Query 030236
Match_columns 181
No_of_seqs 110 out of 159
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 10:39:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030236.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030236hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04719 TAFII28: hTAFII28-lik 100.0 6.3E-35 1.4E-39 218.9 7.2 75 105-179 1-75 (90)
2 KOG3219 Transcription initiati 100.0 2.8E-31 6.1E-36 222.5 11.2 82 97-179 82-163 (195)
3 cd08048 TAF11 TATA Binding Pro 100.0 2.5E-28 5.4E-33 180.9 8.1 66 112-178 1-66 (85)
4 COG5251 TAF40 Transcription in 99.9 2.3E-27 5.1E-32 197.7 7.9 77 103-180 91-167 (199)
5 PF00808 CBFD_NFYB_HMF: Histon 96.0 0.019 4.1E-07 39.4 5.2 49 126-174 1-49 (65)
6 smart00803 TAF TATA box bindin 94.0 0.18 4E-06 35.7 5.6 48 126-174 1-48 (65)
7 smart00417 H4 Histone H4. 84.2 2.9 6.4E-05 30.7 5.1 46 127-173 13-58 (74)
8 KOG3902 Histone acetyltransfer 84.2 3.8 8.3E-05 37.9 6.9 75 98-173 191-272 (352)
9 cd00076 H4 Histone H4, one of 82.6 3.6 7.8E-05 30.9 5.1 47 126-173 12-58 (85)
10 COG2036 HHT1 Histones H3 and H 80.0 4.6 0.0001 30.8 5.0 58 115-173 7-64 (91)
11 cd07981 TAF12 TATA Binding Pro 79.7 6.6 0.00014 27.9 5.4 47 128-174 2-48 (72)
12 PF02969 TAF: TATA box binding 79.2 5.6 0.00012 28.6 5.0 48 126-174 2-49 (66)
13 PTZ00015 histone H4; Provision 78.1 6.2 0.00013 30.7 5.2 47 126-173 29-75 (102)
14 PF00125 Histone: Core histone 75.7 8.3 0.00018 26.5 4.9 49 126-174 4-56 (75)
15 PLN00035 histone H4; Provision 72.9 10 0.00022 29.7 5.2 45 128-173 30-74 (103)
16 cd00074 H2A Histone 2A; H2A is 69.8 12 0.00027 29.4 5.2 47 127-173 20-66 (115)
17 PF13443 HTH_26: Cro/C1-type H 66.5 2.1 4.5E-05 28.2 0.2 52 113-166 7-58 (63)
18 PF07526 POX: Associated with 59.2 65 0.0014 26.0 7.6 40 116-161 89-131 (140)
19 PF09415 CENP-X: CENP-S associ 58.1 22 0.00049 25.8 4.3 45 129-173 1-47 (72)
20 smart00414 H2A Histone 2A. 57.2 28 0.0006 27.0 5.0 47 127-173 9-55 (106)
21 COG5247 BUR6 Class 2 transcrip 55.2 33 0.00071 27.5 5.1 48 123-172 19-68 (113)
22 PF03847 TFIID_20kDa: Transcri 49.3 41 0.00089 24.1 4.5 46 130-175 2-47 (68)
23 COG5262 HTA1 Histone H2A [Chro 49.0 32 0.0007 28.1 4.3 48 126-173 25-72 (132)
24 smart00574 POX domain associat 48.6 93 0.002 25.8 6.9 42 115-162 88-132 (140)
25 PF06309 Torsin: Torsin; Inte 38.5 29 0.00063 27.9 2.5 32 139-170 43-77 (127)
26 PF03540 TFIID_30kDa: Transcri 38.1 1.4E+02 0.003 20.8 5.8 47 127-174 2-48 (51)
27 PF12174 RST: RCD1-SRO-TAF4 (R 37.9 68 0.0015 23.2 4.1 40 105-144 15-58 (70)
28 KOG1819 FYVE finger-containing 36.2 36 0.00078 34.3 3.2 25 74-98 425-449 (990)
29 PF02268 TFIIA_gamma_N: Transc 35.5 10 0.00022 26.1 -0.4 34 119-153 2-35 (49)
30 PF08971 GlgS: Glycogen synthe 35.4 28 0.0006 25.6 1.8 21 105-125 30-54 (66)
31 KOG1659 Class 2 transcription 34.6 80 0.0017 28.0 4.8 50 125-174 11-60 (224)
32 cd04411 Ribosomal_P1_P2_L12p R 34.6 18 0.00039 28.0 0.8 13 77-89 91-103 (105)
33 COG5123 TOA2 Transcription ini 34.3 35 0.00075 27.3 2.3 33 119-152 4-36 (113)
34 PTZ00017 histone H2A; Provisio 33.9 86 0.0019 25.6 4.6 46 128-173 28-73 (134)
35 KOG3463 Transcription initiati 31.4 42 0.00091 26.8 2.4 33 119-152 3-35 (109)
36 PF03115 Astro_capsid: Astrovi 27.3 21 0.00045 36.5 0.0 15 106-120 715-730 (787)
37 PLN00154 histone H2A; Provisio 26.9 1.4E+02 0.003 24.6 4.7 45 128-172 39-84 (136)
38 PTZ00373 60S Acidic ribosomal 26.2 39 0.00084 26.7 1.4 14 77-90 97-110 (112)
39 KOG0870 DNA polymerase epsilon 25.5 1.7E+02 0.0037 25.1 5.1 49 127-175 10-60 (172)
40 KOG3467 Histone H4 [Chromatin 24.7 1.8E+02 0.004 22.8 4.8 45 126-171 28-72 (103)
41 PLN00157 histone H2A; Provisio 24.7 1.5E+02 0.0034 24.2 4.6 46 128-173 27-72 (132)
42 COG3492 Uncharacterized protei 24.6 3.2E+02 0.0069 21.6 6.1 53 109-170 3-56 (104)
43 PRK02922 glycogen synthesis pr 24.6 92 0.002 23.0 2.9 24 105-128 31-58 (67)
44 COG5208 HAP5 CCAAT-binding fac 23.7 1.9E+02 0.0041 26.2 5.3 50 121-170 103-152 (286)
45 PRK13291 metal-dependent hydro 22.7 80 0.0017 25.5 2.6 39 103-143 118-156 (173)
46 cd08320 Pyrin_NALPs Pyrin deat 22.1 3.3E+02 0.0071 20.1 6.5 65 105-172 3-83 (86)
47 PF07462 MSP1_C: Merozoite sur 22.1 1E+02 0.0022 30.7 3.6 12 146-157 464-475 (574)
48 TIGR03693 ocin_ThiF_like putat 21.8 48 0.001 33.3 1.3 23 106-128 110-132 (637)
49 PLN00156 histone H2AX; Provisi 20.6 2.1E+02 0.0046 23.6 4.7 46 128-173 30-75 (139)
50 KOG4054 Uncharacterized conser 20.0 63 0.0014 27.8 1.6 37 122-167 26-62 (183)
No 1
>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=6.3e-35 Score=218.90 Aligned_cols=75 Identities=41% Similarity=0.658 Sum_probs=55.4
Q ss_pred HHHHHhcCCHHHHHHHHHHHhcCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHHHHhhhh
Q 030236 105 MQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNVTQILF 179 (181)
Q Consensus 105 m~~Ll~~fdeEQldRYE~fRRS~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~ewl~~ 179 (181)
|++|+++||+||++|||+||||+|+|++|||||++++|+|+||+|++|+|+||||||||||||+|++||.+|...
T Consensus 1 ~~~L~~~f~~eQ~~Rye~fRRs~~~k~~ikkli~~~~~~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~ 75 (90)
T PF04719_consen 1 MQLLLSNFDEEQLDRYEAFRRSSFNKAAIKKLINQVLGNQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGET 75 (90)
T ss_dssp ---------HHHHHHHHHHHH----HHHHHHHHHHHHS-S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--
T ss_pred ChHHHHcCCHHHHHHHHHHHHccCCHHHHHHHHHHHcCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 789999999999999999999999999999999999988999999999999999999999999999999999754
No 2
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=99.97 E-value=2.8e-31 Score=222.52 Aligned_cols=82 Identities=41% Similarity=0.658 Sum_probs=76.8
Q ss_pred CcHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHHHHh
Q 030236 97 SDPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNVTQ 176 (181)
Q Consensus 97 ~d~~~~~km~~Ll~~fdeEQldRYE~fRRS~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~ew 176 (181)
.++++..||+.||++||+|||+|||+||||+|||+.|||||+++||. +|++|++|||+||||||||||||+|++||.+|
T Consensus 82 ~~~ee~~r~q~L~s~fseEQl~RYEvfRrs~f~Ka~iKkL~~~itg~-~v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~ 160 (195)
T KOG3219|consen 82 VDAEEAQRMQTLLSNFSEEQLSRYEVFRRSAFPKAQIKKLMSSITGQ-SVSENVAIAMAGIAKVFVGEVVEEALDVREEW 160 (195)
T ss_pred cCHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhCC-ccCcceeeeecchhhHhHHHHHHHHHHHHHHh
Confidence 35666779999999999999999999999999999999999999986 59999999999999999999999999999999
Q ss_pred hhh
Q 030236 177 ILF 179 (181)
Q Consensus 177 l~~ 179 (181)
...
T Consensus 161 ~e~ 163 (195)
T KOG3219|consen 161 GES 163 (195)
T ss_pred ccC
Confidence 653
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=99.95 E-value=2.5e-28 Score=180.95 Aligned_cols=66 Identities=50% Similarity=0.732 Sum_probs=64.1
Q ss_pred CCHHHHHHHHHHHhcCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHHHHhhh
Q 030236 112 FTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNVTQIL 178 (181)
Q Consensus 112 fdeEQldRYE~fRRS~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~ewl~ 178 (181)
||+||++|||.|||++|+|+.|||||++++| |+||+|++|+|+||||+|||||||+|++||.+|..
T Consensus 1 f~~eQ~~Rye~~Rra~f~k~~iKr~~~~~~~-~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~ 66 (85)
T cd08048 1 FSEEQMNRYEMFRRSSFPKAAIKRLIQSVTG-QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGE 66 (85)
T ss_pred CCHHHHHHHHHHHHhhccHHHHHHHHHHHcC-CCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 8999999999999999999999999999987 79999999999999999999999999999999976
No 4
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=99.94 E-value=2.3e-27 Score=197.67 Aligned_cols=77 Identities=30% Similarity=0.594 Sum_probs=73.2
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHhcCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHHHHhhhhc
Q 030236 103 AKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNVTQILFA 180 (181)
Q Consensus 103 ~km~~Ll~~fdeEQldRYE~fRRS~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~ewl~~~ 180 (181)
.++.+|+.+||+||++|||.|||++|||+.||||+++|.+ |+|++|++|+|+||+|||||||||.|+.||.+|+..+
T Consensus 91 ~r~k~l~~~~deeq~~RyEvFrrt~lnKt~VKKlastV~n-QtVspNi~I~l~g~~KVfvGEiIElA~~Vq~~w~~sg 167 (199)
T COG5251 91 ERFKLLVTNLDEEQTNRYEVFRRTSLNKTQVKKLASTVAN-QTVSPNIRIFLQGVGKVFVGEIIELAMIVQNKWLTSG 167 (199)
T ss_pred HHHHHHHhhcCHHHHHHHHHHHhcCCCHHHHHHHHHHHhc-cccCCCeeeeeechhHHHHHHHHHHHHHHHHHhcccC
Confidence 6888899999999999999999999999999999988875 8999999999999999999999999999999998754
No 5
>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=96.01 E-value=0.019 Score=39.42 Aligned_cols=49 Identities=14% Similarity=0.189 Sum_probs=40.3
Q ss_pred cCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHHH
Q 030236 126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNV 174 (181)
Q Consensus 126 S~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~ 174 (181)
..||.+.|||||...-+...|+.....+|+=.+-+||.+|...|.++..
T Consensus 1 ~~lP~a~vkri~k~~~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~ 49 (65)
T PF00808_consen 1 ASLPLARVKRIMKSDPDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQ 49 (65)
T ss_dssp -SS-HHHHHHHHHHTSTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCChHHHHHHhccCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3699999999999885555689999999999999999999999987754
No 6
>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=94.03 E-value=0.18 Score=35.67 Aligned_cols=48 Identities=17% Similarity=0.170 Sum_probs=42.4
Q ss_pred cCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHHH
Q 030236 126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNV 174 (181)
Q Consensus 126 S~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~ 174 (181)
+.||++.||+|+.+. |-..++..+.-.++...+.|+-+|+..|..++.
T Consensus 1 ~~~p~~~i~ria~~~-Gi~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~ 48 (65)
T smart00803 1 SWLPKETIKDVAESL-GIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMR 48 (65)
T ss_pred CCCCHHHHHHHHHHC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 358999999998775 656799999999999999999999999998875
No 7
>smart00417 H4 Histone H4.
Probab=84.23 E-value=2.9 Score=30.74 Aligned_cols=46 Identities=22% Similarity=0.253 Sum_probs=39.8
Q ss_pred CCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHH
Q 030236 127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVN 173 (181)
Q Consensus 127 ~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq 173 (181)
.++|+.|+||+... |-.-||..+.-.+.++.|.|+-+|+..|....
T Consensus 13 gI~k~~IrRLaRr~-GvkRIS~~~y~elr~vle~~l~~I~rdav~~a 58 (74)
T smart00417 13 GITKPAIRRLARRG-GVKRISGLIYDETRNVLKSFLENVVRDAVTYT 58 (74)
T ss_pred CCCHHHHHHHHHHc-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 69999999998764 65678989999999999999999999987654
No 8
>KOG3902 consensus Histone acetyltransferase PCAF/SAGA, subunit SUPT3H/SPT3 [Transcription]
Probab=84.20 E-value=3.8 Score=37.94 Aligned_cols=75 Identities=15% Similarity=0.168 Sum_probs=53.1
Q ss_pred cHHHHHHHHH---HHhcCCHHHHHHHHHHHhcCCChHHHHHHHHHhhcC-c---cCCccHHHHhhhhhHHHHHHHHHHHH
Q 030236 98 DPAKMAKMQA---ILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGS-Q---KISLPMTIVVCGIAKMFVGELVETGF 170 (181)
Q Consensus 98 d~~~~~km~~---Ll~~fdeEQldRYE~fRRS~f~K~~IKKLi~svtgs-Q---sVs~nv~IavaGiAKvFVGEIVE~Ar 170 (181)
|+..+++|.. .-..||.+|+--|--.|..+|.+..=||. ...++- + .++..+.=+++=++==-|.-||+.|+
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 4445555543 45789999999999999999988877764 333332 1 23434444567788888999999998
Q ss_pred HHH
Q 030236 171 CVN 173 (181)
Q Consensus 171 ~Vq 173 (181)
-|.
T Consensus 270 lvr 272 (352)
T KOG3902|consen 270 LVR 272 (352)
T ss_pred HHH
Confidence 874
No 9
>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=82.58 E-value=3.6 Score=30.91 Aligned_cols=47 Identities=19% Similarity=0.268 Sum_probs=39.8
Q ss_pred cCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHH
Q 030236 126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVN 173 (181)
Q Consensus 126 S~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq 173 (181)
..|+|+.|+||+... |--.||..+.-.+..+.+.|+-+|+..|....
T Consensus 12 ~gi~k~~I~RLarr~-GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya 58 (85)
T cd00076 12 KGITKPAIRRLARRG-GVKRISGGVYDEVRNVLKSYLEDVIRDAVTYT 58 (85)
T ss_pred ccCCHHHHHHHHHHc-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 359999999998774 55568888889999999999999999887654
No 10
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=79.97 E-value=4.6 Score=30.83 Aligned_cols=58 Identities=17% Similarity=0.277 Sum_probs=47.2
Q ss_pred HHHHHHHHHHhcCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHH
Q 030236 115 DQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVN 173 (181)
Q Consensus 115 EQldRYE~fRRS~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq 173 (181)
-+..||..+-.-.||++.|+||+.+.. ...|+....-.+.-...-|+=+|.+.|-...
T Consensus 7 ~~~r~~~~~~~~~Lp~apv~Ri~r~~~-~~Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A 64 (91)
T COG2036 7 KEIRRYQRSTDLLLPKAPVRRILRKAG-AERVSSSAIEELQEALEEYLEEIAEDAVELA 64 (91)
T ss_pred HHHHhhhhhhhhhcCchHHHHHHHHHh-HHHhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467889999999999999999998874 3467777777888888888888888876654
No 11
>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=79.67 E-value=6.6 Score=27.93 Aligned_cols=47 Identities=23% Similarity=0.342 Sum_probs=42.5
Q ss_pred CChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHHH
Q 030236 128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNV 174 (181)
Q Consensus 128 f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~ 174 (181)
++|..+..|+..+.++..+++.+.-++.-++=-||-.|++.|..+.+
T Consensus 2 ~~k~~l~~lv~~id~~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAk 48 (72)
T cd07981 2 LTKRKLQELLKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAK 48 (72)
T ss_pred CcHHHHHHHHHhhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 67889999999998887899999999999999999999999987764
No 12
>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=79.25 E-value=5.6 Score=28.60 Aligned_cols=48 Identities=10% Similarity=0.134 Sum_probs=35.8
Q ss_pred cCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHHH
Q 030236 126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNV 174 (181)
Q Consensus 126 S~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~ 174 (181)
|-|++..||-+..+ +|-.++++.++..++-=.-.-+.+||+.|..+|.
T Consensus 2 s~~~~esvk~iAes-~Gi~~l~de~a~~La~dveyrlreiiq~a~kfm~ 49 (66)
T PF02969_consen 2 SVFSQESVKDIAES-LGISNLSDEAAKALAEDVEYRLREIIQEALKFMR 49 (66)
T ss_dssp ----HHHHHHHHHH-TT---B-HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CcCCHHHHHHHHHH-cCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45889999987655 5666799999999999999999999999999885
No 13
>PTZ00015 histone H4; Provisional
Probab=78.11 E-value=6.2 Score=30.75 Aligned_cols=47 Identities=26% Similarity=0.328 Sum_probs=40.6
Q ss_pred cCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHH
Q 030236 126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVN 173 (181)
Q Consensus 126 S~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq 173 (181)
..++|+.|+||+... |-..||..+.-.+..+.+.|+-+|+..|..+.
T Consensus 29 ~gI~k~~IrRLarr~-GvkRIS~d~y~e~r~vle~~l~~I~rdav~~a 75 (102)
T PTZ00015 29 RGITKGAIRRLARRG-GVKRISGDIYEEVRGVLKAFLENVVRDSTAYT 75 (102)
T ss_pred cCCCHHHHHHHHHHc-CCccchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 579999999998764 65679999999999999999999999887654
No 14
>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=75.67 E-value=8.3 Score=26.51 Aligned_cols=49 Identities=18% Similarity=0.199 Sum_probs=40.1
Q ss_pred cCCChHHHHHHHHHhhcC----ccCCccHHHHhhhhhHHHHHHHHHHHHHHHH
Q 030236 126 SALQKSNMRRLLVSITGS----QKISLPMTIVVCGIAKMFVGELVETGFCVNV 174 (181)
Q Consensus 126 S~f~K~~IKKLi~svtgs----QsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~ 174 (181)
...+|..|+||+..+... ..++.....+|..+...|+.+|.+.|..+..
T Consensus 4 ~~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~ 56 (75)
T PF00125_consen 4 RLIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLAR 56 (75)
T ss_dssp HSSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHh
Confidence 346788888888777653 4688889999999999999999999987653
No 15
>PLN00035 histone H4; Provisional
Probab=72.88 E-value=10 Score=29.70 Aligned_cols=45 Identities=22% Similarity=0.335 Sum_probs=39.3
Q ss_pred CChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHH
Q 030236 128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVN 173 (181)
Q Consensus 128 f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq 173 (181)
||++.|+||+.+. |--.||..+.-.+..+.+.|+-+|+..|..+.
T Consensus 30 ipk~~IrRLARr~-GvkRIS~~ay~elr~vle~~l~~I~~dav~ya 74 (103)
T PLN00035 30 ITKPAIRRLARRG-GVKRISGLIYEETRGVLKIFLENVIRDAVTYT 74 (103)
T ss_pred CCHHHHHHHHHHc-CcccchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999998774 55578999999999999999999999887664
No 16
>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=69.82 E-value=12 Score=29.38 Aligned_cols=47 Identities=9% Similarity=0.149 Sum_probs=40.9
Q ss_pred CCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHH
Q 030236 127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVN 173 (181)
Q Consensus 127 ~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq 173 (181)
.||-+.|.|+|..-.+...|+....+.++++--.++.||.|.|-...
T Consensus 20 ~fPV~ri~R~Lk~~~~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~a 66 (115)
T cd00074 20 QFPVGRIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELAGNAA 66 (115)
T ss_pred cCcHHHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHH
Confidence 38999999999875666789999999999999999999999987654
No 17
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=66.55 E-value=2.1 Score=28.23 Aligned_cols=52 Identities=17% Similarity=0.207 Sum_probs=28.3
Q ss_pred CHHHHHHHHHHHhcCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHH
Q 030236 113 TEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELV 166 (181)
Q Consensus 113 deEQldRYE~fRRS~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIV 166 (181)
.+-.+.+++..|+++++++.|.++++.-. .+++...+..+|-+-.+=++||+
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 44567888999999999999999986421 23444455555554444455554
No 18
>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=59.24 E-value=65 Score=26.03 Aligned_cols=40 Identities=15% Similarity=0.327 Sum_probs=27.4
Q ss_pred HHHHHHHHHhcCCChHHHHHHHHH---hhcCccCCccHHHHhhhhhHHH
Q 030236 116 QMNRYESFRRSALQKSNMRRLLVS---ITGSQKISLPMTIVVCGIAKMF 161 (181)
Q Consensus 116 QldRYE~fRRS~f~K~~IKKLi~s---vtgsQsVs~nv~IavaGiAKvF 161 (181)
=-.||..|+. .|.-++.+ ++|.-.-..-.++|+..|+|.|
T Consensus 89 Vd~RY~qY~~------Qmq~VvssFe~vaG~gaA~~YtalAlqamSrhF 131 (140)
T PF07526_consen 89 VDRRYRQYYD------QMQAVVSSFEAVAGLGAAAPYTALALQAMSRHF 131 (140)
T ss_pred HHHHHHHHHH------HHHHHHHHHHHHhcCCcchhhHHHHHHHHHHHH
Confidence 3469999974 56666654 4453333445788999999998
No 19
>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=58.14 E-value=22 Score=25.76 Aligned_cols=45 Identities=22% Similarity=0.142 Sum_probs=32.9
Q ss_pred ChHHHHHHHHHhhcC--ccCCccHHHHhhhhhHHHHHHHHHHHHHHH
Q 030236 129 QKSNMRRLLVSITGS--QKISLPMTIVVCGIAKMFVGELVETGFCVN 173 (181)
Q Consensus 129 ~K~~IKKLi~svtgs--QsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq 173 (181)
|+..|.||+.....+ .+++....-+++-+-++||-|-|-+|....
T Consensus 1 p~~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a 47 (72)
T PF09415_consen 1 PPELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQA 47 (72)
T ss_dssp -CHHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ChHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 567788888754332 246777888899999999999998887644
No 20
>smart00414 H2A Histone 2A.
Probab=57.20 E-value=28 Score=27.04 Aligned_cols=47 Identities=13% Similarity=0.193 Sum_probs=40.0
Q ss_pred CCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHH
Q 030236 127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVN 173 (181)
Q Consensus 127 ~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq 173 (181)
.||=+.|.|++..-.....|+....+-++++--.++.||.|.|-...
T Consensus 9 ~fPVgRi~r~Lk~~~~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a 55 (106)
T smart00414 9 QFPVGRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAA 55 (106)
T ss_pred cCchHHHHHHHHcCccccccccccHHHHHHHHHHHHHHHHHHHHHHH
Confidence 37888899999886666788999999999999999999999886543
No 21
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=55.24 E-value=33 Score=27.48 Aligned_cols=48 Identities=13% Similarity=0.303 Sum_probs=30.6
Q ss_pred HHhcCCChHHHHHHHHHh--hcCccCCccHHHHhhhhhHHHHHHHHHHHHHH
Q 030236 123 FRRSALQKSNMRRLLVSI--TGSQKISLPMTIVVCGIAKMFVGELVETGFCV 172 (181)
Q Consensus 123 fRRS~f~K~~IKKLi~sv--tgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~V 172 (181)
|-.++||-+.||||||-- +| +|++..-++++----+|+-+||-+.+..
T Consensus 19 ~~ktrFP~ar~KkIMQ~deDiG--KV~q~tPVIaskalE~Fl~~iv~~s~k~ 68 (113)
T COG5247 19 KKKTRFPIARLKKIMQLDEDIG--KVGQSTPVIASKALEMFLTEIVGLSLKE 68 (113)
T ss_pred hhhhcCCHHHHHHHHHhhhhhh--hhhhcchHHHHHHHHHHHHHHHHHHHHH
Confidence 678899999999999742 23 3444332232333358888888665543
No 22
>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=49.33 E-value=41 Score=24.09 Aligned_cols=46 Identities=17% Similarity=0.273 Sum_probs=35.6
Q ss_pred hHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHHHH
Q 030236 130 KSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNVT 175 (181)
Q Consensus 130 K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~e 175 (181)
|..+..||.++-++..+.+.+--++.-||=-||-.+++.|..+.+-
T Consensus 2 K~~l~~Lv~~iDp~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKh 47 (68)
T PF03847_consen 2 KRKLQELVKQIDPNEKLDPDVEELLLELADDFVDDVVSFACRLAKH 47 (68)
T ss_dssp HHHHHHHHHCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 6778889988877777888888899999999999999999887654
No 23
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=48.96 E-value=32 Score=28.14 Aligned_cols=48 Identities=13% Similarity=0.154 Sum_probs=41.5
Q ss_pred cCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHH
Q 030236 126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVN 173 (181)
Q Consensus 126 S~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq 173 (181)
+-||=..||||+..-...+.|+....+.++++--.++-||.|.|-.+.
T Consensus 25 l~fpvgrvkr~lk~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA 72 (132)
T COG5262 25 LIFPVGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAA 72 (132)
T ss_pred ccccHHHHHHHHHcCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhh
Confidence 568889999999866677788888899999999999999999887664
No 24
>smart00574 POX domain associated with HOX domains.
Probab=48.57 E-value=93 Score=25.76 Aligned_cols=42 Identities=17% Similarity=0.286 Sum_probs=26.8
Q ss_pred HHHHHHHHHHhcCCChHHHHHHHHH---hhcCccCCccHHHHhhhhhHHHH
Q 030236 115 DQMNRYESFRRSALQKSNMRRLLVS---ITGSQKISLPMTIVVCGIAKMFV 162 (181)
Q Consensus 115 EQldRYE~fRRS~f~K~~IKKLi~s---vtgsQsVs~nv~IavaGiAKvFV 162 (181)
|=-.||..|+. .|.-++.+ ++|...-..-.++|+..|++.|=
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 34579999974 56666654 33432223346788888998883
No 25
>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins. Torsion dystonia is an autosomal dominant movement disorder characterised by involuntary, repetitive muscle contractions and twisted postures. The most severe early-onset form of dystonia has been linked to mutations in the human DYT1 (TOR1A) gene encoding a protein termed torsinA. While causative genetic alterations have been identified, the function of torsin proteins and the molecular mechanism underlying dystonia remain unknown. Phylogenetic analysis of the torsin protein family indicates these proteins share distant sequence similarity with the large and diverse family of AAA ATPase, central region containing proteins () proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor
Probab=38.51 E-value=29 Score=27.91 Aligned_cols=32 Identities=19% Similarity=0.336 Sum_probs=22.5
Q ss_pred HhhcCccCCccHHHHh---hhhhHHHHHHHHHHHH
Q 030236 139 SITGSQKISLPMTIVV---CGIAKMFVGELVETGF 170 (181)
Q Consensus 139 svtgsQsVs~nv~Iav---aGiAKvFVGEIVE~Ar 170 (181)
....+...+.|+++.. .|.+|-||+.||.+++
T Consensus 43 ~~l~~~~p~KpLVlSfHG~tGtGKn~v~~liA~~l 77 (127)
T PF06309_consen 43 GHLANPNPRKPLVLSFHGWTGTGKNFVSRLIAEHL 77 (127)
T ss_pred HHHcCCCCCCCEEEEeecCCCCcHHHHHHHHHHHH
Confidence 3333444555666655 7899999999998874
No 26
>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=38.08 E-value=1.4e+02 Score=20.77 Aligned_cols=47 Identities=13% Similarity=0.133 Sum_probs=36.9
Q ss_pred CCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHHH
Q 030236 127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNV 174 (181)
Q Consensus 127 ~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~ 174 (181)
.+|...+..+++. .|-+....++.=.|+=.+-=||-+|+..|++..+
T Consensus 2 ~IPD~v~~~yL~~-~G~~~~D~rv~RLvSLaaQKFisdI~~dA~q~~k 48 (51)
T PF03540_consen 2 TIPDEVTDYYLER-SGFQTSDPRVKRLVSLAAQKFISDIANDAMQYCK 48 (51)
T ss_pred CCCHHHHHHHHHH-CCCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3677888888755 4766666677777888899999999999987665
No 27
>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=37.85 E-value=68 Score=23.20 Aligned_cols=40 Identities=25% Similarity=0.553 Sum_probs=30.8
Q ss_pred HHHHHhcCCHHHHH----HHHHHHhcCCChHHHHHHHHHhhcCc
Q 030236 105 MQAILNQFTEDQMN----RYESFRRSALQKSNMRRLLVSITGSQ 144 (181)
Q Consensus 105 m~~Ll~~fdeEQld----RYE~fRRS~f~K~~IKKLi~svtgsQ 144 (181)
+..|...+++.+++ -|+.||+..++|...=|.+..++|.+
T Consensus 15 ~~~l~~~l~~~~~~~l~~~Y~~~k~~kIsR~~fvr~lR~IVGD~ 58 (70)
T PF12174_consen 15 FSALSKHLPPSKMDLLQKHYEEFKKKKISREEFVRKLRQIVGDQ 58 (70)
T ss_pred HHHHHHHCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHH
Confidence 34456777777764 59999999999999777778888853
No 28
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=36.19 E-value=36 Score=34.29 Aligned_cols=25 Identities=32% Similarity=0.573 Sum_probs=15.7
Q ss_pred cCCccccccccccccccCCCCCCCc
Q 030236 74 NKDEYDEEDDENVDVELGKFPSSSD 98 (181)
Q Consensus 74 ~~~eedeeeed~~d~~l~~~~~~~d 98 (181)
+++++++++||+.||+...+.++.|
T Consensus 425 ~dgdde~eddddidvdeediessdd 449 (990)
T KOG1819|consen 425 EDGDDEAEDDDDIDVDEEDIESSDD 449 (990)
T ss_pred ccCcccccCcccccccccccccccc
Confidence 3344555666677888777776543
No 29
>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=35.47 E-value=10 Score=26.12 Aligned_cols=34 Identities=26% Similarity=0.342 Sum_probs=19.7
Q ss_pred HHHHHHhcCCChHHHHHHHHHhhcCccCCccHHHH
Q 030236 119 RYESFRRSALQKSNMRRLLVSITGSQKISLPMTIV 153 (181)
Q Consensus 119 RYE~fRRS~f~K~~IKKLi~svtgsQsVs~nv~Ia 153 (181)
-|+.||+|.+-.+=..-| ......+.+++.++.-
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 489999999876644443 3333455677776543
No 30
>PF08971 GlgS: Glycogen synthesis protein; InterPro: IPR015065 Members of this protein are involved in glycogen synthesis in Enterobacteria. The structure of the polypeptide chain comprises a bundle of two parallel amphipathic helices, alpha-1 and alpha-3, and a short hydrophobic helix alpha-2 sandwiched between them []. ; GO: 0005978 glycogen biosynthetic process; PDB: 1RRZ_A.
Probab=35.41 E-value=28 Score=25.57 Aligned_cols=21 Identities=33% Similarity=0.692 Sum_probs=15.8
Q ss_pred HHHHHhcCCHHHH----HHHHHHHh
Q 030236 105 MQAILNQFTEDQM----NRYESFRR 125 (181)
Q Consensus 105 m~~Ll~~fdeEQl----dRYE~fRR 125 (181)
...+..+||++|. +||+.||.
T Consensus 30 ~~~I~gnM~ee~r~~F~~R~~~Yr~ 54 (66)
T PF08971_consen 30 VDAITGNMSEEQREWFCERYAHYRQ 54 (66)
T ss_dssp HHHHHHH--TTHHHHHHHHHHHHHH
T ss_pred HHHHhccCCHHHHHHHHHHHHHHHH
Confidence 4567899999995 79999997
No 31
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=34.63 E-value=80 Score=28.01 Aligned_cols=50 Identities=8% Similarity=0.317 Sum_probs=33.1
Q ss_pred hcCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHHH
Q 030236 125 RSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVNV 174 (181)
Q Consensus 125 RS~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~ 174 (181)
-++|+-+.||||||.-----+|.+-|=++|+=---+|+-+||-+++++-.
T Consensus 11 ~trfp~aRiKKIMQ~dEdIGKvaqavPViisralElFl~~l~~~t~~~t~ 60 (224)
T KOG1659|consen 11 KTRFPPARIKKIMQSDEDIGKVAQAVPVIISRALELFLESLLQKTLEITR 60 (224)
T ss_pred hccCCHHHHHHHHhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 57899999999998632111344444333344446899999988887754
No 32
>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=34.55 E-value=18 Score=27.96 Aligned_cols=13 Identities=38% Similarity=0.603 Sum_probs=6.6
Q ss_pred ccccccccccccc
Q 030236 77 EYDEEDDENVDVE 89 (181)
Q Consensus 77 eedeeeed~~d~~ 89 (181)
|+++|+||+|-+.
T Consensus 91 ee~eE~dddmgf~ 103 (105)
T cd04411 91 EEEEEEDEDFGFG 103 (105)
T ss_pred ccccccccccCcc
Confidence 3445555666543
No 33
>COG5123 TOA2 Transcription initiation factor IIA, gamma subunit [Transcription]
Probab=34.26 E-value=35 Score=27.32 Aligned_cols=33 Identities=30% Similarity=0.302 Sum_probs=19.0
Q ss_pred HHHHHHhcCCChHHHHHHHHHhhcCccCCccHHH
Q 030236 119 RYESFRRSALQKSNMRRLLVSITGSQKISLPMTI 152 (181)
Q Consensus 119 RYE~fRRS~f~K~~IKKLi~svtgsQsVs~nv~I 152 (181)
=||.||||.+-|.-.+-|=.-|.- -.++++++.
T Consensus 4 yYElYRrs~ig~~L~dalD~lis~-g~isp~lam 36 (113)
T COG5123 4 YYELYRRSMIGKVLEDALDELISA-GVISPNLAM 36 (113)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhc-CCcCHHHHH
Confidence 399999999877654443222221 135666543
No 34
>PTZ00017 histone H2A; Provisional
Probab=33.90 E-value=86 Score=25.65 Aligned_cols=46 Identities=9% Similarity=0.145 Sum_probs=37.0
Q ss_pred CChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHH
Q 030236 128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVN 173 (181)
Q Consensus 128 f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq 173 (181)
||=..|.|++..-.....|+....+-++++--.++.||.|.|-...
T Consensus 28 FPVgRi~R~Lk~g~~a~RV~a~A~VYLAAVLEYLtaEILELAgNaa 73 (134)
T PTZ00017 28 FPVGRVHRYLKKGRYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAA 73 (134)
T ss_pred cchHHHHHHHhccchhccccccchhhhHHHHHHHHHHHHHHHHHHH
Confidence 6777788888765445568888889999999999999999886543
No 35
>KOG3463 consensus Transcription initiation factor IIA, gamma subunit [Transcription]
Probab=31.43 E-value=42 Score=26.80 Aligned_cols=33 Identities=21% Similarity=0.352 Sum_probs=22.1
Q ss_pred HHHHHHhcCCChHHHHHHHHHhhcCccCCccHHH
Q 030236 119 RYESFRRSALQKSNMRRLLVSITGSQKISLPMTI 152 (181)
Q Consensus 119 RYE~fRRS~f~K~~IKKLi~svtgsQsVs~nv~I 152 (181)
=||.|||+.+-+.-.+-| -.....+.++++++.
T Consensus 3 ~YelYR~ttlG~~L~~tL-De~v~~g~itp~la~ 35 (109)
T KOG3463|consen 3 YYELYRRTTLGNALQKTL-DELVSDGVITPSLAK 35 (109)
T ss_pred HHHHHHHhhHHHHHHHHH-HHHHHcCCCCHHHHH
Confidence 599999999977654443 444444557777654
No 36
>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=27.27 E-value=21 Score=36.47 Aligned_cols=15 Identities=13% Similarity=0.390 Sum_probs=0.0
Q ss_pred HHHH-hcCCHHHHHHH
Q 030236 106 QAIL-NQFTEDQMNRY 120 (181)
Q Consensus 106 ~~Ll-~~fdeEQldRY 120 (181)
..|| ..+++||-.|.
T Consensus 715 nTLVNqGi~eerAari 730 (787)
T PF03115_consen 715 NTLVNQGIPEERAARI 730 (787)
T ss_dssp ----------------
T ss_pred HHHHHcCCCHHHHHhh
Confidence 3355 67888888763
No 37
>PLN00154 histone H2A; Provisional
Probab=26.93 E-value=1.4e+02 Score=24.63 Aligned_cols=45 Identities=11% Similarity=0.178 Sum_probs=35.8
Q ss_pred CChHHHHHHHHHhh-cCccCCccHHHHhhhhhHHHHHHHHHHHHHH
Q 030236 128 LQKSNMRRLLVSIT-GSQKISLPMTIVVCGIAKMFVGELVETGFCV 172 (181)
Q Consensus 128 f~K~~IKKLi~svt-gsQsVs~nv~IavaGiAKvFVGEIVE~Ar~V 172 (181)
||=..|.|++..-+ ..+.|+....+-++++--++..||.|.|-..
T Consensus 39 FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNa 84 (136)
T PLN00154 39 FPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNA 84 (136)
T ss_pred CchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHH
Confidence 67777888877753 3456888888999999999999999988554
No 38
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=26.20 E-value=39 Score=26.72 Aligned_cols=14 Identities=29% Similarity=0.651 Sum_probs=6.9
Q ss_pred cccccccccccccc
Q 030236 77 EYDEEDDENVDVEL 90 (181)
Q Consensus 77 eedeeeed~~d~~l 90 (181)
|+++|+||+|-+.|
T Consensus 97 ee~ee~ddDmgf~L 110 (112)
T PTZ00373 97 EEEEEEEDDLGFSL 110 (112)
T ss_pred cccccccccccccc
Confidence 34345555565543
No 39
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=25.46 E-value=1.7e+02 Score=25.06 Aligned_cols=49 Identities=18% Similarity=0.190 Sum_probs=37.8
Q ss_pred CCChHHHHHHHHHhhcCc--cCCccHHHHhhhhhHHHHHHHHHHHHHHHHH
Q 030236 127 ALQKSNMRRLLVSITGSQ--KISLPMTIVVCGIAKMFVGELVETGFCVNVT 175 (181)
Q Consensus 127 ~f~K~~IKKLi~svtgsQ--sVs~nv~IavaGiAKvFVGEIVE~Ar~Vq~e 175 (181)
.||++.|.|||..++.-. +|+.--..||+-=|-|||=-|.--|.++...
T Consensus 10 ~lP~AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~ 60 (172)
T KOG0870|consen 10 NLPNAIITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKD 60 (172)
T ss_pred hccHHHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 699999999998876421 3455567788888899999998888877643
No 40
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=24.70 E-value=1.8e+02 Score=22.82 Aligned_cols=45 Identities=22% Similarity=0.364 Sum_probs=31.5
Q ss_pred cCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHH
Q 030236 126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFC 171 (181)
Q Consensus 126 S~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~ 171 (181)
+.+.|+.||||... -|--.|.--+---+.+++|+|+-+++-.|..
T Consensus 28 qgitKpaIRRlARr-~GVkRi~G~~yeE~~~~~k~fl~n~i~~A~~ 72 (103)
T KOG3467|consen 28 QGITKPAIRRLARR-GGVKRISGLIYEETRGVLKVFLENVIRDAVT 72 (103)
T ss_pred cccchHHHHHHHHh-cCcchhchhhHHHHHHHHHHHHHHHHHHHHH
Confidence 35679999998654 2333344445555788999999999887754
No 41
>PLN00157 histone H2A; Provisional
Probab=24.68 E-value=1.5e+02 Score=24.15 Aligned_cols=46 Identities=9% Similarity=0.143 Sum_probs=36.3
Q ss_pred CChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHH
Q 030236 128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVN 173 (181)
Q Consensus 128 f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq 173 (181)
||=..|.|++..-.....|+....+-++++--.++.||.|.|-...
T Consensus 27 FPVgRi~R~Lk~g~~a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa 72 (132)
T PLN00157 27 FPVGRIARYLKAGKYATRVGAGAPVYLAAVLEYLAAEVLELAGNAA 72 (132)
T ss_pred cchHHHHHHHhcCchhhhcCCCcHhHHHHHHHHHHHHHHHHHHHHH
Confidence 6667788887664445567778889999999999999999986654
No 42
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.62 E-value=3.2e+02 Score=21.63 Aligned_cols=53 Identities=15% Similarity=0.310 Sum_probs=33.0
Q ss_pred HhcCCHHHHHHHHHHHhcCCChHHHHHHHHHhhcCccCCccH-HHHhhhhhHHHHHHHHHHHH
Q 030236 109 LNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPM-TIVVCGIAKMFVGELVETGF 170 (181)
Q Consensus 109 l~~fdeEQldRYE~fRRS~f~K~~IKKLi~svtgsQsVs~nv-~IavaGiAKvFVGEIVE~Ar 170 (181)
...||++|.+|+++ +..|+|+...--. +=-+|| .+-++||-.--++.-+.+|-
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 4556666553222 223455 45568877766666555443
No 43
>PRK02922 glycogen synthesis protein GlgS; Provisional
Probab=24.58 E-value=92 Score=23.01 Aligned_cols=24 Identities=21% Similarity=0.466 Sum_probs=18.9
Q ss_pred HHHHHhcCCHHHH----HHHHHHHhcCC
Q 030236 105 MQAILNQFTEDQM----NRYESFRRSAL 128 (181)
Q Consensus 105 m~~Ll~~fdeEQl----dRYE~fRRS~f 128 (181)
...+-.+||++|. +||..||.-.+
T Consensus 31 vd~V~gnmsee~r~~F~eRla~Yr~~~~ 58 (67)
T PRK02922 31 IQAVTGNMDEEHRTWFCARYAWYCQQMM 58 (67)
T ss_pred HHHHHhcCCHHHHHHHHHHHHHHHHHHH
Confidence 4567899999996 68899987554
No 44
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=23.68 E-value=1.9e+02 Score=26.23 Aligned_cols=50 Identities=14% Similarity=0.303 Sum_probs=34.7
Q ss_pred HHHHhcCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHH
Q 030236 121 ESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGF 170 (181)
Q Consensus 121 E~fRRS~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar 170 (181)
-.+.--+||=+.||||+..--+---|+.-+-+..+-++-+||-||.-.|-
T Consensus 103 ~~~k~h~LPlARIkkvMKtdedVkMisaEaPvlFak~~EiFI~ELTmRAW 152 (286)
T COG5208 103 ILLKDHNLPLARIKKVMKTDEDVKMISAEAPVLFAKITEIFIEELTMRAW 152 (286)
T ss_pred HHHHhccCcHHHHHHHHhcccchhheecccchHHHHHHHHHHHHHHHHHH
Confidence 55677789999999998653332224444445567778899999976553
No 45
>PRK13291 metal-dependent hydrolase; Provisional
Probab=22.66 E-value=80 Score=25.53 Aligned_cols=39 Identities=13% Similarity=0.156 Sum_probs=26.7
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHhcCCChHHHHHHHHHhhcC
Q 030236 103 AKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGS 143 (181)
Q Consensus 103 ~km~~Ll~~fdeEQldRYE~fRRS~f~K~~IKKLi~svtgs 143 (181)
+++..|+.+|++++++|.- ..+.+.+-.++-++..+.++
T Consensus 118 ~~~i~ll~~l~~e~l~r~~--~~~~~~~~Tl~~~l~~~~~H 156 (173)
T PRK13291 118 KRWVALLESLTEEDLERTF--NHPDGGETTLDEAIGLYAWH 156 (173)
T ss_pred HHHHHHHHcCCHHHHHccc--CCCCCCeeeHHHHHHHHHHH
Confidence 4555688999999998873 33456666677766666554
No 46
>cd08320 Pyrin_NALPs Pyrin death domain found in NALP proteins. Pyrin Death Domain found in NALP (NACHT, LRR and PYD domains) proteins including NALP1 (CARD7, NLRP1), NALP3 (NLRP3, Cryopyrin, CIAS1), and NALP12 (NLRP12, Monarch-1), among others. Mammals contains at least 14 NALP proteins, named NALP1-14 (or NLRP1-14). NALPs are members of the NBS-LRR family of proteins possessing a tripartite domain structure including a C-terminal LRR (leucine-rich repeats), a central nucleotide-binding site (NBS) domain or NACHT (for neuronal apoptosis inhibitor protein, CIITA, HET-E and TP1), and an N-terminal protein-protein interaction domain, which is a Pyrin domain in the case of NALPs. The NBS-LRR family is also referred to as the NLR (Nod-like Receptor) or CATERPILLER (for CARD, transcription enhancer, R-(purine)-binding, pyrin, lots of LRRs) family. NALP1 contains an additional Caspase activation and recruitment domain (CARD) at the C-terminus. NALP1 and NALP3 are both involved in the assembly
Probab=22.14 E-value=3.3e+02 Score=20.07 Aligned_cols=65 Identities=12% Similarity=0.275 Sum_probs=44.9
Q ss_pred HHHHHhcCCHHHHHHHHHHHhc--------CCChHHHHHH--------HHHhhcCccCCccHHHHhhhhhHHHHHHHHHH
Q 030236 105 MQAILNQFTEDQMNRYESFRRS--------ALQKSNMRRL--------LVSITGSQKISLPMTIVVCGIAKMFVGELVET 168 (181)
Q Consensus 105 m~~Ll~~fdeEQldRYE~fRRS--------~f~K~~IKKL--------i~svtgsQsVs~nv~IavaGiAKvFVGEIVE~ 168 (181)
+...|..|+.+++.+|-.|=+. .+|+..|++- +...-|. ..-+-+++.-+-||=.=+|.|+
T Consensus 3 Ll~~Le~L~~~ElkkFK~~L~~~~~~~~~~~Ip~~~le~ad~~dLa~lLv~~y~~---~~A~~~t~~if~~mn~~dL~e~ 79 (86)
T cd08320 3 LLWYLEELSKEELKKFKLLLKTEPLQSGLKPIPWTEVKKADGEDLAELLVEHYGG---QQAWDVTLSIFEKMNLRDLCEK 79 (86)
T ss_pred HHHHHHHcCHHHHHHHHHHHhccchhccCCCCChHhHhcCCHHHHHHHHHHHcCh---hHHHHHHHHHHHHHChHHHHHH
Confidence 4456889999999999888664 4677776551 2122121 2356778888888888888888
Q ss_pred HHHH
Q 030236 169 GFCV 172 (181)
Q Consensus 169 Ar~V 172 (181)
|+.-
T Consensus 80 ~~~e 83 (86)
T cd08320 80 AKRE 83 (86)
T ss_pred HHHH
Confidence 7653
No 47
>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=22.13 E-value=1e+02 Score=30.74 Aligned_cols=12 Identities=17% Similarity=0.232 Sum_probs=5.5
Q ss_pred CCccHHHHhhhh
Q 030236 146 ISLPMTIVVCGI 157 (181)
Q Consensus 146 Vs~nv~IavaGi 157 (181)
|..-+++|=-||
T Consensus 464 IdkDi~tAnDGl 475 (574)
T PF07462_consen 464 IDKDIATANDGL 475 (574)
T ss_pred HhhhHHHhhhHH
Confidence 444455554443
No 48
>TIGR03693 ocin_ThiF_like putative thiazole-containing bacteriocin maturation protein. Members of this protein family are found in a three-gene operon in Bacillus anthracis and related Bacillus species, where the other two genes are clearly identified with maturation of a putative thiazole-containing bacteriocin precursor. While there is no detectable pairwise sequence similarity between members of this family and the proposed cyclodehydratases such as SagC of Streptococcus pyogenes (see family TIGR03603), both families show similarity through PSI-BLAST to ThiF, a protein involved in biosynthesis of the thiazole moiety for thiamine biosynthesis. This family, therefore, may contribute to cyclodehydratase function in heterocycle-containing bacteriocin biosyntheses. In Bacillus licheniformis ATCC 14580, the bacteriocin precursor gene is adjacent to the gene for this protein.
Probab=21.81 E-value=48 Score=33.30 Aligned_cols=23 Identities=9% Similarity=0.179 Sum_probs=19.6
Q ss_pred HHHHhcCCHHHHHHHHHHHhcCC
Q 030236 106 QAILNQFTEDQMNRYESFRRSAL 128 (181)
Q Consensus 106 ~~Ll~~fdeEQldRYE~fRRS~f 128 (181)
-..+++|+.-.-+||+.||+++.
T Consensus 110 I~F~~~fs~s~~~rF~~qR~akV 132 (637)
T TIGR03693 110 IEFIEADADSGALKFELSRNAKI 132 (637)
T ss_pred HHHHHHhccCchhhhhhhhcccE
Confidence 34789999999999999998874
No 49
>PLN00156 histone H2AX; Provisional
Probab=20.57 E-value=2.1e+02 Score=23.59 Aligned_cols=46 Identities=9% Similarity=0.166 Sum_probs=35.6
Q ss_pred CChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHHHHHHHH
Q 030236 128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETGFCVN 173 (181)
Q Consensus 128 f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE~Ar~Vq 173 (181)
||=..|.|++..-.....|+..-.+-++++--.++.||.|.|-...
T Consensus 30 FPVgRi~R~Lk~g~ya~RVga~ApVYLAAVLEYLtaEVLELAgNaa 75 (139)
T PLN00156 30 FPVGRIARFLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAGNAA 75 (139)
T ss_pred cchHHHHHHHhcCChhhccCCccHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6667777777664444557777788999999999999999986654
No 50
>KOG4054 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.05 E-value=63 Score=27.84 Aligned_cols=37 Identities=30% Similarity=0.373 Sum_probs=28.8
Q ss_pred HHHhcCCChHHHHHHHHHhhcCccCCccHHHHhhhhhHHHHHHHHH
Q 030236 122 SFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVE 167 (181)
Q Consensus 122 ~fRRS~f~K~~IKKLi~svtgsQsVs~nv~IavaGiAKvFVGEIVE 167 (181)
.|--|...|+.+|++|- ...+|-+-+++|+++|.+--
T Consensus 26 hYq~s~~~Ks~lK~lif---------vh~lI~v~mlak~~l~hl~~ 62 (183)
T KOG4054|consen 26 HYQMSVTLKSRLKKLIF---------VHALIWVLMLAKMSLGHLRL 62 (183)
T ss_pred HHHHHHHHHHHHHHHHH---------HHHHHHHHHHHHHhhhhhhh
Confidence 35567788999999972 24678888999999998754
Done!