Query 031136
Match_columns 165
No_of_seqs 115 out of 159
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 09:45:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031136.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031136hhsearch_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 3.2E-29 7E-34 185.7 3.6 61 105-165 1-61 (90)
2 KOG3219 Transcription initiati 99.9 3.5E-27 7.5E-32 195.4 7.0 67 98-165 83-149 (195)
3 cd08048 TAF11 TATA Binding Pro 99.9 4.9E-23 1.1E-27 150.7 4.5 53 112-165 1-53 (85)
4 COG5251 TAF40 Transcription in 99.9 2.3E-22 5.1E-27 165.9 5.9 63 102-165 90-152 (199)
5 PF00808 CBFD_NFYB_HMF: Histon 91.4 0.12 2.5E-06 35.0 1.5 40 126-165 1-40 (65)
6 PF13443 HTH_26: Cro/C1-type H 64.9 3.4 7.4E-05 26.8 1.0 50 113-164 7-56 (63)
7 smart00803 TAF TATA box bindin 58.6 9.2 0.0002 26.6 2.3 39 126-165 1-39 (65)
8 smart00417 H4 Histone H4. 44.9 17 0.00036 26.4 1.9 37 127-164 13-49 (74)
9 KOG3463 Transcription initiati 43.5 23 0.0005 27.9 2.6 34 119-153 3-36 (109)
10 cd00076 H4 Histone H4, one of 42.2 19 0.00042 26.6 1.9 38 126-164 12-49 (85)
11 COG2036 HHT1 Histones H3 and H 42.1 19 0.0004 27.2 1.8 46 115-161 7-52 (91)
12 PF07526 POX: Associated with 41.9 1.8E+02 0.0038 23.2 7.4 40 116-161 89-131 (140)
13 COG5123 TOA2 Transcription ini 41.7 25 0.00054 27.8 2.5 33 119-152 4-36 (113)
14 PF02268 TFIIA_gamma_N: Transc 41.2 11 0.00023 25.7 0.4 35 119-154 2-36 (49)
15 PF08971 GlgS: Glycogen synthe 40.1 22 0.00047 25.8 1.8 23 103-125 28-54 (66)
16 PF12174 RST: RCD1-SRO-TAF4 (R 38.1 90 0.0019 22.2 4.7 38 106-143 16-57 (70)
17 smart00574 POX domain associat 37.3 1.6E+02 0.0035 24.0 6.6 47 108-161 82-131 (140)
18 PTZ00015 histone H4; Provision 31.3 37 0.0008 26.1 2.0 39 126-165 29-67 (102)
19 cd04411 Ribosomal_P1_P2_L12p R 30.0 25 0.00053 26.8 0.8 15 76-90 90-104 (105)
20 KOG3902 Histone acetyltransfer 29.7 80 0.0017 29.2 4.1 44 98-142 191-237 (352)
21 PF14165 YtzH: YtzH-like prote 28.3 67 0.0015 24.3 2.9 49 102-154 4-52 (87)
22 PF09574 DUF2374: Protein of 27.6 61 0.0013 21.7 2.2 29 131-162 2-30 (42)
23 PF08802 CytB6-F_Fe-S: Cytochr 26.6 22 0.00048 23.2 0.1 30 132-162 7-36 (39)
24 PRK02922 glycogen synthesis pr 25.6 87 0.0019 22.8 2.9 26 103-128 29-58 (67)
25 COG3492 Uncharacterized protei 24.8 1.4E+02 0.003 23.4 4.1 41 109-158 3-44 (104)
26 PRK10878 hypothetical protein; 24.8 1.1E+02 0.0025 21.9 3.4 34 109-142 16-62 (72)
27 PF13495 Phage_int_SAM_4: Phag 24.3 1.4E+02 0.0031 19.7 3.8 30 110-139 39-70 (85)
28 PTZ00373 60S Acidic ribosomal 24.3 46 0.001 25.9 1.4 15 76-90 96-110 (112)
29 PF02978 SRP_SPB: Signal pepti 23.5 1.1E+02 0.0025 22.9 3.4 35 99-138 47-81 (104)
30 PF07462 MSP1_C: Merozoite sur 23.4 81 0.0018 31.0 3.2 8 106-113 363-370 (574)
31 cd04494 BRCA2DBD_OB2 BRCA2DBD_ 23.0 83 0.0018 27.7 2.9 35 107-141 113-153 (251)
32 PF03115 Astro_capsid: Astrovi 22.6 29 0.00062 35.0 0.0 10 110-119 720-729 (787)
33 PLN00035 histone H4; Provision 22.5 67 0.0015 24.8 2.0 36 128-164 30-65 (103)
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=99.95 E-value=3.2e-29 Score=185.65 Aligned_cols=61 Identities=41% Similarity=0.767 Sum_probs=43.3
Q ss_pred HHHHHhcCCHHHHHHHHHHHhcCCChHHHHHHHHHhhcCccCCccHHHHhhhhhhhhcccC
Q 031136 105 MQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFLEWL 165 (165)
Q Consensus 105 m~~Ll~~fdeEQl~RYE~fRRS~f~K~~IKKLinsvtgsQsVs~nvvIaVaGiAKvFVGEI 165 (165)
|++|+++||+||++|||+||||+|+|++|||||++++|+|+||+|++|+|+||||||||||
T Consensus 1 ~~~L~~~f~~eQ~~Rye~fRRs~~~k~~ikkli~~~~~~qsv~~~v~i~v~g~aKvFVGEi 61 (90)
T PF04719_consen 1 MQLLLSNFDEEQLDRYEAFRRSSFNKAAIKKLINQVLGNQSVSQNVVIAVAGIAKVFVGEI 61 (90)
T ss_dssp ---------HHHHHHHHHHHH----HHHHHHHHHHHHS-S---HHHHHHHHHHHHHHHHHH
T ss_pred ChHHHHcCCHHHHHHHHHHHHccCCHHHHHHHHHHHcCCCCCChhHHHHHHHHHHHHHHHH
Confidence 7899999999999999999999999999999999999889999999999999999999996
No 2
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=99.94 E-value=3.5e-27 Score=195.42 Aligned_cols=67 Identities=43% Similarity=0.762 Sum_probs=63.4
Q ss_pred cHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCChHHHHHHHHHhhcCccCCccHHHHhhhhhhhhcccC
Q 031136 98 DPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFLEWL 165 (165)
Q Consensus 98 de~k~~km~~Ll~~fdeEQl~RYE~fRRS~f~K~~IKKLinsvtgsQsVs~nvvIaVaGiAKvFVGEI 165 (165)
++++..||+.|+++||+||++|||+||||+|||+.|||||++++| ++|++||+|||+||||||||||
T Consensus 83 ~~ee~~r~q~L~s~fseEQl~RYEvfRrs~f~Ka~iKkL~~~itg-~~v~~nv~Ia~~GiaKvFVGEv 149 (195)
T KOG3219|consen 83 DAEEAQRMQTLLSNFSEEQLSRYEVFRRSAFPKAQIKKLMSSITG-QSVSENVAIAMAGIAKVFVGEV 149 (195)
T ss_pred CHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhC-CccCcceeeeecchhhHhHHHH
Confidence 466667999999999999999999999999999999999999998 5699999999999999999996
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=99.87 E-value=4.9e-23 Score=150.70 Aligned_cols=53 Identities=51% Similarity=0.848 Sum_probs=51.7
Q ss_pred CCHHHHHHHHHHHhcCCChHHHHHHHHHhhcCccCCccHHHHhhhhhhhhcccC
Q 031136 112 FTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFLEWL 165 (165)
Q Consensus 112 fdeEQl~RYE~fRRS~f~K~~IKKLinsvtgsQsVs~nvvIaVaGiAKvFVGEI 165 (165)
||+||++|||.|||++|+|+.|||||++++| |+|++||+|+|+||||+|||||
T Consensus 1 f~~eQ~~Rye~~Rra~f~k~~iKr~~~~~~~-~~v~~~v~i~v~glaKvFVGei 53 (85)
T cd08048 1 FSEEQMNRYEMFRRSSFPKAAIKRLIQSVTG-QSVSQNVVIAVAGIAKVFVGEI 53 (85)
T ss_pred CCHHHHHHHHHHHHhhccHHHHHHHHHHHcC-CCCCchHHHHHHHHHHHHHHHH
Confidence 8999999999999999999999999999997 7999999999999999999996
No 4
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=99.86 E-value=2.3e-22 Score=165.90 Aligned_cols=63 Identities=29% Similarity=0.595 Sum_probs=60.5
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHHhcCCChHHHHHHHHHhhcCccCCccHHHHhhhhhhhhcccC
Q 031136 102 MAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFLEWL 165 (165)
Q Consensus 102 ~~km~~Ll~~fdeEQl~RYE~fRRS~f~K~~IKKLinsvtgsQsVs~nvvIaVaGiAKvFVGEI 165 (165)
..|+.+|+.+||+||++|||.|||++|||+.||||+++|++ |+|++|++|+|+||+|||||||
T Consensus 90 ~~r~k~l~~~~deeq~~RyEvFrrt~lnKt~VKKlastV~n-QtVspNi~I~l~g~~KVfvGEi 152 (199)
T COG5251 90 DERFKLLVTNLDEEQTNRYEVFRRTSLNKTQVKKLASTVAN-QTVSPNIRIFLQGVGKVFVGEI 152 (199)
T ss_pred HHHHHHHHhhcCHHHHHHHHHHHhcCCCHHHHHHHHHHHhc-cccCCCeeeeeechhHHHHHHH
Confidence 47788899999999999999999999999999999999996 8999999999999999999996
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=91.40 E-value=0.12 Score=34.96 Aligned_cols=40 Identities=18% Similarity=0.333 Sum_probs=31.4
Q ss_pred cCCChHHHHHHHHHhhcCccCCccHHHHhhhhhhhhcccC
Q 031136 126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFLEWL 165 (165)
Q Consensus 126 S~f~K~~IKKLinsvtgsQsVs~nvvIaVaGiAKvFVGEI 165 (165)
..||.+.|||||...-+...|+.....+|+=.+-+||.+|
T Consensus 1 ~~lP~a~vkri~k~~~~~~~vs~ea~~~i~~a~e~Fi~~l 40 (65)
T PF00808_consen 1 ASLPLARVKRIMKSDPDVMRVSKEAVEAIAKAAEEFIQYL 40 (65)
T ss_dssp -SS-HHHHHHHHHHTSTTSEE-HHHHHHHHHHHHHHHHHH
T ss_pred CCCChHHHHHHhccCCCccchhHHHHHHHHHHHHHHHHHH
Confidence 3699999999999985555689999999998899998653
No 6
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=64.92 E-value=3.4 Score=26.77 Aligned_cols=50 Identities=16% Similarity=0.161 Sum_probs=27.5
Q ss_pred CHHHHHHHHHHHhcCCChHHHHHHHHHhhcCccCCccHHHHhhhhhhhhccc
Q 031136 113 TEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFLEW 164 (165)
Q Consensus 113 deEQl~RYE~fRRS~f~K~~IKKLinsvtgsQsVs~nvvIaVaGiAKvFVGE 164 (165)
.+-.+.+++..|++++++++|.++++.-. ..++-..+..+|-+-.+=++|
T Consensus 7 ~~~~it~~~La~~~gis~~tl~~~~~~~~--~~~~~~~l~~ia~~l~~~~~e 56 (63)
T PF13443_consen 7 AERGITQKDLARKTGISRSTLSRILNGKP--SNPSLDTLEKIAKALNCSPEE 56 (63)
T ss_dssp HHTT--HHHHHHHHT--HHHHHHHHTTT-------HHHHHHHHHHHT--HHH
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHhccc--ccccHHHHHHHHHHcCCCHHH
Confidence 45567889999999999999999988432 245555555555444443433
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=58.60 E-value=9.2 Score=26.63 Aligned_cols=39 Identities=15% Similarity=0.153 Sum_probs=32.0
Q ss_pred cCCChHHHHHHHHHhhcCccCCccHHHHhhhhhhhhcccC
Q 031136 126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFLEWL 165 (165)
Q Consensus 126 S~f~K~~IKKLinsvtgsQsVs~nvvIaVaGiAKvFVGEI 165 (165)
+.||++.||+|..+. |-..++..+.-.++...+.|+-+|
T Consensus 1 ~~~p~~~i~ria~~~-Gi~ris~~a~~~l~~~~e~rl~~i 39 (65)
T smart00803 1 SWLPKETIKDVAESL-GIGNLSDEAAKLLAEDVEYRIKEI 39 (65)
T ss_pred CCCCHHHHHHHHHHC-CCccccHHHHHHHHHHHHHHHHHH
Confidence 358999999999875 555799999999999888887653
No 8
>smart00417 H4 Histone H4.
Probab=44.89 E-value=17 Score=26.42 Aligned_cols=37 Identities=30% Similarity=0.287 Sum_probs=30.6
Q ss_pred CCChHHHHHHHHHhhcCccCCccHHHHhhhhhhhhccc
Q 031136 127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFLEW 164 (165)
Q Consensus 127 ~f~K~~IKKLinsvtgsQsVs~nvvIaVaGiAKvFVGE 164 (165)
.++|+.|+||+... |-.-||..+.-.+.++.|.|+-+
T Consensus 13 gI~k~~IrRLaRr~-GvkRIS~~~y~elr~vle~~l~~ 49 (74)
T smart00417 13 GITKPAIRRLARRG-GVKRISGLIYDETRNVLKSFLEN 49 (74)
T ss_pred CCCHHHHHHHHHHc-CcchhhHHHHHHHHHHHHHHHHH
Confidence 69999999999874 55678888888888888888754
No 9
>KOG3463 consensus Transcription initiation factor IIA, gamma subunit [Transcription]
Probab=43.48 E-value=23 Score=27.87 Aligned_cols=34 Identities=21% Similarity=0.314 Sum_probs=21.5
Q ss_pred HHHHHHhcCCChHHHHHHHHHhhcCccCCccHHHH
Q 031136 119 RYESFRRSALQKSNMRRLLVSITGSQKISLPMTIV 153 (165)
Q Consensus 119 RYE~fRRS~f~K~~IKKLinsvtgsQsVs~nvvIa 153 (165)
=||.|||+.+-+.-.+ .+-...+.+.++++++.=
T Consensus 3 ~YelYR~ttlG~~L~~-tLDe~v~~g~itp~la~~ 36 (109)
T KOG3463|consen 3 YYELYRRTTLGNALQK-TLDELVSDGVITPSLAKK 36 (109)
T ss_pred HHHHHHHhhHHHHHHH-HHHHHHHcCCCCHHHHHH
Confidence 5999999999775333 333333345677776543
No 10
>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=42.21 E-value=19 Score=26.64 Aligned_cols=38 Identities=29% Similarity=0.278 Sum_probs=30.5
Q ss_pred cCCChHHHHHHHHHhhcCccCCccHHHHhhhhhhhhccc
Q 031136 126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFLEW 164 (165)
Q Consensus 126 S~f~K~~IKKLinsvtgsQsVs~nvvIaVaGiAKvFVGE 164 (165)
..|+|+.|+||+... |--.||..+.-.+..+.+.|+-+
T Consensus 12 ~gi~k~~I~RLarr~-GvkRIS~d~y~e~~~~l~~~l~~ 49 (85)
T cd00076 12 KGITKPAIRRLARRG-GVKRISGGVYDEVRNVLKSYLED 49 (85)
T ss_pred ccCCHHHHHHHHHHc-CcchhhHHHHHHHHHHHHHHHHH
Confidence 369999999999875 44578888888888888888754
No 11
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=42.10 E-value=19 Score=27.17 Aligned_cols=46 Identities=17% Similarity=0.271 Sum_probs=33.4
Q ss_pred HHHHHHHHHHhcCCChHHHHHHHHHhhcCccCCccHHHHhhhhhhhh
Q 031136 115 DQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMF 161 (165)
Q Consensus 115 EQl~RYE~fRRS~f~K~~IKKLinsvtgsQsVs~nvvIaVaGiAKvF 161 (165)
-+..||..|-.-.||++.|+||+..+.- ..|+....-.+.-...-|
T Consensus 7 ~~~r~~~~~~~~~Lp~apv~Ri~r~~~~-~Rvs~~A~~~l~~~~e~~ 52 (91)
T COG2036 7 KEIRRYQRSTDLLLPKAPVRRILRKAGA-ERVSSSAIEELQEALEEY 52 (91)
T ss_pred HHHHhhhhhhhhhcCchHHHHHHHHHhH-HHhhHHHHHHHHHHHHHH
Confidence 4678999999999999999999998763 356655554444444333
No 12
>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=41.92 E-value=1.8e+02 Score=23.19 Aligned_cols=40 Identities=15% Similarity=0.327 Sum_probs=27.8
Q ss_pred HHHHHHHHHhcCCChHHHHHHHHH---hhcCccCCccHHHHhhhhhhhh
Q 031136 116 QMNRYESFRRSALQKSNMRRLLVS---ITGSQKISLPMTIVVCGIAKMF 161 (165)
Q Consensus 116 Ql~RYE~fRRS~f~K~~IKKLins---vtgsQsVs~nvvIaVaGiAKvF 161 (165)
=-.||..|+. .|.-++.+ +.|--.-..-.++|+..|+|.|
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 57777765 3443233445789999999988
No 13
>COG5123 TOA2 Transcription initiation factor IIA, gamma subunit [Transcription]
Probab=41.70 E-value=25 Score=27.78 Aligned_cols=33 Identities=30% Similarity=0.302 Sum_probs=18.8
Q ss_pred HHHHHHhcCCChHHHHHHHHHhhcCccCCccHHH
Q 031136 119 RYESFRRSALQKSNMRRLLVSITGSQKISLPMTI 152 (165)
Q Consensus 119 RYE~fRRS~f~K~~IKKLinsvtgsQsVs~nvvI 152 (165)
=||.||||.+-|.-.+-|=.-+.. -.+++|++.
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 399999999877544333222221 245666543
No 14
>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=41.22 E-value=11 Score=25.66 Aligned_cols=35 Identities=31% Similarity=0.332 Sum_probs=19.6
Q ss_pred HHHHHHhcCCChHHHHHHHHHhhcCccCCccHHHHh
Q 031136 119 RYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVV 154 (165)
Q Consensus 119 RYE~fRRS~f~K~~IKKLinsvtgsQsVs~nvvIaV 154 (165)
.|+.||+|.+=.+=..-|-.-+ .++.+++.++.-|
T Consensus 2 ~yelYR~stlG~aL~dtLDeli-~~~~I~p~La~kV 36 (49)
T PF02268_consen 2 YYELYRRSTLGIALTDTLDELI-QEGKITPQLAMKV 36 (49)
T ss_dssp --CGGGCSHHHHHHHHHHHHHH-HTTSS-HHHHHHH
T ss_pred cHHHHHcchHHHHHHHHHHHHH-HcCCCCHHHHHHH
Confidence 4899999998775433333223 3456887765543
No 15
>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=40.11 E-value=22 Score=25.78 Aligned_cols=23 Identities=30% Similarity=0.641 Sum_probs=16.0
Q ss_pred HHHHHHHhcCCHHHH----HHHHHHHh
Q 031136 103 AKMQAILNQFTEDQM----NRYESFRR 125 (165)
Q Consensus 103 ~km~~Ll~~fdeEQl----~RYE~fRR 125 (165)
.....+..+||++|. +||+.||.
T Consensus 28 vd~~~I~gnM~ee~r~~F~~R~~~Yr~ 54 (66)
T PF08971_consen 28 VDVDAITGNMSEEQREWFCERYAHYRQ 54 (66)
T ss_dssp --HHHHHHH--TTHHHHHHHHHHHHHH
T ss_pred CCHHHHhccCCHHHHHHHHHHHHHHHH
Confidence 335568899999995 79999997
No 16
>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=38.05 E-value=90 Score=22.24 Aligned_cols=38 Identities=24% Similarity=0.545 Sum_probs=30.5
Q ss_pred HHHHhcCCHHHHH----HHHHHHhcCCChHHHHHHHHHhhcC
Q 031136 106 QAILNQFTEDQMN----RYESFRRSALQKSNMRRLLVSITGS 143 (165)
Q Consensus 106 ~~Ll~~fdeEQl~----RYE~fRRS~f~K~~IKKLinsvtgs 143 (165)
..|...+++.+++ -|+.||+..++|...=|.+..+.|.
T Consensus 16 ~~l~~~l~~~~~~~l~~~Y~~~k~~kIsR~~fvr~lR~IVGD 57 (70)
T PF12174_consen 16 SALSKHLPPSKMDLLQKHYEEFKKKKISREEFVRKLRQIVGD 57 (70)
T ss_pred HHHHHHCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHH
Confidence 3466777777764 5999999999999988888888874
No 17
>smart00574 POX domain associated with HOX domains.
Probab=37.25 E-value=1.6e+02 Score=24.03 Aligned_cols=47 Identities=17% Similarity=0.344 Sum_probs=29.7
Q ss_pred HHhcCCHHHHHHHHHHHhcCCChHHHHHHHHHh---hcCccCCccHHHHhhhhhhhh
Q 031136 108 ILNQFTEDQMNRYESFRRSALQKSNMRRLLVSI---TGSQKISLPMTIVVCGIAKMF 161 (165)
Q Consensus 108 Ll~~fdeEQl~RYE~fRRS~f~K~~IKKLinsv---tgsQsVs~nvvIaVaGiAKvF 161 (165)
|+.-|+ |=-.||+.|+. .|.-++.+. .|-..-..-.++|+..|++.|
T Consensus 82 Ll~mL~-eVd~RY~qY~~------qmq~v~ssFe~vaG~g~a~~yt~lAl~a~SrhF 131 (140)
T smart00574 82 LLSMLE-EVDRRYKHYYE------QMQTVVSSFDQAAGLGAAKPYTALALKTISRHF 131 (140)
T ss_pred HHHHHH-HHHHHHHHHHH------HHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHH
Confidence 444443 33479999974 577777653 342222344678889999888
No 18
>PTZ00015 histone H4; Provisional
Probab=31.31 E-value=37 Score=26.09 Aligned_cols=39 Identities=33% Similarity=0.397 Sum_probs=31.3
Q ss_pred cCCChHHHHHHHHHhhcCccCCccHHHHhhhhhhhhcccC
Q 031136 126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFLEWL 165 (165)
Q Consensus 126 S~f~K~~IKKLinsvtgsQsVs~nvvIaVaGiAKvFVGEI 165 (165)
..++|+.|+||+... |-.-|+..+.-.+..+.+.|+-+|
T Consensus 29 ~gI~k~~IrRLarr~-GvkRIS~d~y~e~r~vle~~l~~I 67 (102)
T PTZ00015 29 RGITKGAIRRLARRG-GVKRISGDIYEEVRGVLKAFLENV 67 (102)
T ss_pred cCCCHHHHHHHHHHc-CCccchHHHHHHHHHHHHHHHHHH
Confidence 579999999999875 556788888888888888887543
No 19
>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=29.95 E-value=25 Score=26.84 Aligned_cols=15 Identities=40% Similarity=0.672 Sum_probs=8.4
Q ss_pred CCCcccccccccccc
Q 031136 76 DEYDEEDDENVDVEL 90 (165)
Q Consensus 76 de~~eeeed~~dv~l 90 (165)
.|+++|+||+|-+.|
T Consensus 90 ~ee~eE~dddmgf~L 104 (105)
T cd04411 90 EEEEEEEDEDFGFGL 104 (105)
T ss_pred cccccccccccCccc
Confidence 344455666776543
No 20
>KOG3902 consensus Histone acetyltransferase PCAF/SAGA, subunit SUPT3H/SPT3 [Transcription]
Probab=29.73 E-value=80 Score=29.18 Aligned_cols=44 Identities=14% Similarity=0.231 Sum_probs=32.2
Q ss_pred cHHHHHHHHH---HHhcCCHHHHHHHHHHHhcCCChHHHHHHHHHhhc
Q 031136 98 DPAKMAKMQA---ILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITG 142 (165)
Q Consensus 98 de~k~~km~~---Ll~~fdeEQl~RYE~fRRS~f~K~~IKKLinsvtg 142 (165)
++..++||.. ....||-+|+--|--.|..+|.+..=|| ....+|
T Consensus 191 devt~~RLkrADrrTrimt~eqYvefsE~RqaSFt~Rkgkr-FRdwld 237 (352)
T KOG3902|consen 191 DEVTMRRLKRADRRTRIMTGEQYVEFSECRQASFTCRKGKR-FRDWLD 237 (352)
T ss_pred HHHHHHHHHHHHHHHhhccHHHHHHHHHHhhhhhhhhcchh-HHhhhC
Confidence 4445555533 6788999999999999999999877676 344443
No 21
>PF14165 YtzH: YtzH-like protein
Probab=28.34 E-value=67 Score=24.34 Aligned_cols=49 Identities=10% Similarity=0.255 Sum_probs=37.8
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHHhcCCChHHHHHHHHHhhcCccCCccHHHHh
Q 031136 102 MAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVV 154 (165)
Q Consensus 102 ~~km~~Ll~~fdeEQl~RYE~fRRS~f~K~~IKKLinsvtgsQsVs~nvvIaV 154 (165)
+.++.+|-+-|++-|.++|..---. ..|+|||.+.+....|++.|-.++
T Consensus 4 ~hQl~LLkDIL~~hq~DccgTvsEc----EQieRLvksLm~n~~i~~~ik~~L 52 (87)
T PF14165_consen 4 QHQLTLLKDILSNHQLDCCGTVSEC----EQIERLVKSLMANPNIDADIKQTL 52 (87)
T ss_pred HHHHHHHHHHHHhhhhhccCcHHHH----HHHHHHHHHHHcCCCcCHHHHHHH
Confidence 4678899999999999999764432 579999999887667777765554
No 22
>PF09574 DUF2374: Protein of unknown function (Duf2374); InterPro: IPR014175 This very small protein (about 46 amino acids) consists largely of a single predicted membrane-spanning region. It is found in Photobacterium profundum SS9 and in three species of Vibrio, always near periplasmic nitrate reductase genes, but far from the periplasmic nitrate reductase genes in Aeromonas hydrophila ATCC 7966.
Probab=27.62 E-value=61 Score=21.73 Aligned_cols=29 Identities=17% Similarity=0.332 Sum_probs=21.5
Q ss_pred HHHHHHHHHhhcCccCCccHHHHhhhhhhhhc
Q 031136 131 SNMRRLLVSITGSQKISLPMTIVVCGIAKMFL 162 (165)
Q Consensus 131 ~~IKKLinsvtgsQsVs~nvvIaVaGiAKvFV 162 (165)
+++..+|.+++|. +.-.+|.++||+-|.|
T Consensus 2 StlEsviWhvLGY---~AmPvI~L~GF~~Vav 30 (42)
T PF09574_consen 2 STLESVIWHVLGY---AAMPVIILSGFAAVAV 30 (42)
T ss_pred chHHHHHHHHhcc---ccchHHHHhhHHHHHH
Confidence 3567899999985 3455788888887665
No 23
>PF08802 CytB6-F_Fe-S: Cytochrome B6-F complex Fe-S subunit ; InterPro: IPR014909 The cytochrome b6-f complex mediates electron transfer between photosystem II (PSII) and photosystem I (PSI), cyclic electron flow around PSI, and state transitions. The cytochrome b6-f complex has 4 large subunits, these are: cytochrome b6, subunit IV (17 kDa polypeptide, PetD), cytochrome f and the Rieske protein, while the 4 small subunits are: PetG, PetL, PetM and PetN. The complex functions as a dimer. This protein corresponds to the alpha helical transmembrane domain of the cytochrome b6-f complex Rieske iron-sulphur subunit. ; GO: 0009496 plastoquinol-plastocyanin reductase activity, 0051537 2 iron, 2 sulfur cluster binding, 0055114 oxidation-reduction process, 0042651 thylakoid membrane; PDB: 1Q90_R 1VF5_D 2E75_D 2E74_D 2E76_D 2D2C_Q 2ZT9_D.
Probab=26.63 E-value=22 Score=23.23 Aligned_cols=30 Identities=20% Similarity=0.419 Sum_probs=22.6
Q ss_pred HHHHHHHHhhcCccCCccHHHHhhhhhhhhc
Q 031136 132 NMRRLLVSITGSQKISLPMTIVVCGIAKMFL 162 (165)
Q Consensus 132 ~IKKLinsvtgsQsVs~nvvIaVaGiAKvFV 162 (165)
.-|+|+|-++++ .+.-+++-++-.+.|.||
T Consensus 7 ~RR~lmN~ll~G-ava~~a~~~lyP~~~ffv 36 (39)
T PF08802_consen 7 SRRQLMNLLLGG-AVAVPAGGMLYPYVKFFV 36 (39)
T ss_dssp HHHHHHHHHHHH-HHHHHHHHHHHHHHHHHS
T ss_pred hHHHHHHHHHHh-hHHHHHHHHhhhheeEec
Confidence 347888888865 567777777778888886
No 24
>PRK02922 glycogen synthesis protein GlgS; Provisional
Probab=25.59 E-value=87 Score=22.84 Aligned_cols=26 Identities=19% Similarity=0.438 Sum_probs=20.0
Q ss_pred HHHHHHHhcCCHHHH----HHHHHHHhcCC
Q 031136 103 AKMQAILNQFTEDQM----NRYESFRRSAL 128 (165)
Q Consensus 103 ~km~~Ll~~fdeEQl----~RYE~fRRS~f 128 (165)
.....+-.+||++|. +||..||.-..
T Consensus 29 Idvd~V~gnmsee~r~~F~eRla~Yr~~~~ 58 (67)
T PRK02922 29 VDIQAVTGNMDEEHRTWFCARYAWYCQQMM 58 (67)
T ss_pred ccHHHHHhcCCHHHHHHHHHHHHHHHHHHH
Confidence 345668899999996 68899987544
No 25
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.78 E-value=1.4e+02 Score=23.38 Aligned_cols=41 Identities=20% Similarity=0.404 Sum_probs=24.9
Q ss_pred HhcCCHHHHHHHHHHHhcCCChHHHHHHHHHhhcCccCCccH-HHHhhhhh
Q 031136 109 LNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPM-TIVVCGIA 158 (165)
Q Consensus 109 l~~fdeEQl~RYE~fRRS~f~K~~IKKLinsvtgsQsVs~nv-vIaVaGiA 158 (165)
+..||++|.+|+++ +..|+|+.+.--. +=-+|+ .+.++||-
T Consensus 3 ~~~ls~~q~~~leA--------AaFRrLv~HL~~r-sdvQNIDLMnLAgFC 44 (104)
T COG3492 3 MQELSEEQRDRLEA--------AAFRRLVEHLQER-SDVQNIDLMNLAGFC 44 (104)
T ss_pred hHhcCHHHHHHHHH--------HHHHHHHHHHHHh-cccchhHHHHHHHHH
Confidence 46789999999985 4566777664321 223454 34455553
No 26
>PRK10878 hypothetical protein; Provisional
Probab=24.77 E-value=1.1e+02 Score=21.92 Aligned_cols=34 Identities=9% Similarity=0.271 Sum_probs=23.4
Q ss_pred HhcCCHHHHHHHHH-------------HHhcCCChHHHHHHHHHhhc
Q 031136 109 LNQFTEDQMNRYES-------------FRRSALQKSNMRRLLVSITG 142 (165)
Q Consensus 109 l~~fdeEQl~RYE~-------------fRRS~f~K~~IKKLinsvtg 142 (165)
+..||++|+++|+. ..++.-+.+.++++|..+..
T Consensus 16 ~~~l~~~e~~~Fe~LL~~~D~dL~~W~~g~~~p~d~~l~~iV~~Ir~ 62 (72)
T PRK10878 16 YDSLSDDEKRIFIRLLECDDPDLFNWLMNHGKPADAELERMVRLIQT 62 (72)
T ss_pred HhhCCHHHHHHHHHHHcCCCHHHHHHHhCCCCCCCHHHHHHHHHHHH
Confidence 45566666666664 35677778888888877764
No 27
>PF13495 Phage_int_SAM_4: Phage integrase, N-terminal SAM-like domain; PDB: 2A3V_A.
Probab=24.31 E-value=1.4e+02 Score=19.73 Aligned_cols=30 Identities=17% Similarity=0.453 Sum_probs=18.2
Q ss_pred hcCCHHHHHHHHHHHh--cCCChHHHHHHHHH
Q 031136 110 NQFTEDQMNRYESFRR--SALQKSNMRRLLVS 139 (165)
Q Consensus 110 ~~fdeEQl~RYE~fRR--S~f~K~~IKKLins 139 (165)
..+++++..+|-.|-+ .++..++|+..++.
T Consensus 39 ~~it~~~i~~y~~~l~~~~~~s~~T~~~~~~~ 70 (85)
T PF13495_consen 39 DEITPEDIEQYLNYLQNERGLSPSTINQYLSA 70 (85)
T ss_dssp GG--HHHHHHHHHHHHTTT---HHHHHHHHHH
T ss_pred chhHHHHHHHHHHHHHHhcCCCHHHHHHHHHH
Confidence 4667888888888877 56777777776654
No 28
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=24.27 E-value=46 Score=25.94 Aligned_cols=15 Identities=27% Similarity=0.618 Sum_probs=8.5
Q ss_pred CCCcccccccccccc
Q 031136 76 DEYDEEDDENVDVEL 90 (165)
Q Consensus 76 de~~eeeed~~dv~l 90 (165)
.|+++|+||+|-+.|
T Consensus 96 ~ee~ee~ddDmgf~L 110 (112)
T PTZ00373 96 KEEEEEEEDDLGFSL 110 (112)
T ss_pred ccccccccccccccc
Confidence 344455666676654
No 29
>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=23.49 E-value=1.1e+02 Score=22.89 Aligned_cols=35 Identities=23% Similarity=0.404 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCChHHHHHHHH
Q 031136 99 PAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLV 138 (165)
Q Consensus 99 e~k~~km~~Ll~~fdeEQl~RYE~fRRS~f~K~~IKKLin 138 (165)
+.+-.|+..+|++||+++++--..+.. +.++||..
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 334578889999999999977666633 55666654
No 30
>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=23.37 E-value=81 Score=30.98 Aligned_cols=8 Identities=13% Similarity=0.094 Sum_probs=3.4
Q ss_pred HHHHhcCC
Q 031136 106 QAILNQFT 113 (165)
Q Consensus 106 ~~Ll~~fd 113 (165)
..||..+.
T Consensus 363 e~Iv~~~~ 370 (574)
T PF07462_consen 363 ENIVPEGI 370 (574)
T ss_pred hhhhcCcC
Confidence 34444443
No 31
>cd04494 BRCA2DBD_OB2 BRCA2DBD_OB2: A subfamily of OB folds corresponding to the second OB fold (OB2) of the 800-amino acid C-terminal ssDNA binding domain (DBD) of BRCA2 (breast cancer susceptibility gene 2) protein, called BRCA2DBD. BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks. It stimulates the displacement of Replication protein A (RPA), the most abundant eukaryotic ssDNA binding protein. It also facilitates filament formation. Mutations that map throughout the BRCA2 protein are associated with breast cancer susceptibility. BRCA2 is a large nuclear protein and its most conserved region is the C-terminal BRCA2DBD. BRCA2DBD binds ssDNA in vitro, and is composed of five structural domains, three of which are OB folds (OB1, OB2, and OB3). BRCA2DBD OB2 and OB3 are arranged in tandem, and their mode of binding can be considered qualitatively similar to two OB folds of RPA1, DBD-A and DBD-B (the major DBDs of RPA).
Probab=22.97 E-value=83 Score=27.68 Aligned_cols=35 Identities=11% Similarity=0.291 Sum_probs=26.5
Q ss_pred HHHhcCCHHHHHHHHHHHhcCCCh------HHHHHHHHHhh
Q 031136 107 AILNQFTEDQMNRYESFRRSALQK------SNMRRLLVSIT 141 (165)
Q Consensus 107 ~Ll~~fdeEQl~RYE~fRRS~f~K------~~IKKLinsvt 141 (165)
.|..+||++|+.=...||+.-..| ..++|.+...+
T Consensus 113 ~le~~lS~~Q~~~L~~y~~~~~~~kq~~lQ~~~~ka~~~a~ 153 (251)
T cd04494 113 FLEAELSEEQLEALSNYQQLQNEKKQARLQEEFRKAVEEAL 153 (251)
T ss_pred HHHhhCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHH
Confidence 477889999999999999987643 34556665555
No 32
>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=22.59 E-value=29 Score=34.99 Aligned_cols=10 Identities=20% Similarity=0.411 Sum_probs=0.0
Q ss_pred hcCCHHHHHH
Q 031136 110 NQFTEDQMNR 119 (165)
Q Consensus 110 ~~fdeEQl~R 119 (165)
..+++||-.|
T Consensus 720 qGi~eerAar 729 (787)
T PF03115_consen 720 QGIPEERAAR 729 (787)
T ss_dssp ----------
T ss_pred cCCCHHHHHh
Confidence 3456676665
No 33
>PLN00035 histone H4; Provisional
Probab=22.46 E-value=67 Score=24.80 Aligned_cols=36 Identities=33% Similarity=0.394 Sum_probs=28.8
Q ss_pred CChHHHHHHHHHhhcCccCCccHHHHhhhhhhhhccc
Q 031136 128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFLEW 164 (165)
Q Consensus 128 f~K~~IKKLinsvtgsQsVs~nvvIaVaGiAKvFVGE 164 (165)
|+++.|+||+... |---|+..+.-.+..+.+.|+-+
T Consensus 30 ipk~~IrRLARr~-GvkRIS~~ay~elr~vle~~l~~ 65 (103)
T PLN00035 30 ITKPAIRRLARRG-GVKRISGLIYEETRGVLKIFLEN 65 (103)
T ss_pred CCHHHHHHHHHHc-CcccchHHHHHHHHHHHHHHHHH
Confidence 9999999999875 45578888888888888777643
Done!