Query 027954
Match_columns 216
No_of_seqs 124 out of 211
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 04:02:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027954.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027954hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3219 Transcription initiati 100.0 2.8E-44 6.1E-49 307.8 12.2 114 102-216 81-195 (195)
2 PF04719 TAFII28: hTAFII28-lik 100.0 1.7E-42 3.6E-47 266.2 9.4 90 111-200 1-90 (90)
3 cd08048 TAF11 TATA Binding Pro 100.0 5.5E-38 1.2E-42 238.4 10.6 83 118-201 1-85 (85)
4 COG5251 TAF40 Transcription in 100.0 1.6E-31 3.5E-36 226.9 10.1 94 109-203 91-184 (199)
5 KOG3902 Histone acetyltransfer 99.3 1E-11 2.2E-16 113.8 10.2 99 104-203 191-330 (352)
6 PF00808 CBFD_NFYB_HMF: Histon 97.8 5.4E-05 1.2E-09 53.6 6.1 65 132-197 1-65 (65)
7 smart00803 TAF TATA box bindin 96.3 0.021 4.6E-07 41.5 6.9 65 132-198 1-65 (65)
8 cd07981 TAF12 TATA Binding Pro 95.7 0.085 1.8E-06 38.7 8.0 67 134-201 2-68 (72)
9 cd00074 H2A Histone 2A; H2A is 95.3 0.078 1.7E-06 42.8 6.9 66 133-199 20-85 (115)
10 PF00125 Histone: Core histone 94.7 0.12 2.5E-06 37.0 5.8 66 133-199 5-74 (75)
11 COG5262 HTA1 Histone H2A [Chro 94.1 0.13 2.8E-06 42.6 5.5 66 132-198 25-90 (132)
12 KOG0871 Class 2 transcription 93.7 0.33 7.1E-06 41.5 7.5 69 132-201 11-80 (156)
13 PF02969 TAF: TATA box binding 92.9 0.56 1.2E-05 34.6 6.7 65 132-198 2-66 (66)
14 smart00414 H2A Histone 2A. 92.8 0.39 8.4E-06 38.3 6.3 66 133-199 9-74 (106)
15 COG2036 HHT1 Histones H3 and H 92.6 0.62 1.3E-05 36.4 7.0 80 121-202 7-86 (91)
16 cd00076 H4 Histone H4, one of 92.2 0.99 2.1E-05 34.8 7.6 68 132-201 12-79 (85)
17 PTZ00017 histone H2A; Provisio 91.4 0.52 1.1E-05 39.3 5.6 66 133-199 27-92 (134)
18 PTZ00015 histone H4; Provision 90.9 1.4 3E-05 35.2 7.4 68 132-201 29-96 (102)
19 PLN00035 histone H4; Provision 90.7 1.5 3.2E-05 35.1 7.4 66 134-201 30-95 (103)
20 PLN00153 histone H2A; Provisio 89.1 1.2 2.6E-05 37.0 5.9 65 134-199 25-89 (129)
21 PLN00154 histone H2A; Provisio 89.1 1.5 3.3E-05 36.8 6.5 66 133-199 38-104 (136)
22 PLN00157 histone H2A; Provisio 88.7 1.1 2.4E-05 37.3 5.5 65 134-199 27-91 (132)
23 PLN00156 histone H2AX; Provisi 88.7 1.4 2.9E-05 37.1 6.0 65 134-199 30-94 (139)
24 PTZ00252 histone H2A; Provisio 87.5 2 4.4E-05 35.9 6.3 66 134-199 26-92 (134)
25 KOG1659 Class 2 transcription 87.3 1.8 3.8E-05 39.0 6.2 68 131-199 11-78 (224)
26 smart00417 H4 Histone H4. 86.9 2.2 4.8E-05 32.2 5.7 48 133-181 13-60 (74)
27 PF03847 TFIID_20kDa: Transcri 86.3 2.9 6.4E-05 30.8 5.9 64 135-199 1-64 (68)
28 PF09415 CENP-X: CENP-S associ 85.5 1.9 4.1E-05 32.1 4.7 63 135-197 1-65 (72)
29 smart00576 BTP Bromodomain tra 84.9 8.4 0.00018 28.2 7.9 64 136-201 9-72 (77)
30 cd08050 TAF6 TATA Binding Prot 83.0 6.3 0.00014 36.5 8.0 67 136-204 2-68 (343)
31 KOG1756 Histone 2A [Chromatin 81.1 5.6 0.00012 33.3 6.2 65 133-198 27-91 (131)
32 COG5208 HAP5 CCAAT-binding fac 77.9 5.5 0.00012 36.4 5.6 74 125-199 101-174 (286)
33 PF07524 Bromo_TP: Bromodomain 77.0 23 0.00051 25.6 7.8 64 136-201 9-72 (77)
34 COG5247 BUR6 Class 2 transcrip 72.2 13 0.00029 30.3 5.9 68 129-197 19-86 (113)
35 PF07526 POX: Associated with 71.3 35 0.00075 28.3 8.4 40 123-168 90-132 (140)
36 COG5150 Class 2 transcription 70.3 24 0.00051 29.9 7.2 69 132-201 10-79 (148)
37 PRK07194 fliG flagellar motor 67.8 35 0.00076 31.6 8.5 90 110-206 215-323 (334)
38 smart00427 H2B Histone H2B. 67.7 34 0.00075 26.8 7.2 66 139-206 7-72 (89)
39 PRK13916 plasmid segregation p 64.0 6.5 0.00014 31.1 2.5 18 188-205 31-48 (97)
40 PF01706 FliG_C: FliG C-termin 63.6 15 0.00033 28.3 4.6 68 134-206 28-107 (110)
41 PLN00158 histone H2B; Provisio 58.7 58 0.0013 26.8 7.2 62 139-201 33-94 (116)
42 smart00574 POX domain associat 56.3 66 0.0014 27.3 7.4 42 121-168 88-132 (140)
43 PTZ00463 histone H2B; Provisio 52.6 70 0.0015 26.4 6.8 66 139-206 34-99 (117)
44 PRK05686 fliG flagellar motor 51.6 36 0.00079 31.4 5.7 69 133-206 249-329 (339)
45 KOG1757 Histone 2A [Chromatin 51.3 15 0.00032 30.5 2.7 64 134-198 31-95 (131)
46 TIGR00207 fliG flagellar motor 50.8 39 0.00086 31.4 5.8 69 133-206 246-326 (338)
47 KOG1657 CCAAT-binding factor, 47.3 31 0.00067 31.1 4.4 71 128-199 69-139 (236)
48 KOG1142 Transcription initiati 46.9 32 0.0007 31.7 4.5 60 134-194 155-214 (258)
49 cd07978 TAF13 The TATA Binding 46.5 1.3E+02 0.0027 23.3 7.1 63 134-199 4-66 (92)
50 KOG0870 DNA polymerase epsilon 45.2 1.2E+02 0.0026 26.6 7.4 50 132-181 9-60 (172)
51 COG2074 2-phosphoglycerate kin 42.6 38 0.00082 31.8 4.3 80 105-207 56-138 (299)
52 PF13443 HTH_26: Cro/C1-type H 41.7 9.2 0.0002 25.9 0.1 52 119-172 7-58 (63)
53 PF04147 Nop14: Nop14-like fam 40.5 2.5E+02 0.0055 29.5 10.3 70 109-178 429-517 (840)
54 PF12174 RST: RCD1-SRO-TAF4 (R 38.8 92 0.002 23.1 5.1 39 111-149 15-57 (70)
55 PF02269 TFIID-18kDa: Transcri 36.2 47 0.001 25.5 3.3 60 139-199 7-66 (93)
56 PF07462 MSP1_C: Merozoite sur 35.5 47 0.001 33.8 3.9 14 151-164 463-476 (574)
57 cd04411 Ribosomal_P1_P2_L12p R 31.9 21 0.00045 28.4 0.8 11 84-94 92-102 (105)
58 KOG2140 Uncharacterized conser 31.1 2.1E+02 0.0045 29.8 7.6 89 93-181 125-244 (739)
59 PF05236 TAF4: Transcription i 29.8 99 0.0022 27.4 4.7 51 134-184 44-97 (264)
60 PF03540 TFIID_30kDa: Transcri 29.3 2.1E+02 0.0046 20.3 6.3 47 134-181 3-49 (51)
61 PRK14703 glutaminyl-tRNA synth 28.4 40 0.00087 35.2 2.3 95 112-211 586-684 (771)
62 PF11011 DUF2849: Protein of u 28.3 37 0.00079 26.4 1.5 18 183-200 64-81 (90)
63 PTZ00373 60S Acidic ribosomal 27.8 34 0.00074 27.7 1.3 12 84-95 98-109 (112)
64 PRK15398 aldehyde dehydrogenas 27.2 83 0.0018 30.4 4.1 46 137-183 8-53 (465)
65 COG3492 Uncharacterized protei 26.1 2.7E+02 0.0059 22.5 6.1 53 115-176 3-56 (104)
66 COG5123 TOA2 Transcription ini 25.0 68 0.0015 26.2 2.6 39 126-165 5-44 (113)
67 PF11521 TFIIE-A_C-term: C-ter 24.9 62 0.0013 25.1 2.2 20 112-131 59-78 (86)
68 COG3763 Uncharacterized protei 24.5 3.2E+02 0.007 20.8 6.0 43 156-200 8-51 (71)
69 KOG3467 Histone H4 [Chromatin 24.0 2.3E+02 0.0049 22.8 5.2 47 132-179 28-74 (103)
70 KOG3540 Beta amyloid precursor 23.9 8.1E+02 0.018 25.2 12.0 20 184-203 340-359 (615)
71 COG3937 Uncharacterized conser 23.7 1E+02 0.0023 25.1 3.4 36 163-201 43-78 (108)
72 cd07979 TAF9 TATA Binding Prot 23.2 3.9E+02 0.0085 21.3 7.8 63 138-202 6-68 (117)
73 KOG1819 FYVE finger-containing 23.2 86 0.0019 32.4 3.4 22 81-102 426-447 (990)
74 PF15510 CENP-W: Centromere ki 23.1 3.4E+02 0.0074 21.9 6.1 36 166-202 63-98 (102)
75 KOG3871 Cell adhesion complex 22.9 4.4E+02 0.0095 26.1 7.9 49 161-209 145-205 (449)
76 PF02978 SRP_SPB: Signal pepti 22.0 1.2E+02 0.0027 23.7 3.5 35 105-144 47-81 (104)
77 PF02268 TFIIA_gamma_N: Transc 22.0 26 0.00056 24.7 -0.3 34 125-159 2-35 (49)
78 KOG1744 Histone H2B [Chromatin 20.9 4E+02 0.0086 22.3 6.3 78 128-208 33-110 (127)
79 PF03115 Astro_capsid: Astrovi 20.7 33 0.00071 36.0 0.0 15 111-125 714-729 (787)
80 KOG3449 60S acidic ribosomal p 20.6 54 0.0012 26.9 1.2 9 86-94 100-108 (112)
No 1
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=100.00 E-value=2.8e-44 Score=307.84 Aligned_cols=114 Identities=51% Similarity=0.848 Sum_probs=108.7
Q ss_pred CCcHHHHHHHHHHHhcCCHHHHHHHHHHHhccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 027954 102 SSDPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTE 181 (216)
Q Consensus 102 ~~d~e~~~km~~Ll~~fteEQ~dRYE~fRRS~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E 181 (216)
+.+.++..+|+.||++||+||++|||.||||+|+|+.|||||++|||. +|++|++|+|+||||||||||||+|++||++
T Consensus 81 ~~~~ee~~r~q~L~s~fseEQl~RYEvfRrs~f~Ka~iKkL~~~itg~-~v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~ 159 (195)
T KOG3219|consen 81 TVDAEEAQRMQTLLSNFSEEQLSRYEVFRRSAFPKAQIKKLMSSITGQ-SVSENVAIAMAGIAKVFVGEVVEEALDVREE 159 (195)
T ss_pred CcCHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhCC-ccCcceeeeecchhhHhHHHHHHHHHHHHHH
Confidence 335666679999999999999999999999999999999999999986 5999999999999999999999999999999
Q ss_pred hCcCCCCCchHHHHHHHHHHhcCCCC-CCCCCCCCC
Q 027954 182 RNESGPIRPCHIREAYRRLKLEGKVP-KRSVPRLFR 216 (216)
Q Consensus 182 ~~e~gPLqP~HIREA~RRL~~~Gkvp-~r~~~rlfr 216 (216)
|++++||||+|||||||||+.+|++| ++..+++||
T Consensus 160 ~~e~~PLqP~HIREA~rrL~~qgk~~~~~~~~~~fr 195 (195)
T KOG3219|consen 160 WGESGPLQPKHIREAYRRLKLQGKLPNSRYKKSMFR 195 (195)
T ss_pred hccCCCCCcHHHHHHHHHHHhcCCCCCCcccccccC
Confidence 99999999999999999999999999 888999997
No 2
>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=100.00 E-value=1.7e-42 Score=266.23 Aligned_cols=90 Identities=51% Similarity=0.894 Sum_probs=68.4
Q ss_pred HHHHHhcCCHHHHHHHHHHHhccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCc
Q 027954 111 MQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRP 190 (216)
Q Consensus 111 m~~Ll~~fteEQ~dRYE~fRRS~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP 190 (216)
|+.|+++||+||++|||+||||+|+|++|||||++++|+|+||+|++|+|+||||+|||||||+|++||++|++++||+|
T Consensus 1 ~~~L~~~f~~eQ~~Rye~fRRs~~~k~~ikkli~~~~~~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P 80 (90)
T PF04719_consen 1 MQLLLSNFDEEQLDRYEAFRRSSFNKAAIKKLINQVLGNQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQP 80 (90)
T ss_dssp ---------HHHHHHHHHHHH----HHHHHHHHHHHHS-S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--H
T ss_pred ChHHHHcCCHHHHHHHHHHHHccCCHHHHHHHHHHHcCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCc
Confidence 78999999999999999999999999999999999999899999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHH
Q 027954 191 CHIREAYRRL 200 (216)
Q Consensus 191 ~HIREA~RRL 200 (216)
+|||||||||
T Consensus 81 ~hlreA~rrL 90 (90)
T PF04719_consen 81 DHLREAYRRL 90 (90)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHHHHhC
Confidence 9999999998
No 3
>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=100.00 E-value=5.5e-38 Score=238.42 Aligned_cols=83 Identities=59% Similarity=0.965 Sum_probs=80.8
Q ss_pred CCHHHHHHHHHHHhccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCc--CCCCCchHHHH
Q 027954 118 FTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNE--SGPIRPCHIRE 195 (216)
Q Consensus 118 fteEQ~dRYE~fRRS~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e--~gPLqP~HIRE 195 (216)
||+|||+|||.||||+|+|++|||||+++++ |+||+|++|+|+||||+|||||||+|++||++|++ ++||+|+||||
T Consensus 1 f~~eQ~~Rye~~Rra~f~k~~iKr~~~~~~~-~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~Hire 79 (85)
T cd08048 1 FSEEQMNRYEMFRRSSFPKAAIKRLIQSVTG-QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLRE 79 (85)
T ss_pred CCHHHHHHHHHHHHhhccHHHHHHHHHHHcC-CCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHH
Confidence 8999999999999999999999999999987 79999999999999999999999999999999999 89999999999
Q ss_pred HHHHHH
Q 027954 196 AYRRLK 201 (216)
Q Consensus 196 A~RRL~ 201 (216)
|||||+
T Consensus 80 A~rrl~ 85 (85)
T cd08048 80 AYRRLK 85 (85)
T ss_pred HHHHhC
Confidence 999985
No 4
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=99.97 E-value=1.6e-31 Score=226.95 Aligned_cols=94 Identities=36% Similarity=0.653 Sum_probs=90.0
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHhccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCC
Q 027954 109 AKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPI 188 (216)
Q Consensus 109 ~km~~Ll~~fteEQ~dRYE~fRRS~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPL 188 (216)
+++..|+.+||+||+.|||.|||++|||.+||||+++|.+ |+|++|++|+|+|++|||||||||.|+.||.+|.++|||
T Consensus 91 ~r~k~l~~~~deeq~~RyEvFrrt~lnKt~VKKlastV~n-QtVspNi~I~l~g~~KVfvGEiIElA~~Vq~~w~~sgpl 169 (199)
T COG5251 91 ERFKLLVTNLDEEQTNRYEVFRRTSLNKTQVKKLASTVAN-QTVSPNIRIFLQGVGKVFVGEIIELAMIVQNKWLTSGPL 169 (199)
T ss_pred HHHHHHHhhcCHHHHHHHHHHHhcCCCHHHHHHHHHHHhc-cccCCCeeeeeechhHHHHHHHHHHHHHHHHHhcccCCC
Confidence 5788899999999999999999999999999999999875 899999999999999999999999999999999999999
Q ss_pred CchHHHHHHHHHHhc
Q 027954 189 RPCHIREAYRRLKLE 203 (216)
Q Consensus 189 qP~HIREA~RRL~~~ 203 (216)
.|.|+|||||++..+
T Consensus 170 ~p~h~reayr~~~k~ 184 (199)
T COG5251 170 IPFHKREAYRYKLKK 184 (199)
T ss_pred ChHHHHHHHHHHHHh
Confidence 999999999998765
No 5
>KOG3902 consensus Histone acetyltransferase PCAF/SAGA, subunit SUPT3H/SPT3 [Transcription]
Probab=99.31 E-value=1e-11 Score=113.84 Aligned_cols=99 Identities=21% Similarity=0.278 Sum_probs=80.4
Q ss_pred cHHHHHHHHH---HHhcCCHHHHHHHHHHHhccCChhHHHHHHHHhcC----CCCCCccHHHHHHHHHHHHHHHHHHHHH
Q 027954 104 DPAKMAKMQA---ILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITG----SQKISLPMTIVVCGIAKMFVGELVETAR 176 (216)
Q Consensus 104 d~e~~~km~~---Ll~~fteEQ~dRYE~fRRS~f~K~~IKRLi~~vtg----sqsVs~nvvIavaGlaKvFVGELVEeAr 176 (216)
|+..+++|.. .-..||.+||..|..||+++|.+.+-||+ ..+.+ ..+++.++..|++.||...|+-||+.|+
T Consensus 191 devt~~RLkrADrrTrimt~eqYvefsE~RqaSFt~RkgkrF-Rdwld~s~ld~rp~~~~mdILayLafEtVa~Lvd~AL 269 (352)
T KOG3902|consen 191 DEVTMRRLKRADRRTRIMTGEQYVEFSECRQASFTCRKGKRF-RDWLDLSALDLRPPTDTMDILAYLAFETVAALVDYAL 269 (352)
T ss_pred HHHHHHHHHHHHHHHhhccHHHHHHHHHHhhhhhhhhcchhH-HhhhCCchhccCCCccHHHHHHHHHHHHHHHHHHHHH
Confidence 4444444433 55799999999999999999999999986 33333 2267889999999999999999999999
Q ss_pred HHHHHh----------------------------------CcCCCCCchHHHHHHHHHHhc
Q 027954 177 MVMTER----------------------------------NESGPIRPCHIREAYRRLKLE 203 (216)
Q Consensus 177 ~Vq~E~----------------------------------~e~gPLqP~HIREA~RRL~~~ 203 (216)
.|+... ....||+|+||+||||+|+..
T Consensus 270 lvrq~~~~ka~~p~S~~~sa~~s~~~~H~~~e~t~~~G~e~v~~~lqp~hieea~R~~q~~ 330 (352)
T KOG3902|consen 270 LVRQRSDNKATEPYSSVTSAGGSSAMMHVCKEVTLFDGMEVVKPPLQPEHIEEARRRLQMS 330 (352)
T ss_pred HHHhhhhhcccCccccccCCCCchHHhccCcccccccCccccCCCcchHHHHHHHHHHhcc
Confidence 996641 136899999999999999965
No 6
>PF00808 CBFD_NFYB_HMF: Histone-like transcription factor (CBF/NF-Y) and archaeal histone; InterPro: IPR003958 The CCAAT-binding factor (CBF) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin. The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding [, ]. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The A subunit can be split into 3 domains on the basis of sequence similarity, a non-conserved N-terminal 'A domain'; a highly-conserved central 'B domain' involved in DNA-binding; and a C-terminal 'C domain', which contains a number of glutamine and acidic residues involved in protein-protein interactions []. The A subunit shows striking similarity to the HAP3 subunit of the yeast CCAAT-binding heterotrimeric transcription factor [, ]. The Kluyveromyces lactis HAP3 protein has been predicted to contain a 4-cysteine zinc finger, which is thought to be present in similar HAP3 and CBF subunit A proteins, in which the third cysteine is replaced by a serine []. This domain is found in the CCAAT transcription factor and archaeal histones.; GO: 0043565 sequence-specific DNA binding, 0005622 intracellular; PDB: 1F1E_A 2BYM_D 2BYK_D 1HTA_A 1B67_A 1JFI_B 1KU5_B 1N1J_A 1BFM_A 1B6W_A ....
Probab=97.84 E-value=5.4e-05 Score=53.61 Aligned_cols=65 Identities=15% Similarity=0.210 Sum_probs=53.6
Q ss_pred ccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHH
Q 027954 132 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAY 197 (216)
Q Consensus 132 S~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~ 197 (216)
++||.+.|||||...-+...||.+...+|+-.+-+||.+|..+|.++... +.+.=|+|.||..|+
T Consensus 1 ~~lP~a~vkri~k~~~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~-~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 1 ASLPLARVKRIMKSDPDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQR-DKRKTITYEDVAKAV 65 (65)
T ss_dssp -SS-HHHHHHHHHHTSTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TTSSEE-HHHHHHHH
T ss_pred CCCChHHHHHHhccCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCccCHHHHHHHC
Confidence 47999999999999755557999999999999999999999999988774 456789999999885
No 7
>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=96.30 E-value=0.021 Score=41.52 Aligned_cols=65 Identities=20% Similarity=0.236 Sum_probs=55.5
Q ss_pred ccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHH
Q 027954 132 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYR 198 (216)
Q Consensus 132 S~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~R 198 (216)
+.||+..||++..+. |-..+|+++.-.++...+.|+-+|+..|.+.+..-+ +.-|.+.+|.-|++
T Consensus 1 ~~~p~~~i~ria~~~-Gi~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hak-Rktlt~~DI~~Alk 65 (65)
T smart00803 1 SWLPKETIKDVAESL-GIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSK-RTTLTTSDIDSALR 65 (65)
T ss_pred CCCCHHHHHHHHHHC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC-CCeecHHHHHHHhC
Confidence 358999999998875 666899999999999999999999999999988653 44588999988864
No 8
>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=95.73 E-value=0.085 Score=38.68 Aligned_cols=67 Identities=21% Similarity=0.279 Sum_probs=60.1
Q ss_pred CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHHH
Q 027954 134 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK 201 (216)
Q Consensus 134 f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~ 201 (216)
++|.++..|+..+.++..+++++..++.-++=-||-.+++.|..+...++.. -|.++.|.-+++|..
T Consensus 2 ~~k~~l~~lv~~id~~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~-tv~~~Di~l~l~r~~ 68 (72)
T cd07981 2 LTKRKLQELLKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSD-TLEVKDVQLHLERNW 68 (72)
T ss_pred CcHHHHHHHHHhhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCC-CCCHHHHHHHHHHhc
Confidence 5789999999999888889999999999999999999999999998887544 499999999988753
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=95.27 E-value=0.078 Score=42.79 Aligned_cols=66 Identities=15% Similarity=0.260 Sum_probs=57.0
Q ss_pred cCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHH
Q 027954 133 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 199 (216)
Q Consensus 133 ~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 199 (216)
.||-+.|.|+|..-.+...|+....+.++++--.++.||.|.|-...... ...-|.|.||..|++-
T Consensus 20 ~fPV~ri~R~Lk~~~~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~-k~krItp~hi~lAi~n 85 (115)
T cd00074 20 QFPVGRIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDN-KKKRITPRHLQLAVRN 85 (115)
T ss_pred cCcHHHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHc-CCCeEcHHHHHHHHhc
Confidence 57888899999875566789999999999999999999999999886654 4578999999999875
No 10
>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=94.66 E-value=0.12 Score=36.97 Aligned_cols=66 Identities=23% Similarity=0.262 Sum_probs=52.3
Q ss_pred cCChhHHHHHHHHhcCC----CCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHH
Q 027954 133 ALQKSNMRRLLVSITGS----QKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 199 (216)
Q Consensus 133 ~f~K~~IKRLi~~vtgs----qsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 199 (216)
..++.-++|+...+... .+++.....+|..+...|+.+|.+.|..+....+ ..=|.|.||.-|.|.
T Consensus 5 ~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~k-R~tI~~~DI~~A~r~ 74 (75)
T PF00125_consen 5 LIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAK-RKTITPRDIQLAVRI 74 (75)
T ss_dssp SSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-BSEEGHHHHHHHHHH
T ss_pred ccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcC-CcEecHHHHHHHHhc
Confidence 34566677776665443 4789999999999999999999999999877654 445999999999874
No 11
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=94.09 E-value=0.13 Score=42.62 Aligned_cols=66 Identities=18% Similarity=0.255 Sum_probs=56.1
Q ss_pred ccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHH
Q 027954 132 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYR 198 (216)
Q Consensus 132 S~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~R 198 (216)
+-|+=..||||+..-...+.|+....+.++++--.++.||.|.|-.+.... ...-|-|+||+-|.|
T Consensus 25 l~fpvgrvkr~lk~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~-kkkri~PrHlqlAIr 90 (132)
T COG5262 25 LIFPVGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDN-KKKRIIPRHLQLAIR 90 (132)
T ss_pred ccccHHHHHHHHHcCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhc-CcceechHHHHHHhc
Confidence 467888899999866667789999999999999999999999999886643 345789999999987
No 12
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=93.75 E-value=0.33 Score=41.45 Aligned_cols=69 Identities=13% Similarity=0.249 Sum_probs=53.7
Q ss_pred ccCChhHHHHHHHHhcC-CCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHHH
Q 027954 132 SALQKSNMRRLLVSITG-SQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK 201 (216)
Q Consensus 132 S~f~K~~IKRLi~~vtg-sqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~ 201 (216)
.+|||++|-|+|..+.. .-.|....--++---+=.||--|..+|-+|+.+. ...-|-|.|+-.|+..|-
T Consensus 11 ~sLPkAtv~KmIke~lP~d~rvakeareliincCvEFI~liSsEAneic~~e-~KKTIa~EHV~KALe~Lg 80 (156)
T KOG0871|consen 11 LSLPKATVNKMIKEMLPKDVRVAKEARELIINCCVEFINLISSEANEICNKE-AKKTIAPEHVIKALENLG 80 (156)
T ss_pred ccCcHHHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHH-hcccCCHHHHHHHHHHcc
Confidence 47999999999999876 4345555444444455689999999999999875 456799999999988763
No 13
>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=92.92 E-value=0.56 Score=34.58 Aligned_cols=65 Identities=15% Similarity=0.194 Sum_probs=47.5
Q ss_pred ccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHH
Q 027954 132 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYR 198 (216)
Q Consensus 132 S~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~R 198 (216)
+-|++..||-+..+ .|-.+++++++..++-=.-.-+.+||+.|.+.|..- .+.-|.+.+|..|+|
T Consensus 2 s~~~~esvk~iAes-~Gi~~l~de~a~~La~dveyrlreiiq~a~kfm~hs-kR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 2 SVFSQESVKDIAES-LGISNLSDEAAKALAEDVEYRLREIIQEALKFMRHS-KRTKLTTDDINSALR 66 (66)
T ss_dssp ----HHHHHHHHHH-TT---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHT-T-SSB-HHHHHHHH-
T ss_pred CcCCHHHHHHHHHH-cCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCCCCHHHHHHHhC
Confidence 45788999998666 465579999999999999999999999999998854 356799999999876
No 14
>smart00414 H2A Histone 2A.
Probab=92.85 E-value=0.39 Score=38.27 Aligned_cols=66 Identities=18% Similarity=0.293 Sum_probs=54.2
Q ss_pred cCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHH
Q 027954 133 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 199 (216)
Q Consensus 133 ~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 199 (216)
.||=..|.|++..-+-...|+....+-++++--.++.||.|.|-...... ...-|.|.||.-|.+-
T Consensus 9 ~fPVgRi~r~Lk~~~~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~-k~~rItp~hi~lAi~n 74 (106)
T smart00414 9 QFPVGRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDN-KKRRITPRHLQLAIRN 74 (106)
T ss_pred cCchHHHHHHHHcCccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCccchHHHhhhccC
Confidence 46777799999876556789999999999999999999999997765543 4567999999977653
No 15
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=92.64 E-value=0.62 Score=36.42 Aligned_cols=80 Identities=19% Similarity=0.274 Sum_probs=68.5
Q ss_pred HHHHHHHHHHhccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHH
Q 027954 121 DQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRL 200 (216)
Q Consensus 121 EQ~dRYE~fRRS~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL 200 (216)
-+..||..+=...||++.|+|||.++.. ..||....-.+.-....|+-+|.+.|-.+...- .+.-+++..|.-|++++
T Consensus 7 ~~~r~~~~~~~~~Lp~apv~Ri~r~~~~-~Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha-~RKTV~~~DI~la~~~~ 84 (91)
T COG2036 7 KEIRRYQRSTDLLLPKAPVRRILRKAGA-ERVSSSAIEELQEALEEYLEEIAEDAVELAEHA-KRKTVKAEDIKLALKRL 84 (91)
T ss_pred HHHHhhhhhhhhhcCchHHHHHHHHHhH-HHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHc-CCCeecHHHHHHHHHHh
Confidence 4667888888999999999999999754 489999999999999999999999998886654 56789999999999887
Q ss_pred Hh
Q 027954 201 KL 202 (216)
Q Consensus 201 ~~ 202 (216)
..
T Consensus 85 ~~ 86 (91)
T COG2036 85 GR 86 (91)
T ss_pred cc
Confidence 54
No 16
>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=92.21 E-value=0.99 Score=34.79 Aligned_cols=68 Identities=18% Similarity=0.219 Sum_probs=56.3
Q ss_pred ccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHHH
Q 027954 132 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK 201 (216)
Q Consensus 132 S~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~ 201 (216)
+.++|+.|+||+... |-..||..+...+..+.+.|+-+|+..|....+. ..+.-+.+..|.-|++|.-
T Consensus 12 ~gi~k~~I~RLarr~-GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~H-a~RKTVt~~DV~~alkr~g 79 (85)
T cd00076 12 KGITKPAIRRLARRG-GVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEH-AKRKTVTAMDVVYALKRQG 79 (85)
T ss_pred ccCCHHHHHHHHHHc-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCCCcCcHHHHHHHHHHCC
Confidence 369999999998774 6568999999999999999999999999988664 3455588888988877653
No 17
>PTZ00017 histone H2A; Provisional
Probab=91.38 E-value=0.52 Score=39.31 Aligned_cols=66 Identities=17% Similarity=0.264 Sum_probs=52.7
Q ss_pred cCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHH
Q 027954 133 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 199 (216)
Q Consensus 133 ~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 199 (216)
.||=..|.|++..-.-...|+....+-++++--.++.||.|.|-...... ...-|.|.||.-|.+-
T Consensus 27 ~FPVgRi~R~Lk~g~~a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~-kk~RItPrHi~lAI~n 92 (134)
T PTZ00017 27 QFPVGRVHRYLKKGRYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDN-KKKRITPRHIQLAIRN 92 (134)
T ss_pred ccchHHHHHHHhccchhccccccchhhhHHHHHHHHHHHHHHHHHHHHhc-CCCeecHHHHHhhccC
Confidence 35666688888764445578888899999999999999999998776544 3568999999988874
No 18
>PTZ00015 histone H4; Provisional
Probab=90.92 E-value=1.4 Score=35.17 Aligned_cols=68 Identities=21% Similarity=0.266 Sum_probs=57.2
Q ss_pred ccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHHH
Q 027954 132 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK 201 (216)
Q Consensus 132 S~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~ 201 (216)
..++|+.|+||+.. .|-..||.++...+..+.+.|+-+|+..|....+.- .+.-+....|.-|++|..
T Consensus 29 ~gI~k~~IrRLarr-~GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA-~RKTVt~~DV~~AlKr~g 96 (102)
T PTZ00015 29 RGITKGAIRRLARR-GGVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYA-RRKTVTAMDVVYALKRQG 96 (102)
T ss_pred cCCCHHHHHHHHHH-cCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCcccHHHHHHHHHhcC
Confidence 57999999999877 466689999999999999999999999999886543 455688999988877653
No 19
>PLN00035 histone H4; Provisional
Probab=90.72 E-value=1.5 Score=35.14 Aligned_cols=66 Identities=20% Similarity=0.258 Sum_probs=56.7
Q ss_pred CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHHH
Q 027954 134 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK 201 (216)
Q Consensus 134 f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~ 201 (216)
||++.|+||+... |-..||..+...+..+.+.|+-+|+..|....+.- .+.-+....|.-|++|+.
T Consensus 30 ipk~~IrRLARr~-GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA-~RKTV~~~DV~~Alkr~g 95 (103)
T PLN00035 30 ITKPAIRRLARRG-GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHA-RRKTVTAMDVVYALKRQG 95 (103)
T ss_pred CCHHHHHHHHHHc-CcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCcCcHHHHHHHHHHcC
Confidence 9999999998774 66689999999999999999999999999886643 455688999999988764
No 20
>PLN00153 histone H2A; Provisional
Probab=89.10 E-value=1.2 Score=36.98 Aligned_cols=65 Identities=18% Similarity=0.271 Sum_probs=50.9
Q ss_pred CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHH
Q 027954 134 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 199 (216)
Q Consensus 134 f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 199 (216)
||=.-|.|++..-.-...|+....+-++++--.++.||.|.|-...... ....|.|.||.-|.+-
T Consensus 25 FpVgRi~R~Lr~g~~a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~-kk~RItPrHi~lAI~n 89 (129)
T PLN00153 25 FPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDN-KKNRIVPRHIQLAIRN 89 (129)
T ss_pred cchHHHHHHHhcCchhhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhc-CCCccChHHHHhhccC
Confidence 4555677777653334578888889999999999999999998876544 4679999999988764
No 21
>PLN00154 histone H2A; Provisional
Probab=89.09 E-value=1.5 Score=36.75 Aligned_cols=66 Identities=17% Similarity=0.248 Sum_probs=51.4
Q ss_pred cCChhHHHHHHHHhc-CCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHH
Q 027954 133 ALQKSNMRRLLVSIT-GSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 199 (216)
Q Consensus 133 ~f~K~~IKRLi~~vt-gsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 199 (216)
.||=.-|.|++..-+ -.+.|+....+.++++--.+..||.|.|-...... ...-|.|.||.-|.|-
T Consensus 38 ~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~-kk~RItPrHi~lAIrn 104 (136)
T PLN00154 38 QFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDL-KVKRITPRHLQLAIRG 104 (136)
T ss_pred cCchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhh-CCceecHHHhhhhccC
Confidence 355566777777643 24578889999999999999999999997775544 3456999999988764
No 22
>PLN00157 histone H2A; Provisional
Probab=88.73 E-value=1.1 Score=37.27 Aligned_cols=65 Identities=17% Similarity=0.262 Sum_probs=51.5
Q ss_pred CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHH
Q 027954 134 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 199 (216)
Q Consensus 134 f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 199 (216)
|+=.-|.|++..-.-...|+....+-++++--.++.||.|.|-...... ....|.|.||.-|.|-
T Consensus 27 FPVgRi~R~Lk~g~~a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~-kk~RItPrHi~lAI~n 91 (132)
T PLN00157 27 FPVGRIARYLKAGKYATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDN-KKSRIVPRHIQLAVRN 91 (132)
T ss_pred cchHHHHHHHhcCchhhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhc-CCccccHHHHhhcccC
Confidence 5555678887664445578888889999999999999999998876544 3579999999988764
No 23
>PLN00156 histone H2AX; Provisional
Probab=88.67 E-value=1.4 Score=37.13 Aligned_cols=65 Identities=17% Similarity=0.279 Sum_probs=51.2
Q ss_pred CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHH
Q 027954 134 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 199 (216)
Q Consensus 134 f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 199 (216)
|+=.-|.|++..-.-...|+....+.++++--.++.||.|.|-...... ....|.|.||.-|+|-
T Consensus 30 FPVgRi~R~Lk~g~ya~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~-kk~RItPrHi~lAIrn 94 (139)
T PLN00156 30 FPVGRIARFLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDN-KKNRIVPRHIQLAVRN 94 (139)
T ss_pred cchHHHHHHHhcCChhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHc-CCCcCcHHHHHhhccC
Confidence 5555677877654334578888889999999999999999998876544 3579999999988764
No 24
>PTZ00252 histone H2A; Provisional
Probab=87.53 E-value=2 Score=35.93 Aligned_cols=66 Identities=14% Similarity=0.213 Sum_probs=52.1
Q ss_pred CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHh-CcCCCCCchHHHHHHHH
Q 027954 134 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTER-NESGPIRPCHIREAYRR 199 (216)
Q Consensus 134 f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~-~e~gPLqP~HIREA~RR 199 (216)
|+=.-|.|++..-.-...|+....+-++++--.++.||.|.|-...... +...-|.|.||.-|+|-
T Consensus 26 FPVgRi~R~Lr~g~ya~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIrN 92 (134)
T PTZ00252 26 FPVGRVGSLLRRGQYARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVRH 92 (134)
T ss_pred CchHHHHHHHHcCCcccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhccC
Confidence 4445577877654444578888889999999999999999999987543 45689999999988764
No 25
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=87.29 E-value=1.8 Score=38.97 Aligned_cols=68 Identities=10% Similarity=0.345 Sum_probs=52.0
Q ss_pred hccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHH
Q 027954 131 RSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 199 (216)
Q Consensus 131 RS~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 199 (216)
-+.|+-+.|||||+.--.-.+|.+.|=++|+=---+|+.+|+-.+.++-..++ ..-|.|.||+.|+..
T Consensus 11 ~trfp~aRiKKIMQ~dEdIGKvaqavPViisralElFl~~l~~~t~~~t~~~~-aKt~s~~hlkq~v~~ 78 (224)
T KOG1659|consen 11 KTRFPPARIKKIMQSDEDIGKVAQAVPVIISRALELFLESLLQKTLEITRSRG-AKTVSSSHLKQAVES 78 (224)
T ss_pred hccCCHHHHHHHHhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcC-ccccCHHHHHHHHhc
Confidence 46899999999998643222566666566666667999999999999977663 567899999988754
No 26
>smart00417 H4 Histone H4.
Probab=86.91 E-value=2.2 Score=32.17 Aligned_cols=48 Identities=23% Similarity=0.259 Sum_probs=42.6
Q ss_pred cCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 027954 133 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTE 181 (216)
Q Consensus 133 ~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E 181 (216)
.++|+.|+||+.. .|-..||..+...+..+.+.|+-+|+..|....+.
T Consensus 13 gI~k~~IrRLaRr-~GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~h 60 (74)
T smart00417 13 GITKPAIRRLARR-GGVKRISGLIYDETRNVLKSFLENVVRDAVTYTEH 60 (74)
T ss_pred CCCHHHHHHHHHH-cCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 6999999999877 46678999999999999999999999999887653
No 27
>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=86.26 E-value=2.9 Score=30.77 Aligned_cols=64 Identities=17% Similarity=0.273 Sum_probs=47.7
Q ss_pred ChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHH
Q 027954 135 QKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 199 (216)
Q Consensus 135 ~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 199 (216)
+|.++..|+.+|-++..+.+.+.-++.=||=-||-.+++.|..+.+.|+. .-|.++.|.-.+.|
T Consensus 1 ~K~~l~~Lv~~iDp~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s-~tle~~Dv~~~Ler 64 (68)
T PF03847_consen 1 SKRKLQELVKQIDPNEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKS-STLEVKDVQLHLER 64 (68)
T ss_dssp -HHHHHHHHHCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SEE-HHHHHHHHHH
T ss_pred ChHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCC-CCCCHHHHHHHHHh
Confidence 47889999999988888999999999999999999999999999988753 35666666666555
No 28
>PF09415 CENP-X: CENP-S associating Centromere protein X; InterPro: IPR018552 Centromere protein X (CENP-X) is a component of the CENP-S complex. The CENP-S complex is composed of at least of CENP-S and CENP-X and is essential for the stable assembly of the outer kinetchore []. CENP-X is also a DNA-binding component of the Fanconi anemia (FA) core complex involved in DNA damage repair and genome maintenance. The FA complex is composed of CENPS, FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL/PHF9, FANCM, FAAP24 and CENPX. Interacts with CENPS, FANCM and FAAP24 [, ].; PDB: 4DRB_L 4DRA_H 3V9R_D.
Probab=85.49 E-value=1.9 Score=32.13 Aligned_cols=63 Identities=21% Similarity=0.198 Sum_probs=45.0
Q ss_pred ChhHHHHHHHHhcC--CCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHH
Q 027954 135 QKSNMRRLLVSITG--SQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAY 197 (216)
Q Consensus 135 ~K~~IKRLi~~vtg--sqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~ 197 (216)
|+..|.||+..... ..+|+.+.+.+++-+-++||-|-|-.|.......+..+=|.+.||..-.
T Consensus 1 p~~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki~ 65 (72)
T PF09415_consen 1 PPELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKIL 65 (72)
T ss_dssp -CHHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHHC
T ss_pred ChHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHH
Confidence 46678888764332 2368889999999999999999999998876665555458999997644
No 29
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=84.90 E-value=8.4 Score=28.25 Aligned_cols=64 Identities=17% Similarity=0.166 Sum_probs=51.7
Q ss_pred hhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHHH
Q 027954 136 KSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK 201 (216)
Q Consensus 136 K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~ 201 (216)
|..|.+++.. +|..++++...-.+.-+.--|+.+|...++..++--+.+.|. +..|..|+..+.
T Consensus 9 ~~~Vaqil~~-~Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~-~~Dv~~Al~~~g 72 (77)
T smart00576 9 RIAVAQILES-AGFDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPN-LGDVVLALENLG 72 (77)
T ss_pred HHHHHHHHHH-cCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCC-HHHHHHHHHHhC
Confidence 4556666655 577789999999999999999999999999998765556665 899999988764
No 30
>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=82.98 E-value=6.3 Score=36.53 Aligned_cols=67 Identities=13% Similarity=0.224 Sum_probs=56.9
Q ss_pred hhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHHHhcC
Q 027954 136 KSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKLEG 204 (216)
Q Consensus 136 K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~~~G 204 (216)
+..||-++.++ |-..+++.++..++.....++.+|+++|.+.|..- .+.=|.+.||..|+|.+.-+-
T Consensus 2 ~~~i~~ia~~~-Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hs-kR~~l~~~Di~~Al~~~n~ep 68 (343)
T cd08050 2 QESIKLIAESL-GIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHS-KRRKLTTSDVNHALRLRNVEP 68 (343)
T ss_pred hhHHHHHHHHc-CCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCcCCHHHHHHHHHHhCCCc
Confidence 56788877664 54589999999999999999999999999998864 457899999999999887663
No 31
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=81.07 E-value=5.6 Score=33.26 Aligned_cols=65 Identities=18% Similarity=0.293 Sum_probs=48.9
Q ss_pred cCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHH
Q 027954 133 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYR 198 (216)
Q Consensus 133 ~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~R 198 (216)
-||=..|.|++..-...+.++..-.+.|+++--....||.|.|-....+. ...-|.|+||+-|++
T Consensus 27 ~fPvgri~r~Lr~~~~~~ri~~gapV~laavLeYL~Aeile~agnaardn-kk~ri~PrH~~lAI~ 91 (131)
T KOG1756|consen 27 QFPVGRIHRLLRKGRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDN-KKTRITPRHLQLAIR 91 (131)
T ss_pred ccCHHHHHHHHHccchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhc-CccccChHHHHHHHh
Confidence 35555677777652223467777777888999999999999998876643 355789999999998
No 32
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=77.89 E-value=5.5 Score=36.41 Aligned_cols=74 Identities=18% Similarity=0.308 Sum_probs=55.2
Q ss_pred HHHHHHhccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHH
Q 027954 125 RYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 199 (216)
Q Consensus 125 RYE~fRRS~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 199 (216)
|-..+..-+|+-+.|||+|..--+---|+..+-++.+-++-+||.||+-.|--+ .|++.+.-||-..|.+|+.+
T Consensus 101 ~q~~~k~h~LPlARIkkvMKtdedVkMisaEaPvlFak~~EiFI~ELTmRAW~~-ae~NkRRtLQksDia~Av~k 174 (286)
T COG5208 101 RQILLKDHNLPLARIKKVMKTDEDVKMISAEAPVLFAKITEIFIEELTMRAWIN-AEENKRRTLQKSDIAAAVKK 174 (286)
T ss_pred HHHHHHhccCcHHHHHHHHhcccchhheecccchHHHHHHHHHHHHHHHHHHHH-HhHhhhhHHHHHHHHHHHHH
Confidence 335677778999999999864333223566666777889999999999988655 44456677888889988875
No 33
>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=77.04 E-value=23 Score=25.59 Aligned_cols=64 Identities=16% Similarity=0.212 Sum_probs=50.6
Q ss_pred hhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHHH
Q 027954 136 KSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK 201 (216)
Q Consensus 136 K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~ 201 (216)
+..|..++.+ .|..++++...-++.-++.-|+.+|...++..++.-+.+.|. +.+|..|+..+-
T Consensus 9 ~~~va~il~~-~GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~-~~Dv~~al~~~g 72 (77)
T PF07524_consen 9 RRSVAQILKH-AGFDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPN-LQDVEQALEEMG 72 (77)
T ss_pred HHHHHHHHHH-cCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCC-HHHHHHHHHHhC
Confidence 3345555544 576778899999999999999999999999998766667777 888888887653
No 34
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=72.25 E-value=13 Score=30.26 Aligned_cols=68 Identities=10% Similarity=0.207 Sum_probs=43.9
Q ss_pred HHhccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHH
Q 027954 129 FRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAY 197 (216)
Q Consensus 129 fRRS~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~ 197 (216)
|-.++||-+.|||||+---.-.+|++.+-++++----+|+.+||-+.++-.... .+.-+.-.||..|.
T Consensus 19 ~~ktrFP~ar~KkIMQ~deDiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~-~skR~t~e~lk~a~ 86 (113)
T COG5247 19 KKKTRFPIARLKKIMQLDEDIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKK-SSKRMTSEFLKRAT 86 (113)
T ss_pred hhhhcCCHHHHHHHHHhhhhhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhc-cchhhHHHHHHHHH
Confidence 667899999999998743222256665555555555788888888776653322 23445566666554
No 35
>PF07526 POX: Associated with HOX; InterPro: IPR006563 This domain in found exclusively in plant proteins, associated with HOX domains which may suggest these proteins are homeodomain transcription factors.
Probab=71.34 E-value=35 Score=28.34 Aligned_cols=40 Identities=13% Similarity=0.314 Sum_probs=27.9
Q ss_pred HHHHHHHHhccCChhHHHHHHH---HhcCCCCCCccHHHHHHHHHHHHH
Q 027954 123 MNRYESFRRSALQKSNMRRLLV---SITGSQKISLPMTIVVCGIAKMFV 168 (216)
Q Consensus 123 ~dRYE~fRRS~f~K~~IKRLi~---~vtgsqsVs~nvvIavaGlaKvFV 168 (216)
-.||..|+. .|.-++. .++|...-..-...++..|+|.|=
T Consensus 90 d~RY~qY~~------Qmq~VvssFe~vaG~gaA~~YtalAlqamSrhFR 132 (140)
T PF07526_consen 90 DRRYRQYYD------QMQAVVSSFEAVAGLGAAAPYTALALQAMSRHFR 132 (140)
T ss_pred HHHHHHHHH------HHHHHHHHHHHHhcCCcchhhHHHHHHHHHHHHH
Confidence 469999987 5666644 456654444567888999999883
No 36
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=70.29 E-value=24 Score=29.90 Aligned_cols=69 Identities=17% Similarity=0.219 Sum_probs=46.9
Q ss_pred ccCChhHHHHHHHHhcCCC-CCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHHH
Q 027954 132 SALQKSNMRRLLVSITGSQ-KISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK 201 (216)
Q Consensus 132 S~f~K~~IKRLi~~vtgsq-sVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~ 201 (216)
-+|||++|.|.+.++..-. .++...--++---+=.|+--|..+|-+++++. ...-|-|.|+-.|+.-|-
T Consensus 10 ~sLPKATVqKMvS~iLp~dl~ftKearei~in~cieFi~~lsseAne~ce~E-aKKTIa~EHviKALenLe 79 (148)
T COG5150 10 NSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEE-AKKTIAYEHVIKALENLE 79 (148)
T ss_pred ccCcHHHHHHHHHHhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HhccccHHHHHHHHHhcc
Confidence 3799999999988876522 13333222222223368888889999998864 345789999998877653
No 37
>PRK07194 fliG flagellar motor switch protein G; Reviewed
Probab=67.81 E-value=35 Score=31.61 Aligned_cols=90 Identities=13% Similarity=0.299 Sum_probs=60.7
Q ss_pred HHHHHHhcCCHHHHHH-------HHHHHhccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHH----HHHH-H
Q 027954 110 KMQAILNQFTEDQMNR-------YESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELV----ETAR-M 177 (216)
Q Consensus 110 km~~Ll~~fteEQ~dR-------YE~fRRS~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELV----EeAr-~ 177 (216)
.+..-|...+++.... |+... ++....|..|+..+. ++.++.+++|+..-+-.+|+ ..|. .
T Consensus 215 ~il~~L~~~dp~~a~~Ir~~mF~FedL~--~~~~qtia~iL~~v~-----~~~la~aLkg~~~e~r~~il~nmS~Raa~~ 287 (334)
T PRK07194 215 QLMEMLKEHDEEVVNEIEDNMYDFFILS--RQSEETLQRLMDEVP-----MELWAVALKGTEPALRQAILRVMPKRQAQA 287 (334)
T ss_pred HHHHHHHhhCHHHHHHHHHhcCCHHHHh--cCCHHHHHHHHHhCC-----HHHHHHHHccCCHHHHHHHHHHccHHHHHH
Confidence 3444566677777666 55554 366667777776652 45788899888765555544 4444 5
Q ss_pred HHHHhCcCCCCCchHHHHH-------HHHHHhcCCC
Q 027954 178 VMTERNESGPIRPCHIREA-------YRRLKLEGKV 206 (216)
Q Consensus 178 Vq~E~~e~gPLqP~HIREA-------~RRL~~~Gkv 206 (216)
++++....||++...+.+| .|+|-.+|+|
T Consensus 288 l~eele~~gpV~~sdvE~Aq~~Iv~~~r~L~~~G~I 323 (334)
T PRK07194 288 LEAQIERLGPVPLSRVEQARKEIMALVRELAEAGEI 323 (334)
T ss_pred HHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHCCCE
Confidence 5667778999999988876 5677777764
No 38
>smart00427 H2B Histone H2B.
Probab=67.65 E-value=34 Score=26.80 Aligned_cols=66 Identities=14% Similarity=0.200 Sum_probs=48.0
Q ss_pred HHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHHHhcCCC
Q 027954 139 MRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKLEGKV 206 (216)
Q Consensus 139 IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~~~Gkv 206 (216)
|.|++.++-....++....-+|.+|..=+.-.|..+|-.+..- +...-|.+++|+.|+|-+. .|++
T Consensus 7 i~kvLKqVhpd~giS~kam~imnSfvnDiferIa~EAs~L~~~-nkr~TltsreIqtAvrl~L-pgeL 72 (89)
T smart00427 7 IYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASKLARY-NKKSTLSSREIQTAVRLIL-PGEL 72 (89)
T ss_pred HHHHHHHhCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhc-cCCCcCCHHHHHHHHHHHc-cHHH
Confidence 7888888877667777777777777666666676677666553 3567899999999987654 3443
No 39
>PRK13916 plasmid segregation protein ParR; Provisional
Probab=63.96 E-value=6.5 Score=31.14 Aligned_cols=18 Identities=44% Similarity=0.481 Sum_probs=15.7
Q ss_pred CCchHHHHHHHHHHhcCC
Q 027954 188 IRPCHIREAYRRLKLEGK 205 (216)
Q Consensus 188 LqP~HIREA~RRL~~~Gk 205 (216)
-.|.|||+|+|||..+|-
T Consensus 31 T~~~~iR~~L~rYI~~~G 48 (97)
T PRK13916 31 TKTAHIREALRRYIEEIG 48 (97)
T ss_pred CccHHHHHHHHHHHHhcC
Confidence 468999999999999864
No 40
>PF01706 FliG_C: FliG C-terminal domain; InterPro: IPR023087 The flagellar motor switch in Escherichia coli and Salmonella typhimurium regulates the direction of flagellar rotation and hence controls swimming behaviour []. The switch is a complex apparatus that responds to signals transduced by the chemotaxis sensory signalling system during chemotactic behaviour []. CheY, the chemotaxis response regulator, is believed to act directly on the switch to induce tumbles in the swimming pattern, but no physical interactions of CheY and switch proteins have yet been demonstrated. The switch complex comprises at least three proteins - FliG, FliM and FliN. It has been shown that FliG interacts with FliM, FliM interacts with itself, and FliM interacts with FliN []. Several residues within the middle third of FliG appear to be strongly involved in the FliG-FliM interaction, with residues near the N- or C-termini being less important []. Such clustering suggests that FliG-FliM interaction plays a central role in switching. Analysis of the FliG, FliM and FliN sequences shows that none are especially hydrophobic or appear to be integral membrane proteins []. This result is consistent with other evidence suggesting that the proteins may be peripheral to the membrane, possibly mounted on the basal body M ring [, ]. FliG is present in about 25 copies per flagellum. This entry represents the C-terminal domain of FliG, the structure of which is known. This domain functions specifically in motor rotation [].; PDB: 3USY_B 3USW_A 3HJL_A 3AJC_A 1LKV_X 1QC7_B.
Probab=63.55 E-value=15 Score=28.31 Aligned_cols=68 Identities=26% Similarity=0.483 Sum_probs=39.8
Q ss_pred CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHH----HH-HHHHHHHHhCcCCCCCchHHHHH-------HHHHH
Q 027954 134 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGEL----VE-TARMVMTERNESGPIRPCHIREA-------YRRLK 201 (216)
Q Consensus 134 f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGEL----VE-eAr~Vq~E~~e~gPLqP~HIREA-------~RRL~ 201 (216)
++...+.+|+.++. ++.+++++.|-...|.--| -. .|..|+++....||+.+..+.+| .|+|.
T Consensus 28 l~~~~l~~ll~~v~-----~~~la~ALkga~~e~~~~il~nms~r~a~~l~~e~~~~g~v~~~di~~Aq~~iv~~~r~l~ 102 (110)
T PF01706_consen 28 LDDRDLQKLLREVD-----PDDLALALKGASEELREKILSNMSKRAAEMLREEMEALGPVRLSDIEEAQREIVEIVRRLE 102 (110)
T ss_dssp S-HHHHHHHHTTS------HHHHHHHHCTS-HHHHHHHHTTS-HHHHHHHHHHHHHH-S--HHHHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHCC-----HhHHHHHHccCCHHHHHHHHHHcCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHH
Confidence 55556666665542 3568888877665544444 34 34566777778899999988876 45666
Q ss_pred hcCCC
Q 027954 202 LEGKV 206 (216)
Q Consensus 202 ~~Gkv 206 (216)
.+|.+
T Consensus 103 ~~G~I 107 (110)
T PF01706_consen 103 EEGEI 107 (110)
T ss_dssp HTTSS
T ss_pred HCcCE
Confidence 66764
No 41
>PLN00158 histone H2B; Provisional
Probab=58.66 E-value=58 Score=26.78 Aligned_cols=62 Identities=13% Similarity=0.149 Sum_probs=44.3
Q ss_pred HHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHHH
Q 027954 139 MRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK 201 (216)
Q Consensus 139 IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~ 201 (216)
|.|++.+|-....||....-+|.+|..=+.-.|..+|-.+..- +...-|.+.+|+.|+|-+.
T Consensus 33 I~kVLKQVhPd~gIS~kaM~ImnSfvnDiferIA~EAs~La~~-nkr~TltsrEIqtAvrLvL 94 (116)
T PLN00158 33 IYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARY-NKKPTVTSREIQTAVRLIL 94 (116)
T ss_pred HHHHHHHhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhc-cCCCcCCHHHHHHHHHHhc
Confidence 7888888877667777766667766555555566666665442 4567899999999987654
No 42
>smart00574 POX domain associated with HOX domains.
Probab=56.34 E-value=66 Score=27.26 Aligned_cols=42 Identities=14% Similarity=0.271 Sum_probs=26.9
Q ss_pred HHHHHHHHHHhccCChhHHHHHHH---HhcCCCCCCccHHHHHHHHHHHHH
Q 027954 121 DQMNRYESFRRSALQKSNMRRLLV---SITGSQKISLPMTIVVCGIAKMFV 168 (216)
Q Consensus 121 EQ~dRYE~fRRS~f~K~~IKRLi~---~vtgsqsVs~nvvIavaGlaKvFV 168 (216)
|=-.||..|+. .|.-++. .++|...-..-...++..|++.|=
T Consensus 88 eVd~RY~qY~~------qmq~v~ssFe~vaG~g~a~~yt~lAl~a~SrhFr 132 (140)
T smart00574 88 EVDRRYKHYYE------QMQTVVSSFDQAAGLGAAKPYTALALKTISRHFR 132 (140)
T ss_pred HHHHHHHHHHH------HHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHH
Confidence 33579999986 4666544 445543333446778888888884
No 43
>PTZ00463 histone H2B; Provisional
Probab=52.58 E-value=70 Score=26.39 Aligned_cols=66 Identities=12% Similarity=0.124 Sum_probs=44.2
Q ss_pred HHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHHHhcCCC
Q 027954 139 MRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKLEGKV 206 (216)
Q Consensus 139 IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~~~Gkv 206 (216)
|.|++.+|-....||....-+|.+|..=++-.|..+|-.+..- +...-|.+.+|+.|+|-+. .|++
T Consensus 34 I~KVLKqVhPd~gIS~kaM~ImnSfvnDifErIA~EAs~La~~-nkr~TltsrEIQtAvrLlL-pGEL 99 (117)
T PTZ00463 34 IFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATEASRLCKY-TRRDTLSSREIQTAIRLVL-PGEL 99 (117)
T ss_pred HHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCCCcCCHHHHHHHHhhcc-cHHH
Confidence 7888888877667777766667655444444455555555442 4677899999999987554 4554
No 44
>PRK05686 fliG flagellar motor switch protein G; Validated
Probab=51.60 E-value=36 Score=31.36 Aligned_cols=69 Identities=25% Similarity=0.476 Sum_probs=49.6
Q ss_pred cCChhHHHHHHHHhcCCCCCCccHHHHHHHHHH----HHHHHHHHHHH-HHHHHhCcCCCCCchHHHHHH-------HHH
Q 027954 133 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAK----MFVGELVETAR-MVMTERNESGPIRPCHIREAY-------RRL 200 (216)
Q Consensus 133 ~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaK----vFVGELVEeAr-~Vq~E~~e~gPLqP~HIREA~-------RRL 200 (216)
+++...+.+|+..|. ++.+++++.|-.. -|..-|-..+. .++++....||+++..+.+|- |+|
T Consensus 249 ~l~~~~l~~ll~~v~-----~~~L~~ALkga~~~~~~~il~nmS~R~a~~l~eel~~~g~v~~~dve~Aq~~I~~~~r~l 323 (339)
T PRK05686 249 DLDDRSIQRLLREVD-----NDVLALALKGASEELREKFLSNMSKRAAEMLREDLEALGPVRLSDVEEAQKKIVQIARRL 323 (339)
T ss_pred cCCHHHHHHHHHhCC-----HHHHHHHHCCCCHHHHHHHHHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHHH
Confidence 477777888887763 4678999987655 45555556554 556677789999999988774 577
Q ss_pred HhcCCC
Q 027954 201 KLEGKV 206 (216)
Q Consensus 201 ~~~Gkv 206 (216)
-.+|+|
T Consensus 324 ~~~G~I 329 (339)
T PRK05686 324 AEAGEI 329 (339)
T ss_pred HHCCCE
Confidence 777774
No 45
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=51.32 E-value=15 Score=30.55 Aligned_cols=64 Identities=19% Similarity=0.284 Sum_probs=43.9
Q ss_pred CChhHHHHHHHH-hcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHH
Q 027954 134 LQKSNMRRLLVS-ITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYR 198 (216)
Q Consensus 134 f~K~~IKRLi~~-vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~R 198 (216)
||=.-|.|.+.+ ++...+|...-++-+++|-..+-.|+.|.|=..-+.. .-.-|.|.||+-|.|
T Consensus 31 FpVgRihr~LK~r~t~h~rVGataavy~aaileYLTaEVLeLAgNasKdL-KvKRitprHlqLAiR 95 (131)
T KOG1757|consen 31 FPVGRIHRHLKTRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDL-KVKRITPRHLQLAIR 95 (131)
T ss_pred cchHHHHHHHHHhcccccccchHHHHHHHHHHHHHHHHHHHHcccccccc-eeeeccchhheeeec
Confidence 555557776654 3444567778888889999999999999874332211 123488999998876
No 46
>TIGR00207 fliG flagellar motor switch protein FliG. The fliG protein along with fliM and fliN interact to form the switch complex of the bacterial flagellar motor located at the base of the basal body. This complex interacts with chemotaxis proteins (eg CHEY). In addition the complex interacts with other components of the motor that determine the direction of flagellar rotation. The model contains putative members of the fliG family at scores of less than 100 from Agrobacterium radiobacter and Sinorhizobium meliloti as well as fliG-like genes from treponema pallidum and Borrelia burgdorferi. That is why the suggested cutoff is set at 20 but was set at 100 to construct the family.
Probab=50.79 E-value=39 Score=31.37 Aligned_cols=69 Identities=22% Similarity=0.433 Sum_probs=49.8
Q ss_pred cCChhHHHHHHHHhcCCCCCCccHHHHHHHHH----HHHHHHHHHHHH-HHHHHhCcCCCCCchHHHHH-------HHHH
Q 027954 133 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIA----KMFVGELVETAR-MVMTERNESGPIRPCHIREA-------YRRL 200 (216)
Q Consensus 133 ~f~K~~IKRLi~~vtgsqsVs~nvvIavaGla----KvFVGELVEeAr-~Vq~E~~e~gPLqP~HIREA-------~RRL 200 (216)
.+....+.+|+..|. ++.+++++.|-. .-|..-+-..|. .++++....||++...+.+| .|+|
T Consensus 246 ~ld~~~l~~llrev~-----~~~L~~ALkga~~e~~~~il~nmS~R~a~~l~ee~~~~GpV~~sdvE~Aq~~Iv~~~r~L 320 (338)
T TIGR00207 246 DLDDRSIQRVLREVD-----SEDLLLALKGAEQPLREKFLNNMSQRAAEILKEDMEFLGPVRLKDVEEAQKKIVSIVRKL 320 (338)
T ss_pred cCCHHHHHHHHHhCC-----HHHHHHHHCcCCHHHHHHHHHHhhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHH
Confidence 477777888877762 367888887754 456666666554 45667777999999988876 5677
Q ss_pred HhcCCC
Q 027954 201 KLEGKV 206 (216)
Q Consensus 201 ~~~Gkv 206 (216)
-.+|.|
T Consensus 321 ~~~G~I 326 (338)
T TIGR00207 321 EETGEI 326 (338)
T ss_pred HHCCCE
Confidence 888874
No 47
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=47.32 E-value=31 Score=31.10 Aligned_cols=71 Identities=18% Similarity=0.322 Sum_probs=52.6
Q ss_pred HHHhccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHH
Q 027954 128 SFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 199 (216)
Q Consensus 128 ~fRRS~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 199 (216)
.|....|+.+-|||+|.+=-.-++|+....+.++-.+-+||-||...+ .+..+.+.+..|+=.||-.|..+
T Consensus 69 d~~~~~lPlaRiKkimK~dedv~mI~~Eapvl~aka~E~Fi~elt~~s-w~~Tee~~rrtl~~sdia~av~~ 139 (236)
T KOG1657|consen 69 DFKNHILPLARIKKIMKSDEDVSMITAEAPVLFAKACELFITELTLRS-WVHTEENKRRTLQKSDIAAAVTQ 139 (236)
T ss_pred chhhccCcHhhccccccccccccccchhHHHHHHHHHHHHHHHHHHHh-hhhhcccccccchHHHHHHHhcc
Confidence 466779999999999876444457888999999999999999998874 23334445666666777766544
No 48
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=46.87 E-value=32 Score=31.69 Aligned_cols=60 Identities=22% Similarity=0.340 Sum_probs=46.3
Q ss_pred CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHH
Q 027954 134 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIR 194 (216)
Q Consensus 134 f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIR 194 (216)
+.|.++..|+..|.++..+-++|-.+|.=||==||-.||..|..+.+.|+ +.-|..+.|+
T Consensus 155 l~k~kl~dLvqqId~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRK-sdtlEvrDIq 214 (258)
T KOG1142|consen 155 LSKRKLDDLVQQIDGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRK-SDTVEVRDIQ 214 (258)
T ss_pred ccccchhHHHHhhcCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc-cCccchhhee
Confidence 44777888888888877788899999999999999999999988877652 2234444443
No 49
>cd07978 TAF13 The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Several hy
Probab=46.54 E-value=1.3e+02 Score=23.32 Aligned_cols=63 Identities=17% Similarity=0.213 Sum_probs=46.7
Q ss_pred CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHH
Q 027954 134 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 199 (216)
Q Consensus 134 f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 199 (216)
|.+. |+.+|=..-..+.+.+..+.+|-.|.--||-+|+-+|..+.. | ..+.+.+..|.=++|+
T Consensus 4 f~~e-i~~mmy~~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~-r~~k~~~eD~~FliR~ 66 (92)
T cd07978 4 FTKE-IRQMMYGFGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-R-RRGKVKVEDLIFLLRK 66 (92)
T ss_pred cHHH-HHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-c-CCCCCCHHHHHHHHhc
Confidence 4433 777765543344566678888999999999999999999977 4 3445599999888775
No 50
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=45.19 E-value=1.2e+02 Score=26.57 Aligned_cols=50 Identities=18% Similarity=0.222 Sum_probs=41.3
Q ss_pred ccCChhHHHHHHHHhcCC--CCCCccHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 027954 132 SALQKSNMRRLLVSITGS--QKISLPMTIVVCGIAKMFVGELVETARMVMTE 181 (216)
Q Consensus 132 S~f~K~~IKRLi~~vtgs--qsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E 181 (216)
-.||++.|.||+..+..- .+|+.....+|+--|-|||--|..-|..++..
T Consensus 9 l~lP~AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~ 60 (172)
T KOG0870|consen 9 LNLPNAIITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKD 60 (172)
T ss_pred hhccHHHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 368999999998887542 25777788889999999999999999998774
No 51
>COG2074 2-phosphoglycerate kinase [Carbohydrate transport and metabolism]
Probab=42.57 E-value=38 Score=31.84 Aligned_cols=80 Identities=21% Similarity=0.293 Sum_probs=47.4
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHhccCChhHHHHHHH---HhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 027954 105 PAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLV---SITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTE 181 (216)
Q Consensus 105 ~e~~~km~~Ll~~fteEQ~dRYE~fRRS~f~K~~IKRLi~---~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E 181 (216)
.+-++-.+.|+..-++|...||..||+ ||+... -..|+ ++|++|.-| |..|..+
T Consensus 56 ~eir~~~~~l~~k~~~e~a~rY~lwR~-------ir~~~~p~IILIGG----------asGVGkStI------A~ElA~r 112 (299)
T COG2074 56 DEIREVYQKLLEKGDPEVAKRYLLWRR-------IRKMKRPLIILIGG----------ASGVGKSTI------AGELARR 112 (299)
T ss_pred HHHHHHHHHHHHhcCHHHHHHHHHHHH-------HhccCCCeEEEecC----------CCCCChhHH------HHHHHHH
Confidence 344456788999999999999999999 444321 11232 134555433 4444444
Q ss_pred hCcCCCCCchHHHHHHHHHHhcCCCC
Q 027954 182 RNESGPIRPCHIREAYRRLKLEGKVP 207 (216)
Q Consensus 182 ~~e~gPLqP~HIREA~RRL~~~Gkvp 207 (216)
.+=+.-|--++|||-+|.+...-.+|
T Consensus 113 LgI~~visTD~IREvlR~ii~~~l~P 138 (299)
T COG2074 113 LGIRSVISTDSIREVLRKIISPELLP 138 (299)
T ss_pred cCCceeecchHHHHHHHHhCCHHhcc
Confidence 44455556666666666665433333
No 52
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=41.71 E-value=9.2 Score=25.88 Aligned_cols=52 Identities=17% Similarity=0.207 Sum_probs=26.7
Q ss_pred CHHHHHHHHHHHhccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHH
Q 027954 119 TEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELV 172 (216)
Q Consensus 119 teEQ~dRYE~fRRS~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELV 172 (216)
.+-.+..++..+++.++++.|.++++.-. .+++-..+..++-+-.+=++||+
T Consensus 7 ~~~~it~~~La~~~gis~~tl~~~~~~~~--~~~~~~~l~~ia~~l~~~~~el~ 58 (63)
T PF13443_consen 7 AERGITQKDLARKTGISRSTLSRILNGKP--SNPSLDTLEKIAKALNCSPEELF 58 (63)
T ss_dssp HHTT--HHHHHHHHT--HHHHHHHHTTT-------HHHHHHHHHHHT--HHHCT
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHhccc--ccccHHHHHHHHHHcCCCHHHHh
Confidence 34456788889999999999999986421 23444444444444333344443
No 53
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=40.51 E-value=2.5e+02 Score=29.45 Aligned_cols=70 Identities=17% Similarity=0.290 Sum_probs=45.1
Q ss_pred HHHHHHHhcCCHHH----HHHHHHHHhccC---ChhHHHHHHH----Hh--cCCCCCCc------cHHHHHHHHHHHHHH
Q 027954 109 AKMQAILNQFTEDQ----MNRYESFRRSAL---QKSNMRRLLV----SI--TGSQKISL------PMTIVVCGIAKMFVG 169 (216)
Q Consensus 109 ~km~~Ll~~fteEQ----~dRYE~fRRS~f---~K~~IKRLi~----~v--tgsqsVs~------nvvIavaGlaKvFVG 169 (216)
+.+..||...+.++ ..|.-.|-..+| ||.++.+|+. .+ ..++.-+. .++-.|-.||+.|.-
T Consensus 429 eel~~lL~~~~~~~~~~iI~RIrk~~hpsLa~~NK~Kl~~f~~vLlq~i~~la~~~~~~~~~~ld~L~~~L~~Laq~~p~ 508 (840)
T PF04147_consen 429 EELLELLDGYSPEDQPTIIQRIRKCYHPSLAEGNKEKLQVFFGVLLQHILYLASQDSPPPFEVLDSLIPHLYDLAQKYPE 508 (840)
T ss_pred HHHHHHHhcCCHHHHhHHHHHHHHhCCCCCCcchHHHHHHHHHHHHHHHHHHhcccCCcCHHHHHHHHHHHHHHHHHHHH
Confidence 56788898888775 367788888887 6777776622 11 11221022 245557788888887
Q ss_pred HHHHHHHHH
Q 027954 170 ELVETARMV 178 (216)
Q Consensus 170 ELVEeAr~V 178 (216)
.+.+..+.+
T Consensus 509 ~~a~~~r~~ 517 (840)
T PF04147_consen 509 EAAECFREV 517 (840)
T ss_pred HHHHHHHHH
Confidence 777777766
No 54
>PF12174 RST: RCD1-SRO-TAF4 (RST) plant domain; InterPro: IPR022003 This domain is found in many plant proteins including SROs and RCD1s; it is required for interaction with multiple plant transcription factors.
Probab=38.82 E-value=92 Score=23.07 Aligned_cols=39 Identities=23% Similarity=0.544 Sum_probs=30.4
Q ss_pred HHHHHhcCCHHHHH----HHHHHHhccCChhHHHHHHHHhcCC
Q 027954 111 MQAILNQFTEDQMN----RYESFRRSALQKSNMRRLLVSITGS 149 (216)
Q Consensus 111 m~~Ll~~fteEQ~d----RYE~fRRS~f~K~~IKRLi~~vtgs 149 (216)
+..|...+++.+++ .|+.||+..++|...=|.+..|+|.
T Consensus 15 ~~~l~~~l~~~~~~~l~~~Y~~~k~~kIsR~~fvr~lR~IVGD 57 (70)
T PF12174_consen 15 FSALSKHLPPSKMDLLQKHYEEFKKKKISREEFVRKLRQIVGD 57 (70)
T ss_pred HHHHHHHCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHH
Confidence 34456777777764 7999999999999977777888875
No 55
>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=36.19 E-value=47 Score=25.52 Aligned_cols=60 Identities=18% Similarity=0.196 Sum_probs=27.8
Q ss_pred HHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHH
Q 027954 139 MRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 199 (216)
Q Consensus 139 IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 199 (216)
|+.+|=..-.+..+.+..+.+|--|...||-+|+-.|..+...+ .++-|.+.+|.=++|+
T Consensus 7 I~~mMy~fGD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~r-g~~~i~~eDl~F~lR~ 66 (93)
T PF02269_consen 7 IRQMMYGFGDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRR-GSKKIKVEDLLFLLRK 66 (93)
T ss_dssp CHHHHHCTTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC----------------------
T ss_pred HHHHHHHcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhcc-ccCcCcHHHHHHHHhc
Confidence 56665443223456667888899999999999999999985554 5778999999888886
No 56
>PF07462 MSP1_C: Merozoite surface protein 1 (MSP1) C-terminus; InterPro: IPR010901 This entry represents the C-terminal region of merozoite surface protein 1 (MSP1), which is found in a number of Plasmodium species. MSP-1 is a 200 kDa protein expressed on the surface of the Plasmodium vivax merozoite. MSP-1 of Plasmodium species is synthesised as a high-molecular-weight precursor and then processed into several fragments. At the time of red cell invasion by the merozoite, only the 19 kDa C-terminal fragment (MSP-119), which contains two epidermal growth factor-like domains, remains on the surface. Antibodies against MSP-119 inhibit merozoite entry into red cells, and immunisation with MSP-119 protects monkeys from challenging infections. Hence, MSP-119 is considered a promising vaccine candidate [].; GO: 0009405 pathogenesis, 0016020 membrane
Probab=35.50 E-value=47 Score=33.79 Aligned_cols=14 Identities=21% Similarity=0.259 Sum_probs=7.9
Q ss_pred CCCccHHHHHHHHH
Q 027954 151 KISLPMTIVVCGIA 164 (216)
Q Consensus 151 sVs~nvvIavaGla 164 (216)
+|..+|+++=-||+
T Consensus 463 SIdkDi~tAnDGl~ 476 (574)
T PF07462_consen 463 SIDKDIATANDGLA 476 (574)
T ss_pred HHhhhHHHhhhHHH
Confidence 46666666644443
No 57
>cd04411 Ribosomal_P1_P2_L12p Ribosomal protein P1, P2, and L12p. Ribosomal proteins P1 and P2 are the eukaryotic proteins that are functionally equivalent to bacterial L7/L12. L12p is the archaeal homolog. Unlike other ribosomal proteins, the archaeal L12p and eukaryotic P1 and P2 do not share sequence similarity with their bacterial counterparts. They are part of the ribosomal stalk (called the L7/L12 stalk in bacteria), along with 28S rRNA and the proteins L11 and P0 in eukaryotes (23S rRNA, L11, and L10e in archaea). In bacterial ribosomes, L7/L12 homodimers bind the extended C-terminal helix of L10 to anchor the L7/L12 molecules to the ribosome. Eukaryotic P1/P2 heterodimers and archaeal L12p homodimers are believed to bind the L10 equivalent proteins, eukaryotic P0 and archaeal L10e, in a similar fashion. P1 and P2 (L12p, L7/L12) are the only proteins in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain
Probab=31.89 E-value=21 Score=28.35 Aligned_cols=11 Identities=36% Similarity=0.628 Sum_probs=5.3
Q ss_pred ccccccccccc
Q 027954 84 YDEEDDENVDV 94 (216)
Q Consensus 84 ~~~e~ed~~~~ 94 (216)
+++|+||||-+
T Consensus 92 e~eE~dddmgf 102 (105)
T cd04411 92 EEEEEDEDFGF 102 (105)
T ss_pred cccccccccCc
Confidence 33444555544
No 58
>KOG2140 consensus Uncharacterized conserved protein [General function prediction only]
Probab=31.15 E-value=2.1e+02 Score=29.81 Aligned_cols=89 Identities=22% Similarity=0.334 Sum_probs=57.2
Q ss_pred cccccCCCCCC-cHHHHHHHHHHHhcCCHHHHHH--HHHHHhc------cCChhHHHHHHH----------------Hhc
Q 027954 93 DVELGKFPSSS-DPAKMAKMQAILNQFTEDQMNR--YESFRRS------ALQKSNMRRLLV----------------SIT 147 (216)
Q Consensus 93 ~~~l~~~~~~~-d~e~~~km~~Ll~~fteEQ~dR--YE~fRRS------~f~K~~IKRLi~----------------~vt 147 (216)
++..+....+. .|.+-+.|+.-+..=+..+|.| ||+.|.+ ++|..+|+-+|. +|.
T Consensus 125 ~l~~trtGG~YIPPaKL~~mq~qi~Dk~s~~yQRmnWEalkksInglInkvn~sNi~~ii~eLfqeNiirgRgl~crsv~ 204 (739)
T KOG2140|consen 125 DLLRTRTGGAYIPPAKLRMMQAQITDKNSIEYQRMNWEALKKSINGLINKVNASNIQEIIRELFQENIIRGRGLLCRSVM 204 (739)
T ss_pred HHhhccCCCeecCHHHHHHHHHHhcccchHHHHHHHHHHHHHHhHHHHhhhhHHHHHHHHHHHHHHHHHhccchhHHHHH
Confidence 34443333322 5566667777776666566666 8888876 667777766632 233
Q ss_pred CCCCCCccHHHHHHHHHHHH------HHHHHHHHHHHHHH
Q 027954 148 GSQKISLPMTIVVCGIAKMF------VGELVETARMVMTE 181 (216)
Q Consensus 148 gsqsVs~nvvIavaGlaKvF------VGELVEeAr~Vq~E 181 (216)
-.|.-+++.+-|.++|+-|+ ||||+-+-+-||..
T Consensus 205 ~aq~asp~ft~vyaALvAviNskfP~IgElLlkrLilqf~ 244 (739)
T KOG2140|consen 205 QAQAASPGFTPVYAALVAVINSKFPQIGELLLKRLILQFK 244 (739)
T ss_pred HHHhcCCCCcHHHHHHHHHHccCCchHHHHHHHHHHHHHH
Confidence 33455667777777777765 89998888877764
No 59
>PF05236 TAF4: Transcription initiation factor TFIID component TAF4 family; InterPro: IPR007900 Accurate transcription initiation at protein-coding genes by RNA polymerase II requires the assembly of a multiprotein complex around the mRNA start site. Transcription factor TFIID is one of the general factors involved in this process. Yeast TFIID comprises the TATA binding protein and 14 TBP-associated factors (TAFIIs), nine of which contain histone-fold domains (IPR007124 from INTERPRO). The C-terminal region of the TFIID-specific yeast TAF4 (yTAF4) containing the HFD shares strong sequence similarity with Drosophila (d)TAF4 and human TAF4. A structure/function analysis of yTAF4 demonstrates that the HFD, a short conserved C-terminal domain (CCTD), and the region separating them are all required for yTAF4 function. This region of similarity is found in Transcription initiation factor TFIID component TAF4 []. ; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_C.
Probab=29.80 E-value=99 Score=27.45 Aligned_cols=51 Identities=16% Similarity=0.247 Sum_probs=32.3
Q ss_pred CChhHHHHHHHHhc---CCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCc
Q 027954 134 LQKSNMRRLLVSIT---GSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNE 184 (216)
Q Consensus 134 f~K~~IKRLi~~vt---gsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e 184 (216)
|+...+.+.|..|. |...+..+++-.|+--++.++-.|||.+..+...|-+
T Consensus 44 L~~~~L~~~i~~i~~~~g~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~ 97 (264)
T PF05236_consen 44 LNPSPLQKRIQKIAKKHGLKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRD 97 (264)
T ss_dssp S-HHHHHHHHHHHHHCTT--EE-TCHHHHHHHHHHHHHHHHHHHHH--------
T ss_pred cCHHHHHHHHHHHHHHcCCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence 56666666666654 4346888999999999999999999999998776643
No 60
>PF03540 TFIID_30kDa: Transcription initiation factor TFIID 23-30kDa subunit; InterPro: IPR003923 Transcription initiation factor TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. The complex includes TATA binding protein (TBP) and various TBP-associated factors (TAFS). TFIID a bona fide RNA polymerase II-specific TATA-binding protein-associated factor (TAF) and is essential for viability []. TFIID acts to nucleate the transcription complex, recruiting the rest of the factors through a direct interaction with TFIIB. The TBP subunit of TFIID is sufficient for TATA-element binding and TFIIB interaction, and can support basal transcription. The protein belongs to the TAF2H family.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus
Probab=29.27 E-value=2.1e+02 Score=20.29 Aligned_cols=47 Identities=15% Similarity=0.129 Sum_probs=36.8
Q ss_pred CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 027954 134 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTE 181 (216)
Q Consensus 134 f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E 181 (216)
+|...+..+++. .|-+.....++=.|+=.+-=||-+|+..|...++-
T Consensus 3 IPD~v~~~yL~~-~G~~~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~ 49 (51)
T PF03540_consen 3 IPDEVTDYYLER-SGFQTSDPRVKRLVSLAAQKFISDIANDAMQYCKI 49 (51)
T ss_pred CCHHHHHHHHHH-CCCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 566777777766 47665556788889999999999999999887653
No 61
>PRK14703 glutaminyl-tRNA synthetase/YqeY domain fusion protein; Provisional
Probab=28.35 E-value=40 Score=35.22 Aligned_cols=95 Identities=17% Similarity=0.200 Sum_probs=59.6
Q ss_pred HHHHhcCCHHHHHHHHHHHhc-cCChhHHHHHHHHhcCCCCCCccHHH---HHHHHHHHHHHHHHHHHHHHHHHhCcCCC
Q 027954 112 QAILNQFTEDQMNRYESFRRS-ALQKSNMRRLLVSITGSQKISLPMTI---VVCGIAKMFVGELVETARMVMTERNESGP 187 (216)
Q Consensus 112 ~~Ll~~fteEQ~dRYE~fRRS-~f~K~~IKRLi~~vtgsqsVs~nvvI---avaGlaKvFVGELVEeAr~Vq~E~~e~gP 187 (216)
+.=+..||++|-.|.+-|-.. +|+..-.+-|+++..... .-..++- --..+|..+++||.....+- . -..-|
T Consensus 586 ~~~~~~~~~~~~~r~~Rlv~eyGLs~~dA~~L~~d~~la~-yFE~~v~~~~~pk~aANWl~~El~~~Lne~--~-i~~~~ 661 (771)
T PRK14703 586 RAEAAALNPEQRARFDRYLSELGLNEEDARTLARDPALAA-FFEAALAAGKSPVQLANWVVNDLAGLLRDR--E-LAALP 661 (771)
T ss_pred ccccccCCHhHHHHHHHHHHHcCCCHHHHHHHHcChHHHH-HHHHHHHcCCCHHHHHHHHHHHHHHHHhcC--C-CccCC
Confidence 345678999999999999865 888887766643221100 0001110 01246788888888776653 1 24568
Q ss_pred CCchHHHHHHHHHHhcCCCCCCCC
Q 027954 188 IRPCHIREAYRRLKLEGKVPKRSV 211 (216)
Q Consensus 188 LqP~HIREA~RRL~~~Gkvp~r~~ 211 (216)
|.|.||-+-+ .|...|+|-.+..
T Consensus 662 l~pe~LaeLv-~lV~~g~IS~~~A 684 (771)
T PRK14703 662 FTPAALARLV-ALVDAGRISTRIA 684 (771)
T ss_pred CCHHHHHHHH-HHHHcCCccHHHH
Confidence 9999999987 5556687755443
No 62
>PF11011 DUF2849: Protein of unknown function (DUF2849); InterPro: IPR021270 This bacterial family of proteins has no known function.
Probab=28.35 E-value=37 Score=26.44 Aligned_cols=18 Identities=39% Similarity=0.630 Sum_probs=15.1
Q ss_pred CcCCCCCchHHHHHHHHH
Q 027954 183 NESGPIRPCHIREAYRRL 200 (216)
Q Consensus 183 ~e~gPLqP~HIREA~RRL 200 (216)
...|.++|.|+||.+|..
T Consensus 64 ~~dG~~~P~~~RE~iRa~ 81 (90)
T PF11011_consen 64 GADGRPRPVHLRERIRAR 81 (90)
T ss_pred cCCCCccchhHHHhhhcc
Confidence 457889999999998863
No 63
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=27.80 E-value=34 Score=27.72 Aligned_cols=12 Identities=17% Similarity=0.548 Sum_probs=5.5
Q ss_pred cccccccccccc
Q 027954 84 YDEEDDENVDVE 95 (216)
Q Consensus 84 ~~~e~ed~~~~~ 95 (216)
+++|+||||-+.
T Consensus 98 e~ee~ddDmgf~ 109 (112)
T PTZ00373 98 EEEEEEDDLGFS 109 (112)
T ss_pred cccccccccccc
Confidence 334444555543
No 64
>PRK15398 aldehyde dehydrogenase EutE; Provisional
Probab=27.19 E-value=83 Score=30.35 Aligned_cols=46 Identities=20% Similarity=0.303 Sum_probs=35.5
Q ss_pred hHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Q 027954 137 SNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERN 183 (216)
Q Consensus 137 ~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~ 183 (216)
..||++|.+...||+||++.+.-+-|..+. |-+.|+.|+.-+.+|.
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d-v~~av~~A~~A~~~w~ 53 (465)
T PRK15398 8 QVVKAVLAEMLSSQTVSPPAAVGEMGVFAS-VDDAVAAAKVAQQRYQ 53 (465)
T ss_pred HHHHHHHHHhhcccccccccccccccHHHH-HHHHHHHHHHHHHHHH
Confidence 357888888888899999887777777666 5577888887777773
No 65
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.13 E-value=2.7e+02 Score=22.45 Aligned_cols=53 Identities=17% Similarity=0.333 Sum_probs=34.2
Q ss_pred HhcCCHHHHHHHHHHHhccCChhHHHHHHHHhcCCCCCCccH-HHHHHHHHHHHHHHHHHHHH
Q 027954 115 LNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPM-TIVVCGIAKMFVGELVETAR 176 (216)
Q Consensus 115 l~~fteEQ~dRYE~fRRS~f~K~~IKRLi~~vtgsqsVs~nv-vIavaGlaKvFVGELVEeAr 176 (216)
..+||++|.+|+++ +..|+|+.+.--. +=-+|| .+.++||+.--++.-+.+|-
T Consensus 3 ~~~ls~~q~~~leA--------AaFRrLv~HL~~r-sdvQNIDLMnLAgFCRNCLs~Wy~eaa 56 (104)
T COG3492 3 MQELSEEQRDRLEA--------AAFRRLVEHLQER-SDVQNIDLMNLAGFCRNCLSNWYREAA 56 (104)
T ss_pred hHhcCHHHHHHHHH--------HHHHHHHHHHHHh-cccchhHHHHHHHHHHHHHHHHHHHHH
Confidence 35789999999985 3455666554321 112344 45678988888777766553
No 66
>COG5123 TOA2 Transcription initiation factor IIA, gamma subunit [Transcription]
Probab=25.05 E-value=68 Score=26.20 Aligned_cols=39 Identities=31% Similarity=0.314 Sum_probs=21.9
Q ss_pred HHHHHhccCChhHHHHHHHHhcCCCCCCccHHH-HHHHHHH
Q 027954 126 YESFRRSALQKSNMRRLLVSITGSQKISLPMTI-VVCGIAK 165 (216)
Q Consensus 126 YE~fRRS~f~K~~IKRLi~~vtgsqsVs~nvvI-avaGlaK 165 (216)
||.|||+.+-|.-.+-|=.-|.. ..++++.+. ++-.+-|
T Consensus 5 YElYRrs~ig~~L~dalD~lis~-g~isp~lam~vLetFDk 44 (113)
T COG5123 5 YELYRRSMIGKVLEDALDELISA-GVISPNLAMHVLETFDK 44 (113)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhc-CCcCHHHHHHHHHHhhh
Confidence 99999998776655444222222 256776543 2334444
No 67
>PF11521 TFIIE-A_C-term: C-terminal general transcription factor TFIIE alpha; InterPro: IPR021600 TFIIE is compiled of two subunits, alpha and beta. This family of proteins are the C-terminal domain of the alpha subunit of the protein which is the largest subunit and contains several functional domains which are important for basal transcription and cell growth. The C-terminal end of the protein binds directly to the amino-terminal PH domain of p62/Tfb1 (of IIH) which is involved in the recruitment of the general transcription factor IIH to the transcription preinitiation complex. P53 competes for the same binding site as TFIIE alpha which shows their structural similarity. Like p53, TFIIE alpha 336-439 can activate transcription in vivo []. ; PDB: 2RNR_A 2RNQ_A 2JTX_A.
Probab=24.94 E-value=62 Score=25.10 Aligned_cols=20 Identities=15% Similarity=0.328 Sum_probs=15.1
Q ss_pred HHHHhcCCHHHHHHHHHHHh
Q 027954 112 QAILNQFTEDQMNRYESFRR 131 (216)
Q Consensus 112 ~~Ll~~fteEQ~dRYE~fRR 131 (216)
-.|+..||+++...|-.--+
T Consensus 59 p~LV~qMT~~EKEaYi~v~Q 78 (86)
T PF11521_consen 59 PELVAQMTPEEKEAYIQVGQ 78 (86)
T ss_dssp HHHHHHS-HHHHHHHHHHHH
T ss_pred hHHHHHcCHHHHHHHHHHHH
Confidence 46899999999999965443
No 68
>COG3763 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.47 E-value=3.2e+02 Score=20.81 Aligned_cols=43 Identities=23% Similarity=0.343 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH-HHHHhCcCCCCCchHHHHHHHHH
Q 027954 156 MTIVVCGIAKMFVGELVETARM-VMTERNESGPIRPCHIREAYRRL 200 (216)
Q Consensus 156 vvIavaGlaKvFVGELVEeAr~-Vq~E~~e~gPLqP~HIREA~RRL 200 (216)
+.|+++-++-+|.|-.| |++ ++++..+..||-++-||.-+-.+
T Consensus 8 l~ivl~ll~G~~~G~fi--ark~~~k~lk~NPpine~~iR~M~~qm 51 (71)
T COG3763 8 LLIVLALLAGLIGGFFI--ARKQMKKQLKDNPPINEEMIRMMMAQM 51 (71)
T ss_pred HHHHHHHHHHHHHHHHH--HHHHHHHHHhhCCCCCHHHHHHHHHHh
Confidence 56777888888888766 444 45567899999998888766544
No 69
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=23.96 E-value=2.3e+02 Score=22.75 Aligned_cols=47 Identities=23% Similarity=0.334 Sum_probs=34.7
Q ss_pred ccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHH
Q 027954 132 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVM 179 (216)
Q Consensus 132 S~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq 179 (216)
+.++|..||||... .|--.|+--+---..++.|+|+-..+.-|..--
T Consensus 28 qgitKpaIRRlARr-~GVkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt 74 (103)
T KOG3467|consen 28 QGITKPAIRRLARR-GGVKRISGLIYEETRGVLKVFLENVIRDAVTYT 74 (103)
T ss_pred cccchHHHHHHHHh-cCcchhchhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 36779999998654 343355555666678999999999999887653
No 70
>KOG3540 consensus Beta amyloid precursor protein [General function prediction only]
Probab=23.86 E-value=8.1e+02 Score=25.24 Aligned_cols=20 Identities=25% Similarity=0.468 Sum_probs=17.2
Q ss_pred cCCCCCchHHHHHHHHHHhc
Q 027954 184 ESGPIRPCHIREAYRRLKLE 203 (216)
Q Consensus 184 e~gPLqP~HIREA~RRL~~~ 203 (216)
-..|=+|+|+-.|+|||.+-
T Consensus 340 qa~pprp~~Vl~aLkrYvRA 359 (615)
T KOG3540|consen 340 QADPPRPHRVLQALKRYVRA 359 (615)
T ss_pred hcCCCChHHHHHHHHHHHHH
Confidence 46899999999999999753
No 71
>COG3937 Uncharacterized conserved protein [Function unknown]
Probab=23.73 E-value=1e+02 Score=25.10 Aligned_cols=36 Identities=33% Similarity=0.402 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHHH
Q 027954 163 IAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK 201 (216)
Q Consensus 163 laKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~ 201 (216)
=+|-||-+|+..++.-+.+|.+. .|..|++....|-
T Consensus 43 Eak~~vddl~~q~k~~~~e~e~K---~~r~i~~ml~~~~ 78 (108)
T COG3937 43 EAKRFVDDLLRQAKEAQGELEEK---IPRKIEEMLSDLE 78 (108)
T ss_pred HHHHHHHHHHHHHHHHhhhHHHh---hhHHHHHHHhhcc
Confidence 46889999999999777777555 7788887776654
No 72
>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=23.20 E-value=3.9e+02 Score=21.32 Aligned_cols=63 Identities=11% Similarity=0.119 Sum_probs=49.4
Q ss_pred HHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHHHh
Q 027954 138 NMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKL 202 (216)
Q Consensus 138 ~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~~ 202 (216)
.|++|+.+. |-..+++.++..+.=++.-++.+|...|......- .+.-|....|+-|......
T Consensus 6 ~v~~iLk~~-Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA-~r~tV~~eDV~lAi~~r~~ 68 (117)
T cd07979 6 VIAAILKSM-GITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHA-GKANIDADDVKLAIQSRVD 68 (117)
T ss_pred HHHHHHHHC-CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHc-CCCCCCHHHHHHHHHHHhc
Confidence 477777664 55578999999999999999999999999886543 4567788888888766543
No 73
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=23.19 E-value=86 Score=32.36 Aligned_cols=22 Identities=32% Similarity=0.558 Sum_probs=11.2
Q ss_pred CCcccccccccccccccCCCCC
Q 027954 81 KDEYDEEDDENVDVELGKFPSS 102 (216)
Q Consensus 81 ~~e~~~e~ed~~~~~l~~~~~~ 102 (216)
+.|+++++||+-||+.....+.
T Consensus 426 dgdde~eddddidvdeediess 447 (990)
T KOG1819|consen 426 DGDDEAEDDDDIDVDEEDIESS 447 (990)
T ss_pred cCcccccCcccccccccccccc
Confidence 3344455555556655554443
No 74
>PF15510 CENP-W: Centromere kinetochore component W
Probab=23.10 E-value=3.4e+02 Score=21.88 Aligned_cols=36 Identities=33% Similarity=0.444 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHHHh
Q 027954 166 MFVGELVETARMVMTERNESGPIRPCHIREAYRRLKL 202 (216)
Q Consensus 166 vFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~~ 202 (216)
+||-.|-|+|+.=.-| +..+-|.++|+..|...+..
T Consensus 63 LFvhrLAEEaRtnA~E-nK~~~Ik~~Hv~AaaKviLK 98 (102)
T PF15510_consen 63 LFVHRLAEEARTNACE-NKCGTIKKEHVLAAAKVILK 98 (102)
T ss_pred HHHHHHHHHHHHHHHH-HhhccccHHHHHHHHHHHHH
Confidence 7999999999865433 35889999999998876653
No 75
>KOG3871 consensus Cell adhesion complex protein bystin [Extracellular structures]
Probab=22.95 E-value=4.4e+02 Score=26.14 Aligned_cols=49 Identities=24% Similarity=0.324 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhC------cCCCCCchHHHHHHHHHH------hcCCCCCC
Q 027954 161 CGIAKMFVGELVETARMVMTERN------ESGPIRPCHIREAYRRLK------LEGKVPKR 209 (216)
Q Consensus 161 aGlaKvFVGELVEeAr~Vq~E~~------e~gPLqP~HIREA~RRL~------~~Gkvp~r 209 (216)
..|++++..-|-|+--+|..+.- -..|=.|-.+-|.|.... ..||+|.-
T Consensus 145 ~tL~diIm~ki~ekead~~~~~~~~~~~e~~~~~ldpkV~e~Y~~Vg~~lskyrsGKlPKa 205 (449)
T KOG3871|consen 145 YTLADIIMAKIREKEADVETEQSDPDENEFPMPALDPKVIEMYEGVGSVLSKYRSGKLPKA 205 (449)
T ss_pred ccHHHHHHHHHHHHHhhHHhhhcccccccCCCCCCCHHHHHHHHHHHHHHHHhhcCCCchh
Confidence 56777777777775555544321 133444555667776542 45888754
No 76
>PF02978 SRP_SPB: Signal peptide binding domain; InterPro: IPR004125 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the M domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle; PDB: 2FFH_B 3NDB_B 2V3C_C 1QZW_G 1QZX_B 3KL4_A 2JQE_A 1HQ1_A 1RY1_W 1MFQ_C ....
Probab=22.04 E-value=1.2e+02 Score=23.69 Aligned_cols=35 Identities=23% Similarity=0.404 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHhccCChhHHHHHHH
Q 027954 105 PAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLV 144 (216)
Q Consensus 105 ~e~~~km~~Ll~~fteEQ~dRYE~fRRS~f~K~~IKRLi~ 144 (216)
+.+..++..++++||+++++--..+.. +-++||..
T Consensus 47 ~~~lk~~~~Ii~SMT~~Er~~p~ll~~-----sR~~RIA~ 81 (104)
T PF02978_consen 47 EKKLKRMEAIIDSMTPEERDNPKLLNE-----SRRRRIAR 81 (104)
T ss_dssp HHHHHHHHHHHTTSBHHHHHCGGGHHH-----HHHHHHHH
T ss_pred HHHHHHHHHHHHCcCHHHHhCccccch-----HHHHHHHH
Confidence 344578999999999999977776643 55777643
No 77
>PF02268 TFIIA_gamma_N: Transcription initiation factor IIA, gamma subunit, helical domain; InterPro: IPR015872 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the alpha-helical domain found at the N-terminal of the gamma subunit of transcription factor TFIIA.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_D 1RM1_B 1YTF_D 1NH2_D.
Probab=22.01 E-value=26 Score=24.67 Aligned_cols=34 Identities=26% Similarity=0.342 Sum_probs=19.3
Q ss_pred HHHHHHhccCChhHHHHHHHHhcCCCCCCccHHHH
Q 027954 125 RYESFRRSALQKSNMRRLLVSITGSQKISLPMTIV 159 (216)
Q Consensus 125 RYE~fRRS~f~K~~IKRLi~~vtgsqsVs~nvvIa 159 (216)
-|+.||+|++-.+=..-| .....++.+++.++.-
T Consensus 2 ~yelYR~stlG~aL~dtL-Deli~~~~I~p~La~k 35 (49)
T PF02268_consen 2 YYELYRRSTLGIALTDTL-DELIQEGKITPQLAMK 35 (49)
T ss_dssp --CGGGCSHHHHHHHHHH-HHHHHTTSS-HHHHHH
T ss_pred cHHHHHcchHHHHHHHHH-HHHHHcCCCCHHHHHH
Confidence 489999998766544444 3333345788876543
No 78
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=20.94 E-value=4e+02 Score=22.31 Aligned_cols=78 Identities=19% Similarity=0.215 Sum_probs=45.1
Q ss_pred HHHhccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHHHhcCCCC
Q 027954 128 SFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKLEGKVP 207 (216)
Q Consensus 128 ~fRRS~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~~~Gkvp 207 (216)
.+|..+|..- |.|++.+|-.+..++..-..||.+|--.++-.|.-+|=....-.+.. -|--+||+-|+|-| +.|+++
T Consensus 33 ~~~~e~~s~y-v~kvlk~Vhpd~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krs-tisSreiqta~rLl-lPgel~ 109 (127)
T KOG1744|consen 33 TRRKESYSEY-VYKVLKQVHPDLGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRS-TISSREIQTAVRLL-LPGELA 109 (127)
T ss_pred ccccCceeee-hhhhhhcccCCCCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCC-cccHHHHHHHHHHh-CchHHh
Confidence 4445555443 44466665544456666666666655555555555555554434333 48899999977655 447655
Q ss_pred C
Q 027954 208 K 208 (216)
Q Consensus 208 ~ 208 (216)
.
T Consensus 110 k 110 (127)
T KOG1744|consen 110 K 110 (127)
T ss_pred h
Confidence 3
No 79
>PF03115 Astro_capsid: Astrovirus capsid protein precursor; InterPro: IPR004337 The astrovirus genome is apparently organised with nonstructural proteins encoded at the 5' end and structural proteins at the 3' end []. Proteins in this family are encoded by astrovirus ORF2, one of the three astrovirus ORFs (1a, 1b, 2). The proteins contain a viral RNA-dependent RNA polymerase motif []. The 87kDa precursor polyprotein undergoes an intracellular cleavage to form a 79kDa protein. Subsequently, extracellular trypsin cleavage yields the three proteins forming the infectious virion [].; PDB: 3QSQ_A 3TS3_D.
Probab=20.74 E-value=33 Score=36.02 Aligned_cols=15 Identities=13% Similarity=0.441 Sum_probs=0.0
Q ss_pred HHHHH-hcCCHHHHHH
Q 027954 111 MQAIL-NQFTEDQMNR 125 (216)
Q Consensus 111 m~~Ll-~~fteEQ~dR 125 (216)
|..|| ..+++||-.|
T Consensus 714 ~nTLVNqGi~eerAar 729 (787)
T PF03115_consen 714 FNTLVNQGIPEERAAR 729 (787)
T ss_dssp ----------------
T ss_pred HHHHHHcCCCHHHHHh
Confidence 34455 6777777776
No 80
>KOG3449 consensus 60S acidic ribosomal protein P2 [Translation, ribosomal structure and biogenesis]
Probab=20.60 E-value=54 Score=26.88 Aligned_cols=9 Identities=33% Similarity=0.708 Sum_probs=4.6
Q ss_pred ccccccccc
Q 027954 86 EEDDENVDV 94 (216)
Q Consensus 86 ~e~ed~~~~ 94 (216)
||.||||.+
T Consensus 100 eesddDmgf 108 (112)
T KOG3449|consen 100 EESDDDMGF 108 (112)
T ss_pred ccccccccc
Confidence 444555554
Done!