Query 046088
Match_columns 193
No_of_seqs 166 out of 461
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 08:36:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046088.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046088hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00154 histone H2A; Provisio 100.0 2.1E-51 4.5E-56 330.2 11.8 134 60-193 1-136 (136)
2 PLN00153 histone H2A; Provisio 100.0 2.3E-49 4.9E-54 316.2 10.6 110 82-192 11-121 (129)
3 PLN00156 histone H2AX; Provisi 100.0 3.9E-49 8.4E-54 318.1 11.0 110 81-191 15-125 (139)
4 PLN00157 histone H2A; Provisio 100.0 4.8E-49 1E-53 315.3 10.8 109 82-191 13-122 (132)
5 PTZ00017 histone H2A; Provisio 100.0 1.1E-48 2.3E-53 314.1 10.9 110 82-192 14-124 (134)
6 PTZ00252 histone H2A; Provisio 100.0 1.7E-47 3.6E-52 306.9 9.9 107 83-190 13-122 (134)
7 smart00414 H2A Histone 2A. 100.0 3.2E-46 7E-51 289.0 9.5 104 87-191 1-105 (106)
8 KOG1756 Histone 2A [Chromatin 100.0 5.6E-46 1.2E-50 295.9 9.1 110 82-192 14-124 (131)
9 cd00074 H2A Histone 2A; H2A is 100.0 3.3E-45 7.1E-50 287.0 10.8 108 82-190 7-115 (115)
10 COG5262 HTA1 Histone H2A [Chro 100.0 3.2E-45 7E-50 289.5 9.0 111 82-193 13-124 (132)
11 KOG1757 Histone 2A [Chromatin 100.0 2.5E-44 5.4E-49 283.1 4.8 112 82-193 17-128 (131)
12 PLN00155 histone H2A; Provisio 99.8 7.6E-22 1.7E-26 139.1 4.4 48 82-130 11-58 (58)
13 PF00125 Histone: Core histone 99.6 3.6E-15 7.8E-20 105.8 5.7 74 89-162 2-75 (75)
14 COG5247 BUR6 Class 2 transcrip 99.3 2.2E-12 4.7E-17 100.7 6.0 79 91-170 19-97 (113)
15 KOG1659 Class 2 transcription 99.0 3.6E-10 7.8E-15 97.6 6.3 77 93-170 11-87 (224)
16 PF00808 CBFD_NFYB_HMF: Histon 98.8 1.5E-08 3.1E-13 70.9 6.9 64 95-159 2-65 (65)
17 PLN00035 histone H4; Provision 98.3 1.1E-06 2.4E-11 68.5 5.6 73 85-161 21-93 (103)
18 PTZ00015 histone H4; Provision 98.2 3.5E-06 7.5E-11 65.6 6.3 70 87-160 24-93 (102)
19 smart00803 TAF TATA box bindin 98.1 1E-05 2.2E-10 57.8 6.8 64 95-160 2-65 (65)
20 COG2036 HHT1 Histones H3 and H 97.9 3.1E-05 6.7E-10 59.2 5.3 66 93-160 17-82 (91)
21 KOG1657 CCAAT-binding factor, 97.7 3.5E-05 7.7E-10 67.4 4.2 84 87-171 66-149 (236)
22 COG5208 HAP5 CCAAT-binding fac 97.6 0.0001 2.2E-09 65.0 5.4 76 94-170 108-183 (286)
23 cd00076 H4 Histone H4, one of 97.5 0.00032 6.9E-09 53.0 6.4 69 89-161 9-77 (85)
24 smart00417 H4 Histone H4. 97.3 0.00044 9.5E-09 51.1 5.1 61 96-158 14-74 (74)
25 cd07981 TAF12 TATA Binding Pro 97.2 0.0016 3.5E-08 47.0 6.6 65 97-162 3-67 (72)
26 cd08048 TAF11 TATA Binding Pro 96.9 0.0042 9.1E-08 46.7 6.6 63 96-160 17-82 (85)
27 PF02969 TAF: TATA box binding 96.5 0.012 2.7E-07 42.5 6.3 64 95-160 3-66 (66)
28 cd07979 TAF9 TATA Binding Prot 96.4 0.01 2.2E-07 46.8 6.3 61 99-161 5-65 (117)
29 PTZ00463 histone H2B; Provisio 96.2 0.034 7.4E-07 44.6 8.4 61 99-160 32-92 (117)
30 PF04719 TAFII28: hTAFII28-lik 96.2 0.012 2.5E-07 45.0 5.2 64 96-160 24-88 (90)
31 smart00427 H2B Histone H2B. 95.9 0.026 5.6E-07 43.3 6.0 60 100-160 6-65 (89)
32 cd08050 TAF6 TATA Binding Prot 95.9 0.023 5E-07 51.6 6.6 58 101-160 5-62 (343)
33 PLN00158 histone H2B; Provisio 95.6 0.04 8.7E-07 44.1 6.3 62 98-160 30-91 (116)
34 KOG3219 Transcription initiati 95.5 0.018 3.8E-07 49.7 4.2 65 94-160 111-176 (195)
35 smart00428 H3 Histone H3. 95.0 0.08 1.7E-06 41.5 6.2 68 93-160 27-99 (105)
36 smart00576 BTP Bromodomain tra 94.5 0.15 3.3E-06 36.9 6.2 59 101-161 12-70 (77)
37 PF09415 CENP-X: CENP-S associ 92.6 0.52 1.1E-05 34.5 6.2 62 97-158 1-64 (72)
38 PF15630 CENP-S: Kinetochore c 92.5 0.5 1.1E-05 34.9 6.1 48 118-165 26-76 (76)
39 KOG0869 CCAAT-binding factor, 92.0 0.5 1.1E-05 40.0 6.2 66 95-160 32-97 (168)
40 PF03847 TFIID_20kDa: Transcri 90.0 1.7 3.6E-05 31.5 6.6 61 100-161 4-64 (68)
41 KOG3467 Histone H4 [Chromatin 89.3 0.84 1.8E-05 35.5 4.8 71 86-160 22-92 (103)
42 KOG1744 Histone H2B [Chromatin 88.8 2.2 4.7E-05 34.8 7.1 69 88-160 33-101 (127)
43 KOG0871 Class 2 transcription 87.6 1.9 4.2E-05 36.2 6.2 70 91-161 8-78 (156)
44 PF15511 CENP-T: Centromere ki 85.0 1.9 4.2E-05 40.4 5.6 73 82-154 338-414 (414)
45 PTZ00018 histone H3; Provision 83.8 2.9 6.2E-05 34.3 5.4 68 93-160 60-130 (136)
46 PF02861 Clp_N: Clp amino term 82.9 1.3 2.8E-05 28.5 2.5 34 138-171 1-36 (53)
47 PLN00121 histone H3; Provision 82.7 3.4 7.3E-05 33.9 5.4 68 93-160 60-130 (136)
48 PF02291 TFIID-31kDa: Transcri 82.4 4.9 0.00011 32.5 6.2 59 98-161 15-76 (129)
49 KOG0870 DNA polymerase epsilon 81.9 5 0.00011 34.2 6.3 68 93-160 8-76 (172)
50 PF02269 TFIID-18kDa: Transcri 81.2 1.9 4E-05 32.7 3.2 42 123-164 25-69 (93)
51 cd07978 TAF13 The TATA Binding 79.3 4.9 0.00011 30.5 5.0 38 126-164 29-69 (92)
52 PF07524 Bromo_TP: Bromodomain 78.9 9.3 0.0002 27.2 6.1 57 102-160 13-69 (77)
53 PLN00160 histone H3; Provision 77.1 7.7 0.00017 30.2 5.5 68 93-160 19-90 (97)
54 KOG1658 DNA polymerase epsilon 77.0 2.6 5.7E-05 35.6 3.1 75 94-170 58-133 (162)
55 PLN00161 histone H3; Provision 69.5 14 0.00031 30.3 5.7 69 92-160 52-124 (135)
56 KOG1142 Transcription initiati 65.1 8.9 0.00019 34.6 3.9 69 96-165 155-223 (258)
57 KOG1745 Histones H3 and H4 [Ch 57.1 12 0.00026 30.9 3.1 64 96-160 67-131 (137)
58 COG5251 TAF40 Transcription in 52.8 19 0.0004 31.2 3.7 63 96-160 116-179 (199)
59 COG5150 Class 2 transcription 49.2 30 0.00066 28.7 4.2 67 93-161 9-77 (148)
60 PRK11034 clpA ATP-dependent Cl 46.4 30 0.00064 35.3 4.5 40 131-170 6-45 (758)
61 PF13654 AAA_32: AAA domain; P 45.7 39 0.00084 32.8 5.0 30 132-161 476-505 (509)
62 TIGR02639 ClpA ATP-dependent C 44.1 33 0.00071 34.2 4.4 39 132-170 6-44 (731)
63 PF13335 Mg_chelatase_2: Magne 42.9 29 0.00063 26.1 3.1 47 114-160 42-94 (96)
64 PF08369 PCP_red: Proto-chloro 42.3 58 0.0013 21.6 4.1 27 132-158 18-44 (45)
65 COG1067 LonB Predicted ATP-dep 41.4 29 0.00063 34.9 3.6 39 132-170 369-407 (647)
66 COG3636 Predicted transcriptio 38.7 47 0.001 26.2 3.6 53 118-170 22-83 (100)
67 CHL00095 clpC Clp protease ATP 36.3 45 0.00097 33.8 4.0 33 132-164 10-42 (821)
68 PF12096 DUF3572: Protein of u 35.5 18 0.00039 27.7 0.9 57 99-160 22-81 (88)
69 TIGR02928 orc1/cdc6 family rep 35.3 1.4E+02 0.003 26.1 6.6 46 115-160 221-272 (365)
70 PF04604 L_biotic_typeA: Type- 33.7 24 0.00053 24.6 1.2 22 161-184 16-37 (51)
71 KOG3901 Transcription initiati 33.3 67 0.0015 25.7 3.8 38 123-164 37-74 (109)
72 KOG3334 Transcription initiati 32.0 1.6E+02 0.0035 24.7 6.0 57 100-161 18-77 (148)
73 TIGR03346 chaperone_ClpB ATP-d 31.1 68 0.0015 32.8 4.4 33 131-163 5-37 (852)
74 PRK00411 cdc6 cell division co 30.0 1.9E+02 0.0041 25.7 6.6 69 93-161 201-281 (394)
75 COG5094 TAF9 Transcription ini 28.2 2.4E+02 0.0051 23.5 6.2 63 98-162 17-82 (145)
76 TIGR03345 VI_ClpV1 type VI sec 27.9 79 0.0017 32.5 4.2 33 131-163 5-37 (852)
77 COG4430 Uncharacterized protei 27.5 61 0.0013 28.4 2.9 61 95-171 95-158 (200)
78 PF15510 CENP-W: Centromere ki 27.5 1.5E+02 0.0033 23.3 4.8 64 95-159 16-93 (102)
79 COG1474 CDC6 Cdc6-related prot 26.2 76 0.0016 29.4 3.5 76 92-168 183-270 (366)
80 TIGR02263 benz_CoA_red_C benzo 25.5 1.2E+02 0.0026 27.9 4.7 45 126-171 136-180 (380)
81 TIGR02639 ClpA ATP-dependent C 24.4 84 0.0018 31.4 3.6 34 131-164 82-115 (731)
82 TIGR00764 lon_rel lon-related 24.3 92 0.002 30.8 3.8 32 132-163 361-392 (608)
83 PRK10865 protein disaggregatio 24.3 1E+02 0.0022 31.7 4.3 39 131-169 10-50 (857)
84 CHL00095 clpC Clp protease ATP 24.1 97 0.0021 31.5 4.0 34 131-164 84-117 (821)
85 KOG2235 Uncharacterized conser 23.2 2.9E+02 0.0063 28.6 7.0 44 93-143 478-521 (776)
86 KOG2549 Transcription initiati 22.0 1.7E+02 0.0037 29.4 5.1 47 114-160 28-74 (576)
87 PF01405 PsbT: Photosystem II 21.5 45 0.00098 20.9 0.7 18 23-40 12-29 (29)
88 KOG1051 Chaperone HSP104 and r 21.1 1E+02 0.0022 32.4 3.6 44 126-171 8-54 (898)
89 cd05031 S-100A10_like S-100A10 21.0 3.3E+02 0.0071 19.6 5.6 52 127-179 3-68 (94)
90 cd01028 TOPRIM_TopoIA TOPRIM_T 20.5 90 0.002 24.5 2.5 32 128-161 105-141 (142)
91 PHA02669 hypothetical protein; 20.0 1.3E+02 0.0027 26.2 3.3 31 119-152 12-42 (210)
No 1
>PLN00154 histone H2A; Provisional
Probab=100.00 E-value=2.1e-51 Score=330.18 Aligned_cols=134 Identities=89% Similarity=1.240 Sum_probs=117.2
Q ss_pred cCCCCCCccccccc--cccCCCCCCCCCCCcccccCcccchhhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHH
Q 046088 60 MSGKGAKGLIMGKA--SASNKDKDKKKPISRSSRAGLQFPVGRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLEL 137 (193)
Q Consensus 60 ~~~~~~~~~~~~~~--~~~~~~~~~k~~~SrSsRAGLqFPVsRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILEL 137 (193)
|++.+|+++.|++. .++.+++.+++..|||+||||||||+||||+||++++..+||+++||||||||||||++|||||
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~k~~srS~rAgL~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLEL 80 (136)
T PLN00154 1 MSGKGGKGLLAAKTTAAAAKKDKDKKKPTSRSSRAGLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLEL 80 (136)
T ss_pred CCCccccccccCCcCCcccccccCCcCCcCcccccCccCchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHH
Confidence 45555555555443 1222345577899999999999999999999999985334999999999999999999999999
Q ss_pred HHHHHhhcCCceechhhHHHHhhCchHHhHhhhccccCCcccCCCCcccccCCCCC
Q 046088 138 AGNASKDLKVKRITPRHLQLAIRGDEELDTLIKGTIAGGGVIPHIHKSLINKSTKD 193 (193)
Q Consensus 138 AGnaA~~~kkkRItPrHIqlAI~nDeEL~~Lf~~tIa~GGv~P~i~~~ll~k~~k~ 193 (193)
|||+|+|++++|||||||++||+||+||++||+.||++|||+|+||++|++|+.+|
T Consensus 81 AGNaA~d~kk~RItPrHi~lAIrnDeEL~~Ll~~TIa~GGVlP~i~~~l~~k~~~~ 136 (136)
T PLN00154 81 AGNASKDLKVKRITPRHLQLAIRGDEELDTLIKGTIAGGGVIPHIHKSLINKSTKK 136 (136)
T ss_pred HHHHHHhhCCceecHHHhhhhccCcHHHHHHhcCCccCCccCCCcchhhcccccCC
Confidence 99999999999999999999999999999999889999999999999999999875
No 2
>PLN00153 histone H2A; Provisional
Probab=100.00 E-value=2.3e-49 Score=316.19 Aligned_cols=110 Identities=65% Similarity=0.948 Sum_probs=106.2
Q ss_pred CCCCCCcccccCcccchhhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhhC
Q 046088 82 KKKPISRSSRAGLQFPVGRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG 161 (193)
Q Consensus 82 ~k~~~SrSsRAGLqFPVsRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~n 161 (193)
+++.+|||+||||||||+||+|+|++++|+. ||+++||||||||||||++||||||+|+|++++++||+||||++||+|
T Consensus 11 ~~k~~srS~ragL~FpVgRi~R~Lr~g~~a~-Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~n 89 (129)
T PLN00153 11 GKKAVSRSAKAGLQFPVGRIARYLKKGKYAE-RIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIRN 89 (129)
T ss_pred ccCccCcccccCcccchHHHHHHHhcCchhh-ccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhccC
Confidence 3467899999999999999999999999997 999999999999999999999999999999999999999999999999
Q ss_pred chHHhHhhhc-cccCCcccCCCCcccccCCCC
Q 046088 162 DEELDTLIKG-TIAGGGVIPHIHKSLINKSTK 192 (193)
Q Consensus 162 DeEL~~Lf~~-tIa~GGv~P~i~~~ll~k~~k 192 (193)
|+||++||++ ||++|||+|+||++|++||.+
T Consensus 90 DeEL~~Ll~~vTIa~GGV~P~i~~~l~~kk~~ 121 (129)
T PLN00153 90 DEELGKLLGEVTIASGGVLPNIHAVLLPKKTK 121 (129)
T ss_pred cHHHHHHHCCCccCCCccCCCcchhhcCcccC
Confidence 9999999999 999999999999999999863
No 3
>PLN00156 histone H2AX; Provisional
Probab=100.00 E-value=3.9e-49 Score=318.08 Aligned_cols=110 Identities=62% Similarity=0.945 Sum_probs=107.0
Q ss_pred CCCCCCCcccccCcccchhhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhh
Q 046088 81 DKKKPISRSSRAGLQFPVGRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 160 (193)
Q Consensus 81 ~~k~~~SrSsRAGLqFPVsRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~ 160 (193)
.+++.+|||+||||||||+||+|+|++++|++ ||+++||||||||||||++||||||+|+|++++++||+||||++||+
T Consensus 15 ~~~k~~srS~rAgL~FPVgRi~R~Lk~g~ya~-RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIr 93 (139)
T PLN00156 15 KATKSVSRSSKAGLQFPVGRIARFLKAGKYAE-RVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR 93 (139)
T ss_pred cccCCcCcccccCcccchHHHHHHHhcCChhh-ccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhcc
Confidence 36788999999999999999999999999997 99999999999999999999999999999999999999999999999
Q ss_pred CchHHhHhhhc-cccCCcccCCCCcccccCCC
Q 046088 161 GDEELDTLIKG-TIAGGGVIPHIHKSLINKST 191 (193)
Q Consensus 161 nDeEL~~Lf~~-tIa~GGv~P~i~~~ll~k~~ 191 (193)
||+||++||++ ||++|||+|+||++|++||.
T Consensus 94 nDeEL~~Ll~~vTIa~GGV~P~i~~~l~~kk~ 125 (139)
T PLN00156 94 NDEELSKLLGSVTIAAGGVLPNIHQTLLPKKV 125 (139)
T ss_pred CcHHHHHHHCCCccCCCccCCCccHhhccccc
Confidence 99999999999 99999999999999999986
No 4
>PLN00157 histone H2A; Provisional
Probab=100.00 E-value=4.8e-49 Score=315.35 Aligned_cols=109 Identities=64% Similarity=0.949 Sum_probs=106.1
Q ss_pred CCCCCCcccccCcccchhhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhhC
Q 046088 82 KKKPISRSSRAGLQFPVGRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG 161 (193)
Q Consensus 82 ~k~~~SrSsRAGLqFPVsRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~n 161 (193)
+++..|||+||||||||+||+|+|++++|+. ||+++||||||||||||++||||||+|+|++++++||+||||++||+|
T Consensus 13 ~~k~~srS~ragL~FPVgRi~R~Lk~g~~a~-RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~n 91 (132)
T PLN00157 13 GKKATSRSAKAGLQFPVGRIARYLKAGKYAT-RVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVRN 91 (132)
T ss_pred CcCCcCcccccCcccchHHHHHHHhcCchhh-hcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhcccC
Confidence 4578999999999999999999999999997 999999999999999999999999999999999999999999999999
Q ss_pred chHHhHhhhc-cccCCcccCCCCcccccCCC
Q 046088 162 DEELDTLIKG-TIAGGGVIPHIHKSLINKST 191 (193)
Q Consensus 162 DeEL~~Lf~~-tIa~GGv~P~i~~~ll~k~~ 191 (193)
|+||++||++ ||++|||+|+||++|++||.
T Consensus 92 DeEL~~Ll~~vtIa~GGV~P~i~~~ll~kk~ 122 (132)
T PLN00157 92 DEELSKLLGGVTIAAGGVLPNIHSVLLPKKS 122 (132)
T ss_pred cHHHHHHHcCceecCCccCCCcchhhcCCCC
Confidence 9999999999 99999999999999999986
No 5
>PTZ00017 histone H2A; Provisional
Probab=100.00 E-value=1.1e-48 Score=314.07 Aligned_cols=110 Identities=72% Similarity=1.057 Sum_probs=106.4
Q ss_pred CCCCCCcccccCcccchhhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhhC
Q 046088 82 KKKPISRSSRAGLQFPVGRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG 161 (193)
Q Consensus 82 ~k~~~SrSsRAGLqFPVsRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~n 161 (193)
+++..|||+||||||||+||+|+|++++|+. ||+++||||||||||||++||||||+|+|++++++|||||||++||+|
T Consensus 14 ~~k~~srS~ragL~FPVgRi~R~Lk~g~~a~-RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~n 92 (134)
T PTZ00017 14 KKKPVSRSAKAGLQFPVGRVHRYLKKGRYAK-RVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIRN 92 (134)
T ss_pred CcCcccccccCCcccchHHHHHHHhccchhc-cccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhccC
Confidence 4578999999999999999999999999997 999999999999999999999999999999999999999999999999
Q ss_pred chHHhHhhhc-cccCCcccCCCCcccccCCCC
Q 046088 162 DEELDTLIKG-TIAGGGVIPHIHKSLINKSTK 192 (193)
Q Consensus 162 DeEL~~Lf~~-tIa~GGv~P~i~~~ll~k~~k 192 (193)
|+||++||++ ||++|||+|+||++|++|+.+
T Consensus 93 DeEL~~Ll~~vtIa~GGV~P~i~~~l~~k~~~ 124 (134)
T PTZ00017 93 DEELNKLLAGVTIASGGVLPNIHKVLLPKKSK 124 (134)
T ss_pred cHHHHHHHcCCcccCCccCCCccHhhccCCCC
Confidence 9999999998 999999999999999999863
No 6
>PTZ00252 histone H2A; Provisional
Probab=100.00 E-value=1.7e-47 Score=306.89 Aligned_cols=107 Identities=50% Similarity=0.806 Sum_probs=101.4
Q ss_pred CCCCCcccccCcccchhhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhh--cCCceechhhHHHHhh
Q 046088 83 KKPISRSSRAGLQFPVGRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKD--LKVKRITPRHLQLAIR 160 (193)
Q Consensus 83 k~~~SrSsRAGLqFPVsRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~--~kkkRItPrHIqlAI~ 160 (193)
+...+||+|||||||||||+|+|++++|++ ||+++||||||||||||++||||||+|+|++ ++++||+||||++||+
T Consensus 13 ~~~~~rS~rAGL~FPVgRi~R~Lr~g~ya~-RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIr 91 (134)
T PTZ00252 13 KSGSGRSAKAGLIFPVGRVGSLLRRGQYAR-RIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVR 91 (134)
T ss_pred ccccccccccCccCchHHHHHHHHcCCccc-ccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhcc
Confidence 334449999999999999999999999997 9999999999999999999999999999976 7889999999999999
Q ss_pred CchHHhHhhhc-cccCCcccCCCCcccccCC
Q 046088 161 GDEELDTLIKG-TIAGGGVIPHIHKSLINKS 190 (193)
Q Consensus 161 nDeEL~~Lf~~-tIa~GGv~P~i~~~ll~k~ 190 (193)
||+||++||++ ||++|||+|+||++|++|+
T Consensus 92 NDeEL~~Ll~~vTIa~GGVlP~i~~~l~~k~ 122 (134)
T PTZ00252 92 HDDDLGSLLKNVTLSRGGVMPSLNKALAKKH 122 (134)
T ss_pred ChHHHHHHHcCCccCCCccCCCccHhhcccc
Confidence 99999999999 9999999999999999983
No 7
>smart00414 H2A Histone 2A.
Probab=100.00 E-value=3.2e-46 Score=289.00 Aligned_cols=104 Identities=75% Similarity=1.082 Sum_probs=101.9
Q ss_pred CcccccCcccchhhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhhCchHHh
Q 046088 87 SRSSRAGLQFPVGRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELD 166 (193)
Q Consensus 87 SrSsRAGLqFPVsRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~nDeEL~ 166 (193)
|||+||||||||+||+|+|++++|+. ||+++||||||||||||++||||||+|+|++++++||||+||++||+||+||+
T Consensus 1 srS~ragL~fPVgRi~r~Lk~~~~~~-Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~nD~EL~ 79 (106)
T smart00414 1 SRSARAGLQFPVGRIHRLLRKGTYAK-RVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIRNDEELN 79 (106)
T ss_pred CccccCCccCchHHHHHHHHcCcccc-ccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhccCCHHHH
Confidence 68999999999999999999999997 99999999999999999999999999999999999999999999999999999
Q ss_pred Hhhhc-cccCCcccCCCCcccccCCC
Q 046088 167 TLIKG-TIAGGGVIPHIHKSLINKST 191 (193)
Q Consensus 167 ~Lf~~-tIa~GGv~P~i~~~ll~k~~ 191 (193)
+||++ ||++|||+|+||++|++||.
T Consensus 80 ~L~~~vti~~ggv~p~i~~~l~~~~~ 105 (106)
T smart00414 80 KLLKGVTIAQGGVLPNIHKVLLPKKT 105 (106)
T ss_pred HHHcCcccCCCccCCCcchhhcccCC
Confidence 99999 99999999999999999884
No 8
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=100.00 E-value=5.6e-46 Score=295.93 Aligned_cols=110 Identities=67% Similarity=0.944 Sum_probs=106.7
Q ss_pred CCCCCCcccccCcccchhhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhhC
Q 046088 82 KKKPISRSSRAGLQFPVGRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG 161 (193)
Q Consensus 82 ~k~~~SrSsRAGLqFPVsRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~n 161 (193)
++...|||.|+|||||||||+|+||+++|++ ||+++|||||+||||||++||||+|+|+|+|++++||+||||++||+|
T Consensus 14 ~~~~~srs~~agl~fPvgri~r~Lr~~~~~~-ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~N 92 (131)
T KOG1756|consen 14 AKAKSSRSSRAGLQFPVGRIHRLLRKGRYAQ-RVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIRN 92 (131)
T ss_pred hhhhcchhhhcccccCHHHHHHHHHccchhh-hccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHhC
Confidence 5678899999999999999999999999997 999999999999999999999999999999999999999999999999
Q ss_pred chHHhHhhhc-cccCCcccCCCCcccccCCCC
Q 046088 162 DEELDTLIKG-TIAGGGVIPHIHKSLINKSTK 192 (193)
Q Consensus 162 DeEL~~Lf~~-tIa~GGv~P~i~~~ll~k~~k 192 (193)
||||++|+++ ||++|||+|+||+.||+|+..
T Consensus 93 DeEL~~lL~~vtIa~GGvlPnI~~~lLpKk~~ 124 (131)
T KOG1756|consen 93 DEELNKLLGKVTIAQGGVLPNIQAILLPKKTG 124 (131)
T ss_pred cHHHHHHhccceeccCCcccccchhhcccccc
Confidence 9999999999 999999999999999999863
No 9
>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=100.00 E-value=3.3e-45 Score=287.00 Aligned_cols=108 Identities=72% Similarity=1.029 Sum_probs=104.8
Q ss_pred CCCCCCcccccCcccchhhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhhC
Q 046088 82 KKKPISRSSRAGLQFPVGRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG 161 (193)
Q Consensus 82 ~k~~~SrSsRAGLqFPVsRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~n 161 (193)
+++.+|||+||||+|||+||+|+|++++++. ||+++|+|||+||||||++||||+|+|+|++++++||||+||++||+|
T Consensus 7 ~~~~~s~s~ragL~fPV~ri~R~Lk~~~~a~-RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~n 85 (115)
T cd00074 7 KSKKRSRSARAGLQFPVGRIHRYLKKGRYAE-RVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRN 85 (115)
T ss_pred CcCccccccccCccCcHHHHHHHHHcCcccc-ccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhc
Confidence 5677899999999999999999999999996 999999999999999999999999999999999999999999999999
Q ss_pred chHHhHhhhc-cccCCcccCCCCcccccCC
Q 046088 162 DEELDTLIKG-TIAGGGVIPHIHKSLINKS 190 (193)
Q Consensus 162 DeEL~~Lf~~-tIa~GGv~P~i~~~ll~k~ 190 (193)
|+||++||++ ||++|||+|+||++|++|+
T Consensus 86 D~EL~~L~~~vtI~~ggv~p~i~~~l~~~~ 115 (115)
T cd00074 86 DEELNKLLKGVTIASGGVLPNIHKVLLPKK 115 (115)
T ss_pred cHHHHHHHcCCcccCCccCCCcchhhcCCC
Confidence 9999999999 9999999999999999875
No 10
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=100.00 E-value=3.2e-45 Score=289.49 Aligned_cols=111 Identities=60% Similarity=0.899 Sum_probs=106.9
Q ss_pred CCCCCCcccccCcccchhhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhhC
Q 046088 82 KKKPISRSSRAGLQFPVGRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG 161 (193)
Q Consensus 82 ~k~~~SrSsRAGLqFPVsRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~n 161 (193)
.+...|+|+++||+|||+||+|+|++++|.. ||+++|+||++||||||++||||+|+|+|++++++||+|||||+||+|
T Consensus 13 ~r~~~s~sa~agl~fpvgrvkr~lk~~~~~~-Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIrn 91 (132)
T COG5262 13 ARVSQSRSAKAGLIFPVGRVKRLLKKGNYRM-RIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIRN 91 (132)
T ss_pred chhccchhhhcCccccHHHHHHHHHcCccce-eecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhcC
Confidence 5667899999999999999999999999985 999999999999999999999999999999999999999999999999
Q ss_pred chHHhHhhhc-cccCCcccCCCCcccccCCCCC
Q 046088 162 DEELDTLIKG-TIAGGGVIPHIHKSLINKSTKD 193 (193)
Q Consensus 162 DeEL~~Lf~~-tIa~GGv~P~i~~~ll~k~~k~ 193 (193)
|+||++|+++ ||++|||+|+|++.|+++.+||
T Consensus 92 D~EL~~l~~~~tIa~GGvlp~I~~~ll~k~skK 124 (132)
T COG5262 92 DEELNKLLGDVTIAQGGVLPNINPGLLPKSSKK 124 (132)
T ss_pred cHHHHHHhhhheeecCCcccccChhhhhhhhcc
Confidence 9999999998 9999999999999999998764
No 11
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=100.00 E-value=2.5e-44 Score=283.10 Aligned_cols=112 Identities=90% Similarity=1.243 Sum_probs=108.2
Q ss_pred CCCCCCcccccCcccchhhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhhC
Q 046088 82 KKKPISRSSRAGLQFPVGRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG 161 (193)
Q Consensus 82 ~k~~~SrSsRAGLqFPVsRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~n 161 (193)
+.+.+|+|+||||||||+||||+|+....+.+||++.++||++|+|||||+||||||||+++|.+.+||||||+|+|||.
T Consensus 17 ~~k~vs~s~raGlqFpVgRihr~LK~r~t~h~rVGataavy~aaileYLTaEVLeLAgNasKdLKvKRitprHlqLAiRG 96 (131)
T KOG1757|consen 17 KAKAVSRSARAGLQFPVGRIHRHLKTRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG 96 (131)
T ss_pred hhhhhhHHHhcccccchHHHHHHHHHhcccccccchHHHHHHHHHHHHHHHHHHHHcccccccceeeeccchhheeeecC
Confidence 67889999999999999999999999988889999999999999999999999999999999999999999999999999
Q ss_pred chHHhHhhhccccCCcccCCCCcccccCCCCC
Q 046088 162 DEELDTLIKGTIAGGGVIPHIHKSLINKSTKD 193 (193)
Q Consensus 162 DeEL~~Lf~~tIa~GGv~P~i~~~ll~k~~k~ 193 (193)
|||||.|++.||++|||+||||++|+.|+.++
T Consensus 97 DeELDtLIk~TiagGgViPhihk~l~~k~~~~ 128 (131)
T KOG1757|consen 97 DEELDTLIKATIAGGGVIPHIHKSLINKKGKK 128 (131)
T ss_pred cHHHHHHHHHhhccCccccchHHHHhcccccc
Confidence 99999999999999999999999999988753
No 12
>PLN00155 histone H2A; Provisional
Probab=99.85 E-value=7.6e-22 Score=139.11 Aligned_cols=48 Identities=65% Similarity=0.948 Sum_probs=45.4
Q ss_pred CCCCCCcccccCcccchhhHHhhhhccCCcccccCcchHHHHHHHHHHH
Q 046088 82 KKKPISRSSRAGLQFPVGRIHRLLKSRTTAHGRVGATAAVYSAAILEYL 130 (193)
Q Consensus 82 ~k~~~SrSsRAGLqFPVsRI~RlLke~~~a~~RIss~ApVYLAAVLEYL 130 (193)
+++.+|||+||||||||+||+|+|++++|++ ||+++||||||||||||
T Consensus 11 ~~k~~srS~rAgL~FPVgri~r~Lr~g~~a~-Rvga~apVYlAAVLEYL 58 (58)
T PLN00155 11 GKKAVSRSAKAGLQFPVGRIARYLKKGKYAE-RIGAGAPVYLAAVLEYL 58 (58)
T ss_pred ccCccCcccccccccchHHHHHHHhcCChhh-cccCCcHHHHHHHHHhC
Confidence 3467899999999999999999999999998 99999999999999997
No 13
>PF00125 Histone: Core histone H2A/H2B/H3/H4 histone h2a signature histone h2b signature histone h3 signature histone h4 signature; InterPro: IPR007125 The core histones together with some other DNA binding proteins appear to form a superfamily defined by a common fold and distant sequence similarities [, ]. Some proteins contain local homology domains related to the histone fold [].; GO: 0003677 DNA binding; PDB: 2YFW_D 2YFV_B 1U35_H 2F8N_D 2PYO_D 2NQB_D 3AN2_C 3AZJ_C 3AV1_G 3AZM_G ....
Probab=99.57 E-value=3.6e-15 Score=105.82 Aligned_cols=74 Identities=39% Similarity=0.547 Sum_probs=69.2
Q ss_pred ccccCcccchhhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhhCc
Q 046088 89 SSRAGLQFPVGRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGD 162 (193)
Q Consensus 89 SsRAGLqFPVsRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~nD 162 (193)
+.+..+.||+.|+.|-+..+.+..+||++.|.+||.+++||++.+|+|+|++.|..+++++|+|+||++|++.|
T Consensus 2 ~~~~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r~~ 75 (75)
T PF00125_consen 2 TRRLIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVRID 75 (75)
T ss_dssp HSHSSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHHHT
T ss_pred cccccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHhcC
Confidence 45778999999999999998776569999999999999999999999999999999999999999999999876
No 14
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=99.33 E-value=2.2e-12 Score=100.70 Aligned_cols=79 Identities=25% Similarity=0.485 Sum_probs=74.1
Q ss_pred ccCcccchhhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhhCchHHhHhhh
Q 046088 91 RAGLQFPVGRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDTLIK 170 (193)
Q Consensus 91 RAGLqFPVsRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~nDeEL~~Lf~ 170 (193)
+-.-+||++|++++||.+++. ++|++.+||.++..||+++++|+.+++..|+....+|||.+||..|+.+||.+++|=.
T Consensus 19 ~~ktrFP~ar~KkIMQ~deDi-GKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sdekFdFL~~ 97 (113)
T COG5247 19 KKKTRFPIARLKKIMQLDEDI-GKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDEKFDFLKN 97 (113)
T ss_pred hhhhcCCHHHHHHHHHhhhhh-hhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhHHHHHHHH
Confidence 445669999999999999987 5999999999999999999999999999999999999999999999999999998864
No 15
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=99.04 E-value=3.6e-10 Score=97.62 Aligned_cols=77 Identities=23% Similarity=0.416 Sum_probs=72.7
Q ss_pred CcccchhhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhhCchHHhHhhh
Q 046088 93 GLQFPVGRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDTLIK 170 (193)
Q Consensus 93 GLqFPVsRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~nDeEL~~Lf~ 170 (193)
.-.||++||+++||.++.. ++|...+||.+...||.|+.+|+..++.+++..+-+|+++.||..||.+|+.|++|=.
T Consensus 11 ~trfp~aRiKKIMQ~dEdI-GKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~~FdFLk~ 87 (224)
T KOG1659|consen 11 KTRFPPARIKKIMQSDEDI-GKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDPKFDFLKE 87 (224)
T ss_pred hccCCHHHHHHHHhhhhhh-hhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccchhHHHHH
Confidence 3459999999999999997 5999999999999999999999999999999999999999999999999999998854
No 16
>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=98.82 E-value=1.5e-08 Score=70.86 Aligned_cols=64 Identities=25% Similarity=0.275 Sum_probs=57.1
Q ss_pred ccchhhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHh
Q 046088 95 QFPVGRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAI 159 (193)
Q Consensus 95 qFPVsRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI 159 (193)
.||.++|+|+||...... +|+.+|...++...|.++.++...|...|...+++.|+++||..|+
T Consensus 2 ~lP~a~vkri~k~~~~~~-~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 2 SLPLARVKRIMKSDPDVM-RVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp SS-HHHHHHHHHHTSTTS-EE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred CCChHHHHHHhccCCCcc-chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 599999999999995544 9999999999999999999999999999999999999999999886
No 17
>PLN00035 histone H4; Provisional
Probab=98.32 E-value=1.1e-06 Score=68.49 Aligned_cols=73 Identities=16% Similarity=0.224 Sum_probs=64.5
Q ss_pred CCCcccccCcccchhhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhhC
Q 046088 85 PISRSSRAGLQFPVGRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG 161 (193)
Q Consensus 85 ~~SrSsRAGLqFPVsRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~n 161 (193)
+..+-+-+| +|..-|.|+.+.+.. + |||.++-..+..+||.+..+|+.-|...|+..+++.|+.+||.+|++.
T Consensus 21 k~~~d~i~~--ipk~~IrRLARr~Gv-k-RIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr 93 (103)
T PLN00035 21 KVLRDNIQG--ITKPAIRRLARRGGV-K-RISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 93 (103)
T ss_pred HHHHhhhcc--CCHHHHHHHHHHcCc-c-cchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHH
Confidence 344555566 788889999999874 5 999999999999999999999999999999999999999999999873
No 18
>PTZ00015 histone H4; Provisional
Probab=98.21 E-value=3.5e-06 Score=65.60 Aligned_cols=70 Identities=17% Similarity=0.231 Sum_probs=61.4
Q ss_pred CcccccCcccchhhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhh
Q 046088 87 SRSSRAGLQFPVGRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 160 (193)
Q Consensus 87 SrSsRAGLqFPVsRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~ 160 (193)
.|.+-.| +|..-|.|+.+.+.. + |||.++-..+..+||.+..+|+.-|...|+..+++.|+.+||.+|++
T Consensus 24 ~r~~i~g--I~k~~IrRLarr~Gv-k-RIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlK 93 (102)
T PTZ00015 24 LRDNIRG--ITKGAIRRLARRGGV-K-RISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALK 93 (102)
T ss_pred HhhcccC--CCHHHHHHHHHHcCC-c-cchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHH
Confidence 3444456 556679999998866 4 99999999999999999999999999999999999999999999986
No 19
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=98.13 E-value=1e-05 Score=57.83 Aligned_cols=64 Identities=22% Similarity=0.213 Sum_probs=59.6
Q ss_pred ccchhhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhh
Q 046088 95 QFPVGRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 160 (193)
Q Consensus 95 qFPVsRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~ 160 (193)
.+|..-|+|+.+.... . ||+..+...|+-.+||...||++-|.+.++..+++++|++||..|++
T Consensus 2 ~~p~~~i~ria~~~Gi-~-ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 2 WLPKETIKDVAESLGI-G-NLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred CCCHHHHHHHHHHCCC-c-cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 4788999999998866 4 99999999999999999999999999999999999999999999874
No 20
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=97.85 E-value=3.1e-05 Score=59.21 Aligned_cols=66 Identities=24% Similarity=0.335 Sum_probs=60.6
Q ss_pred CcccchhhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhh
Q 046088 93 GLQFPVGRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 160 (193)
Q Consensus 93 GLqFPVsRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~ 160 (193)
.+-+|+.=|.|+||+... + ||+++|-..|.-++|-+..+|.|.|...|...+++.|+++||++|++
T Consensus 17 ~~~Lp~apv~Ri~r~~~~-~-Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~ 82 (91)
T COG2036 17 DLLLPKAPVRRILRKAGA-E-RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALK 82 (91)
T ss_pred hhhcCchHHHHHHHHHhH-H-HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHH
Confidence 455788889999998765 4 99999999999999999999999999999999999999999999986
No 21
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=97.71 E-value=3.5e-05 Score=67.44 Aligned_cols=84 Identities=19% Similarity=0.210 Sum_probs=75.9
Q ss_pred CcccccCcccchhhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhhCchHHh
Q 046088 87 SRSSRAGLQFPVGRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELD 166 (193)
Q Consensus 87 SrSsRAGLqFPVsRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~nDeEL~ 166 (193)
....-....||.+||+++||.+.... -|++.|||.++-+.|+++.|+-..|+..+.+++++.+.-.||..|+.+.+-++
T Consensus 66 ~~~d~~~~~lPlaRiKkimK~dedv~-mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av~~s~~fd 144 (236)
T KOG1657|consen 66 GQLDFKNHILPLARIKKIMKSDEDVS-MITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAVTQSETFD 144 (236)
T ss_pred cccchhhccCcHhhcccccccccccc-ccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHhccCCCcc
Confidence 33334467799999999999999987 89999999999999999999999999999999999999999999999999999
Q ss_pred Hhhhc
Q 046088 167 TLIKG 171 (193)
Q Consensus 167 ~Lf~~ 171 (193)
+|...
T Consensus 145 FL~Di 149 (236)
T KOG1657|consen 145 FLRDI 149 (236)
T ss_pred ceecc
Confidence 99853
No 22
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=97.60 E-value=0.0001 Score=65.02 Aligned_cols=76 Identities=24% Similarity=0.333 Sum_probs=71.0
Q ss_pred cccchhhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhhCchHHhHhhh
Q 046088 94 LQFPVGRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDTLIK 170 (193)
Q Consensus 94 LqFPVsRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~nDeEL~~Lf~ 170 (193)
+.+|..||+++|+.+...+ =|++.|||.+|.+-|-+++|+--.|.-.|..|+++.+.-.+|..|+...|-+++|+.
T Consensus 108 h~LPlARIkkvMKtdedVk-MisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~kSeMfDFLid 183 (286)
T COG5208 108 HNLPLARIKKVMKTDEDVK-MISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKKSEMFDFLID 183 (286)
T ss_pred ccCcHHHHHHHHhcccchh-heecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHHHHHHhHHhh
Confidence 4499999999999999987 799999999999999999999999999999999988999999999999999999883
No 23
>cd00076 H4 Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution
Probab=97.52 E-value=0.00032 Score=52.98 Aligned_cols=69 Identities=17% Similarity=0.191 Sum_probs=61.5
Q ss_pred ccccCcccchhhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhhC
Q 046088 89 SSRAGLQFPVGRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG 161 (193)
Q Consensus 89 SsRAGLqFPVsRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~n 161 (193)
.+-+| +|..-|.|+.+.+.. . |||.++-.-+..+||.+..+|+..|...|...+++.|+.+||.+|++.
T Consensus 9 ~~~~g--i~k~~I~RLarr~Gv-k-RIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr 77 (85)
T cd00076 9 DNIKG--ITKPAIRRLARRGGV-K-RISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKR 77 (85)
T ss_pred Hhhcc--CCHHHHHHHHHHcCc-c-hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHH
Confidence 33445 677789999999875 5 999999999999999999999999999999999999999999999874
No 24
>smart00417 H4 Histone H4.
Probab=97.34 E-value=0.00044 Score=51.08 Aligned_cols=61 Identities=16% Similarity=0.164 Sum_probs=55.4
Q ss_pred cchhhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHH
Q 046088 96 FPVGRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLA 158 (193)
Q Consensus 96 FPVsRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlA 158 (193)
+|..-|.|+++.+.. + |||.++-..+..+||.+..+|+..|...|...+++.|+.+|+..|
T Consensus 14 I~k~~IrRLaRr~Gv-k-RIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~a 74 (74)
T smart00417 14 ITKPAIRRLARRGGV-K-RISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74 (74)
T ss_pred CCHHHHHHHHHHcCc-c-hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHheeC
Confidence 567789999999866 5 999999999999999999999999999999999999999998653
No 25
>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=97.18 E-value=0.0016 Score=46.98 Aligned_cols=65 Identities=17% Similarity=0.230 Sum_probs=57.8
Q ss_pred chhhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhhCc
Q 046088 97 PVGRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGD 162 (193)
Q Consensus 97 PVsRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~nD 162 (193)
+-..+..++++..... |++.+|-..|..+.|=+..+|++.|...|+..+++.|.++||+++++..
T Consensus 3 ~k~~l~~lv~~id~~~-~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r~ 67 (72)
T cd07981 3 TKRKLQELLKEIDPRE-QLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLERN 67 (72)
T ss_pred cHHHHHHHHHhhCCCC-CcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence 4456777888765554 9999999999999999999999999999999999999999999999864
No 26
>cd08048 TAF11 TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypothes
Probab=96.88 E-value=0.0042 Score=46.74 Aligned_cols=63 Identities=30% Similarity=0.472 Sum_probs=55.4
Q ss_pred cchhhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcC---CceechhhHHHHhh
Q 046088 96 FPVGRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLK---VKRITPRHLQLAIR 160 (193)
Q Consensus 96 FPVsRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~k---kkRItPrHIqlAI~ 160 (193)
||-..++|++..-.. + .++....+.|+++-.-++.||+|.|...-.+.+ ...|.|+||+.|.+
T Consensus 17 f~k~~iKr~~~~~~~-~-~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~r 82 (85)
T cd08048 17 FPKAAIKRLIQSVTG-Q-SVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYR 82 (85)
T ss_pred ccHHHHHHHHHHHcC-C-CCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHH
Confidence 788889999987665 4 899999999999999999999999998866554 47899999999976
No 27
>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex. TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.
Probab=96.46 E-value=0.012 Score=42.50 Aligned_cols=64 Identities=20% Similarity=0.225 Sum_probs=48.9
Q ss_pred ccchhhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhh
Q 046088 95 QFPVGRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 160 (193)
Q Consensus 95 qFPVsRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~ 160 (193)
.||..-|+.+-..-... .++..+.-.||-=+||-+.||++-|.+..+..+++++|+.||+.|++
T Consensus 3 ~~~~esvk~iAes~Gi~--~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 3 VFSQESVKDIAESLGIS--NLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp ---HHHHHHHHHHTT-----B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred cCCHHHHHHHHHHcCCC--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 46667776666655553 58999999999999999999999999999999999999999999975
No 28
>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=96.44 E-value=0.01 Score=46.79 Aligned_cols=61 Identities=21% Similarity=0.126 Sum_probs=55.3
Q ss_pred hhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhhC
Q 046088 99 GRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG 161 (193)
Q Consensus 99 sRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~n 161 (193)
--|+++|++... . +++..++..|.-.++-.+.+|+.-|...|+..+++.|+.+||++||..
T Consensus 5 ~~v~~iLk~~Gv-~-~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~ 65 (117)
T cd07979 5 RVIAAILKSMGI-T-EYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQS 65 (117)
T ss_pred HHHHHHHHHCCC-C-ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 358899998644 3 899999999999999999999999999999999999999999999974
No 29
>PTZ00463 histone H2B; Provisional
Probab=96.25 E-value=0.034 Score=44.55 Aligned_cols=61 Identities=18% Similarity=0.165 Sum_probs=50.6
Q ss_pred hhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhh
Q 046088 99 GRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 160 (193)
Q Consensus 99 sRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~ 160 (193)
-.|++.|++-.... -|++.|.-.|...+.=+...|-..|.+.|+-+++..|++|+||.|++
T Consensus 32 ~YI~KVLKqVhPd~-gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvr 92 (117)
T PTZ00463 32 LYIFKVLKQVHPDT-GISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIR 92 (117)
T ss_pred HHHHHHHHhhCCCC-CccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHh
Confidence 46999999877654 79888887777777777777777777788889999999999999998
No 30
>PF04719 TAFII28: hTAFII28-like protein conserved region; InterPro: IPR006809 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C terminus of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3 [, ].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005634 nucleus; PDB: 1BH9_B 1BH8_B.
Probab=96.18 E-value=0.012 Score=44.99 Aligned_cols=64 Identities=22% Similarity=0.361 Sum_probs=46.6
Q ss_pred cchhhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhc-CCceechhhHHHHhh
Q 046088 96 FPVGRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDL-KVKRITPRHLQLAIR 160 (193)
Q Consensus 96 FPVsRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~-kkkRItPrHIqlAI~ 160 (193)
||=+.|+|++..-...+ -|+....+.++++--.+..||+|.|-...... ....|.|.||+.|.+
T Consensus 24 ~~k~~ikkli~~~~~~q-sv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~hlreA~r 88 (90)
T PF04719_consen 24 FNKAAIKKLINQVLGNQ-SVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDHLREAYR 88 (90)
T ss_dssp --HHHHHHHHHHHHS-S----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHHHHHHHH
T ss_pred CCHHHHHHHHHHHcCCC-CCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHH
Confidence 78888999998754424 79999999999999999999999998885543 445899999999875
No 31
>smart00427 H2B Histone H2B.
Probab=95.91 E-value=0.026 Score=43.26 Aligned_cols=60 Identities=17% Similarity=0.220 Sum_probs=52.9
Q ss_pred hHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhh
Q 046088 100 RIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 160 (193)
Q Consensus 100 RI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~ 160 (193)
.|+|.|++-.... -|++.|.-.|...+..+...|-.-|.+-++-++++.|++|+||.|++
T Consensus 6 Yi~kvLKqVhpd~-giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvr 65 (89)
T smart00427 6 YIYKVLKQVHPDT-GISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVR 65 (89)
T ss_pred HHHHHHHHhCCCc-cccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHH
Confidence 5889999887765 79999988888888888888888888889999999999999999998
No 32
>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=95.86 E-value=0.023 Score=51.57 Aligned_cols=58 Identities=21% Similarity=0.255 Sum_probs=50.4
Q ss_pred HHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhh
Q 046088 101 IHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 160 (193)
Q Consensus 101 I~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~ 160 (193)
|+-+.+.- .+. |++.+|...|+..+||...+|++.|.+.++..++++++++||+.|++
T Consensus 5 i~~ia~~~-Gi~-~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~ 62 (343)
T cd08050 5 IKLIAESL-GID-SLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALR 62 (343)
T ss_pred HHHHHHHc-CCC-cCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHH
Confidence 33344433 334 99999999999999999999999999999999999999999999987
No 33
>PLN00158 histone H2B; Provisional
Probab=95.63 E-value=0.04 Score=44.12 Aligned_cols=62 Identities=19% Similarity=0.225 Sum_probs=54.0
Q ss_pred hhhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhh
Q 046088 98 VGRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 160 (193)
Q Consensus 98 VsRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~ 160 (193)
-..|+|.|++-.... -|++.|.-.|...+..+...|-..|.+.|+-+++..|++|+||.|++
T Consensus 30 ~~YI~kVLKQVhPd~-gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvr 91 (116)
T PLN00158 30 KIYIYKVLKQVHPDT-GISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVR 91 (116)
T ss_pred HHHHHHHHHHhCCCC-CccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHH
Confidence 356999999877754 79999988888888888888888888889999999999999999988
No 34
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=95.50 E-value=0.018 Score=49.69 Aligned_cols=65 Identities=28% Similarity=0.394 Sum_probs=55.9
Q ss_pred cccchhhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhh-cCCceechhhHHHHhh
Q 046088 94 LQFPVGRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKD-LKVKRITPRHLQLAIR 160 (193)
Q Consensus 94 LqFPVsRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~-~kkkRItPrHIqlAI~ 160 (193)
.-||=+.|+++|..-.-. -|+..+.++++++-.-|+-||+|.|...... .....+.|.||+.|.+
T Consensus 111 s~f~Ka~iKkL~~~itg~--~v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~r 176 (195)
T KOG3219|consen 111 SAFPKAQIKKLMSSITGQ--SVSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAYR 176 (195)
T ss_pred hcCCHHHHHHHHHHHhCC--ccCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHHH
Confidence 349999999999987663 4999999999999999999999999888554 4455799999999987
No 35
>smart00428 H3 Histone H3.
Probab=95.05 E-value=0.08 Score=41.52 Aligned_cols=68 Identities=22% Similarity=0.207 Sum_probs=54.7
Q ss_pred CcccchhhHHhhhhccC---Cc--ccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhh
Q 046088 93 GLQFPVGRIHRLLKSRT---TA--HGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 160 (193)
Q Consensus 93 GLqFPVsRI~RlLke~~---~a--~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~ 160 (193)
+|.+|-.-+.|+.++-. .. .+|++++|-..|-.+.|....+++|-|..-|...++..|+|+|+++|.+
T Consensus 27 ~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~r 99 (105)
T smart00428 27 DLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARR 99 (105)
T ss_pred ccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHH
Confidence 45555555555554421 11 3599999999999999999999999999999999999999999999954
No 36
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=94.54 E-value=0.15 Score=36.91 Aligned_cols=59 Identities=15% Similarity=0.076 Sum_probs=52.2
Q ss_pred HHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhhC
Q 046088 101 IHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG 161 (193)
Q Consensus 101 I~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~n 161 (193)
|.++|+...+ + +++.+|--.|+-++|=.+.++.+.+-+.|...+++..++.||.+|+.+
T Consensus 12 Vaqil~~~Gf-~-~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~ 70 (77)
T smart00576 12 VAQILESAGF-D-SFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALEN 70 (77)
T ss_pred HHHHHHHcCc-c-ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 4456777666 3 899999999999999999999999999999999999999999999864
No 37
>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=92.58 E-value=0.52 Score=34.47 Aligned_cols=62 Identities=21% Similarity=0.237 Sum_probs=47.0
Q ss_pred chhhHHhhhhccC-CcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCce-echhhHHHH
Q 046088 97 PVGRIHRLLKSRT-TAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKR-ITPRHLQLA 158 (193)
Q Consensus 97 PVsRI~RlLke~~-~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkR-ItPrHIqlA 158 (193)
|-.-|.|+|+... ...-||+.+|---++..|+-|+.|-+-.|...|++.+... |..+||+..
T Consensus 1 p~~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki 64 (72)
T PF09415_consen 1 PPELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKI 64 (72)
T ss_dssp -CHHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHH
T ss_pred ChHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHH
Confidence 4445677776421 1224999999999999999999999999999999999888 999999864
No 38
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=92.52 E-value=0.5 Score=34.95 Aligned_cols=48 Identities=21% Similarity=0.265 Sum_probs=37.9
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHH---HhhcCCceechhhHHHHhhCchHH
Q 046088 118 TAAVYSAAILEYLTAEVLELAGNA---SKDLKVKRITPRHLQLAIRGDEEL 165 (193)
Q Consensus 118 ~ApVYLAAVLEYLtAEILELAGna---A~~~kkkRItPrHIqlAI~nDeEL 165 (193)
-+|-|++|+.|-....+-.+|..- |+.-|++.|++.|+.+..|.++.|
T Consensus 26 ~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~Rrn~~L 76 (76)
T PF15630_consen 26 VSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARRNPSL 76 (76)
T ss_dssp E-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT-HHH
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhcCCCC
Confidence 478999999999888888777543 778899999999999999998876
No 39
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=92.02 E-value=0.5 Score=39.97 Aligned_cols=66 Identities=18% Similarity=0.220 Sum_probs=51.7
Q ss_pred ccchhhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhh
Q 046088 95 QFPVGRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 160 (193)
Q Consensus 95 qFPVsRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~ 160 (193)
-+|+.-|-|+||+.-....+|+.+|--.+--++--|++=|---|-..+...++|.|+-.||-+|+.
T Consensus 32 ~LPIANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~ 97 (168)
T KOG0869|consen 32 FLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMS 97 (168)
T ss_pred hccHHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHH
Confidence 389999999999988887899999987765444444444455555557778899999999999986
No 40
>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=89.98 E-value=1.7 Score=31.45 Aligned_cols=61 Identities=13% Similarity=0.242 Sum_probs=47.8
Q ss_pred hHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhhC
Q 046088 100 RIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG 161 (193)
Q Consensus 100 RI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~n 161 (193)
++..++++-... .++...+--.|.-+.+=|+.+|++.|...|+..+...+.+++|++.+..
T Consensus 4 ~l~~Lv~~iDp~-~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Ler 64 (68)
T PF03847_consen 4 KLQELVKQIDPN-EKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLER 64 (68)
T ss_dssp HHHHHHHCC-SS-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHH
T ss_pred HHHHHHHHcCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHh
Confidence 566677766554 4899999999999999999999999999999999999999999998764
No 41
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=89.34 E-value=0.84 Score=35.50 Aligned_cols=71 Identities=20% Similarity=0.285 Sum_probs=54.1
Q ss_pred CCcccccCcccchhhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhh
Q 046088 86 ISRSSRAGLQFPVGRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 160 (193)
Q Consensus 86 ~SrSsRAGLqFPVsRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~ 160 (193)
.-+.+-.|++-|. |.|+-+.+.. . ||+..---=.-.|+.-++.+++-.|...+...+++.||..++-.++.
T Consensus 22 ~LsDnIqgitKpa--IRRlARr~GV-k-Ri~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LK 92 (103)
T KOG3467|consen 22 VLRDNIQGITKPA--IRRLARRGGV-K-RISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALK 92 (103)
T ss_pred HHHhhccccchHH--HHHHHHhcCc-c-hhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHH
Confidence 3344556777776 8888888866 4 89876655566677777788899999888888999999998877654
No 42
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=88.80 E-value=2.2 Score=34.80 Aligned_cols=69 Identities=17% Similarity=0.170 Sum_probs=53.1
Q ss_pred cccccCcccchhhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhh
Q 046088 88 RSSRAGLQFPVGRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 160 (193)
Q Consensus 88 rSsRAGLqFPVsRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~ 160 (193)
+....+..++|-| .|++-...- -|+..|.-.+-+.+.-+...|...|+..|+-+++..|+.++||.|++
T Consensus 33 ~~~~e~~s~yv~k---vlk~Vhpd~-gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~r 101 (127)
T KOG1744|consen 33 TRRKESYSEYVYK---VLKQVHPDL-GISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVR 101 (127)
T ss_pred ccccCceeeehhh---hhhcccCCC-CcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHH
Confidence 4444555566655 566654443 48888888888887777888888999999999999999999999987
No 43
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=87.60 E-value=1.9 Score=36.16 Aligned_cols=70 Identities=19% Similarity=0.282 Sum_probs=51.4
Q ss_pred ccCcccchhhHHhhhhccCCcccccCcchHH-HHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhhC
Q 046088 91 RAGLQFPVGRIHRLLKSRTTAHGRVGATAAV-YSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG 161 (193)
Q Consensus 91 RAGLqFPVsRI~RlLke~~~a~~RIss~ApV-YLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~n 161 (193)
.-.+.+|-.-|..++++.-....||...|-- ++...+||+ -=|---|-..|....++.|.|+|+..|+.|
T Consensus 8 dde~sLPkAtv~KmIke~lP~d~rvakeareliincCvEFI-~liSsEAneic~~e~KKTIa~EHV~KALe~ 78 (156)
T KOG0871|consen 8 DDELSLPKATVNKMIKEMLPKDVRVAKEARELIINCCVEFI-NLISSEANEICNKEAKKTIAPEHVIKALEN 78 (156)
T ss_pred cccccCcHHHHHHHHHHhCCcccccchHHHHHHHHHHHHHH-HHHHHHHHHHHhHHhcccCCHHHHHHHHHH
Confidence 3467889899999999886644688887654 555556654 344444555677778899999999999986
No 44
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=84.99 E-value=1.9 Score=40.43 Aligned_cols=73 Identities=14% Similarity=0.142 Sum_probs=42.9
Q ss_pred CCCCCCcccccCcccchhhHHhhhhc----cCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhh
Q 046088 82 KKKPISRSSRAGLQFPVGRIHRLLKS----RTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRH 154 (193)
Q Consensus 82 ~k~~~SrSsRAGLqFPVsRI~RlLke----~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrH 154 (193)
++++.||-.-.+-.+|.+-|++++.. ..|++.||+..|---|.-++||+...+-+-=.-+|+.-|+|.|.+.|
T Consensus 338 k~~k~Skhgi~~P~lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 338 KQKKVSKHGIPYPSLPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp --------------S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred cccCCCCCCCCCCCCCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 45666777677778999999888743 46677899999999999999999999987777788888999998865
No 45
>PTZ00018 histone H3; Provisional
Probab=83.76 E-value=2.9 Score=34.34 Aligned_cols=68 Identities=21% Similarity=0.181 Sum_probs=54.6
Q ss_pred CcccchhhHHhhhhccC---CcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhh
Q 046088 93 GLQFPVGRIHRLLKSRT---TAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 160 (193)
Q Consensus 93 GLqFPVsRI~RlLke~~---~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~ 160 (193)
.|.+|-.-+.|+.+|-. ...+|+...|-.-|--+-|..+..++|.+.-.|...++..|.|+|+++|.+
T Consensus 60 ~lLI~k~pF~RLVREI~~~~~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~r 130 (136)
T PTZ00018 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
T ss_pred hhccccccHHHHHHHHHHHcCCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHHH
Confidence 55566666666665531 123699999999999999999999999998888888999999999999843
No 46
>PF02861 Clp_N: Clp amino terminal domain; InterPro: IPR004176 This short domain is found in one or two copies at the amino terminus of ClpA and ClpB proteins from bacteria and eukaryotes. The function of these domains is uncertain but they may form a protein binding site []. The proteins are thought to be subunits of ATP-dependent proteases which act as chaperones to target the proteases to substrates.; GO: 0019538 protein metabolic process; PDB: 3FH2_A 3ZRJ_A 3ZRI_A 1QVR_C 3FES_C 2Y1R_F 3PXG_D 2Y1Q_A 3PXI_C 2K77_A ....
Probab=82.91 E-value=1.3 Score=28.49 Aligned_cols=34 Identities=26% Similarity=0.370 Sum_probs=26.3
Q ss_pred HHHHHhhcCCceechhhHHHHhhCch--HHhHhhhc
Q 046088 138 AGNASKDLKVKRITPRHLQLAIRGDE--ELDTLIKG 171 (193)
Q Consensus 138 AGnaA~~~kkkRItPrHIqlAI~nDe--EL~~Lf~~ 171 (193)
|-+.|+..+...|+|+||-+|+-.|+ ....+|+.
T Consensus 1 A~~~A~~~~~~~i~~eHlL~all~~~~~~~~~il~~ 36 (53)
T PF02861_consen 1 AQELARERGHQYISPEHLLLALLEDPDSIAARILKK 36 (53)
T ss_dssp HHHHHHHTTBSSE-HHHHHHHHHHHTTSHHHHHHHH
T ss_pred CHHHHHHcCCCcccHHHHHHHHHhhhhHHHHHHHHH
Confidence 45678899999999999999987665 66666654
No 47
>PLN00121 histone H3; Provisional
Probab=82.67 E-value=3.4 Score=33.94 Aligned_cols=68 Identities=21% Similarity=0.181 Sum_probs=54.4
Q ss_pred CcccchhhHHhhhhccC---CcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhh
Q 046088 93 GLQFPVGRIHRLLKSRT---TAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 160 (193)
Q Consensus 93 GLqFPVsRI~RlLke~~---~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~ 160 (193)
.|.+|-.-+.|+.+|-. ...+|+..+|-.-|--+-|..+-.++|.+.--|...++..|.|+|++++.+
T Consensus 60 ~lLI~k~pF~RLVREI~~~~~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~r 130 (136)
T PLN00121 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
T ss_pred ccccccccHHHHHHHHHHHhCccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHHH
Confidence 56666666666665422 123699999999999999999999999998888888999999999999843
No 48
>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=82.38 E-value=4.9 Score=32.49 Aligned_cols=59 Identities=29% Similarity=0.299 Sum_probs=43.4
Q ss_pred hhhHHhhhhccCCcccccCcchHHHHHHHHHHH---HHHHHHHHHHHHhhcCCceechhhHHHHhhC
Q 046088 98 VGRIHRLLKSRTTAHGRVGATAAVYSAAILEYL---TAEVLELAGNASKDLKVKRITPRHLQLAIRG 161 (193)
Q Consensus 98 VsRI~RlLke~~~a~~RIss~ApVYLAAVLEYL---tAEILELAGnaA~~~kkkRItPrHIqlAI~n 161 (193)
+--|+.+|++.. |...-|-...-.|||. +.+||+-|-..|...+++.|+..|+++||..
T Consensus 15 a~~i~~iL~~~G-----v~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~ 76 (129)
T PF02291_consen 15 ARVIHLILKSMG-----VTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQS 76 (129)
T ss_dssp HHHHHHHHHHTT--------B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHH
T ss_pred HHHHHHHHHHcC-----CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHH
Confidence 345778888763 4555677777778875 6788999999999999999999999999983
No 49
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=81.89 E-value=5 Score=34.22 Aligned_cols=68 Identities=21% Similarity=0.225 Sum_probs=53.1
Q ss_pred CcccchhhHHhhhhccCCc-ccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhh
Q 046088 93 GLQFPVGRIHRLLKSRTTA-HGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 160 (193)
Q Consensus 93 GLqFPVsRI~RlLke~~~a-~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~ 160 (193)
-|-||-+-|-|+.++--.- ..-|+..|...++-.---|+..+.-.|.+.|++.+++.|++.++-.|+.
T Consensus 8 dl~lP~AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~ 76 (172)
T KOG0870|consen 8 DLNLPNAIITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALD 76 (172)
T ss_pred HhhccHHHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHH
Confidence 4678988888776654221 1247777777777777777788888999999999999999999999987
No 50
>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=81.25 E-value=1.9 Score=32.66 Aligned_cols=42 Identities=17% Similarity=0.277 Sum_probs=9.4
Q ss_pred HHHHHHHHHHHHHHHHH---HHHhhcCCceechhhHHHHhhCchH
Q 046088 123 SAAILEYLTAEVLELAG---NASKDLKVKRITPRHLQLAIRGDEE 164 (193)
Q Consensus 123 LAAVLEYLtAEILELAG---naA~~~kkkRItPrHIqlAI~nDeE 164 (193)
...+-|+++.+|.++.- +.|...+.++|+++|+..++|+|+.
T Consensus 25 v~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~D~~ 69 (93)
T PF02269_consen 25 VDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRKDPK 69 (93)
T ss_dssp HHHHHHHHHHHHHHHHHHHHC------------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhcCHH
Confidence 33455555555555554 4566677789999999999999986
No 51
>cd07978 TAF13 The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Several hy
Probab=79.33 E-value=4.9 Score=30.54 Aligned_cols=38 Identities=16% Similarity=0.322 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHHHHH---HhhcCCceechhhHHHHhhCchH
Q 046088 126 ILEYLTAEVLELAGNA---SKDLKVKRITPRHLQLAIRGDEE 164 (193)
Q Consensus 126 VLEYLtAEILELAGna---A~~~kkkRItPrHIqlAI~nDeE 164 (193)
+=|+++..|.++.-++ |. .++.+|+++|+.-+||+|+.
T Consensus 29 lE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR~D~~ 69 (92)
T cd07978 29 LEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLRKDPK 69 (92)
T ss_pred HHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHhcCHH
Confidence 3344444455554444 44 46778899999999999986
No 52
>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=78.89 E-value=9.3 Score=27.21 Aligned_cols=57 Identities=14% Similarity=0.081 Sum_probs=48.8
Q ss_pred HhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhh
Q 046088 102 HRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 160 (193)
Q Consensus 102 ~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~ 160 (193)
.++|+...+ . .++.+|---|+-+++..+.++...+-..|...++...++.|+..|+.
T Consensus 13 a~il~~~GF-~-~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~ 69 (77)
T PF07524_consen 13 AQILKHAGF-D-SASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALE 69 (77)
T ss_pred HHHHHHcCc-c-ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 345666656 3 78899999999999988999999999999999999999999999875
No 53
>PLN00160 histone H3; Provisional
Probab=77.09 E-value=7.7 Score=30.15 Aligned_cols=68 Identities=21% Similarity=0.120 Sum_probs=53.0
Q ss_pred CcccchhhHHhhhhccC----CcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhh
Q 046088 93 GLQFPVGRIHRLLKSRT----TAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 160 (193)
Q Consensus 93 GLqFPVsRI~RlLke~~----~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~ 160 (193)
+|.+|-.-+.|+.++-. ....|..++|-.-|--+-|..+-.++|-+.--|...++..|.|+|+++|.+
T Consensus 19 ~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~r 90 (97)
T PLN00160 19 DLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLARR 90 (97)
T ss_pred hhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHHH
Confidence 45555555555554421 122599999999999999999999999998888888999999999999854
No 54
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=77.05 E-value=2.6 Score=35.57 Aligned_cols=75 Identities=21% Similarity=0.205 Sum_probs=63.8
Q ss_pred cccchhhHHhhhhccCCcccccCc-chHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhhCchHHhHhhh
Q 046088 94 LQFPVGRIHRLLKSRTTAHGRVGA-TAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDTLIK 170 (193)
Q Consensus 94 LqFPVsRI~RlLke~~~a~~RIss-~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~nDeEL~~Lf~ 170 (193)
.++|.+||+.+++.+... ++.. .+...++-.-|-+..++=..++..+...+++.+.-+++..||..-+|+.+|-.
T Consensus 58 ~rLpL~rik~vvkl~pdl--~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai~~~de~~fle~ 133 (162)
T KOG1658|consen 58 SRLPLARIKQVVKLDPDL--TLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAIEAVDEFAFLEG 133 (162)
T ss_pred hhccHHHHHhhccCCcch--hhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccccchHHHHHHhh
Confidence 569999999999988774 5555 45555677899999999999999999999999999999999999999888774
No 55
>PLN00161 histone H3; Provisional
Probab=69.49 E-value=14 Score=30.32 Aligned_cols=69 Identities=22% Similarity=0.151 Sum_probs=53.7
Q ss_pred cCcccchhhHHhhhhccC----CcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhh
Q 046088 92 AGLQFPVGRIHRLLKSRT----TAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 160 (193)
Q Consensus 92 AGLqFPVsRI~RlLke~~----~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~ 160 (193)
.+|.+|-.-+.|+.+|-. ...+|+.+.|-.-|--+-|..+-.++|-|.--|...++..|.|+|+++|.+
T Consensus 52 t~lLIpklPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~r 124 (135)
T PLN00161 52 TELLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARR 124 (135)
T ss_pred cccccccccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHH
Confidence 355566555566655421 123699999999999999999999999998888888999999999999854
No 56
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=65.14 E-value=8.9 Score=34.62 Aligned_cols=69 Identities=10% Similarity=0.195 Sum_probs=59.1
Q ss_pred cchhhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhhCchHH
Q 046088 96 FPVGRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEEL 165 (193)
Q Consensus 96 FPVsRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~nDeEL 165 (193)
.-.-+++.++++-.-. ..+...+--+|.-+.|=|+..|...|+.-|+..++..|..+||++.+.++--+
T Consensus 155 l~k~kl~dLvqqId~~-~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr~~Nm 223 (258)
T KOG1142|consen 155 LSKRKLDDLVQQIDGT-TKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLERNFNM 223 (258)
T ss_pred ccccchhHHHHhhcCc-ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeeccccc
Confidence 3356778888876443 48999999999999999999999999999999999999999999999987543
No 57
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=57.14 E-value=12 Score=30.92 Aligned_cols=64 Identities=23% Similarity=0.244 Sum_probs=49.4
Q ss_pred cchhhHHh-hhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhh
Q 046088 96 FPVGRIHR-LLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 160 (193)
Q Consensus 96 FPVsRI~R-lLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~ 160 (193)
.|-.|+-| ..++..- ..|+.++|-.-|--..|...-+++|.+.--|-..++-.|.|.|||+|.+
T Consensus 67 ~PFqRlvrei~q~f~~-dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArr 131 (137)
T KOG1745|consen 67 LPFQRLVREIAQDFKT-DLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 131 (137)
T ss_pred CcHHHHhHHHHhcccc-cceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhh
Confidence 34455555 3333333 3689999998888888888889999888778888999999999999976
No 58
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=52.76 E-value=19 Score=31.22 Aligned_cols=63 Identities=17% Similarity=0.252 Sum_probs=47.9
Q ss_pred cchhhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHh-hcCCceechhhHHHHhh
Q 046088 96 FPVGRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASK-DLKVKRITPRHLQLAIR 160 (193)
Q Consensus 96 FPVsRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~-~~kkkRItPrHIqlAI~ 160 (193)
||-..|+.+.-.--. + -|+..-.|++.++---+..||+|||...-. +.-.....|.|++.|++
T Consensus 116 lnKt~VKKlastV~n-Q-tVspNi~I~l~g~~KVfvGEiIElA~~Vq~~w~~sgpl~p~h~reayr 179 (199)
T COG5251 116 LNKTQVKKLASTVAN-Q-TVSPNIRIFLQGVGKVFVGEIIELAMIVQNKWLTSGPLIPFHKREAYR 179 (199)
T ss_pred CCHHHHHHHHHHHhc-c-ccCCCeeeeeechhHHHHHHHHHHHHHHHHHhcccCCCChHHHHHHHH
Confidence 556666666543322 3 688889999999999999999999976633 33455789999999987
No 59
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=49.21 E-value=30 Score=28.65 Aligned_cols=67 Identities=15% Similarity=0.258 Sum_probs=39.6
Q ss_pred CcccchhhHHhhhhccCCccccc-CcchHHHHHHHHHHHHHHHHHHHHHH-HhhcCCceechhhHHHHhhC
Q 046088 93 GLQFPVGRIHRLLKSRTTAHGRV-GATAAVYSAAILEYLTAEVLELAGNA-SKDLKVKRITPRHLQLAIRG 161 (193)
Q Consensus 93 GLqFPVsRI~RlLke~~~a~~RI-ss~ApVYLAAVLEYLtAEILELAGna-A~~~kkkRItPrHIqlAI~n 161 (193)
.+.+|-.-|..++-+.-....-+ -...-+++-+.+||+. +|..-.|. |.+..++.|.|+|+-.|+.|
T Consensus 9 e~sLPKATVqKMvS~iLp~dl~ftKearei~in~cieFi~--~lsseAne~ce~EaKKTIa~EHviKALen 77 (148)
T COG5150 9 ENSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFIN--MLSSEANEACEEEAKKTIAYEHVIKALEN 77 (148)
T ss_pred cccCcHHHHHHHHHHhccccccccHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHhccccHHHHHHHHHh
Confidence 34455555555443321111011 2345678889999874 33333333 45567889999999999986
No 60
>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional
Probab=46.43 E-value=30 Score=35.25 Aligned_cols=40 Identities=18% Similarity=0.208 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHHhhcCCceechhhHHHHhhCchHHhHhhh
Q 046088 131 TAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDTLIK 170 (193)
Q Consensus 131 tAEILELAGnaA~~~kkkRItPrHIqlAI~nDeEL~~Lf~ 170 (193)
+.++|+.|.+.|+..+...|+|+|+-+|+-.|.++..+|.
T Consensus 6 ~~~~l~~a~~~a~~~~~~~~~~~h~l~~l~~~~~~~~~~~ 45 (758)
T PRK11034 6 LELSLNMAFARAREHRHEFMTVEHLLLALLSNPSAREALE 45 (758)
T ss_pred HHHHHHHHHHHHHHcCCCcchHHHHHHHHHcChhHHHHHH
Confidence 4678899999999999999999999999998887777665
No 61
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=45.66 E-value=39 Score=32.82 Aligned_cols=30 Identities=30% Similarity=0.325 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHhhcCCceechhhHHHHhhC
Q 046088 132 AEVLELAGNASKDLKVKRITPRHLQLAIRG 161 (193)
Q Consensus 132 AEILELAGnaA~~~kkkRItPrHIqlAI~n 161 (193)
.++|.-|...|+..+...|+..||+.||..
T Consensus 476 ~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~~ 505 (509)
T PF13654_consen 476 ADLLREANYWARKEGAKVITAEHVEQAIEE 505 (509)
T ss_dssp HHHHHHHHHHHHHCT-SSB-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhCCCccCHHHHHHHHHc
Confidence 788888988999999999999999999974
No 62
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA.
Probab=44.09 E-value=33 Score=34.24 Aligned_cols=39 Identities=21% Similarity=0.268 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHhhcCCceechhhHHHHhhCchHHhHhhh
Q 046088 132 AEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDTLIK 170 (193)
Q Consensus 132 AEILELAGnaA~~~kkkRItPrHIqlAI~nDeEL~~Lf~ 170 (193)
.++|+.|-+.|+..+...|+|+||-+|+-.+++...+++
T Consensus 6 ~~~L~~A~~~A~~~~h~~V~~EHLLlaLL~~~~~~~iL~ 44 (731)
T TIGR02639 6 ERILDAALEEAKKRRHEFVTLEHILLALLFDSDAIEILE 44 (731)
T ss_pred HHHHHHHHHHHHHhCCCcCcHHHHHHHHHcCchHHHHHH
Confidence 567889999999999999999999999988776555554
No 63
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=42.94 E-value=29 Score=26.14 Aligned_cols=47 Identities=21% Similarity=0.196 Sum_probs=37.9
Q ss_pred ccCcchHHHHHHHHHHH------HHHHHHHHHHHHhhcCCceechhhHHHHhh
Q 046088 114 RVGATAAVYSAAILEYL------TAEVLELAGNASKDLKVKRITPRHLQLAIR 160 (193)
Q Consensus 114 RIss~ApVYLAAVLEYL------tAEILELAGnaA~~~kkkRItPrHIqlAI~ 160 (193)
.++..+-.+|-.+++-+ ..-||.+|-..|.-.+..+|++.||..|+.
T Consensus 42 ~l~~~~~~~l~~~~~~~~lS~R~~~rilrvARTIADL~~~~~I~~~hi~EAl~ 94 (96)
T PF13335_consen 42 PLSSEAKKLLEQAAEKLNLSARGYHRILRVARTIADLEGSERITREHIAEALS 94 (96)
T ss_pred CCCHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHhHcCCCCCCHHHHHHHHh
Confidence 56666777776666654 356899999999999999999999999974
No 64
>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=42.28 E-value=58 Score=21.60 Aligned_cols=27 Identities=15% Similarity=0.151 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHhhcCCceechhhHHHH
Q 046088 132 AEVLELAGNASKDLKVKRITPRHLQLA 158 (193)
Q Consensus 132 AEILELAGnaA~~~kkkRItPrHIqlA 158 (193)
..+=..+-..|++.|..+||+.++..|
T Consensus 18 ~~~r~~~E~~Ar~~G~~~IT~e~v~~A 44 (45)
T PF08369_consen 18 KKLRDAAEKYARERGYDEITVEVVDAA 44 (45)
T ss_dssp HHHHHHHHHHHHHCT-SEE-HHHHHHH
T ss_pred HHHHHHHHHHHHHcCCCeECHHHHHhh
Confidence 444455667799999999999999865
No 65
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=41.44 E-value=29 Score=34.88 Aligned_cols=39 Identities=18% Similarity=0.195 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHhhcCCceechhhHHHHhhCchHHhHhhh
Q 046088 132 AEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDTLIK 170 (193)
Q Consensus 132 AEILELAGnaA~~~kkkRItPrHIqlAI~nDeEL~~Lf~ 170 (193)
..++..|+..|...+++.|+++|++.|+++.......+.
T Consensus 369 ~~lv~~A~~ia~~~~~~~I~ae~Ve~a~~~~~~~e~~l~ 407 (647)
T COG1067 369 GNLVREAGDIAVSEGRKLITAEDVEEALQKRELREGQLA 407 (647)
T ss_pred HHHHHHhhHHHhcCCcccCcHHHHHHHHHhhhhHHHHHH
Confidence 456778899999999999999999999999666554443
No 66
>COG3636 Predicted transcriptional regulator [Transcription]
Probab=38.73 E-value=47 Score=26.20 Aligned_cols=53 Identities=21% Similarity=0.264 Sum_probs=34.8
Q ss_pred chHHHHHHHHHHHHHHHH-------HHHHHHHhhcCCceechhhHHHHhh--CchHHhHhhh
Q 046088 118 TAAVYSAAILEYLTAEVL-------ELAGNASKDLKVKRITPRHLQLAIR--GDEELDTLIK 170 (193)
Q Consensus 118 ~ApVYLAAVLEYLtAEIL-------ELAGnaA~~~kkkRItPrHIqlAI~--nDeEL~~Lf~ 170 (193)
.+.+||.++||=-=.+.+ ..+++-++--++.-++-+||..|++ .+++|+.+++
T Consensus 22 ~ia~yL~~~le~~d~a~i~~alg~var~~GMsqvA~~aGlsRe~LYkaLS~~GNPtf~Til~ 83 (100)
T COG3636 22 AIAAYLNAALEEGDPALIAAALGVVARSRGMSQVARKAGLSREGLYKALSPGGNPTFDTILA 83 (100)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHhcCHHHHHHHhCccHHHHHHHhCCCCCCcHHHHHH
Confidence 478999999974333322 3333333333455688999999998 5678888875
No 67
>CHL00095 clpC Clp protease ATP binding subunit
Probab=36.28 E-value=45 Score=33.82 Aligned_cols=33 Identities=15% Similarity=0.303 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHhhcCCceechhhHHHHhhCchH
Q 046088 132 AEVLELAGNASKDLKVKRITPRHLQLAIRGDEE 164 (193)
Q Consensus 132 AEILELAGnaA~~~kkkRItPrHIqlAI~nDeE 164 (193)
.++|+.|-+.|+..+...|+|+|+-+|+-.+++
T Consensus 10 ~~vL~~A~~~A~~~~h~~V~~EHLLLaLL~~~~ 42 (821)
T CHL00095 10 IKVIMLSQEEARRLGHNFVGTEQILLGLIGEGT 42 (821)
T ss_pred HHHHHHHHHHHHHhCCCcCcHHHHHHHHHhCCC
Confidence 467889999999999999999999999987654
No 68
>PF12096 DUF3572: Protein of unknown function (DUF3572); InterPro: IPR021955 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 100 amino acids in length.
Probab=35.51 E-value=18 Score=27.73 Aligned_cols=57 Identities=25% Similarity=0.300 Sum_probs=35.1
Q ss_pred hhHHhhhhccCCc--ccccCcchHHHHHHHHHHHHHH-HHHHHHHHHhhcCCceechhhHHHHhh
Q 046088 99 GRIHRLLKSRTTA--HGRVGATAAVYSAAILEYLTAE-VLELAGNASKDLKVKRITPRHLQLAIR 160 (193)
Q Consensus 99 sRI~RlLke~~~a--~~RIss~ApVYLAAVLEYLtAE-ILELAGnaA~~~kkkRItPrHIqlAI~ 160 (193)
.++.|+|-..... ..|-..+-|.||++||+||+.+ -.-++.-.+ .-|.|+++..|-+
T Consensus 22 e~l~rFLa~TG~~p~~LR~~a~dp~FL~~VLdFl~~de~~l~af~~a-----~~~~p~~v~~Ar~ 81 (88)
T PF12096_consen 22 ERLPRFLALTGLSPDDLRAAAGDPAFLAAVLDFLLMDEAWLLAFCDA-----AGIPPEAVAAARQ 81 (88)
T ss_pred HHHHHHHHHhCCCHHHHHHHccChHHHHHHHHHHHcchHHHHHHHHH-----cCcChhHHHHHHH
Confidence 4566666544332 2466778899999999999864 222332222 2467777776643
No 69
>TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
Probab=35.28 E-value=1.4e+02 Score=26.15 Aligned_cols=46 Identities=20% Similarity=0.273 Sum_probs=33.0
Q ss_pred cCcchHHHHHHHHHH------HHHHHHHHHHHHHhhcCCceechhhHHHHhh
Q 046088 115 VGATAAVYSAAILEY------LTAEVLELAGNASKDLKVKRITPRHLQLAIR 160 (193)
Q Consensus 115 Iss~ApVYLAAVLEY------LtAEILELAGnaA~~~kkkRItPrHIqlAI~ 160 (193)
++..+.-|++.+.+. ..-++++.|...|...+...|+++|++.|+.
T Consensus 221 ~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~ 272 (365)
T TIGR02928 221 LDDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQE 272 (365)
T ss_pred CChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 555555566665542 3345777888778777888999999998875
No 70
>PF04604 L_biotic_typeA: Type-A lantibiotic; InterPro: IPR007682 Lantibiotics are antibiotic peptides distinguished by the presence of the rare thioether amino acids lanthionine and/or methyllanthionine. They are produced by Gram-positive bacteria as gene-encoded precursor peptides and undergo post-translational modification to generate the mature peptide. Based on their structural and functional features lantibiotics are currently divided into two major groups: the flexible amphiphilic type-A and the rather rigid and globular type-B. Type-A lantibiotics act primarily by pore formation in the bacterial membrane by a mechanism involving the interaction with specific docking molecules such as the membrane precursor lipid II [].; GO: 0019748 secondary metabolic process, 0005576 extracellular region
Probab=33.67 E-value=24 Score=24.64 Aligned_cols=22 Identities=50% Similarity=0.866 Sum_probs=17.3
Q ss_pred CchHHhHhhhccccCCcccCCCCc
Q 046088 161 GDEELDTLIKGTIAGGGVIPHIHK 184 (193)
Q Consensus 161 nDeEL~~Lf~~tIa~GGv~P~i~~ 184 (193)
.|+||+++++.. .+||++.|..
T Consensus 16 s~eELd~ilGg~--g~Gv~~Tis~ 37 (51)
T PF04604_consen 16 SDEELDQILGGA--GNGVIKTISH 37 (51)
T ss_pred CHHHHHHHhCCC--CCCceeeccc
Confidence 589999999663 7788887654
No 71
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=33.30 E-value=67 Score=25.66 Aligned_cols=38 Identities=24% Similarity=0.411 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhhCchH
Q 046088 123 SAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEE 164 (193)
Q Consensus 123 LAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~nDeE 164 (193)
=.-|+||++ |++..|-++. ++-+..-+++..+|+.|+-
T Consensus 37 e~iV~~Yi~-elt~~a~~~g---~rgk~~veD~~f~lRkDpk 74 (109)
T KOG3901|consen 37 EDIVLEYIT-ELTHAAMEIG---KRGKVKVEDFKFLLRKDPK 74 (109)
T ss_pred HHHHHHHHH-HHHHHHHHhc---ccCceeHHHHHHHHHhChH
Confidence 344555553 3355555444 4446788999999999975
No 72
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=32.02 E-value=1.6e+02 Score=24.68 Aligned_cols=57 Identities=28% Similarity=0.262 Sum_probs=44.7
Q ss_pred hHHhhhhccCCcccccCcchHHHHHHHHHHH---HHHHHHHHHHHHhhcCCceechhhHHHHhhC
Q 046088 100 RIHRLLKSRTTAHGRVGATAAVYSAAILEYL---TAEVLELAGNASKDLKVKRITPRHLQLAIRG 161 (193)
Q Consensus 100 RI~RlLke~~~a~~RIss~ApVYLAAVLEYL---tAEILELAGnaA~~~kkkRItPrHIqlAI~n 161 (193)
-|+.+|++. =|...-|-...-.|||- +..||+-|-=.+...++..|+-+|+++|++.
T Consensus 18 ~i~~iL~s~-----GI~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~ 77 (148)
T KOG3334|consen 18 VIASILKSL-----GIQEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQM 77 (148)
T ss_pred HHHHHHHHc-----CccccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHH
Confidence 367777764 35555677777778874 5678999988888889999999999999974
No 73
>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB. Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.
Probab=31.06 E-value=68 Score=32.76 Aligned_cols=33 Identities=27% Similarity=0.316 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHhhcCCceechhhHHHHhhCch
Q 046088 131 TAEVLELAGNASKDLKVKRITPRHLQLAIRGDE 163 (193)
Q Consensus 131 tAEILELAGnaA~~~kkkRItPrHIqlAI~nDe 163 (193)
+.++|+.|-..|+..+...|+|+||-+|+-.++
T Consensus 5 a~~vL~~A~~~A~~~~h~~V~~EHLLlaLl~~~ 37 (852)
T TIGR03346 5 FQEALQAAQSLALGRDHQQIEPEHLLKALLDQE 37 (852)
T ss_pred HHHHHHHHHHHHHHcCCCcccHHHHHHHHHhCC
Confidence 356788999999999999999999999988766
No 74
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=30.03 E-value=1.9e+02 Score=25.71 Aligned_cols=69 Identities=20% Similarity=0.253 Sum_probs=40.6
Q ss_pred Ccccc---hhhHHhhhhccC---CcccccCcchHHHHHHHHHHH------HHHHHHHHHHHHhhcCCceechhhHHHHhh
Q 046088 93 GLQFP---VGRIHRLLKSRT---TAHGRVGATAAVYSAAILEYL------TAEVLELAGNASKDLKVKRITPRHLQLAIR 160 (193)
Q Consensus 93 GLqFP---VsRI~RlLke~~---~a~~RIss~ApVYLAAVLEYL------tAEILELAGnaA~~~kkkRItPrHIqlAI~ 160 (193)
-+.|| ...+..+|++.- ....-++..+.-++++..+.. .-+++..|...|...+...|+++|++.|+.
T Consensus 201 ~i~f~py~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~ 280 (394)
T PRK00411 201 EIYFPPYTADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYE 280 (394)
T ss_pred eeecCCCCHHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHH
Confidence 34554 355555555321 101135555555555544331 124566777677777888999999999887
Q ss_pred C
Q 046088 161 G 161 (193)
Q Consensus 161 n 161 (193)
.
T Consensus 281 ~ 281 (394)
T PRK00411 281 K 281 (394)
T ss_pred H
Confidence 3
No 75
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=28.17 E-value=2.4e+02 Score=23.46 Aligned_cols=63 Identities=22% Similarity=0.174 Sum_probs=43.8
Q ss_pred hhhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceech---hhHHHHhhCc
Q 046088 98 VGRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITP---RHLQLAIRGD 162 (193)
Q Consensus 98 VsRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItP---rHIqlAI~nD 162 (193)
|--||-+|+.-..- -.+...|.-|--.----|.++||-|.-.|+..++..|++ +|+++|+..-
T Consensus 17 vrlihliL~Slgi~--~ye~~VplQLl~FAhRYTq~vl~Dalvya~htgrg~~a~l~veDvrLA~at~ 82 (145)
T COG5094 17 VRLIHLILRSLGIE--EYEPKVPLQLLEFAHRYTQDVLEDALVYAKHTGRGHIATLGVEDVRLALATK 82 (145)
T ss_pred hhHHHHHHHhcCch--hhCccchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHHHHHHH
Confidence 44566667653321 234445555444444468899999999999999999999 9999999753
No 76
>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family. Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.
Probab=27.87 E-value=79 Score=32.53 Aligned_cols=33 Identities=18% Similarity=0.140 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHhhcCCceechhhHHHHhhCch
Q 046088 131 TAEVLELAGNASKDLKVKRITPRHLQLAIRGDE 163 (193)
Q Consensus 131 tAEILELAGnaA~~~kkkRItPrHIqlAI~nDe 163 (193)
+.++|+.|-..|+..+...|+|+||-+|+-.++
T Consensus 5 a~~~L~~A~~~A~~~~h~~I~~eHLLlaLL~~~ 37 (852)
T TIGR03345 5 SRRALEQAAALCVARGHPEVELEHWLLALLDQP 37 (852)
T ss_pred HHHHHHHHHHHHHHhCCCcccHHHHHHHHHhcc
Confidence 357889999999999999999999999987653
No 77
>COG4430 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.48 E-value=61 Score=28.38 Aligned_cols=61 Identities=23% Similarity=0.265 Sum_probs=42.3
Q ss_pred ccchhhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHH--HHHHHHH-hhcCCceechhhHHHHhhCchHHhHhhhc
Q 046088 95 QFPVGRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVL--ELAGNAS-KDLKVKRITPRHLQLAIRGDEELDTLIKG 171 (193)
Q Consensus 95 qFPVsRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEIL--ELAGnaA-~~~kkkRItPrHIqlAI~nDeEL~~Lf~~ 171 (193)
|+....|.+++-+++. +++=++|+. |.||..+ -+....-+.|++|+.|+..++.|..+|..
T Consensus 95 qirf~nv~El~e~~~m----------------i~ayL~e~~~a~~aG~~~~~~~~~e~~IPeeLq~alda~palk~~f~~ 158 (200)
T COG4430 95 QIRFTNVQELSEEGRM----------------IKAYLAEAIAAEKAGRWVALKKNEELIIPEELQDALDANPALKTAFEA 158 (200)
T ss_pred eeehhhHHHHHHhHHH----------------HHHHHHHHHHHHhcCCccCCCcccccCCcHHHHHHHhcCHHHHHHHHh
Confidence 6667777777766543 333334443 4456653 33345569999999999999999999976
No 78
>PF15510 CENP-W: Centromere kinetochore component W
Probab=27.47 E-value=1.5e+02 Score=23.30 Aligned_cols=64 Identities=19% Similarity=0.245 Sum_probs=40.9
Q ss_pred ccchhhHHhhhhccCCcccccCcchHHHH----------H--HHHH--HHHHHHHHHHHHHHhhcCCceechhhHHHHh
Q 046088 95 QFPVGRIHRLLKSRTTAHGRVGATAAVYS----------A--AILE--YLTAEVLELAGNASKDLKVKRITPRHLQLAI 159 (193)
Q Consensus 95 qFPVsRI~RlLke~~~a~~RIss~ApVYL----------A--AVLE--YLtAEILELAGnaA~~~kkkRItPrHIqlAI 159 (193)
.-|-|.++|++++...- .|+...+-+.. . .=|. .+...+-|-|-.-|.+++-..|-++|+..|-
T Consensus 16 kaPrgfLkrv~Kr~Kph-lRl~~~~Dllv~~~~f~~~~~~~~vhLncLLFvhrLAEEaRtnA~EnK~~~Ik~~Hv~Aaa 93 (102)
T PF15510_consen 16 KAPRGFLKRVFKRQKPH-LRLETSGDLLVRFCPFSGWQWGGEVHLNCLLFVHRLAEEARTNACENKCGTIKKEHVLAAA 93 (102)
T ss_pred hCchHHHHHHHHhcCCc-eeecccccHHHhhcccccccccceeehhHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHH
Confidence 36888999999865442 47776554430 0 0111 1334555666666778888899999998774
No 79
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=26.16 E-value=76 Score=29.36 Aligned_cols=76 Identities=20% Similarity=0.352 Sum_probs=52.7
Q ss_pred cCcccch---hhHHhhhhccCC---cccccCcchHHHHHHHHHHHH------HHHHHHHHHHHhhcCCceechhhHHHHh
Q 046088 92 AGLQFPV---GRIHRLLKSRTT---AHGRVGATAAVYSAAILEYLT------AEVLELAGNASKDLKVKRITPRHLQLAI 159 (193)
Q Consensus 92 AGLqFPV---sRI~RlLke~~~---a~~RIss~ApVYLAAVLEYLt------AEILELAGnaA~~~kkkRItPrHIqlAI 159 (193)
-.+.||. ..+..+|+++.. ..+.++.++--+.|+.-.+-. -++|+.|++.|...+...+++.|+..|
T Consensus 183 ~~I~F~pY~a~el~~Il~~R~~~~~~~~~~~~~vl~lia~~~a~~~GDAR~aidilr~A~eiAe~~~~~~v~~~~v~~a- 261 (366)
T COG1474 183 SEIVFPPYTAEELYDILRERVEEGFSAGVIDDDVLKLIAALVAAESGDARKAIDILRRAGEIAEREGSRKVSEDHVREA- 261 (366)
T ss_pred ceeeeCCCCHHHHHHHHHHHHHhhccCCCcCccHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHhhCCCCcCHHHHHHH-
Confidence 3488886 566666654322 224666677766665555433 578999999999999999999999999
Q ss_pred hCchHHhHh
Q 046088 160 RGDEELDTL 168 (193)
Q Consensus 160 ~nDeEL~~L 168 (193)
+.+.|.+.+
T Consensus 262 ~~~~~~~~~ 270 (366)
T COG1474 262 QEEIERDVL 270 (366)
T ss_pred HHHhhHHHH
Confidence 434444443
No 80
>TIGR02263 benz_CoA_red_C benzoyl-CoA reductase, subunit C. This model describes C subunit of benzoyl-CoA reductase, a 4-subunit enzyme. Many aromatic compounds are metabolized by way of benzoyl-CoA. This enzyme acts under anaerobic conditions.
Probab=25.52 E-value=1.2e+02 Score=27.87 Aligned_cols=45 Identities=24% Similarity=0.173 Sum_probs=37.0
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhhCchHHhHhhhc
Q 046088 126 ILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDTLIKG 171 (193)
Q Consensus 126 VLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~nDeEL~~Lf~~ 171 (193)
.++|+..|+-++.-...+..|+ .||++.|+.||+.-.+...+++.
T Consensus 136 ~~~Y~~~el~~l~~~LE~~~G~-~it~e~L~~aI~~~N~~R~~~~~ 180 (380)
T TIGR02263 136 GGEFYTAELNELCEGLEHLSGK-KITDDAIRASIAVFNDNRKLIQA 180 (380)
T ss_pred HHHHHHHHHHHHHHHHHHHHCC-CCCHHHHHHHHHHHHHHHHHHHH
Confidence 3899999999988877777776 58999999999988777777754
No 81
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA.
Probab=24.43 E-value=84 Score=31.41 Aligned_cols=34 Identities=24% Similarity=0.173 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHhhcCCceechhhHHHHhhCchH
Q 046088 131 TAEVLELAGNASKDLKVKRITPRHLQLAIRGDEE 164 (193)
Q Consensus 131 tAEILELAGnaA~~~kkkRItPrHIqlAI~nDeE 164 (193)
+.++|+.|..+|...+...|.+.||-+|+-.|++
T Consensus 82 lk~vL~~A~~~A~~~g~~~I~teHLLLALl~~~~ 115 (731)
T TIGR02639 82 VQRVLQRALLHVKSAGKKEIGIGDILVALFDEED 115 (731)
T ss_pred HHHHHHHHHHHHHHcCCCccCHHHHHHHHhcCcc
Confidence 3678899999999999999999999999876643
No 82
>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=24.34 E-value=92 Score=30.79 Aligned_cols=32 Identities=19% Similarity=0.202 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHhhcCCceechhhHHHHhhCch
Q 046088 132 AEVLELAGNASKDLKVKRITPRHLQLAIRGDE 163 (193)
Q Consensus 132 AEILELAGnaA~~~kkkRItPrHIqlAI~nDe 163 (193)
.+|+..|...|+..+...|+.+|++.|++.-.
T Consensus 361 ~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~~~ 392 (608)
T TIGR00764 361 GGLVRAAGDIAKSSGKVYVTAEHVLKAKKLAK 392 (608)
T ss_pred HHHHHHHHHHHHhcCCceecHHHHHHHHHHHH
Confidence 45677787778888888999999999977443
No 83
>PRK10865 protein disaggregation chaperone; Provisional
Probab=24.34 E-value=1e+02 Score=31.65 Aligned_cols=39 Identities=23% Similarity=0.186 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHHhhcCCceechhhHHHHhhCchH--HhHhh
Q 046088 131 TAEVLELAGNASKDLKVKRITPRHLQLAIRGDEE--LDTLI 169 (193)
Q Consensus 131 tAEILELAGnaA~~~kkkRItPrHIqlAI~nDeE--L~~Lf 169 (193)
+.++|+.|-..|+..+...|+|+||-+|+-+++. +..++
T Consensus 10 ~~~~l~~a~~~a~~~~~~~~~~~hll~~l~~~~~~~~~~~l 50 (857)
T PRK10865 10 FQLALADAQSLALGHDNQFIEPLHLMSALLNQEGGSVRPLL 50 (857)
T ss_pred HHHHHHHHHHHHHHcCCCcccHHHHHHHHHhCCccHHHHHH
Confidence 4567889999999999999999999999987663 44443
No 84
>CHL00095 clpC Clp protease ATP binding subunit
Probab=24.08 E-value=97 Score=31.46 Aligned_cols=34 Identities=32% Similarity=0.431 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHhhcCCceechhhHHHHhhCchH
Q 046088 131 TAEVLELAGNASKDLKVKRITPRHLQLAIRGDEE 164 (193)
Q Consensus 131 tAEILELAGnaA~~~kkkRItPrHIqlAI~nDeE 164 (193)
+.++|+.|...|...+...|+|.|+-+|+-.|++
T Consensus 84 ~~~vL~~A~~~A~~~~~~~I~~eHLLlALL~~~d 117 (821)
T CHL00095 84 AKRVLEMSLEEARDLGHNYIGTEHLLLALLEEGE 117 (821)
T ss_pred HHHHHHHHHHHHHHhCCCcccHHHHHHHHHhCCC
Confidence 3577888888898888899999999999877654
No 85
>KOG2235 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.18 E-value=2.9e+02 Score=28.56 Aligned_cols=44 Identities=11% Similarity=0.037 Sum_probs=29.7
Q ss_pred CcccchhhHHhhhhccCCcccccCcchHHHHHHHHHHHHHHHHHHHHHHHh
Q 046088 93 GLQFPVGRIHRLLKSRTTAHGRVGATAAVYSAAILEYLTAEVLELAGNASK 143 (193)
Q Consensus 93 GLqFPVsRI~RlLke~~~a~~RIss~ApVYLAAVLEYLtAEILELAGnaA~ 143 (193)
.+.|-+.-++-|+++.+.. ---+|.-+.||+.-++.......++
T Consensus 478 ~~~k~~d~v~~~~~~~qe~-------peeiLs~iae~l~~~ln~tl~er~q 521 (776)
T KOG2235|consen 478 NISKNSDIVEIWLRESQEV-------PEEILSVIAEKLNQELNTTLLERVQ 521 (776)
T ss_pred eeeechhhHHHHHHhhhhc-------hHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3556677777777776553 2457788889988888666655443
No 86
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=21.98 E-value=1.7e+02 Score=29.40 Aligned_cols=47 Identities=23% Similarity=0.273 Sum_probs=44.9
Q ss_pred ccCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCceechhhHHHHhh
Q 046088 114 RVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 160 (193)
Q Consensus 114 RIss~ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItPrHIqlAI~ 160 (193)
.|...++-.|+-=+||=+.||...|...-+..++.+.|-.||..|++
T Consensus 28 nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr 74 (576)
T KOG2549|consen 28 NLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALR 74 (576)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHh
Confidence 68999999999999999999999999999999999999999999987
No 87
>PF01405 PsbT: Photosystem II reaction centre T protein; InterPro: IPR001743 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. This family represents the low molecular weight transmembrane protein PsbT found in PSII, which is thought to be associated with the D1 (PsbA) - D2 (PsbD) heterodimer. PsbT may be involved in the formation and/or stabilisation of dimeric PSII complexes, because in the absence of this protein dimeric PSII complexes were found to be less abundant. Furthermore, although PsbT does not confer photo-protection, it is required for the efficient recovery of photo-damaged PSII [].; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009539 photosystem II reaction center, 0016020 membrane; PDB: 3BZ1_T 1S5L_t 2AXT_t 3KZI_T 3PRQ_T 3BZ2_T 3PRR_T 4FBY_g 3A0H_t 3A0B_T ....
Probab=21.52 E-value=45 Score=20.88 Aligned_cols=18 Identities=17% Similarity=0.488 Sum_probs=11.3
Q ss_pred hhhhhhhhhhcccCCCce
Q 046088 23 CVLSLVFCSLALKPHPSF 40 (193)
Q Consensus 23 ~~~~~~~~~~~~~~~~~~ 40 (193)
+.|.++|+.++++-+|.+
T Consensus 12 ~tlgilffAI~FRePPrI 29 (29)
T PF01405_consen 12 GTLGILFFAIFFREPPRI 29 (29)
T ss_dssp HHHHHHHHHHHSS-----
T ss_pred HHHHHHHhhhhccCCCCC
Confidence 567889999999998863
No 88
>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]
Probab=21.13 E-value=1e+02 Score=32.41 Aligned_cols=44 Identities=20% Similarity=0.307 Sum_probs=34.7
Q ss_pred HHHHHH---HHHHHHHHHHHhhcCCceechhhHHHHhhCchHHhHhhhc
Q 046088 126 ILEYLT---AEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDTLIKG 171 (193)
Q Consensus 126 VLEYLt---AEILELAGnaA~~~kkkRItPrHIqlAI~nDeEL~~Lf~~ 171 (193)
+-|.|| +.+|..|.+.|+..++.-+||.|+-.|+-.++ ..++..
T Consensus 8 ~~q~lT~~Aa~~L~~a~~~Arrrgh~qvtplH~~~~LLs~~--t~~lr~ 54 (898)
T KOG1051|consen 8 VQQTLTEEAATVLKQAVTEARRRGHAQVTPLHVASTLLSSP--TGILRR 54 (898)
T ss_pred hHhhhCHHHHHHHHHHHHHHHHcCCCCcchHHHHHHHHcCC--chHHHH
Confidence 445454 56799999999999999999999999988776 444444
No 89
>cd05031 S-100A10_like S-100A10_like: S-100A10 domain found in proteins similar to S100A10. S100A10 is a member of the S100 family of EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100A1_like group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins are expressed exclusively in vertebrates, and are implicated in intracellular and extracellular regulatory activities. A unique feature of S100A10 is that it contains mutation in both of the calcium binding sites, making it calcium insensitive. S100A10 has been detected in brain, heart, gastrointestinal tract, kidney, liver, lung, spleen, testes, epidermis, aorta, and thymus. Structural data supports the homo- and hetero-dimeric as well as hetero-tetrameric nature of the protein. S100A10 has multiple binding partners in its calcium free state and is therefore involved in many diverse biological functions.
Probab=20.99 E-value=3.3e+02 Score=19.57 Aligned_cols=52 Identities=12% Similarity=0.145 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHHHHHHhh-cC-CceechhhHHHHhh-----------CchHHhHhhhc-cccCCccc
Q 046088 127 LEYLTAEVLELAGNASKD-LK-VKRITPRHLQLAIR-----------GDEELDTLIKG-TIAGGGVI 179 (193)
Q Consensus 127 LEYLtAEILELAGnaA~~-~k-kkRItPrHIqlAI~-----------nDeEL~~Lf~~-tIa~GGv~ 179 (193)
||+..+++.+ +-+.-.+ ++ .-.|+...+..+++ .+++++.+++. .....|.+
T Consensus 3 ~~~~~~~l~~-~F~~~D~~dg~dG~Is~~El~~~l~~~~g~~lg~~~s~~ei~~~~~~~D~~~dg~I 68 (94)
T cd05031 3 LEHAMESLIL-TFHRYAGKDGDKNTLSRKELKKLMEKELSEFLKNQKDPMAVDKIMKDLDQNRDGKV 68 (94)
T ss_pred HHHHHHHHHH-HHHHHhccCCCCCeECHHHHHHHHHHHhHHHhhccccHHHHHHHHHHhCCCCCCcC
Confidence 5555555544 4444333 54 57899999998765 34678888876 44444443
No 90
>cd01028 TOPRIM_TopoIA TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IA family of DNA topoisomerases (TopoIA). This subgroup contains proteins similar to the Type I DNA topoisomerases: E. coli topisomerases I and III, eukaryotic topoisomerase III and, ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA. These enzymes cleave one strand of the DNA duplex, covalently link to the 5' phosphoryl end of the DNA break and allow the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general b
Probab=20.51 E-value=90 Score=24.48 Aligned_cols=32 Identities=31% Similarity=0.484 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHHHHHhhcCCc-----eechhhHHHHhhC
Q 046088 128 EYLTAEVLELAGNASKDLKVK-----RITPRHLQLAIRG 161 (193)
Q Consensus 128 EYLtAEILELAGnaA~~~kkk-----RItPrHIqlAI~n 161 (193)
|.+..||++.++. .+...+ -||+++|+.|+.|
T Consensus 105 E~I~~~i~~~~~~--~~~~v~R~~fsslT~~~I~~A~~n 141 (142)
T cd01028 105 ELIAWEILEVLKC--DNKPVKRAWFSEITPKAIREAFKN 141 (142)
T ss_pred HHHHHHHHHHhCC--CCCCeEEEEEccCCHHHHHHHHhC
Confidence 5666788888875 222222 3899999999876
No 91
>PHA02669 hypothetical protein; Provisional
Probab=20.03 E-value=1.3e+02 Score=26.23 Aligned_cols=31 Identities=32% Similarity=0.405 Sum_probs=19.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhhcCCceech
Q 046088 119 AAVYSAAILEYLTAEVLELAGNASKDLKVKRITP 152 (193)
Q Consensus 119 ApVYLAAVLEYLtAEILELAGnaA~~~kkkRItP 152 (193)
|.+||+++.-||.-||= || +-+.+++.|..-
T Consensus 12 avi~LTgAaiYlLiEiG-LA--aERanKrsRvK~ 42 (210)
T PHA02669 12 AVIYLTGAAIYLLIEIG-LA--AERANKRSRVKA 42 (210)
T ss_pred HHHHHHHHHHHHHHHHH-HH--HHHhhhHHHHHH
Confidence 67899999999987752 33 223345555433
Done!