRLVREIAQDFK-TDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKD 81 (102)
Q Consensus 3 ~valrEIr~yQkst~lLIpk~pF~RLVrEI~~~~~-~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kD 81 (102)
+|||+|||+|||||++||||+||+||||||++++. +++|||++|+.|||||+|+|||++|||+++||+||||||||++|
T Consensus 5 t~aLrEIR~yQkst~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD 84 (97)
T PLN00160 5 EKALKEIKMYQKSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKD 84 (97)
T ss_pred cHHHHHHHHHccchhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhh
Confidence 68999999999999999999999999999999986 56999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhh
Q psy1398 82 IQLAAESVENA 92 (102)
Q Consensus 82 i~La~ri~~~~ 92 (102)
|+|+.+|+|+.
T Consensus 85 ~~L~~rirg~~ 95 (97)
T PLN00160 85 MQLARRIRGQT 95 (97)
T ss_pred HHHHHHhhccc
Confidence 99999999874
No 2
>PLN00161 histone H3; Provisional
Probab=100.00 E-value=3.9e-45 Score=261.73 Aligned_cols=90 Identities=60% Similarity=0.833 Sum_probs=86.9
Q ss_pred chhhhhhhcccccchhhcccchHHHHHHHHHhhcc-cccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCccc
Q psy1398 3 WVARERFQKPMKSTELLIRKLPFQRLVREIAQDFK-TDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKD 81 (102)
Q Consensus 3 ~valrEIr~yQkst~lLIpk~pF~RLVrEI~~~~~-~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kD 81 (102)
+|||+|||+||+||+|||||+||+||||||++++. +++|||++|+.|||||+|+|||++|||+|+||+||||||||++|
T Consensus 39 tvaLrEIR~yQkst~lLIpklPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kD 118 (135)
T PLN00161 39 TVALREIRKYQKSTELLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKD 118 (135)
T ss_pred chHHHHHHHHccccccccccccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhh
Confidence 68999999999999999999999999999999996 58999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhh
Q psy1398 82 IQLAAESVENA 92 (102)
Q Consensus 82 i~La~ri~~~~ 92 (102)
|+||.+|+|..
T Consensus 119 m~La~rirg~~ 129 (135)
T PLN00161 119 MQLARRIRGPI 129 (135)
T ss_pred HHHHHHhcccc
Confidence 99999999753
No 3
>smart00428 H3 Histone H3.
Probab=100.00 E-value=8.9e-45 Score=250.81 Aligned_cols=89 Identities=76% Similarity=0.975 Sum_probs=87.0
Q ss_pred chhhhhhhcccccchhhcccchHHHHHHHHHhhccc--ccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcc
Q psy1398 3 WVARERFQKPMKSTELLIRKLPFQRLVREIAQDFKT--DLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPK 80 (102)
Q Consensus 3 ~valrEIr~yQkst~lLIpk~pF~RLVrEI~~~~~~--~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~k 80 (102)
+|||+|||+||+||++||||+||+||||||++++++ ++|||++|++||||++|+|++++||||++||+||||||||++
T Consensus 13 ~~aLrEIr~yQkst~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~k 92 (105)
T smart00428 13 QVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPK 92 (105)
T ss_pred chHHHHHHHHccCcccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHh
Confidence 689999999999999999999999999999999987 999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHHHh
Q psy1398 81 DIQLAAESVEN 91 (102)
Q Consensus 81 Di~La~ri~~~ 91 (102)
||+||.+|+|+
T Consensus 93 Di~La~rir~~ 103 (105)
T smart00428 93 DIQLARRIRGE 103 (105)
T ss_pred hHHHHHHHhcc
Confidence 99999999985
No 4
>PTZ00018 histone H3; Provisional
Probab=100.00 E-value=6.1e-45 Score=261.19 Aligned_cols=89 Identities=81% Similarity=1.064 Sum_probs=87.2
Q ss_pred chhhhhhhcccccchhhcccchHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccH
Q psy1398 3 WVARERFQKPMKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDI 82 (102)
Q Consensus 3 ~valrEIr~yQkst~lLIpk~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi 82 (102)
.|||+|||+||+||+|||||+||+||||||++++++++|||++|++|||||+|+|||++|||+|+||+||||||||++||
T Consensus 46 t~aLrEIr~yQkst~lLI~k~pF~RLVREI~~~~~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~ 125 (136)
T PTZ00018 46 TVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDI 125 (136)
T ss_pred hhHHHHHHHHcccchhccccccHHHHHHHHHHHcCCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHh
Q psy1398 83 QLAAESVEN 91 (102)
Q Consensus 83 ~La~ri~~~ 91 (102)
+|+.+|+|+
T Consensus 126 ~L~~rirg~ 134 (136)
T PTZ00018 126 QLARRIRGE 134 (136)
T ss_pred HHHHHhccc
Confidence 999999975
No 5
>PLN00121 histone H3; Provisional
Probab=100.00 E-value=8.1e-45 Score=260.55 Aligned_cols=89 Identities=82% Similarity=1.066 Sum_probs=87.2
Q ss_pred chhhhhhhcccccchhhcccchHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccH
Q psy1398 3 WVARERFQKPMKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDI 82 (102)
Q Consensus 3 ~valrEIr~yQkst~lLIpk~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi 82 (102)
.|||+|||+||+||+|||||+||+||||||++++++++|||++|++|||||+|+|||++|||+++||+||||||||++||
T Consensus 46 t~aLrEIr~yQkst~lLI~k~pF~RLVREI~~~~~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~ 125 (136)
T PLN00121 46 TVALREIRKYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDI 125 (136)
T ss_pred hHHHHHHHHhccccccccccccHHHHHHHHHHHhCccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhH
Confidence 48999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHh
Q psy1398 83 QLAAESVEN 91 (102)
Q Consensus 83 ~La~ri~~~ 91 (102)
+|+.+|+|+
T Consensus 126 ~L~~rirg~ 134 (136)
T PLN00121 126 QLARRIRGE 134 (136)
T ss_pred HHHHHhccc
Confidence 999999975
No 6
>KOG1745|consensus
Probab=100.00 E-value=7.9e-44 Score=255.37 Aligned_cols=89 Identities=80% Similarity=1.048 Sum_probs=87.2
Q ss_pred chhhhhhhcccccchhhcccchHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccH
Q psy1398 3 WVARERFQKPMKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDI 82 (102)
Q Consensus 3 ~valrEIr~yQkst~lLIpk~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi 82 (102)
.||++|||+|||||+|||+|+||+||||||+++|..++|||++|+.|||||+|+|||+||||+|+||+||||||||++||
T Consensus 47 ~~al~eirkyQkstdLlI~K~PFqRlvrei~q~f~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdi 126 (137)
T KOG1745|consen 47 TVALREIRKYQKSTDLLIRKLPFQRLVREIAQDFKTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDI 126 (137)
T ss_pred hHHHHHHHHHHhhhHHHhhcCcHHHHhHHHHhcccccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccce
Confidence 48999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHh
Q psy1398 83 QLAAESVEN 91 (102)
Q Consensus 83 ~La~ri~~~ 91 (102)
|||++|+|.
T Consensus 127 QlArrirg~ 135 (137)
T KOG1745|consen 127 QLARRIRGE 135 (137)
T ss_pred ehhhhcccC
Confidence 999999985
No 7
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.95 E-value=3.9e-28 Score=164.26 Aligned_cols=85 Identities=38% Similarity=0.465 Sum_probs=80.9
Q ss_pred chhhhhhhcccccchhhcccchHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccH
Q psy1398 3 WVARERFQKPMKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDI 82 (102)
Q Consensus 3 ~valrEIr~yQkst~lLIpk~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi 82 (102)
.++++|+|+||+|+.++||++||+|++|+. ++.|||++|.++||+++|.|+.+++++|+.||.|+||+||+++||
T Consensus 3 ~~~~~~~r~~~~~~~~~Lp~apv~Ri~r~~-----~~~Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI 77 (91)
T COG2036 3 AVGLKEIRRYQRSTDLLLPKAPVRRILRKA-----GAERVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDI 77 (91)
T ss_pred cchHHHHHhhhhhhhhhcCchHHHHHHHHH-----hHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHH
Confidence 578999999999999999999999999999 555999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhh
Q psy1398 83 QLAAESVENA 92 (102)
Q Consensus 83 ~La~ri~~~~ 92 (102)
+|+.+.++..
T Consensus 78 ~la~~~~~~~ 87 (91)
T COG2036 78 KLALKRLGRR 87 (91)
T ss_pred HHHHHHhccc
Confidence 9999988754
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=99.86 E-value=8e-22 Score=125.70 Aligned_cols=75 Identities=45% Similarity=0.612 Sum_probs=71.3
Q ss_pred cchhhcccchHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHHHH
Q psy1398 15 STELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAESV 89 (102)
Q Consensus 15 st~lLIpk~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri~ 89 (102)
+|..+||+.||.|++|++..+....+||+++|+.+||.++|.+++++|++|+.+|.|+||+||+++||++|.+++
T Consensus 1 ~~~~~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r~~ 75 (75)
T PF00125_consen 1 RTRRLIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVRID 75 (75)
T ss_dssp HHSHSSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHHHT
T ss_pred CcccccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHhcC
Confidence 467899999999999999998877799999999999999999999999999999999999999999999999874
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=99.45 E-value=2.7e-13 Score=87.47 Aligned_cols=64 Identities=28% Similarity=0.349 Sum_probs=56.7
Q ss_pred cccchHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHH
Q psy1398 20 IRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAE 87 (102)
Q Consensus 20 Ipk~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~r 87 (102)
++|--.+.|++++ .+..|++++|.++||+.+|+|+.+++++|..+|.|+||+||+++||+|+.+
T Consensus 2 ~~k~~l~~lv~~i----d~~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~ 65 (72)
T cd07981 2 LTKRKLQELLKEI----DPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLE 65 (72)
T ss_pred CcHHHHHHHHHhh----CCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 4555566777777 346999999999999999999999999999999999999999999999964
No 10
>PLN00035 histone H4; Provisional
Probab=99.35 E-value=1.7e-12 Score=89.76 Aligned_cols=67 Identities=21% Similarity=0.218 Sum_probs=64.3
Q ss_pred cccchHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHHHHHh
Q psy1398 20 IRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAESVEN 91 (102)
Q Consensus 20 Ipk~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri~~~ 91 (102)
||++|..||+|.. +..|++.+|.+++.++.|.|+.++..||...|.||+|+||+.+|+.+|.+-.++
T Consensus 30 ipk~~IrRLARr~-----GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~ 96 (103)
T PLN00035 30 ITKPAIRRLARRG-----GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGR 96 (103)
T ss_pred CCHHHHHHHHHHc-----CcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCC
Confidence 9999999999998 899999999999999999999999999999999999999999999999876654
No 11
>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=99.35 E-value=1.3e-12 Score=87.40 Aligned_cols=68 Identities=24% Similarity=0.240 Sum_probs=64.4
Q ss_pred hhcccchHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHHHHH
Q psy1398 18 LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAESVE 90 (102)
Q Consensus 18 lLIpk~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri~~ 90 (102)
-=|||+|..||+|.- |..|++.++.+++.++.|.|+.++..||...|.||+|+||+..|+.++.+-.|
T Consensus 12 ~gi~k~~I~RLarr~-----GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g 79 (85)
T cd00076 12 KGITKPAIRRLARRG-----GVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQG 79 (85)
T ss_pred ccCCHHHHHHHHHHc-----CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCC
Confidence 349999999999988 89999999999999999999999999999999999999999999999987665
No 12
>PTZ00015 histone H4; Provisional
Probab=99.29 E-value=4.7e-12 Score=87.38 Aligned_cols=69 Identities=20% Similarity=0.186 Sum_probs=64.9
Q ss_pred hhcccchHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHHHHHh
Q psy1398 18 LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAESVEN 91 (102)
Q Consensus 18 lLIpk~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri~~~ 91 (102)
--||++|..||+|.. +..|++.++.+.+.++.|.|+.++..||..+|.||+|+||+.+|+.+|.+-.++
T Consensus 29 ~gI~k~~IrRLarr~-----GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~ 97 (102)
T PTZ00015 29 RGITKGAIRRLARRG-----GVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGR 97 (102)
T ss_pred cCCCHHHHHHHHHHc-----CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCC
Confidence 349999999999988 999999999999999999999999999999999999999999999999876554
No 13
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=99.27 E-value=9.8e-12 Score=79.17 Aligned_cols=64 Identities=19% Similarity=0.194 Sum_probs=61.0
Q ss_pred hcccchHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHH
Q psy1398 19 LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAE 87 (102)
Q Consensus 19 LIpk~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~r 87 (102)
.+|+.|..|+.+.. |-.|++++|..+|.+..|.++-++.++|..++.|+||.||+++||.+|.+
T Consensus 2 ~~p~~~i~ria~~~-----Gi~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 2 WLPKETIKDVAESL-----GIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred CCCHHHHHHHHHHC-----CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 57999999999988 88999999999999999999999999999999999999999999999863
No 14
>smart00417 H4 Histone H4.
Probab=99.20 E-value=1.4e-11 Score=80.65 Aligned_cols=62 Identities=21% Similarity=0.211 Sum_probs=59.0
Q ss_pred hhcccchHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHH
Q psy1398 18 LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQL 84 (102)
Q Consensus 18 lLIpk~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~L 84 (102)
--|||+|..||+|.- |..|+++++.+.+.++.|.|+.++..||..+|.||+|+||+..|+..
T Consensus 12 ~gI~k~~IrRLaRr~-----GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~ 73 (74)
T smart00417 12 QGITKPAIRRLARRG-----GVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVY 73 (74)
T ss_pred cCCCHHHHHHHHHHc-----CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHhee
Confidence 349999999999988 99999999999999999999999999999999999999999999864
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=98.83 E-value=8.9e-09 Score=64.29 Aligned_cols=62 Identities=26% Similarity=0.306 Sum_probs=53.5
Q ss_pred cccchHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHH
Q psy1398 20 IRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLA 85 (102)
Q Consensus 20 Ipk~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La 85 (102)
+|.+...|++|+. .+..+++.+|..+++.++|.|+..|...|+..|.+.+|.||+.+|+.-|
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 6788888888876 3567899999999999999999999999999999999999999999866
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=98.81 E-value=2e-08 Score=70.28 Aligned_cols=65 Identities=20% Similarity=0.345 Sum_probs=58.4
Q ss_pred HHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHHHHHh
Q psy1398 26 QRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAESVEN 91 (102)
Q Consensus 26 ~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri~~~ 91 (102)
.++|..|..+. |..++++++...|-|.++.|..++..||...|.||||.||+.+|++||...+..
T Consensus 4 ~~~v~~iLk~~-Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~ 68 (117)
T cd07979 4 ARVIAAILKSM-GITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVD 68 (117)
T ss_pred HHHHHHHHHHC-CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhc
Confidence 46666676544 677999999999999999999999999999999999999999999999888776
No 17
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=98.52 E-value=3.4e-07 Score=59.31 Aligned_cols=51 Identities=27% Similarity=0.197 Sum_probs=48.2
Q ss_pred cccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHHH
Q psy1398 38 TDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAES 88 (102)
Q Consensus 38 ~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri 88 (102)
|-.+++++|++.|.+..|.|+..+.+.+...|.|++|.++++.|+.++..-
T Consensus 20 Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~ 70 (77)
T smart00576 20 GFDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALEN 70 (77)
T ss_pred CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 677999999999999999999999999999999999999999999998743
No 18
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=98.47 E-value=4.6e-07 Score=59.52 Aligned_cols=65 Identities=26% Similarity=0.245 Sum_probs=52.4
Q ss_pred chHHHHHHHHHhhc--ccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHH
Q psy1398 23 LPFQRLVREIAQDF--KTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAE 87 (102)
Q Consensus 23 ~pF~RLVrEI~~~~--~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~r 87 (102)
+.+..-|-+|+++- ..+..++++++.+|-|.+=.++..+.+|--..|.||||.||+++|+.|..|
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 34444555666654 367899999999999999999999999999999999999999999999864
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=98.45 E-value=2.9e-07 Score=64.64 Aligned_cols=73 Identities=21% Similarity=0.203 Sum_probs=64.6
Q ss_pred hhhcccchHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHHHHHhhccc
Q psy1398 17 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAESVENARLR 95 (102)
Q Consensus 17 ~lLIpk~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri~~~~~~~ 95 (102)
.|.+|-.++.|+.|+-. ...|++++|...|-...|.+..+++|.|...|.|.|+.+|+++|++++.+ .+..|+
T Consensus 18 gL~fPV~ri~R~Lk~~~----~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~--nD~EL~ 90 (115)
T cd00074 18 GLQFPVGRIHRYLKKGR----YAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVR--NDEELN 90 (115)
T ss_pred CccCcHHHHHHHHHcCc----cccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHh--ccHHHH
Confidence 78999999999999731 57899999999999999999999999999999999999999999999954 444443
No 20
>KOG0870|consensus
Probab=98.23 E-value=2e-06 Score=64.01 Aligned_cols=70 Identities=24% Similarity=0.320 Sum_probs=64.3
Q ss_pred chhhcccchHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHH
Q psy1398 16 TELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAE 87 (102)
Q Consensus 16 t~lLIpk~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~r 87 (102)
.+|.+|++-..||||+...+. +.-++++|..|++.+|--|+.-|.-.|+..|.-.+|+|++++|+-=++.
T Consensus 7 ~dl~lP~AiI~rlvke~l~E~--~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~ 76 (172)
T KOG0870|consen 7 EDLNLPNAIITRLVKEVLPES--NVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALD 76 (172)
T ss_pred HHhhccHHHHHHHHHHhCccc--cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHH
Confidence 368899999999999998865 5889999999999999999999999999999999999999999876654
No 21
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=98.16 E-value=3.4e-06 Score=69.52 Aligned_cols=61 Identities=26% Similarity=0.293 Sum_probs=42.6
Q ss_pred ccchHHHHHHHHHhh-cccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCccc
Q psy1398 21 RKLPFQRLVREIAQD-FKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKD 81 (102)
Q Consensus 21 pk~pF~RLVrEI~~~-~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kD 81 (102)
|..+..+|+.-.++. +....+++++|+.+|.+++|-|.-+|-+|--..|.||||+||...|
T Consensus 353 P~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 353 PPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp -HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred CccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 444444444444442 3367899999999999999999999999999999999999999877
No 22
>cd08050 TAF6 TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as
Probab=98.08 E-value=1e-05 Score=65.02 Aligned_cols=64 Identities=17% Similarity=0.163 Sum_probs=56.2
Q ss_pred HHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHHHHHhh
Q psy1398 28 LVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAESVENA 92 (102)
Q Consensus 28 LVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri~~~~ 92 (102)
.|+.|+... |..|.+.+|..+|.+-+|.++-++.++|..+|.|+||.|++++||++|.+.+.-.
T Consensus 4 ~i~~ia~~~-Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~e 67 (343)
T cd08050 4 SIKLIAESL-GIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNVE 67 (343)
T ss_pred HHHHHHHHc-CCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCCC
Confidence 456665543 5669999999999999999999999999999999999999999999999887543
No 23
>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=97.99 E-value=3.1e-05 Score=49.67 Aligned_cols=59 Identities=25% Similarity=0.287 Sum_probs=46.6
Q ss_pred HHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHH
Q psy1398 28 LVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAE 87 (102)
Q Consensus 28 LVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~r 87 (102)
-||.+++..+ -.-.+.++..+|.+-+|.-+-++.++|..++.|+||.+++++|+..|.|
T Consensus 8 svk~iAes~G-i~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 8 SVKDIAESLG-ISNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp HHHHHHHHTT----B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred HHHHHHHHcC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 4566666554 2357899999999999999999999999999999999999999998864
No 24
>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=97.91 E-value=5.1e-05 Score=48.78 Aligned_cols=60 Identities=25% Similarity=0.309 Sum_probs=47.6
Q ss_pred hHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHH
Q psy1398 24 PFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAE 87 (102)
Q Consensus 24 pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~r 87 (102)
-++.||++| .+...+.+++-+.|.+.|++|+.+..+.|..+|.|.|--||.++|+++...
T Consensus 4 ~l~~Lv~~i----Dp~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Le 63 (68)
T PF03847_consen 4 KLQELVKQI----DPNEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLE 63 (68)
T ss_dssp HHHHHHHCC-----SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHH
T ss_pred HHHHHHHHc----CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHH
Confidence 355666666 568899999999999999999999999999999999999999999999863
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=97.67 E-value=0.0002 Score=51.21 Aligned_cols=64 Identities=28% Similarity=0.348 Sum_probs=51.9
Q ss_pred HHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHHHHH
Q psy1398 26 QRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAESVE 90 (102)
Q Consensus 26 ~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri~~ 90 (102)
.|++..|..+.+ -..+++.++.-|-|.+=.|..++++||...|.||+|.+|..+|++||...+-
T Consensus 15 a~~i~~iL~~~G-v~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~ 78 (129)
T PF02291_consen 15 ARVIHLILKSMG-VTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRL 78 (129)
T ss_dssp HHHHHHHHHHTT----B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT-
T ss_pred HHHHHHHHHHcC-CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHH
Confidence 478888887775 3357999999999999999999999999999999999999999999976553
No 26
>KOG1142|consensus
Probab=97.50 E-value=0.00017 Score=56.87 Aligned_cols=72 Identities=19% Similarity=0.271 Sum_probs=64.2
Q ss_pred cccccchhhcccchHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHH
Q psy1398 11 KPMKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAA 86 (102)
Q Consensus 11 ~yQkst~lLIpk~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ 86 (102)
.++-+++.++-|--...||++| .++....+++-+.|.|.|++|+.++-.-|-.+|+|.|--||.++||+|+.
T Consensus 146 ~~~~~~~~il~k~kl~dLvqqI----d~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhL 217 (258)
T KOG1142|consen 146 QDEPGNNPILSKRKLDDLVQQI----DGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHL 217 (258)
T ss_pred cccCCCCccccccchhHHHHhh----cCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeee
Confidence 4556777788888888888888 46778889999999999999999999999999999999999999999986
No 27
>KOG3467|consensus
Probab=96.76 E-value=0.0041 Score=42.57 Aligned_cols=64 Identities=22% Similarity=0.217 Sum_probs=55.2
Q ss_pred ccchHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHHHH
Q psy1398 21 RKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAESV 89 (102)
Q Consensus 21 pk~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri~ 89 (102)
-|....||.|-- +--|+..-..+....++..|+.+...+|...+.||||+||+.-|+--+.+-.
T Consensus 31 tKpaIRRlARr~-----GVkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~ 94 (103)
T KOG3467|consen 31 TKPAIRRLARRG-----GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQ 94 (103)
T ss_pred chHHHHHHHHhc-----CcchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHc
Confidence 367777888766 6678888888999999999999999999999999999999999997776533
No 28
>KOG0869|consensus
Probab=96.74 E-value=0.0035 Score=46.67 Aligned_cols=69 Identities=14% Similarity=0.192 Sum_probs=61.4
Q ss_pred chhhcccchHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHH
Q psy1398 16 TELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAE 87 (102)
Q Consensus 16 t~lLIpk~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~r 87 (102)
.+-++|.+-..|+.|.+.- .+-+++++|-+..||.+-.|+-=+-..|..-+---||+||+.+|+-.|+-
T Consensus 29 qDr~LPIANV~RIMK~~lP---~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~ 97 (168)
T KOG0869|consen 29 QDRFLPIANVSRIMKKALP---ANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMS 97 (168)
T ss_pred hhhhccHHHHHHHHHhcCC---cccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHH
Confidence 3567899999999999854 77899999999999999999998888888888899999999999988864
No 29
>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=96.69 E-value=0.0062 Score=38.90 Aligned_cols=48 Identities=27% Similarity=0.204 Sum_probs=45.3
Q ss_pred cccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHH
Q psy1398 40 LRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAE 87 (102)
Q Consensus 40 ~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~r 87 (102)
-..+++|++.|-+.+..|+..+...+...|-|++|-...+.|+.++..
T Consensus 22 ~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~ 69 (77)
T PF07524_consen 22 DSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALE 69 (77)
T ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 478999999999999999999999999999999999999999998864
No 30
>KOG3334|consensus
Probab=96.25 E-value=0.027 Score=41.35 Aligned_cols=65 Identities=22% Similarity=0.360 Sum_probs=53.2
Q ss_pred HHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHHHHHhh
Q psy1398 27 RLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAESVENA 92 (102)
Q Consensus 27 RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri~~~~ 92 (102)
+++..|..+++ -.-+....+.-|=|.+=.|.+.+++||...+.||++-||..+|++||...+.+.
T Consensus 17 ~~i~~iL~s~G-I~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~~ 81 (148)
T KOG3334|consen 17 RVIASILKSLG-IQEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRVDH 81 (148)
T ss_pred HHHHHHHHHcC-ccccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHhcc
Confidence 55666655554 334567778888899999999999999999999999999999999998776543
No 31
>smart00427 H2B Histone H2B.
Probab=95.92 E-value=0.065 Score=36.32 Aligned_cols=61 Identities=15% Similarity=0.205 Sum_probs=50.3
Q ss_pred HHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHHHH
Q psy1398 29 VREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAESV 89 (102)
Q Consensus 29 VrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri~ 89 (102)
+..+......+..+++.|+..+--..-+..-.+..+|..++...||.||+.+|||-|.++.
T Consensus 7 i~kvLKqVhpd~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~ 67 (89)
T smart00427 7 IYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLI 67 (89)
T ss_pred HHHHHHHhCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHH
Confidence 3334334456778999999998888888888888889999999999999999999998864
No 32
>PLN00158 histone H2B; Provisional
Probab=95.72 E-value=0.074 Score=37.68 Aligned_cols=69 Identities=13% Similarity=0.197 Sum_probs=58.0
Q ss_pred ccchHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHHHH
Q psy1398 21 RKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAESV 89 (102)
Q Consensus 21 pk~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri~ 89 (102)
++-.|..-+..+......+..+++.|+..+--...++...+..+|..++...+|.||..+|||-+.++.
T Consensus 25 r~esy~~YI~kVLKQVhPd~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLv 93 (116)
T PLN00158 25 KTETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLI 93 (116)
T ss_pred ccccHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHh
Confidence 355666666666666677889999999998888888888888899999999999999999999998764
No 33
>PLN00154 histone H2A; Provisional
Probab=95.55 E-value=0.028 Score=40.80 Aligned_cols=74 Identities=18% Similarity=0.147 Sum_probs=62.7
Q ss_pred hhhcccchHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHHHHHhhccc
Q psy1398 17 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAESVENARLR 95 (102)
Q Consensus 17 ~lLIpk~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri~~~~~~~ 95 (102)
.|.+|-....|+.|+-.. ...|+.++|..-|-.+.|....+++|-|...|...|+..|++++++||. +.+..|+
T Consensus 36 gL~FPVgRi~r~Lk~g~~---~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAI--rnDeEL~ 109 (136)
T PLN00154 36 GLQFPVGRIHRQLKQRVS---AHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAI--RGDEELD 109 (136)
T ss_pred CccCchHHHHHHHHhhhh---hccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhc--cCcHHHH
Confidence 677888888888888632 3579999999999999999999999999999999999999999999995 4444443
No 34
>PTZ00463 histone H2B; Provisional
Probab=95.54 E-value=0.084 Score=37.47 Aligned_cols=68 Identities=10% Similarity=0.102 Sum_probs=57.3
Q ss_pred cchHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHHHH
Q psy1398 22 KLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAESV 89 (102)
Q Consensus 22 k~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri~ 89 (102)
+-.|..-+..+......+..+++.|+..+--...+....+..+|..++...+|.||..+|||-+.++.
T Consensus 27 ~esy~~YI~KVLKqVhPd~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLl 94 (117)
T PTZ00463 27 YDSYGLYIFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLV 94 (117)
T ss_pred cchHHHHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhc
Confidence 45566666666666677888999999998888888888888899999999999999999999998864
No 35
>smart00414 H2A Histone 2A.
Probab=95.48 E-value=0.018 Score=39.89 Aligned_cols=72 Identities=24% Similarity=0.222 Sum_probs=60.6
Q ss_pred hhhcccchHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHHHHHhhcc
Q psy1398 17 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAESVENARL 94 (102)
Q Consensus 17 ~lLIpk~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri~~~~~~ 94 (102)
+|.+|-.-|.|+.|+- ....|+.++|..-|-...|....+++|-|...|...|+..|+++|++++. +.+..|
T Consensus 7 gL~fPVgRi~r~Lk~~----~~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi--~nD~EL 78 (106)
T smart00414 7 GLQFPVGRIHRLLRKG----TYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAI--RNDEEL 78 (106)
T ss_pred CccCchHHHHHHHHcC----ccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhc--cCCHHH
Confidence 5777888888888765 23569999999999999999999999999999999999999999999994 444443
No 36
>KOG0871|consensus
Probab=95.37 E-value=0.05 Score=40.18 Aligned_cols=69 Identities=17% Similarity=0.267 Sum_probs=62.5
Q ss_pred cchhhcccchHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHH
Q psy1398 15 STELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAA 86 (102)
Q Consensus 15 st~lLIpk~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ 86 (102)
.-++-+||+..+.+|+|+.. .+.||..+|-+.+++.+=.|+--+...||..+---.++||.++-+.=|.
T Consensus 8 dde~sLPkAtv~KmIke~lP---~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KAL 76 (156)
T KOG0871|consen 8 DDELSLPKATVNKMIKEMLP---KDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKAL 76 (156)
T ss_pred cccccCcHHHHHHHHHHhCC---cccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHH
Confidence 34677999999999999964 7899999999999999999999999999999999999999998876554
No 37
>PTZ00017 histone H2A; Provisional
Probab=95.16 E-value=0.023 Score=41.09 Aligned_cols=73 Identities=22% Similarity=0.194 Sum_probs=62.2
Q ss_pred hhhcccchHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHHHHHhhccc
Q psy1398 17 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAESVENARLR 95 (102)
Q Consensus 17 ~lLIpk~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri~~~~~~~ 95 (102)
.|.+|-..+.|+.|+-. ...|+.+.|..-|-.+.|....+++|-|...|...|+..|++++++|+. +.+..|+
T Consensus 25 gL~FPVgRi~R~Lk~g~----~a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI--~nDeEL~ 97 (134)
T PTZ00017 25 GLQFPVGRVHRYLKKGR----YAKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAI--RNDEELN 97 (134)
T ss_pred CcccchHHHHHHHhccc----hhccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhc--cCcHHHH
Confidence 68888888888887642 4569999999999999999999999999999999999999999999994 4444443
No 38
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=95.08 E-value=0.037 Score=39.64 Aligned_cols=72 Identities=22% Similarity=0.275 Sum_probs=58.4
Q ss_pred hhcccchHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHHHHHhhccc
Q psy1398 18 LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAESVENARLR 95 (102)
Q Consensus 18 lLIpk~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri~~~~~~~ 95 (102)
+..|--...|+.| .-....|+.++|..++-...|....++.|-|-..|.--|-+.|+|+-+||| ||++-.|+
T Consensus 25 l~fpvgrvkr~lk----~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlA--IrnD~EL~ 96 (132)
T COG5262 25 LIFPVGRVKRLLK----KGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLA--IRNDEELN 96 (132)
T ss_pred ccccHHHHHHHHH----cCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHH--hcCcHHHH
Confidence 4444444444444 334789999999999999999999999999999999999999999999999 66666554
No 39
>PLN00156 histone H2AX; Provisional
Probab=94.30 E-value=0.055 Score=39.36 Aligned_cols=73 Identities=23% Similarity=0.220 Sum_probs=60.7
Q ss_pred hhhcccchHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHHHHHhhccc
Q psy1398 17 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAESVENARLR 95 (102)
Q Consensus 17 ~lLIpk~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri~~~~~~~ 95 (102)
.|.+|-..+.|+.|+- ....|+.+.|...|-...|....+++|-|...|...|+..|+++.++|+. +.+..|+
T Consensus 27 gL~FPVgRi~R~Lk~g----~ya~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAI--rnDeEL~ 99 (139)
T PLN00156 27 GLQFPVGRIARFLKAG----KYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAV--RNDEELS 99 (139)
T ss_pred CcccchHHHHHHHhcC----ChhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhc--cCcHHHH
Confidence 5777777777777764 24579999999999999999999999999999999999999999999994 4444443
No 40
>PLN00157 histone H2A; Provisional
Probab=94.29 E-value=0.049 Score=39.29 Aligned_cols=73 Identities=23% Similarity=0.221 Sum_probs=61.4
Q ss_pred hhhcccchHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHHHHHhhccc
Q psy1398 17 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAESVENARLR 95 (102)
Q Consensus 17 ~lLIpk~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri~~~~~~~ 95 (102)
.|.+|-..+.|+.|+- ....|+.+.|..-|-...|....+++|-|...|...|+..|++++++|+. +.+..|+
T Consensus 24 gL~FPVgRi~R~Lk~g----~~a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI--~nDeEL~ 96 (132)
T PLN00157 24 GLQFPVGRIARYLKAG----KYATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAV--RNDEELS 96 (132)
T ss_pred CcccchHHHHHHHhcC----chhhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhcc--cCcHHHH
Confidence 6778877788887763 24679999999999999999999999999999999999999999999994 4444443
No 41
>PLN00153 histone H2A; Provisional
Probab=94.04 E-value=0.065 Score=38.54 Aligned_cols=73 Identities=23% Similarity=0.210 Sum_probs=61.2
Q ss_pred hhhcccchHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHHHHHhhccc
Q psy1398 17 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAESVENARLR 95 (102)
Q Consensus 17 ~lLIpk~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri~~~~~~~ 95 (102)
.|.+|-..+.|+.|+- ....|+.+.|..-|-...|....+++|-|...|...|+..|+++.++|+. +.+..|+
T Consensus 22 gL~FpVgRi~R~Lr~g----~~a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI--~nDeEL~ 94 (129)
T PLN00153 22 GLQFPVGRIARYLKKG----KYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAI--RNDEELG 94 (129)
T ss_pred CcccchHHHHHHHhcC----chhhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhc--cCcHHHH
Confidence 6777777777877763 24679999999999999999999999999999999999999999999994 4444443
No 42
>KOG1756|consensus
Probab=94.04 E-value=0.079 Score=38.21 Aligned_cols=73 Identities=23% Similarity=0.240 Sum_probs=59.6
Q ss_pred hhhcccchHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHHHHHhhccc
Q psy1398 17 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAESVENARLR 95 (102)
Q Consensus 17 ~lLIpk~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri~~~~~~~ 95 (102)
++..|---..|+.|+ -....|+..+|...|-...|....++.|.|-..|.-.++..|+++-++|| |+.+.+||
T Consensus 25 gl~fPvgri~r~Lr~----~~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lA--I~NDeEL~ 97 (131)
T KOG1756|consen 25 GLQFPVGRIHRLLRK----GRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLA--IRNDEELN 97 (131)
T ss_pred ccccCHHHHHHHHHc----cchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHH--HhCcHHHH
Confidence 455565556666666 23788999999999998889888999999999999999999999999999 55555554
No 43
>PF02269 TFIID-18kDa: Transcription initiation factor IID, 18kD subunit; InterPro: IPR003195 This family includes the Spt3 yeast transcription factors and the 18 kDa subunit from human transcription initiation factor IID (TFIID-18). Determination of the crystal structure reveals an atypical histone fold [].; GO: 0006366 transcription from RNA polymerase II promoter; PDB: 1BH9_A 1BH8_A.
Probab=93.76 E-value=0.043 Score=36.84 Aligned_cols=59 Identities=14% Similarity=0.181 Sum_probs=29.6
Q ss_pred HHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHH
Q psy1398 29 VREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAE 87 (102)
Q Consensus 29 VrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~r 87 (102)
++++.-.|+....=.++.+..+.+..-.|++.+...|..+|.+.++.+|+++|+..+.|
T Consensus 7 I~~mMy~fGD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR 65 (93)
T PF02269_consen 7 IRQMMYGFGDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLR 65 (93)
T ss_dssp CHHHHHCTTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC--------------------
T ss_pred HHHHHHHcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHh
Confidence 34455556655667788999999999999999999999999999999999999998865
No 44
>PTZ00252 histone H2A; Provisional
Probab=93.04 E-value=0.15 Score=37.01 Aligned_cols=73 Identities=19% Similarity=0.199 Sum_probs=58.7
Q ss_pred hhhcccchHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhh--cCccccCcccHHHHHHHHHhhcc
Q psy1398 17 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIH--AKRVTIMPKDIQLAAESVENARL 94 (102)
Q Consensus 17 ~lLIpk~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~H--akRvTi~~kDi~La~ri~~~~~~ 94 (102)
.|.+|-..+.|+.|+- ....|+.+.|..-|-...|....+++|-|...|.. .|+..|+++.++|+.+ .+..|
T Consensus 23 GL~FPVgRi~R~Lr~g----~ya~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIr--NDeEL 96 (134)
T PTZ00252 23 GLIFPVGRVGSLLRRG----QYARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVR--HDDDL 96 (134)
T ss_pred CccCchHHHHHHHHcC----CcccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhcc--ChHHH
Confidence 6777777777777765 24679999999999999999999999999998864 5778899999999954 44444
Q ss_pred c
Q psy1398 95 R 95 (102)
Q Consensus 95 ~ 95 (102)
+
T Consensus 97 ~ 97 (134)
T PTZ00252 97 G 97 (134)
T ss_pred H
Confidence 3
No 45
>KOG2549|consensus
Probab=92.51 E-value=0.41 Score=41.71 Aligned_cols=53 Identities=21% Similarity=0.303 Sum_probs=48.4
Q ss_pred cccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHHHHH
Q psy1398 38 TDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAESVE 90 (102)
Q Consensus 38 ~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri~~ 90 (102)
|-..+..+|..+|-+-.|.-+-++.++|.+++.|+||-+++++|+.-|.+.+.
T Consensus 25 Gi~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~n 77 (576)
T KOG2549|consen 25 GITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLN 77 (576)
T ss_pred CccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhcc
Confidence 55668899999999999999999999999999999999999999998887653
No 46
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=91.89 E-value=0.57 Score=34.08 Aligned_cols=69 Identities=22% Similarity=0.203 Sum_probs=61.3
Q ss_pred cchhhcccchHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHH
Q psy1398 15 STELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAA 86 (102)
Q Consensus 15 st~lLIpk~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ 86 (102)
+.++-+||+-.+..|-+|.. .++-|+.+|-+-+++++=.|+--+--.|+.++-.-+.+||-.+-+-=|.
T Consensus 7 dDe~sLPKATVqKMvS~iLp---~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKAL 75 (148)
T COG5150 7 DDENSLPKATVQKMVSSILP---KDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKAL 75 (148)
T ss_pred cccccCcHHHHHHHHHHhcc---ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHH
Confidence 44677899999999999965 8899999999999999999999999999999999999999988765443
No 47
>KOG1744|consensus
Probab=90.75 E-value=0.78 Score=32.98 Aligned_cols=64 Identities=20% Similarity=0.208 Sum_probs=50.8
Q ss_pred HHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHHHHHh
Q psy1398 28 LVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAESVEN 91 (102)
Q Consensus 28 LVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri~~~ 91 (102)
-|..+......+.-+++.|+..+--..-+++-.+...|..+|..-||-||..++|+.+.++.--
T Consensus 42 yv~kvlk~Vhpd~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLllP 105 (127)
T KOG1744|consen 42 YVYKVLKQVHPDLGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLLLP 105 (127)
T ss_pred ehhhhhhcccCCCCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHhCc
Confidence 3333433334456699999998888777788888889999999999999999999999987643
No 48
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=90.61 E-value=0.94 Score=32.88 Aligned_cols=60 Identities=25% Similarity=0.357 Sum_probs=44.0
Q ss_pred HHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCc---ccHHHHHH
Q psy1398 27 RLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMP---KDIQLAAE 87 (102)
Q Consensus 27 RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~---kDi~La~r 87 (102)
||+.=|..+.+ -.........-|-+.|-.|..++.+||...|.|++|-.+.. +|++||.-
T Consensus 18 rlihliL~Slg-i~~ye~~VplQLl~FAhRYTq~vl~Dalvya~htgrg~~a~l~veDvrLA~a 80 (145)
T COG5094 18 RLIHLILRSLG-IEEYEPKVPLQLLEFAHRYTQDVLEDALVYAKHTGRGHIATLGVEDVRLALA 80 (145)
T ss_pred hHHHHHHHhcC-chhhCccchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHHHHH
Confidence 55555544333 23344555666778899999999999999999999876555 99999853
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=87.93 E-value=3.9 Score=27.45 Aligned_cols=62 Identities=16% Similarity=0.235 Sum_probs=47.2
Q ss_pred HHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHH
Q psy1398 25 FQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAE 87 (102)
Q Consensus 25 F~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~r 87 (102)
|..=++...--|+..-.=..+.+..+-+..-.|+.++.-.|..+|. .+|-.++++|+..+.|
T Consensus 4 f~~ei~~mmy~~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR 65 (92)
T cd07978 4 FTKEIRQMMYGFGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLR 65 (92)
T ss_pred cHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHh
Confidence 3333444554555444556788899999999999999999999998 5666669999998864
No 50
>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=87.79 E-value=2 Score=32.32 Aligned_cols=56 Identities=18% Similarity=0.210 Sum_probs=49.9
Q ss_pred hhhcccchHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcC
Q psy1398 17 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAK 73 (102)
Q Consensus 17 ~lLIpk~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~Hak 73 (102)
..++...|+.+-++.|+...+-. -+..+.+..|..|+|.+|-.+.++...++.|-.
T Consensus 42 ~~fl~~~~l~~~~~~i~~~~g~~-~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~ 97 (212)
T cd08045 42 PSFLNPSPLAKKIRKIAKKHGLK-EVDEDVLDLISLALEERLRNLLEKLIEVSEHRV 97 (212)
T ss_pred hhccCHHHHHHHHHHHHHHcCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 46788899999999998876643 789999999999999999999999999999963
No 51
>PF05236 TAF4: Transcription initiation factor TFIID component TAF4 family; InterPro: IPR007900 Accurate transcription initiation at protein-coding genes by RNA polymerase II requires the assembly of a multiprotein complex around the mRNA start site. Transcription factor TFIID is one of the general factors involved in this process. Yeast TFIID comprises the TATA binding protein and 14 TBP-associated factors (TAFIIs), nine of which contain histone-fold domains (IPR007124 from INTERPRO). The C-terminal region of the TFIID-specific yeast TAF4 (yTAF4) containing the HFD shares strong sequence similarity with Drosophila (d)TAF4 and human TAF4. A structure/function analysis of yTAF4 demonstrates that the HFD, a short conserved C-terminal domain (CCTD), and the region separating them are all required for yTAF4 function. This region of similarity is found in Transcription initiation factor TFIID component TAF4 []. ; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_C.
Probab=86.99 E-value=1.1 Score=34.67 Aligned_cols=58 Identities=21% Similarity=0.265 Sum_probs=38.9
Q ss_pred hhhcccchHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCcc
Q psy1398 17 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRV 75 (102)
Q Consensus 17 ~lLIpk~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRv 75 (102)
.+++...|+++-+++|+..++ ...+.++.+..|--|+|.+|-+|.+++...|.|....
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 466788889999999987665 5678999999999999999999999999999995443
No 52
>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=85.60 E-value=2.2 Score=31.09 Aligned_cols=64 Identities=23% Similarity=0.283 Sum_probs=48.4
Q ss_pred HHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHHHHHhhc
Q psy1398 25 FQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAESVENAR 93 (102)
Q Consensus 25 F~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri~~~~~ 93 (102)
|+|+.|+. ..+=+.++=+.-+-+..|.-+..||.-|+..|..-+|-+|.+.|+.+...+.+.++
T Consensus 1 fe~lFR~a-----a~LdvdK~d~~r~~d~V~~Kl~DLl~va~~~Ak~ngRdvI~~~DLPITkGlqesi~ 64 (138)
T PF09123_consen 1 FERLFRKA-----AGLDVDKNDAKRYSDFVEKKLYDLLLVAQENAKANGRDVIEPRDLPITKGLQESIR 64 (138)
T ss_dssp HHHHHHHH-----HS----HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS---HHHHHHHH
T ss_pred ChHHHHHH-----hccCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeeccccCCccHHHHHHHH
Confidence 67888877 34556677788888999999999999999999999999999999999988877665
No 53
>KOG2389|consensus
Probab=84.52 E-value=2.4 Score=35.12 Aligned_cols=50 Identities=24% Similarity=0.148 Sum_probs=45.8
Q ss_pred cccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHH
Q psy1398 38 TDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAE 87 (102)
Q Consensus 38 ~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~r 87 (102)
+---++.+|++-|+..+-.|+-++-+.|-..+-|++|+-....|+-++..
T Consensus 43 g~~~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~ 92 (353)
T KOG2389|consen 43 GYSSTQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQ 92 (353)
T ss_pred CCcccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHH
Confidence 34467888999999999999999999999999999999999999999864
No 54
>KOG4336|consensus
Probab=84.25 E-value=2.4 Score=34.66 Aligned_cols=48 Identities=17% Similarity=0.151 Sum_probs=44.2
Q ss_pred ccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHHH
Q psy1398 41 RFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAES 88 (102)
Q Consensus 41 R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri 88 (102)
-++..|++.|-++.-.|+-++|+.+-..+.|+||--.+..|+.|...-
T Consensus 22 ~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~ 69 (323)
T KOG4336|consen 22 SISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIE 69 (323)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHH
Confidence 377889999999999999999999999999999999999999999754
No 55
>KOG1757|consensus
Probab=82.71 E-value=1.8 Score=30.89 Aligned_cols=70 Identities=20% Similarity=0.224 Sum_probs=57.0
Q ss_pred chHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHHHHHhhcc
Q psy1398 23 LPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAESVENARL 94 (102)
Q Consensus 23 ~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri~~~~~~ 94 (102)
.|..|+-|..-+.....-|+...|..-.-...|....+.+|-|...+.--|=+.|+++-.||+ |||+..|
T Consensus 31 FpVgRihr~LK~r~t~h~rVGataavy~aaileYLTaEVLeLAgNasKdLKvKRitprHlqLA--iRGDeEL 100 (131)
T KOG1757|consen 31 FPVGRIHRHLKTRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLA--IRGDEEL 100 (131)
T ss_pred cchHHHHHHHHHhcccccccchHHHHHHHHHHHHHHHHHHHHcccccccceeeeccchhheee--ecCcHHH
Confidence 577788887777667788999988888888888888889999999888888888999999998 5555444
No 56
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=77.71 E-value=14 Score=26.34 Aligned_cols=61 Identities=16% Similarity=0.181 Sum_probs=48.1
Q ss_pred HHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHH
Q psy1398 25 FQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAE 87 (102)
Q Consensus 25 F~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~r 87 (102)
|..=++...--|+...-=..+.+++|.|..-+|++.+-..|--+|- .|-.++.+|.+.+.|
T Consensus 11 F~KDikslmYayGDvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq--~rnK~k~eDfkfaLr 71 (126)
T COG5248 11 FMKDIKSLMYAYGDVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQ--VRNKTKTEDFKFALR 71 (126)
T ss_pred HHHHHHHHHHHhCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHH--hcccchHHHHHHHHh
Confidence 4444555555566555666788999999999999999988888877 677789999999975
No 57
>KOG3901|consensus
Probab=77.16 E-value=16 Score=25.66 Aligned_cols=64 Identities=20% Similarity=0.250 Sum_probs=49.7
Q ss_pred ccchHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHH
Q psy1398 21 RKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAE 87 (102)
Q Consensus 21 pk~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~r 87 (102)
+|--|++=+|...-.|+.+.-=-.+.+++|.+..=.|++.+...|..+. +|=.+.++|+..+.|
T Consensus 7 rk~lF~Kdl~~mmYgfGDd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~lR 70 (109)
T KOG3901|consen 7 RKHLFSKDLRSMMYGFGDDVNPYPETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLLR 70 (109)
T ss_pred HHHHHHHHHHHHHHhcCCCCCccHhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHHH
Confidence 3445777777777777755555578899999999999999976666555 888899999998854
No 58
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=69.42 E-value=9.6 Score=31.93 Aligned_cols=62 Identities=19% Similarity=0.283 Sum_probs=51.6
Q ss_pred HHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHHHH
Q psy1398 27 RLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAESV 89 (102)
Q Consensus 27 RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri~ 89 (102)
.-+|++++..+ -.-+..+++.||---.|--+-++-+.|.+.+.|.||--++.+||.-|.|-+
T Consensus 9 et~KdvAeslG-i~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~l 70 (450)
T COG5095 9 ETLKDVAESLG-ISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSL 70 (450)
T ss_pred HHHHHHHHHcC-CcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhc
Confidence 34566665443 445778999999999999999999999999999999999999999887643
No 59
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=67.89 E-value=12 Score=31.89 Aligned_cols=71 Identities=27% Similarity=0.388 Sum_probs=56.5
Q ss_pred hhcccchHHH-HHHHHHhhc-c-cccccchHHHHHHHHHHHH----HHHHHhHhHHHHhhhcCccccCcccHHHHHHH
Q psy1398 18 LLIRKLPFQR-LVREIAQDF-K-TDLRFQSSAVMALQEASEA----YLVGLFEDTNLCAIHAKRVTIMPKDIQLAAES 88 (102)
Q Consensus 18 lLIpk~pF~R-LVrEI~~~~-~-~~~R~~~~Al~aLQeaaE~----~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri 88 (102)
|+|+-.|+.+ =+|||..-- + .+.-.+++|++-|-...|. |.++|.+-|+..|.-.++.+|..+|++=|..+
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 4566677764 467775432 2 5778899999999776665 99999999999999999999999999988654
No 60
>KOG1657|consensus
Probab=60.94 E-value=15 Score=28.60 Aligned_cols=72 Identities=19% Similarity=0.216 Sum_probs=58.1
Q ss_pred ccchhhcccchHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHH
Q psy1398 14 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAA 86 (102)
Q Consensus 14 kst~lLIpk~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ 86 (102)
...++....+|..|+.+ |...-..---++.+|..-.-.++|.++..|-.-|..-+--++|.|+.-.|+.-+.
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-IMKSDEDVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAV 137 (236)
T ss_pred cccchhhccCcHhhccc-cccccccccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHh
Confidence 45678889999999765 3221111227899999999999999999999999999999999999998887664
No 61
>PF10911 DUF2717: Protein of unknown function (DUF2717); InterPro: IPR020121 The proteins in this entry are uncharacterised.
Probab=60.26 E-value=17 Score=24.13 Aligned_cols=60 Identities=23% Similarity=0.392 Sum_probs=45.4
Q ss_pred hhhhhcccccchhhcccchHHHHHHHHHh-hcccccccchHHHHHHHH--HHHHHHHHHhHhHHHH
Q psy1398 6 RERFQKPMKSTELLIRKLPFQRLVREIAQ-DFKTDLRFQSSAVMALQE--ASEAYLVGLFEDTNLC 68 (102)
Q Consensus 6 lrEIr~yQkst~lLIpk~pF~RLVrEI~~-~~~~~~R~~~~Al~aLQe--aaE~~lv~lfe~a~~~ 68 (102)
|++|.+|+...+= ||-.| |.+.|-.+ .|+.++-.++..+..|++ -+|+|+.++.+..+.+
T Consensus 2 L~~I~h~l~np~D-iP~ip--ra~aeyLqvrfN~~yl~~sG~i~~lr~~G~SE~~I~Gfl~Gl~~A 64 (77)
T PF10911_consen 2 LKPIQHLLDNPDD-IPDIP--RAAAEYLQVRFNAAYLMASGIISALRKQGWSESYILGFLAGLQYA 64 (77)
T ss_pred cchHHHHhcCCcc-cCCcc--HHHHHHHHHHhcHHHHHHhhhHHHHHHccccHHHHHHHHHHHHHH
Confidence 6889999988753 46544 66677655 366777777888888875 4899999999888776
No 62
>KOG1658|consensus
Probab=57.15 E-value=8.5 Score=28.74 Aligned_cols=50 Identities=24% Similarity=0.244 Sum_probs=42.7
Q ss_pred cccccccchH-HHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHH
Q psy1398 36 FKTDLRFQSS-AVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLA 85 (102)
Q Consensus 36 ~~~~~R~~~~-Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La 85 (102)
...++++..+ |+..+-.++|.++-.|-..++-|+--.||+|+..+|...+
T Consensus 71 l~pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~a 121 (162)
T KOG1658|consen 71 LDPDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTA 121 (162)
T ss_pred CCcchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhccccc
Confidence 3478887754 5567889999999999999999999999999999987665
No 63
>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=57.01 E-value=17 Score=23.35 Aligned_cols=55 Identities=9% Similarity=0.111 Sum_probs=38.7
Q ss_pred HHHHHhh-cc-cccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccc-cCcccHH
Q psy1398 29 VREIAQD-FK-TDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVT-IMPKDIQ 83 (102)
Q Consensus 29 VrEI~~~-~~-~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvT-i~~kDi~ 83 (102)
+..|.+. |+ ...|++++|+....+..+-|..+-.--|..-+.--+--+ |.++|++
T Consensus 5 i~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LE 62 (72)
T PF09415_consen 5 IARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLE 62 (72)
T ss_dssp HHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHH
T ss_pred HHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHH
Confidence 3444443 43 678999999999999999998888888877776666666 8888875
No 64
>PF10788 DUF2603: Protein of unknown function (DUF2603); InterPro: IPR019724 This entry represents a conserved protein in epsilon-Proteobacteria. The function is not known.
Probab=54.47 E-value=8.5 Score=27.98 Aligned_cols=32 Identities=22% Similarity=0.349 Sum_probs=26.7
Q ss_pred chhhhhhhcccccchhhcccchHHHHHHHHHhh
Q psy1398 3 WVARERFQKPMKSTELLIRKLPFQRLVREIAQD 35 (102)
Q Consensus 3 ~valrEIr~yQkst~lLIpk~pF~RLVrEI~~~ 35 (102)
.||+.||+++..+..-+ |..-+.+||++|-.+
T Consensus 97 ~VAm~ei~~~~~~~~~~-~~id~~~lvk~IKk~ 128 (137)
T PF10788_consen 97 AVAMDEIKKMRQKDGNL-PNIDLDKLVKNIKKE 128 (137)
T ss_pred HHHHHHHHHHHhcCCCc-CCCCHHHHHHHHHHh
Confidence 48999999997666555 999999999999554
No 65
>TIGR02902 spore_lonB ATP-dependent protease LonB. Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.
Probab=53.21 E-value=49 Score=28.21 Aligned_cols=50 Identities=18% Similarity=0.225 Sum_probs=40.2
Q ss_pred cccccchHHHHHHHHHHHH--HHHHHhHhHHHHhhhcCccccCcccHHHHHH
Q psy1398 38 TDLRFQSSAVMALQEASEA--YLVGLFEDTNLCAIHAKRVTIMPKDIQLAAE 87 (102)
Q Consensus 38 ~~~R~~~~Al~aLQeaaE~--~lv~lfe~a~~~A~HakRvTi~~kDi~La~r 87 (102)
..+.++++|++.|...+.+ .+..+.+.|...|...+|.+|+.+|++-+..
T Consensus 279 ~~i~is~~al~~I~~y~~n~Rel~nll~~Aa~~A~~~~~~~It~~dI~~vl~ 330 (531)
T TIGR02902 279 IGINLEKHALELIVKYASNGREAVNIVQLAAGIALGEGRKRILAEDIEWVAE 330 (531)
T ss_pred cCCCcCHHHHHHHHHhhhhHHHHHHHHHHHHHHHhhCCCcEEcHHHHHHHhC
Confidence 3467889999887666553 6788888888888888999999999998853
No 66
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=49.98 E-value=38 Score=26.95 Aligned_cols=68 Identities=22% Similarity=0.283 Sum_probs=53.3
Q ss_pred chHHHHHHHHHhhccccc-ccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHHHHHhh
Q psy1398 23 LPFQRLVREIAQDFKTDL-RFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAESVENA 92 (102)
Q Consensus 23 ~pF~RLVrEI~~~~~~~~-R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri~~~~ 92 (102)
+||.|+-|=. +...+. =++++|=...-.++|-|+.+|---|-+.|...||-|+...||.-|.+-.+-.
T Consensus 110 LPlARIkkvM--KtdedVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~kSeMf 178 (286)
T COG5208 110 LPLARIKKVM--KTDEDVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKKSEMF 178 (286)
T ss_pred CcHHHHHHHH--hcccchhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHHHHHH
Confidence 7888876633 222333 3567777778899999999999999999999999999999999887655433
No 67
>TIGR00764 lon_rel lon-related putative ATP-dependent protease. Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.
Probab=49.73 E-value=98 Score=27.03 Aligned_cols=64 Identities=16% Similarity=0.097 Sum_probs=45.2
Q ss_pred HHHHHHHHhhcccccccchHHHHHHHHH-H------------HHHHHHHhHhHHHHhhhcCccccCcccHHHHHHHH
Q psy1398 26 QRLVREIAQDFKTDLRFQSSAVMALQEA-S------------EAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAESV 89 (102)
Q Consensus 26 ~RLVrEI~~~~~~~~R~~~~Al~aLQea-a------------E~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri~ 89 (102)
.+.+.....+.+.-..|+.+|+..|-+. + ...+.++...|...|...+..+|+.+|++-|...+
T Consensus 315 ~~~i~~~~~r~G~l~~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~~ 391 (608)
T TIGR00764 315 VQFVAQEVKKDGRIPHFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKLA 391 (608)
T ss_pred HHHHHHHHHHhCCCCcCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHHH
Confidence 3344443333322348999999998642 2 35788889999888888899999999998775544
No 68
>KOG2680|consensus
Probab=47.11 E-value=66 Score=27.21 Aligned_cols=70 Identities=20% Similarity=0.331 Sum_probs=53.7
Q ss_pred hcccchHH-HHHHHHHhh-c-ccccccchHHHHHHHHHHHH----HHHHHhHhHHHHhhhcCccccCcccHHHHHHH
Q psy1398 19 LIRKLPFQ-RLVREIAQD-F-KTDLRFQSSAVMALQEASEA----YLVGLFEDTNLCAIHAKRVTIMPKDIQLAAES 88 (102)
Q Consensus 19 LIpk~pF~-RLVrEI~~~-~-~~~~R~~~~Al~aLQeaaE~----~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri 88 (102)
+|.-.|+. +=+++|..- + ..+.-.+++|++-|-...|+ |...|...|++.+...|-.++..+|++=|.++
T Consensus 352 II~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 352 IISTQPYTEEDIKKILRIRCQEEDVEMNPDALDLLTKIGEATSLRYAIHLITAASLVCLKRKGKVVEVDDIERVYRL 428 (454)
T ss_pred eeecccCcHHHHHHHHHhhhhhhccccCHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhcCceeehhHHHHHHHH
Confidence 34444554 345555432 1 16778899999999877776 99999999999999999999999999988764
No 69
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=46.18 E-value=55 Score=25.26 Aligned_cols=59 Identities=19% Similarity=0.240 Sum_probs=45.5
Q ss_pred HHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhh--cCccccCcccHHHHH
Q psy1398 26 QRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIH--AKRVTIMPKDIQLAA 86 (102)
Q Consensus 26 ~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~H--akRvTi~~kDi~La~ 86 (102)
.+.|++.+++ ....++.+|+..|.+.++.=+..+-..-.+++.. ++..+|+.+|++-+.
T Consensus 136 ~~~i~~~~~~--~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v 196 (326)
T PRK07452 136 KQLVERTAQE--LGVKLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALV 196 (326)
T ss_pred HHHHHHHHHH--cCCCCCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHh
Confidence 3444444433 4577999999999999998888888888888887 568889999998764
No 70
>cd08048 TAF11 TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypothes
Probab=42.44 E-value=98 Score=20.37 Aligned_cols=63 Identities=14% Similarity=0.256 Sum_probs=51.2
Q ss_pred cccchHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCc---cccCcccHHHHHH
Q psy1398 20 IRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKR---VTIMPKDIQLAAE 87 (102)
Q Consensus 20 Ipk~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakR---vTi~~kDi~La~r 87 (102)
+||....|++..+ .+-..+.+.+.++.-.+..|+.++-|.|..+...-+. --|.++.+.-|.+
T Consensus 17 f~k~~iKr~~~~~-----~~~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~r 82 (85)
T cd08048 17 FPKAAIKRLIQSV-----TGQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYR 82 (85)
T ss_pred ccHHHHHHHHHHH-----cCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHH
Confidence 7888888887777 4578889999999999999999999999988877554 4577777766654
No 71
>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=39.33 E-value=1.2e+02 Score=22.36 Aligned_cols=49 Identities=16% Similarity=0.131 Sum_probs=40.2
Q ss_pred ccccchHHHHHHHHHHHH---HHHHHhHhHHHHhhhcCccccCcccHHHHHH
Q psy1398 39 DLRFQSSAVMALQEASEA---YLVGLFEDTNLCAIHAKRVTIMPKDIQLAAE 87 (102)
Q Consensus 39 ~~R~~~~Al~aLQeaaE~---~lv~lfe~a~~~A~HakRvTi~~kDi~La~r 87 (102)
+..|++++++.|.+.+.- ++..+...+...|.-.+..+|+.+|++-+.+
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 356999999999999987 7777777787777777778999999987754
No 72
>smart00350 MCM minichromosome maintenance proteins.
Probab=34.49 E-value=64 Score=27.22 Aligned_cols=32 Identities=9% Similarity=0.047 Sum_probs=23.4
Q ss_pred HhHhHHHHhhhcCccccCcccHHHHHHHHHhh
Q psy1398 61 LFEDTNLCAIHAKRVTIMPKDIQLAAESVENA 92 (102)
Q Consensus 61 lfe~a~~~A~HakRvTi~~kDi~La~ri~~~~ 92 (102)
+..-|...|.=..|-+|+++|++-|.++....
T Consensus 476 liRla~A~A~l~~r~~V~~~Dv~~ai~l~~~s 507 (509)
T smart00350 476 IIRLSEAHAKMRLSDVVEEADVEEAIRLLRES 507 (509)
T ss_pred HHHHHHHHHHHcCCCccCHHHHHHHHHHHHHh
Confidence 33444445666779999999999999887653
No 73
>PRK05907 hypothetical protein; Provisional
Probab=33.65 E-value=99 Score=24.65 Aligned_cols=66 Identities=12% Similarity=0.045 Sum_probs=50.4
Q ss_pred cccchHHHHHHHHHhhcc-cccccchHHHHHHHHHH-HHHHHHHhHhHHHHhhh-cCccccCcccHHHH
Q psy1398 20 IRKLPFQRLVREIAQDFK-TDLRFQSSAVMALQEAS-EAYLVGLFEDTNLCAIH-AKRVTIMPKDIQLA 85 (102)
Q Consensus 20 Ipk~pF~RLVrEI~~~~~-~~~R~~~~Al~aLQeaa-E~~lv~lfe~a~~~A~H-akRvTi~~kDi~La 85 (102)
.++..-..|.+=|.+.++ ....++.+|+..|-+.+ +.-|..+...-.+++.. +++.+|+.+|++.+
T Consensus 131 ~~~l~e~~L~~Wi~~~~~~~g~~i~~~a~~~L~~~~~~~nL~~l~~EleKL~ly~g~~~~It~e~V~~l 199 (311)
T PRK05907 131 WFADRDKRIAQLLIQRAKELGISCSLGLASLFVSKFPQTGLFEILSEFQKLLCQMGKKESLEASDIQSF 199 (311)
T ss_pred cCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHccCCCHHHHHHHHHHHHHhcCCCCeECHHHHHHH
Confidence 444445677777766665 67789999999988888 67777777777777777 66889999999876
No 74
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=32.93 E-value=2.5e+02 Score=24.16 Aligned_cols=66 Identities=26% Similarity=0.297 Sum_probs=47.9
Q ss_pred chHHHHHHHHHhhcccccccchHHHHHHHHHHH-----------HHHHHHhHhHHHHhhhcCccccCcccHHHHHHHH
Q psy1398 23 LPFQRLVREIAQDFKTDLRFQSSAVMALQEASE-----------AYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAESV 89 (102)
Q Consensus 23 ~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE-----------~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri~ 89 (102)
..|.++|..++++.+ -.-|+.+|+.+|=+.+= ..+.+++..|+..|.-.+...|..+|++-|..-+
T Consensus 430 ~~~~~~i~~~~~~~~-L~~~~~~Av~~li~~~~R~~q~kLsl~~~~l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~~r 506 (509)
T PF13654_consen 430 RQYARFIASICQKEG-LPPFDRSAVARLIEYSARLDQDKLSLRFSWLADLLREANYWARKEGAKVITAEHVEQAIEER 506 (509)
T ss_dssp HHHHHHHHHHHHHHS-S--BBHHHHHHHHHHHHHCC-SEEE--HHHHHHHHHHHHHHHHHCT-SSB-HHHHHHHHHH-
T ss_pred HHHHHHHHHHHHhCC-CCCCCHHHHHHHHHHHHHHhCCEeCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHcc
Confidence 357778888877653 34688899888665543 3789999999999999999999999999986543
No 75
>PF04914 DltD_C: DltD C-terminal region; InterPro: IPR006998 The dlt operon (dltA to dltD) of Lactobacillus rhamnosus 7469 encodes four proteins responsible for the esterification of lipoteichoic acid (LTA) by D-alanine. These esters play an important role in controlling the net anionic charge of the poly (GroP) moiety of LTA. DltA and DltC encode the D-alanine-D-alanyl carrier protein ligase (Dcl) and D-alanyl carrier protein (Dcp), respectively. Whereas the functions of DltA and DltC are defined, the functions of DltB and DltD are unknown. In vitro assays showed that DltD bound Dcp for ligation with D-alanine by Dcl in the presence of ATP. In contrast, the homologue of Dcp, the Escherichia coli acyl carrier protein (ACP), involved in fatty acid biosynthesis, was not bound to DltD and thus was not ligated with D-alanine. DltD also catalyzed the hydrolysis of the mischarged D-alanyl-ACP. The hydrophobic N-terminal sequence of DltD was required for anchoring the protein in the membrane. It is hypothesized that this membrane-associated DltD facilitates the binding of Dcp and Dcl for ligation of Dcp with D-alanine and that the resulting D-alanyl-Dcp is translocated to the primary site of D-alanylation []. These sequences contain the C-terminal region of DltD.; PDB: 3BMA_C.
Probab=32.52 E-value=33 Score=24.31 Aligned_cols=24 Identities=17% Similarity=0.350 Sum_probs=19.3
Q ss_pred cccHHHHHHHHHhhccceeeccCC
Q psy1398 79 PKDIQLAAESVENARLRIRLISTP 102 (102)
Q Consensus 79 ~kDi~La~ri~~~~~~~~~~~~~~ 102 (102)
-+|.+|++.++.+.+++.-+|..|
T Consensus 35 y~Dl~l~L~~~k~~g~~~lfVi~P 58 (130)
T PF04914_consen 35 YDDLQLLLDVCKELGIDVLFVIQP 58 (130)
T ss_dssp HHHHHHHHHHHHHTT-EEEEEE--
T ss_pred HHHHHHHHHHHHHcCCceEEEecC
Confidence 369999999999999999999887
No 76
>KOG1942|consensus
Probab=32.21 E-value=1.5e+02 Score=25.08 Aligned_cols=52 Identities=25% Similarity=0.284 Sum_probs=44.4
Q ss_pred cccccchHHHHHHHH----HHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHHHH
Q psy1398 38 TDLRFQSSAVMALQE----ASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAESV 89 (102)
Q Consensus 38 ~~~R~~~~Al~aLQe----aaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri~ 89 (102)
..+.+.++|++-|-+ .+-.|.++|..-+..||.-.+|..|.++|++=+..+-
T Consensus 383 E~l~~~e~a~~~l~~~gt~tsLRy~vqLl~p~~~~ak~~g~~~i~v~dvee~~~Lf 438 (456)
T KOG1942|consen 383 EGLQVEEEALDLLAEIGTSTSLRYAVQLLTPASILAKTNGRKEISVEDVEEVTELF 438 (456)
T ss_pred hcceecHHHHHHHHhhccchhHHHHHHhcCHHHHHHHHcCCceeecccHHHHHHHH
Confidence 567888999988876 4556999999999999999999999999998776543
No 77
>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I. This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria.
Probab=31.47 E-value=1.2e+02 Score=24.46 Aligned_cols=56 Identities=16% Similarity=0.129 Sum_probs=42.5
Q ss_pred cccccchHHHHHHHHHHHHHHH-------HHhHhHHHHhhhcCccccCcccHHHHHHHHHhhc
Q psy1398 38 TDLRFQSSAVMALQEASEAYLV-------GLFEDTNLCAIHAKRVTIMPKDIQLAAESVENAR 93 (102)
Q Consensus 38 ~~~R~~~~Al~aLQeaaE~~lv-------~lfe~a~~~A~HakRvTi~~kDi~La~ri~~~~~ 93 (102)
.+..++++.+..+.+.+.+.=+ .+...|...|.-.+|-.|+++|++.+....=.-|
T Consensus 251 ~~V~v~d~~~~~i~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~~dDv~~~a~~vL~HR 313 (337)
T TIGR02030 251 PQVTIPYDVLVKVAELCAELDVDGLRGELTLNRAAKALAAFEGRTEVTVDDIRRVAVLALRHR 313 (337)
T ss_pred ccCcCCHHHHHHHHHHHHHHCCCCCcHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHh
Confidence 5667778887777776666433 3778888899999999999999998876554333
No 78
>PF07962 Swi3: Replication Fork Protection Component Swi3; InterPro: IPR012923 Replication fork pausing is required to initiate recombination events. More specifically, Swi1 is required for recombination near the mat1 locus. Swi3 has been found to co-purify with Swi1. Together they define a fork protection complex that coordinates leading- and lagging-strand synthesis and stabilises stalled replication forks []. This complex is required for accurate replication, fork protection and replication checkpoint signalling [, ].; GO: 0006974 response to DNA damage stimulus, 0007049 cell cycle, 0048478 replication fork protection, 0005634 nucleus
Probab=29.90 E-value=23 Score=23.09 Aligned_cols=24 Identities=17% Similarity=0.204 Sum_probs=20.8
Q ss_pred hhcccccchhhcccchHHHHHHHH
Q psy1398 9 FQKPMKSTELLIRKLPFQRLVREI 32 (102)
Q Consensus 9 Ir~yQkst~lLIpk~pF~RLVrEI 32 (102)
+..||.=..-|.|+++|...+.-+
T Consensus 39 l~~Yq~W~h~LfPk~~F~d~i~~v 62 (83)
T PF07962_consen 39 LQFYQLWAHRLFPKASFEDFIERV 62 (83)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHH
Confidence 567888888999999999999877
No 79
>PF11823 DUF3343: Protein of unknown function (DUF3343); InterPro: IPR021778 This family of proteins are functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are typically between 78 to 102 amino acids in length.
Probab=29.44 E-value=51 Score=20.38 Aligned_cols=22 Identities=32% Similarity=0.501 Sum_probs=16.4
Q ss_pred cHHHHHHHHHhhccceeeccCC
Q psy1398 81 DIQLAAESVENARLRIRLISTP 102 (102)
Q Consensus 81 Di~La~ri~~~~~~~~~~~~~~ 102 (102)
|.--+.+...+.++..|++.||
T Consensus 13 ~a~~~ek~lk~~gi~~~liP~P 34 (73)
T PF11823_consen 13 DAMKAEKLLKKNGIPVRLIPTP 34 (73)
T ss_pred HHHHHHHHHHHCCCcEEEeCCC
Confidence 3344556788888889998887
No 80
>PF06709 DUF1196: Protein of unknown function (DUF1196); InterPro: IPR009585 This family consists of several hypothetical bacterial proteins of around 51 residues in length which seem to be specific to Vibrio cholerae. The function of this family is unknown.
Probab=29.20 E-value=36 Score=20.63 Aligned_cols=19 Identities=26% Similarity=0.478 Sum_probs=16.0
Q ss_pred hhhcccchHHHHHHHHHhh
Q psy1398 17 ELLIRKLPFQRLVREIAQD 35 (102)
Q Consensus 17 ~lLIpk~pF~RLVrEI~~~ 35 (102)
-+++|-.||.++.+.|..+
T Consensus 12 V~~~~t~~FK~v~KGI~~K 30 (51)
T PF06709_consen 12 VFLCPTLPFKGVAKGIYAK 30 (51)
T ss_pred HHHHccchHHHHHHHHHHh
Confidence 4689999999999999553
No 81
>PRK14562 haloacid dehalogenase superfamily protein; Provisional
Probab=27.08 E-value=89 Score=23.49 Aligned_cols=25 Identities=36% Similarity=0.313 Sum_probs=20.0
Q ss_pred cccccchHHHHHHHHHHHHHHHHHh
Q psy1398 38 TDLRFQSSAVMALQEASEAYLVGLF 62 (102)
Q Consensus 38 ~~~R~~~~Al~aLQeaaE~~lv~lf 62 (102)
..++|+...-.++||.+|+....-+
T Consensus 71 ~~~~y~~~~~~~lQEyvEA~~f~~~ 95 (204)
T PRK14562 71 PELYYAGYVGTALQEYVEALLVYSL 95 (204)
T ss_pred chhhhhhhcchHHHHHHHHHHHHHH
Confidence 5678888888999999998666554
No 82
>PRK05629 hypothetical protein; Validated
Probab=25.96 E-value=1.8e+02 Score=22.56 Aligned_cols=59 Identities=17% Similarity=0.135 Sum_probs=39.9
Q ss_pred HHHHHHHHhhcc-cccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHH
Q psy1398 26 QRLVREIAQDFK-TDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLA 85 (102)
Q Consensus 26 ~RLVrEI~~~~~-~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La 85 (102)
..+.+=|.+.+. ....++.+|++.|-+.++.=+..+-..-.+++.+.+ -+|+.+|++-+
T Consensus 129 ~~l~~wi~~~~~~~g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~-~~It~e~V~~~ 188 (318)
T PRK05629 129 RERPGWVTQEFKNHGVRPTPDVVHALLEGVGSDLRELASAISQLVEDTQ-GNVTVEKVRAY 188 (318)
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHCccHHHHHHHHHHHHhcCC-CCcCHHHHHHH
Confidence 334444444443 567899999999999888766666555555666654 36889998765
No 83
>COG2118 DNA-binding protein [General function prediction only]
Probab=24.98 E-value=1.6e+02 Score=20.90 Aligned_cols=32 Identities=28% Similarity=0.232 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHHHH
Q psy1398 50 LQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAESV 89 (102)
Q Consensus 50 LQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri~ 89 (102)
+-+++|.+|+.|. -.||+|.+.+|=+|..-+.
T Consensus 68 ~AeavE~qLi~La--------qtGri~~~I~e~~lk~IL~ 99 (116)
T COG2118 68 LAEAVENQLIQLA--------QTGRITHKIDEEELKEILE 99 (116)
T ss_pred HHHHHHHHHHHHH--------HcCCCCCCCCHHHHHHHHH
Confidence 5689999999986 4799999999998885443
No 84
>PRK08487 DNA polymerase III subunit delta; Validated
Probab=24.62 E-value=2.1e+02 Score=22.38 Aligned_cols=47 Identities=23% Similarity=0.111 Sum_probs=39.4
Q ss_pred cccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHH
Q psy1398 38 TDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAA 86 (102)
Q Consensus 38 ~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ 86 (102)
....++.+|+..|-+.++.-+..+-..-.+++..++ +|+.+|++.+.
T Consensus 151 ~g~~i~~~a~~~L~~~~g~dl~~l~~ELeKL~ly~~--~It~edV~~~v 197 (328)
T PRK08487 151 LGLDIDQNALNHLYFIHNEDLALAANELEKLAILNE--PITLKDIQELV 197 (328)
T ss_pred hCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHHhcC--CCCHHHHHHHh
Confidence 567899999999999999888888888888888877 68999988763
No 85
>PF06075 DUF936: Plant protein of unknown function (DUF936); InterPro: IPR010341 This family consists of several hypothetical proteins from plants. The function of this family is unknown.
Probab=24.21 E-value=1.5e+02 Score=26.07 Aligned_cols=41 Identities=37% Similarity=0.371 Sum_probs=28.8
Q ss_pred HHHHHHHHHhhcccccccchHHHHHHHHH--HHHHHHHHhHhHHHH
Q psy1398 25 FQRLVREIAQDFKTDLRFQSSAVMALQEA--SEAYLVGLFEDTNLC 68 (102)
Q Consensus 25 F~RLVrEI~~~~~~~~R~~~~Al~aLQea--aE~~lv~lfe~a~~~ 68 (102)
..+|-||+++ .-.=-+..|++||||| +|..+-.|-..|.+|
T Consensus 325 L~kLGKEa~~---~Rd~A~~aA~eALqEASAaE~lir~Ls~fseL~ 367 (579)
T PF06075_consen 325 LAKLGKEAMQ---QRDAAQKAAVEALQEASAAESLIRCLSMFSELC 367 (579)
T ss_pred HHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5688888876 2233457899999997 466666666667776
No 86
>COG5624 TAF61 Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=22.98 E-value=19 Score=30.98 Aligned_cols=71 Identities=18% Similarity=0.146 Sum_probs=51.4
Q ss_pred ccchHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHHHHHHHhhccceee
Q psy1398 21 RKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAESVENARLRIRL 98 (102)
Q Consensus 21 pk~pF~RLVrEI~~~~~~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri~~~~~~~~~~ 98 (102)
-|--...|++.+. .+...+..+.-+.|-+.|-.|....-+-|-.+|.|.|-.||.++|++|-. +.+-|||+
T Consensus 385 skrkL~el~~~~v---d~eekie~eveelll~~ad~fve~vt~FsCrlakhrkSdtlevrD~qlhl----ErnwnIr~ 455 (505)
T COG5624 385 SKRKLEELQHGGV---DEEEKIENEVEELLLSRADGFVEPVTEFSCRLAKHRKSDTLEVRDGQLHL----ERNWNIRC 455 (505)
T ss_pred hhhhHHHHHhhcc---CcceeccchHHHHHHhhhcccccccchheeEeeccCCCCceeeccceeee----ccccceec
Confidence 3333444555442 36677888888888888888887777777779999999999999999864 44556663
No 87
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=22.63 E-value=3.8e+02 Score=20.98 Aligned_cols=48 Identities=13% Similarity=0.174 Sum_probs=36.7
Q ss_pred ccchHHHHHHHHHHHH------HHHHHhHhHHHHhhhcCccccCcccHHHHHHH
Q psy1398 41 RFQSSAVMALQEASEA------YLVGLFEDTNLCAIHAKRVTIMPKDIQLAAES 88 (102)
Q Consensus 41 R~~~~Al~aLQeaaE~------~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri 88 (102)
-|.+++++.+.+.+.. ++..+...|...|...+..+|+.+|++-|..-
T Consensus 228 ~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~ 281 (394)
T PRK00411 228 VVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEK 281 (394)
T ss_pred CCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHH
Confidence 4788888888777744 45566777777788788889999999877643
No 88
>PRK07914 hypothetical protein; Reviewed
Probab=20.78 E-value=2.1e+02 Score=22.32 Aligned_cols=59 Identities=12% Similarity=0.124 Sum_probs=39.6
Q ss_pred HHHHHHHHhhcc-cccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCccccCcccHHHH
Q psy1398 26 QRLVREIAQDFK-TDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLA 85 (102)
Q Consensus 26 ~RLVrEI~~~~~-~~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRvTi~~kDi~La 85 (102)
.++.+=|.+.++ ....++++|+..|.+.++.-+..+-..-.+++.+.+ .+|+.+|++-+
T Consensus 131 ~~l~~wi~~~a~~~g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~-~~It~e~V~~~ 190 (320)
T PRK07914 131 AERADFVRKEFRSLRVKVDDDTVTALLDAVGSDLRELASACSQLVADTG-GAVDAAAVRRY 190 (320)
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHCccHHHHHHHHHHHhcCCC-CCcCHHHHHHH
Confidence 444444444443 567899999999999998766666655556665544 45778887755
No 89
>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=20.57 E-value=1.4e+02 Score=17.29 Aligned_cols=18 Identities=17% Similarity=-0.025 Sum_probs=10.0
Q ss_pred HhhhcCccccCcccHHHH
Q psy1398 68 CAIHAKRVTIMPKDIQLA 85 (102)
Q Consensus 68 ~A~HakRvTi~~kDi~La 85 (102)
.|...|...|+++++.-|
T Consensus 27 ~Ar~~G~~~IT~e~v~~A 44 (45)
T PF08369_consen 27 YARERGYDEITVEVVDAA 44 (45)
T ss_dssp HHHHCT-SEE-HHHHHHH
T ss_pred HHHHcCCCeECHHHHHhh
Confidence 456667777777666543
No 90
>PF08145 BOP1NT: BOP1NT (NUC169) domain; InterPro: IPR012953 WD-40 repeats (also known as WD or beta-transducin repeats) are short ~40 amino acid motifs, often terminating in a Trp-Asp (W-D) dipeptide. WD40 repeats usually assume a 7-8 bladed beta-propeller fold, but proteins have been found with 4 to 16 repeated units, which also form a circularised beta-propeller structure. WD-repeat proteins are a large family found in all eukaryotes and are implicated in a variety of functions ranging from signal transduction and transcription regulation to cell cycle control and apoptosis. Repeated WD40 motifs act as a site for protein-protein interaction, and proteins containing WD40 repeats are known to serve as platforms for the assembly of protein complexes or mediators of transient interplay among other proteins. The specificity of the proteins is determined by the sequences outside the repeats themselves. Examples of such complexes are G proteins (beta subunit is a beta-propeller), TAFII transcription factor, and E3 ubiquitin ligase [, ]. In Arabidopsis spp., several WD40-containing proteins act as key regulators of plant-specific developmental events. This N-terminal domain is found in BOP1-like WD40 proteins. Bop1 is a nucleolar protein involved in rRNA processing, thereby controlling the cell cycle []. It is required for the maturation of the 25S and 5.8S ribosomal RNAs. It may serve as an essential factor in ribosome formation that coordinates processing of the spacer regions in pre-rRNA. The Pes1-Bop1 complex has several components: BOP1, GRWD1, PES1, ORC6L, and RPL3 and is involved in ribosome biogenesis and altered chromosome segregation. The overexpression of BOP1 increases the percentage of multipolar spindles in human cells. Deregulation of the BOP1 pathway may contribute to colorectal tumourigenesis in humans []. Elevated levels of Bop1 induces Bop1/WDR12 and Bop1/Pes1 subcomplexes and the assembly and integrity of the PeBoW complex is highly sensitive to changes in Bop1 protein levels []. Nop7p-Erb1p-Ytm1p, found in yeast, is potentially the homologous complex of Pes1-Bop1-WDR12 as it is involved in the control of ribosome biogenesis and S phase entry. The integrity of the PeBoW complex is required for ribosome biogenesis and cell proliferation in mammalian cells []. In Giardia, the species specific cytoskeleton protein, beta-giardin, interacts with Bop1 []. ; GO: 0006364 rRNA processing, 0005634 nucleus
Probab=20.26 E-value=34 Score=27.26 Aligned_cols=44 Identities=9% Similarity=0.296 Sum_probs=35.4
Q ss_pred chHHHHHHHHHHH--HHHHHHhHhHHHHhhhcCccccCcccHHHHHHHHHh
Q psy1398 43 QSSAVMALQEASE--AYLVGLFEDTNLCAIHAKRVTIMPKDIQLAAESVEN 91 (102)
Q Consensus 43 ~~~Al~aLQeaaE--~~lv~lfe~a~~~A~HakRvTi~~kDi~La~ri~~~ 91 (102)
+.++|+.+=...| .++..++. ...++-|+|+.+|++|+.||+..
T Consensus 21 ~~d~LD~fL~~~ddp~~Wrtv~D-----~~~g~~v~Lt~eel~lI~ri~~g 66 (260)
T PF08145_consen 21 KGDALDKFLDSMDDPNYWRTVYD-----KKNGREVVLTDEELELIRRIQKG 66 (260)
T ss_pred chhHHHHHHHhccCccCCceeEc-----CCCCceeeeCHHHHHHHHHHHcC
Confidence 5778888877777 57777776 45678899999999999999854
No 91
>PRK13877 conjugal transfer relaxosome component TraJ; Provisional
Probab=20.23 E-value=1.7e+02 Score=20.35 Aligned_cols=52 Identities=6% Similarity=-0.050 Sum_probs=38.7
Q ss_pred ccccchHHHHHHHHHHHHHHHHHhHhHHHHhhhcCcc--ccCcccHHHHHHHHHh
Q psy1398 39 DLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRV--TIMPKDIQLAAESVEN 91 (102)
Q Consensus 39 ~~R~~~~Al~aLQeaaE~~lv~lfe~a~~~A~HakRv--Ti~~kDi~La~ri~~~ 91 (102)
.+|++++=-..+++-|+..-.++.+....|+. +.++ .+..+++.=..+|.++
T Consensus 14 ~vrvt~eE~~~I~~kA~~AGlS~SeYLR~~aL-g~~I~s~~D~e~v~eL~~in~d 67 (114)
T PRK13877 14 RVPVLPDEKAEIEANAAAAGLSVARYLRDVGQ-GYQIKGVIDYEYVRELARINGD 67 (114)
T ss_pred EEEeCHHHHHHHHHHHHHhCCCHHHHHHHHHc-CCCccccCCHHHHHHHHHhccc
Confidence 56888888899999998888899999999999 6666 3544455444444444
No 92
>cd00913 PCD_DCoH_subfamily_a PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by associating with specific DNA binding proteins such as HNF-1alpha (hepatocyte nuclear factor-1) and Xenopus enhancer of rudimentary homologue (XERH). DCoH also catalyzes the dehydration of 4alpha- hydroxy- tetrahydrobiopterin (4alpha-OH-BH4) to quinoiddihydrobiopterin, a percursor of the phenylalanine hydroxylase cofactor BH4 (tetrahydrobiopterin). The DCoH homodimer has a saddle-shaped structure similar to that of TBP (TATA binding protein).
Probab=20.21 E-value=55 Score=20.56 Aligned_cols=14 Identities=21% Similarity=0.230 Sum_probs=11.7
Q ss_pred cCcccHHHHHHHHH
Q psy1398 77 IMPKDIQLAAESVE 90 (102)
Q Consensus 77 i~~kDi~La~ri~~ 90 (102)
|+.+|+.||.+|-+
T Consensus 62 lT~~D~~lA~~id~ 75 (76)
T cd00913 62 LSENDFIMAAKIDA 75 (76)
T ss_pred CCHHHHHHHHHHhc
Confidence 77899999998853
No 93
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=20.18 E-value=2.8e+02 Score=22.66 Aligned_cols=57 Identities=14% Similarity=0.122 Sum_probs=43.1
Q ss_pred cccccchHHHHHHHHHHHHHH-------HHHhHhHHHHhhhcCccccCcccHHHHHHHHHhhcc
Q psy1398 38 TDLRFQSSAVMALQEASEAYL-------VGLFEDTNLCAIHAKRVTIMPKDIQLAAESVENARL 94 (102)
Q Consensus 38 ~~~R~~~~Al~aLQeaaE~~l-------v~lfe~a~~~A~HakRvTi~~kDi~La~ri~~~~~~ 94 (102)
....++++.+..+.+.+.+.- ..+...|...|.-.+|-.|.++|++.+....=.-|+
T Consensus 264 ~~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~pdDv~~~a~~vL~HR~ 327 (350)
T CHL00081 264 PKVEIDYDLRVKISQICSELDVDGLRGDIVTNRAAKALAAFEGRTEVTPKDIFKVITLCLRHRL 327 (350)
T ss_pred CCCccCHHHHHHHHHHHHHHCCCCChHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHhC
Confidence 456777777777777777643 356678888999999999999999998776544433
Done!