Query 032407
Match_columns 141
No_of_seqs 112 out of 126
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 13:41:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032407.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032407hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04719 TAFII28: hTAFII28-lik 99.6 2.1E-16 4.6E-21 114.7 2.7 37 105-141 1-37 (90)
2 KOG3219 Transcription initiati 99.6 1.1E-15 2.4E-20 124.3 6.2 48 94-141 79-126 (195)
3 COG5251 TAF40 Transcription in 99.2 1.4E-11 3E-16 100.4 5.0 39 103-141 91-129 (199)
4 cd08048 TAF11 TATA Binding Pro 99.2 1.6E-11 3.4E-16 88.0 3.7 30 112-141 1-30 (85)
5 PF13443 HTH_26: Cro/C1-type H 46.3 10 0.00022 23.8 0.9 26 114-139 8-33 (63)
6 PF08971 GlgS: Glycogen synthe 46.1 18 0.00038 25.7 2.1 23 103-125 28-54 (66)
7 PF13495 Phage_int_SAM_4: Phag 41.1 43 0.00094 21.7 3.3 32 109-140 38-71 (85)
8 PF02978 SRP_SPB: Signal pepti 40.6 38 0.00083 24.8 3.2 26 98-123 46-71 (104)
9 COG2036 HHT1 Histones H3 and H 38.5 27 0.00059 25.7 2.2 26 115-140 7-32 (91)
10 KOG3902 Histone acetyltransfer 35.6 37 0.0008 30.6 2.9 38 98-135 191-231 (352)
11 smart00529 HTH_DTXR Helix-turn 31.5 1.4E+02 0.003 20.0 4.6 30 111-140 66-95 (96)
12 PF12174 RST: RCD1-SRO-TAF4 (R 29.8 1.2E+02 0.0027 21.0 4.2 36 105-140 15-54 (70)
13 PRK02922 glycogen synthesis pr 27.3 80 0.0017 22.5 3.0 27 103-129 29-59 (67)
14 PF07462 MSP1_C: Merozoite sur 24.6 71 0.0015 30.7 3.0 8 106-113 363-370 (574)
15 PF09339 HTH_IclR: IclR helix- 24.3 73 0.0016 19.7 2.1 23 118-140 20-42 (52)
16 PF08199 E2: Bacteriophage E2- 23.4 56 0.0012 20.8 1.4 14 101-114 12-25 (37)
17 PF08281 Sigma70_r4_2: Sigma-7 22.2 1.9E+02 0.0042 17.5 4.2 31 103-133 2-32 (54)
18 PF02268 TFIIA_gamma_N: Transc 21.5 14 0.0003 24.6 -1.7 13 119-131 2-14 (49)
19 PRK13291 metal-dependent hydro 21.4 85 0.0018 24.3 2.4 35 103-139 118-152 (173)
20 PF08411 Exonuc_X-T_C: Exonucl 20.2 1.2E+02 0.0026 25.5 3.2 24 109-132 206-229 (269)
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=99.61 E-value=2.1e-16 Score=114.66 Aligned_cols=37 Identities=43% Similarity=0.843 Sum_probs=23.1
Q ss_pred HHHHHhcCCHHHHHHHHHHHhccCChHHHHHHHHhhC
Q 032407 105 MQAILNQFTEDQMNRYESFRRSALQKSNMRRLLLEWL 141 (141)
Q Consensus 105 m~~Ll~~FSeEQmdRYE~fRRS~f~Ka~VKKLinsvL 141 (141)
|++||++||+||++|||+||||+|+|++||||||+++
T Consensus 1 ~~~L~~~f~~eQ~~Rye~fRRs~~~k~~ikkli~~~~ 37 (90)
T PF04719_consen 1 MQLLLSNFDEEQLDRYEAFRRSSFNKAAIKKLINQVL 37 (90)
T ss_dssp ---------HHHHHHHHHHHH----HHHHHHHHHHHH
T ss_pred ChHHHHcCCHHHHHHHHHHHHccCCHHHHHHHHHHHc
Confidence 6899999999999999999999999999999999874
No 2
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=99.60 E-value=1.1e-15 Score=124.35 Aligned_cols=48 Identities=35% Similarity=0.681 Sum_probs=43.2
Q ss_pred CCCCcHHHHHHHHHHHhcCCHHHHHHHHHHHhccCChHHHHHHHHhhC
Q 032407 94 PSSSDPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLLEWL 141 (141)
Q Consensus 94 ~sT~dEee~~km~~Ll~~FSeEQmdRYE~fRRS~f~Ka~VKKLinsvL 141 (141)
..+.++++..+|+.||++||+|||+|||+||||+|||++|||||++|.
T Consensus 79 ~~~~~~ee~~r~q~L~s~fseEQl~RYEvfRrs~f~Ka~iKkL~~~it 126 (195)
T KOG3219|consen 79 KPTVDAEEAQRMQTLLSNFSEEQLSRYEVFRRSAFPKAQIKKLMSSIT 126 (195)
T ss_pred CCCcCHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCHHHHHHHHHHHh
Confidence 334467788899999999999999999999999999999999999874
No 3
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=99.21 E-value=1.4e-11 Score=100.35 Aligned_cols=39 Identities=31% Similarity=0.621 Sum_probs=36.9
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHhccCChHHHHHHHHhhC
Q 032407 103 AKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLLEWL 141 (141)
Q Consensus 103 ~km~~Ll~~FSeEQmdRYE~fRRS~f~Ka~VKKLinsvL 141 (141)
.+++.|+.+||+|||+|||+|||++|||.+||||+++||
T Consensus 91 ~r~k~l~~~~deeq~~RyEvFrrt~lnKt~VKKlastV~ 129 (199)
T COG5251 91 ERFKLLVTNLDEEQTNRYEVFRRTSLNKTQVKKLASTVA 129 (199)
T ss_pred HHHHHHHhhcCHHHHHHHHHHHhcCCCHHHHHHHHHHHh
Confidence 677889999999999999999999999999999999885
No 4
>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=99.19 E-value=1.6e-11 Score=88.01 Aligned_cols=30 Identities=50% Similarity=0.857 Sum_probs=28.9
Q ss_pred CCHHHHHHHHHHHhccCChHHHHHHHHhhC
Q 032407 112 FTEDQMNRYESFRRSALQKSNMRRLLLEWL 141 (141)
Q Consensus 112 FSeEQmdRYE~fRRS~f~Ka~VKKLinsvL 141 (141)
||+|||+|||+||||+|+|+.||||||+++
T Consensus 1 f~~eQ~~Rye~~Rra~f~k~~iKr~~~~~~ 30 (85)
T cd08048 1 FSEEQMNRYEMFRRSSFPKAAIKRLIQSVT 30 (85)
T ss_pred CCHHHHHHHHHHHHhhccHHHHHHHHHHHc
Confidence 899999999999999999999999999875
No 5
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=46.31 E-value=10 Score=23.79 Aligned_cols=26 Identities=19% Similarity=0.400 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHhccCChHHHHHHHHh
Q 032407 114 EDQMNRYESFRRSALQKSNMRRLLLE 139 (141)
Q Consensus 114 eEQmdRYE~fRRS~f~Ka~VKKLins 139 (141)
.-.+.+++..|++++++++|.++++.
T Consensus 8 ~~~it~~~La~~~gis~~tl~~~~~~ 33 (63)
T PF13443_consen 8 ERGITQKDLARKTGISRSTLSRILNG 33 (63)
T ss_dssp HTT--HHHHHHHHT--HHHHHHHHTT
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 44567888889999999999998875
No 6
>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=46.13 E-value=18 Score=25.68 Aligned_cols=23 Identities=30% Similarity=0.641 Sum_probs=16.3
Q ss_pred HHHHHHHhcCCHHHH----HHHHHHHh
Q 032407 103 AKMQAILNQFTEDQM----NRYESFRR 125 (141)
Q Consensus 103 ~km~~Ll~~FSeEQm----dRYE~fRR 125 (141)
..+..+..+||++|. +||+.||.
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 345668999999995 79999997
No 7
>PF13495 Phage_int_SAM_4: Phage integrase, N-terminal SAM-like domain; PDB: 2A3V_A.
Probab=41.09 E-value=43 Score=21.69 Aligned_cols=32 Identities=16% Similarity=0.371 Sum_probs=22.8
Q ss_pred HhcCCHHHHHHHHHHHh--ccCChHHHHHHHHhh
Q 032407 109 LNQFTEDQMNRYESFRR--SALQKSNMRRLLLEW 140 (141)
Q Consensus 109 l~~FSeEQmdRYE~fRR--S~f~Ka~VKKLinsv 140 (141)
+..+++++..+|-.|-+ -++..++|+..++++
T Consensus 38 ~~~it~~~i~~y~~~l~~~~~~s~~T~~~~~~~l 71 (85)
T PF13495_consen 38 PDEITPEDIEQYLNYLQNERGLSPSTINQYLSAL 71 (85)
T ss_dssp GGG--HHHHHHHHHHHHTTT---HHHHHHHHHHH
T ss_pred cchhHHHHHHHHHHHHHHhcCCCHHHHHHHHHHH
Confidence 45778999999999988 779999999888764
No 8
>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=40.58 E-value=38 Score=24.82 Aligned_cols=26 Identities=23% Similarity=0.469 Sum_probs=20.6
Q ss_pred cHHHHHHHHHHHhcCCHHHHHHHHHH
Q 032407 98 DPAKMAKMQAILNQFTEDQMNRYESF 123 (141)
Q Consensus 98 dEee~~km~~Ll~~FSeEQmdRYE~f 123 (141)
++.+..++..+|++||+++++--..+
T Consensus 46 ~~~~lk~~~~Ii~SMT~~Er~~p~ll 71 (104)
T PF02978_consen 46 DEKKLKRMEAIIDSMTPEERDNPKLL 71 (104)
T ss_dssp HHHHHHHHHHHHTTSBHHHHHCGGGH
T ss_pred hHHHHHHHHHHHHCcCHHHHhCcccc
Confidence 34556888999999999998766665
No 9
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=38.54 E-value=27 Score=25.65 Aligned_cols=26 Identities=27% Similarity=0.422 Sum_probs=23.1
Q ss_pred HHHHHHHHHHhccCChHHHHHHHHhh
Q 032407 115 DQMNRYESFRRSALQKSNMRRLLLEW 140 (141)
Q Consensus 115 EQmdRYE~fRRS~f~Ka~VKKLinsv 140 (141)
-+..||..|=.-.||++.|+|||+.+
T Consensus 7 ~~~r~~~~~~~~~Lp~apv~Ri~r~~ 32 (91)
T COG2036 7 KEIRRYQRSTDLLLPKAPVRRILRKA 32 (91)
T ss_pred HHHHhhhhhhhhhcCchHHHHHHHHH
Confidence 46789999999999999999999875
No 10
>KOG3902 consensus Histone acetyltransferase PCAF/SAGA, subunit SUPT3H/SPT3 [Transcription]
Probab=35.56 E-value=37 Score=30.62 Aligned_cols=38 Identities=16% Similarity=0.288 Sum_probs=29.1
Q ss_pred cHHHHHHHHH---HHhcCCHHHHHHHHHHHhccCChHHHHH
Q 032407 98 DPAKMAKMQA---ILNQFTEDQMNRYESFRRSALQKSNMRR 135 (141)
Q Consensus 98 dEee~~km~~---Ll~~FSeEQmdRYE~fRRS~f~Ka~VKK 135 (141)
++..+++|.. ....||-+|+-.|--+|.++|.+-.=||
T Consensus 191 devt~~RLkrADrrTrimt~eqYvefsE~RqaSFt~Rkgkr 231 (352)
T KOG3902|consen 191 DEVTMRRLKRADRRTRIMTGEQYVEFSECRQASFTCRKGKR 231 (352)
T ss_pred HHHHHHHHHHHHHHHhhccHHHHHHHHHHhhhhhhhhcchh
Confidence 4445555543 7789999999999999999998765554
No 11
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=31.46 E-value=1.4e+02 Score=19.96 Aligned_cols=30 Identities=13% Similarity=0.005 Sum_probs=27.9
Q ss_pred cCCHHHHHHHHHHHhccCChHHHHHHHHhh
Q 032407 111 QFTEDQMNRYESFRRSALQKSNMRRLLLEW 140 (141)
Q Consensus 111 ~FSeEQmdRYE~fRRS~f~Ka~VKKLinsv 140 (141)
.|++++...+-......++...+++|.|.+
T Consensus 66 ~~~~~e~~~l~~~l~~~~~~~~~~~~~~~~ 95 (96)
T smart00529 66 GVDEEEVHEEAERLEHVLSDELEDRLDRFL 95 (96)
T ss_pred CCCHHHHHHHHHHHHccCCHHHHHHHHHHh
Confidence 899999999999999999999999999864
No 12
>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=29.80 E-value=1.2e+02 Score=21.01 Aligned_cols=36 Identities=19% Similarity=0.482 Sum_probs=27.4
Q ss_pred HHHHHhcCCHHHHH----HHHHHHhccCChHHHHHHHHhh
Q 032407 105 MQAILNQFTEDQMN----RYESFRRSALQKSNMRRLLLEW 140 (141)
Q Consensus 105 m~~Ll~~FSeEQmd----RYE~fRRS~f~Ka~VKKLinsv 140 (141)
+.+|...+++.+|+ -|+.||+.+++|...=|.+..|
T Consensus 15 ~~~l~~~l~~~~~~~l~~~Y~~~k~~kIsR~~fvr~lR~I 54 (70)
T PF12174_consen 15 FSALSKHLPPSKMDLLQKHYEEFKKKKISREEFVRKLRQI 54 (70)
T ss_pred HHHHHHHCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHH
Confidence 45577778888775 6999999999998866655543
No 13
>PRK02922 glycogen synthesis protein GlgS; Provisional
Probab=27.31 E-value=80 Score=22.52 Aligned_cols=27 Identities=22% Similarity=0.455 Sum_probs=20.7
Q ss_pred HHHHHHHhcCCHHHH----HHHHHHHhccCC
Q 032407 103 AKMQAILNQFTEDQM----NRYESFRRSALQ 129 (141)
Q Consensus 103 ~km~~Ll~~FSeEQm----dRYE~fRRS~f~ 129 (141)
.....+..+||++|. +||.-||.-.+.
T Consensus 29 Idvd~V~gnmsee~r~~F~eRla~Yr~~~~~ 59 (67)
T PRK02922 29 VDIQAVTGNMDEEHRTWFCARYAWYCQQMMQ 59 (67)
T ss_pred ccHHHHHhcCCHHHHHHHHHHHHHHHHHHHH
Confidence 345668899999996 689999976543
No 14
>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=24.59 E-value=71 Score=30.65 Aligned_cols=8 Identities=13% Similarity=0.094 Sum_probs=3.6
Q ss_pred HHHHhcCC
Q 032407 106 QAILNQFT 113 (141)
Q Consensus 106 ~~Ll~~FS 113 (141)
..||..|.
T Consensus 363 e~Iv~~~~ 370 (574)
T PF07462_consen 363 ENIVPEGI 370 (574)
T ss_pred hhhhcCcC
Confidence 34444443
No 15
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=24.34 E-value=73 Score=19.73 Aligned_cols=23 Identities=35% Similarity=0.300 Sum_probs=17.6
Q ss_pred HHHHHHHhccCChHHHHHHHHhh
Q 032407 118 NRYESFRRSALQKSNMRRLLLEW 140 (141)
Q Consensus 118 dRYE~fRRS~f~Ka~VKKLinsv 140 (141)
.-=+.-++.+++|+++.|+++..
T Consensus 20 t~~eia~~~gl~~stv~r~L~tL 42 (52)
T PF09339_consen 20 TLSEIARALGLPKSTVHRLLQTL 42 (52)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHHHHHH
Confidence 34466789999999999999863
No 16
>PF08199 E2: Bacteriophage E2-like protein; InterPro: IPR013184 This is a family of short conserved proteins of 37 amino acids, described in Lactococcus phage c2 and in related phage. The function of these proteins is unknown.
Probab=23.38 E-value=56 Score=20.79 Aligned_cols=14 Identities=21% Similarity=0.574 Sum_probs=11.2
Q ss_pred HHHHHHHHHhcCCH
Q 032407 101 KMAKMQAILNQFTE 114 (141)
Q Consensus 101 e~~km~~Ll~~FSe 114 (141)
+..|.++|++|||.
T Consensus 12 k~ikrrilidnfsn 25 (37)
T PF08199_consen 12 KFIKRRILIDNFSN 25 (37)
T ss_pred HHHHHHHhhhcccc
Confidence 34788999999984
No 17
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=22.24 E-value=1.9e+02 Score=17.46 Aligned_cols=31 Identities=16% Similarity=0.147 Sum_probs=17.6
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHhccCChHHH
Q 032407 103 AKMQAILNQFTEDQMNRYESFRRSALQKSNM 133 (141)
Q Consensus 103 ~km~~Ll~~FSeEQmdRYE~fRRS~f~Ka~V 133 (141)
+.+...|..|++.|..-+..+.--+++-..|
T Consensus 2 ~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eI 32 (54)
T PF08281_consen 2 EALQQALAQLPERQREIFLLRYFQGMSYAEI 32 (54)
T ss_dssp HHHHHHHHCS-HHHHHHHHHHHTS---HHHH
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCcCHHHH
Confidence 4566678888888877777765554444333
No 18
>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=21.49 E-value=14 Score=24.59 Aligned_cols=13 Identities=46% Similarity=0.687 Sum_probs=8.4
Q ss_pred HHHHHHhccCChH
Q 032407 119 RYESFRRSALQKS 131 (141)
Q Consensus 119 RYE~fRRS~f~Ka 131 (141)
-|+.||+|.+-.+
T Consensus 2 ~yelYR~stlG~a 14 (49)
T PF02268_consen 2 YYELYRRSTLGIA 14 (49)
T ss_dssp --CGGGCSHHHHH
T ss_pred cHHHHHcchHHHH
Confidence 4899999976443
No 19
>PRK13291 metal-dependent hydrolase; Provisional
Probab=21.42 E-value=85 Score=24.30 Aligned_cols=35 Identities=17% Similarity=0.301 Sum_probs=26.0
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHhccCChHHHHHHHHh
Q 032407 103 AKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLLE 139 (141)
Q Consensus 103 ~km~~Ll~~FSeEQmdRYE~fRRS~f~Ka~VKKLins 139 (141)
+++-.|+.+|++++++|. |..+.+.+-+++-++.-
T Consensus 118 ~~~i~ll~~l~~e~l~r~--~~~~~~~~~Tl~~~l~~ 152 (173)
T PRK13291 118 KRWVALLESLTEEDLERT--FNHPDGGETTLDEAIGL 152 (173)
T ss_pred HHHHHHHHcCCHHHHHcc--cCCCCCCeeeHHHHHHH
Confidence 444559999999999987 55566777777776654
No 20
>PF08411 Exonuc_X-T_C: Exonuclease C-terminal; InterPro: IPR013620 This bacterial domain is found at the C terminus of exodeoxyribonuclease I/Exonuclease I (IPR013520 from INTERPRO), which is a single-strand specific DNA nuclease affecting recombination and expression pathways. The exonuclease I protein in Escherichia coli is associated with DNA deoxyribophosphodiesterase (dRPase) []. ; GO: 0008852 exodeoxyribonuclease I activity, 0006281 DNA repair; PDB: 2QXF_A 3C94_A 3HL8_A 3C95_A 1FXX_A 3HP9_A.
Probab=20.17 E-value=1.2e+02 Score=25.49 Aligned_cols=24 Identities=13% Similarity=0.440 Sum_probs=19.0
Q ss_pred HhcCCHHHHHHHHHHHhccCChHH
Q 032407 109 LNQFTEDQMNRYESFRRSALQKSN 132 (141)
Q Consensus 109 l~~FSeEQmdRYE~fRRS~f~Ka~ 132 (141)
-..++++++.||..||+..|....
T Consensus 206 P~tL~~~E~~~W~~~~~~rL~~~~ 229 (269)
T PF08411_consen 206 PETLSEEEQQRWQEYCQQRLTDPD 229 (269)
T ss_dssp GGG--HHHHHHHHHHHHHHS-HHH
T ss_pred hhhCCHHHHHHHHHHHHHHccCCc
Confidence 367899999999999999999877
Done!