Query 031510
Match_columns 158
No_of_seqs 105 out of 133
Neff 3.2
Searched_HMMs 46136
Date Fri Mar 29 15:08:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031510.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031510hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3219 Transcription initiati 99.9 1.3E-22 2.8E-27 167.2 9.7 63 94-157 79-141 (195)
2 PF04719 TAFII28: hTAFII28-lik 99.8 1.4E-22 3E-27 149.4 0.4 52 105-157 1-53 (90)
3 COG5251 TAF40 Transcription in 99.7 4E-17 8.7E-22 134.4 6.8 54 103-157 91-144 (199)
4 cd08048 TAF11 TATA Binding Pro 99.7 5.8E-18 1.3E-22 123.1 1.6 45 112-157 1-45 (85)
5 PF12174 RST: RCD1-SRO-TAF4 (R 59.9 29 0.00063 24.6 5.0 38 105-142 15-56 (70)
6 PF00808 CBFD_NFYB_HMF: Histon 55.3 1.7 3.8E-05 28.9 -1.7 24 126-149 1-24 (65)
7 PF02978 SRP_SPB: Signal pepti 45.0 34 0.00073 25.6 3.6 26 98-123 46-71 (104)
8 KOG3902 Histone acetyltransfer 44.3 26 0.00057 32.1 3.4 46 98-144 191-239 (352)
9 PF08971 GlgS: Glycogen synthe 43.4 20 0.00043 25.9 2.0 23 103-125 28-54 (66)
10 PF13443 HTH_26: Cro/C1-type H 40.1 20 0.00043 22.9 1.5 27 114-140 8-34 (63)
11 COG2036 HHT1 Histones H3 and H 38.1 31 0.00068 25.8 2.5 28 115-142 7-34 (91)
12 PF13495 Phage_int_SAM_4: Phag 35.8 66 0.0014 21.3 3.6 33 109-141 38-72 (85)
13 PRK13291 metal-dependent hydro 35.1 43 0.00093 26.5 3.0 39 103-143 118-156 (173)
14 PRK10878 hypothetical protein; 28.9 1.1E+02 0.0025 21.7 4.0 36 109-144 16-64 (72)
15 smart00529 HTH_DTXR Helix-turn 28.1 1.7E+02 0.0038 19.8 4.8 30 111-140 66-95 (96)
16 COG3492 Uncharacterized protei 26.9 90 0.002 24.2 3.4 33 109-150 3-35 (104)
17 PRK02922 glycogen synthesis pr 26.5 82 0.0018 22.8 2.9 27 103-129 29-59 (67)
18 COG5123 TOA2 Transcription ini 26.3 50 0.0011 26.0 1.9 30 119-149 4-33 (113)
19 cd02432 Nodulin-21_like_1 Nodu 23.7 2.2E+02 0.0048 23.7 5.5 41 103-143 75-115 (218)
20 PF11521 TFIIE-A_C-term: C-ter 22.8 75 0.0016 23.5 2.2 23 100-122 53-75 (86)
21 PF09339 HTH_IclR: IclR helix- 21.9 1.1E+02 0.0024 19.2 2.7 26 118-143 20-45 (52)
22 PF08199 E2: Bacteriophage E2- 21.7 63 0.0014 20.9 1.4 14 101-114 12-25 (37)
23 PF07462 MSP1_C: Merozoite sur 21.6 1.1E+02 0.0023 30.0 3.6 8 106-113 363-370 (574)
24 PF08281 Sigma70_r4_2: Sigma-7 20.5 1.9E+02 0.0042 17.8 3.6 34 103-136 2-35 (54)
No 1
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=99.88 E-value=1.3e-22 Score=167.24 Aligned_cols=63 Identities=25% Similarity=0.502 Sum_probs=58.8
Q ss_pred CCCCcHHHHHHHHHHHhcCCHHHHHHHHHHHhccCChHHHHHHHHHHhhcCCCCCceEEEeecc
Q 031510 94 PSSSDPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRVFIASLNSLNLVRLFMFSVTLL 157 (158)
Q Consensus 94 ~sT~~eee~~km~~Lls~FSeEQldRYE~yRRS~f~Ka~IKRLinsv~gqS~V~qnVvIAV~~~ 157 (158)
..+.++++..||+.||++||+|||+|||+||||+|||++|||||++|+||+ |++||+|||+++
T Consensus 79 ~~~~~~ee~~r~q~L~s~fseEQl~RYEvfRrs~f~Ka~iKkL~~~itg~~-v~~nv~Ia~~Gi 141 (195)
T KOG3219|consen 79 KPTVDAEEAQRMQTLLSNFSEEQLSRYEVFRRSAFPKAQIKKLMSSITGQS-VSENVAIAMAGI 141 (195)
T ss_pred CCCcCHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhCCc-cCcceeeeecch
Confidence 334467888899999999999999999999999999999999999999999 999999999986
No 2
>PF04719 TAFII28: hTAFII28-like protein conserved region; InterPro: IPR006809 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C terminus of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3 [, ].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005634 nucleus; PDB: 1BH9_B 1BH8_B.
Probab=99.85 E-value=1.4e-22 Score=149.36 Aligned_cols=52 Identities=31% Similarity=0.600 Sum_probs=35.0
Q ss_pred HHHHHhcCCHHHHHHHHHHHhccCChHHHHHHHHHHhh-cCCCCCceEEEeecc
Q 031510 105 MQAILNQFTEDQMNRYESFRRSALQKSNMRRVFIASLN-SLNLVRLFMFSVTLL 157 (158)
Q Consensus 105 m~~Lls~FSeEQldRYE~yRRS~f~Ka~IKRLinsv~g-qS~V~qnVvIAV~~~ 157 (158)
|++||++||+|||+|||+||||+|+|+.||||||+++| |+ |++||+|+|+|+
T Consensus 1 ~~~L~~~f~~eQ~~Rye~fRRs~~~k~~ikkli~~~~~~qs-v~~~v~i~v~g~ 53 (90)
T PF04719_consen 1 MQLLLSNFDEEQLDRYEAFRRSSFNKAAIKKLINQVLGNQS-VSQNVVIAVAGI 53 (90)
T ss_dssp ---------HHHHHHHHHHHH----HHHHHHHHHHHHS-S----HHHHHHHHHH
T ss_pred ChHHHHcCCHHHHHHHHHHHHccCCHHHHHHHHHHHcCCCC-CChhHHHHHHHH
Confidence 78999999999999999999999999999999999999 87 999999999985
No 3
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=99.69 E-value=4e-17 Score=134.36 Aligned_cols=54 Identities=22% Similarity=0.422 Sum_probs=52.2
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHhccCChHHHHHHHHHHhhcCCCCCceEEEeecc
Q 031510 103 AKMQAILNQFTEDQMNRYESFRRSALQKSNMRRVFIASLNSLNLVRLFMFSVTLL 157 (158)
Q Consensus 103 ~km~~Lls~FSeEQldRYE~yRRS~f~Ka~IKRLinsv~gqS~V~qnVvIAV~~~ 157 (158)
.++++|+.+||+|||+|||+|||++|||.+||||+++|+||+ |++||+|+|+++
T Consensus 91 ~r~k~l~~~~deeq~~RyEvFrrt~lnKt~VKKlastV~nQt-VspNi~I~l~g~ 144 (199)
T COG5251 91 ERFKLLVTNLDEEQTNRYEVFRRTSLNKTQVKKLASTVANQT-VSPNIRIFLQGV 144 (199)
T ss_pred HHHHHHHhhcCHHHHHHHHHHHhcCCCHHHHHHHHHHHhccc-cCCCeeeeeech
Confidence 677889999999999999999999999999999999999999 999999999986
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=99.69 E-value=5.8e-18 Score=123.14 Aligned_cols=45 Identities=33% Similarity=0.589 Sum_probs=43.8
Q ss_pred CCHHHHHHHHHHHhccCChHHHHHHHHHHhhcCCCCCceEEEeecc
Q 031510 112 FTEDQMNRYESFRRSALQKSNMRRVFIASLNSLNLVRLFMFSVTLL 157 (158)
Q Consensus 112 FSeEQldRYE~yRRS~f~Ka~IKRLinsv~gqS~V~qnVvIAV~~~ 157 (158)
||+|||+|||+||||+|+|+.||||||+++||+ |+|||+|+|++|
T Consensus 1 f~~eQ~~Rye~~Rra~f~k~~iKr~~~~~~~~~-v~~~v~i~v~gl 45 (85)
T cd08048 1 FSEEQMNRYEMFRRSSFPKAAIKRLIQSVTGQS-VSQNVVIAVAGI 45 (85)
T ss_pred CCHHHHHHHHHHHHhhccHHHHHHHHHHHcCCC-CCchHHHHHHHH
Confidence 899999999999999999999999999999998 999999999986
No 5
>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=59.86 E-value=29 Score=24.59 Aligned_cols=38 Identities=16% Similarity=0.444 Sum_probs=31.9
Q ss_pred HHHHHhcCCHHHHH----HHHHHHhccCChHHHHHHHHHHhh
Q 031510 105 MQAILNQFTEDQMN----RYESFRRSALQKSNMRRVFIASLN 142 (158)
Q Consensus 105 m~~Lls~FSeEQld----RYE~yRRS~f~Ka~IKRLinsv~g 142 (158)
+.+|...+++.+|+ -|+.||+.+++|...=|.+..|+|
T Consensus 15 ~~~l~~~l~~~~~~~l~~~Y~~~k~~kIsR~~fvr~lR~IVG 56 (70)
T PF12174_consen 15 FSALSKHLPPSKMDLLQKHYEEFKKKKISREEFVRKLRQIVG 56 (70)
T ss_pred HHHHHHHCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH
Confidence 34577777777765 699999999999999999999988
No 6
>PF00808 CBFD_NFYB_HMF: Histone-like transcription factor (CBF/NF-Y) and archaeal histone; InterPro: IPR003958 The CCAAT-binding factor (CBF) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin. The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding [, ]. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The A subunit can be split into 3 domains on the basis of sequence similarity, a non-conserved N-terminal 'A domain'; a highly-conserved central 'B domain' involved in DNA-binding; and a C-terminal 'C domain', which contains a number of glutamine and acidic residues involved in protein-protein interactions []. The A subunit shows striking similarity to the HAP3 subunit of the yeast CCAAT-binding heterotrimeric transcription factor [, ]. The Kluyveromyces lactis HAP3 protein has been predicted to contain a 4-cysteine zinc finger, which is thought to be present in similar HAP3 and CBF subunit A proteins, in which the third cysteine is replaced by a serine []. This domain is found in the CCAAT transcription factor and archaeal histones.; GO: 0043565 sequence-specific DNA binding, 0005622 intracellular; PDB: 1F1E_A 2BYM_D 2BYK_D 1HTA_A 1B67_A 1JFI_B 1KU5_B 1N1J_A 1BFM_A 1B6W_A ....
Probab=55.26 E-value=1.7 Score=28.93 Aligned_cols=24 Identities=8% Similarity=0.296 Sum_probs=15.6
Q ss_pred ccCChHHHHHHHHHHhhcCCCCCc
Q 031510 126 SALQKSNMRRVFIASLNSLNLVRL 149 (158)
Q Consensus 126 S~f~Ka~IKRLinsv~gqS~V~qn 149 (158)
..||.+.|||||...-+...|+..
T Consensus 1 ~~lP~a~vkri~k~~~~~~~vs~e 24 (65)
T PF00808_consen 1 ASLPLARVKRIMKSDPDVMRVSKE 24 (65)
T ss_dssp -SS-HHHHHHHHHHTSTTSEE-HH
T ss_pred CCCChHHHHHHhccCCCccchhHH
Confidence 369999999999998444434443
No 7
>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=45.01 E-value=34 Score=25.59 Aligned_cols=26 Identities=23% Similarity=0.469 Sum_probs=20.9
Q ss_pred cHHHHHHHHHHHhcCCHHHHHHHHHH
Q 031510 98 DPAKMAKMQAILNQFTEDQMNRYESF 123 (158)
Q Consensus 98 ~eee~~km~~Lls~FSeEQldRYE~y 123 (158)
++.+..++..+|++||+++++.-..+
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 34556899999999999999766666
No 8
>KOG3902 consensus Histone acetyltransferase PCAF/SAGA, subunit SUPT3H/SPT3 [Transcription]
Probab=44.28 E-value=26 Score=32.06 Aligned_cols=46 Identities=17% Similarity=0.260 Sum_probs=35.5
Q ss_pred cHHHHHHHHH---HHhcCCHHHHHHHHHHHhccCChHHHHHHHHHHhhcC
Q 031510 98 DPAKMAKMQA---ILNQFTEDQMNRYESFRRSALQKSNMRRVFIASLNSL 144 (158)
Q Consensus 98 ~eee~~km~~---Lls~FSeEQldRYE~yRRS~f~Ka~IKRLinsv~gqS 144 (158)
++..+++|.. ....||-+|+-.|--.|..+|.+..=|| ....+|.|
T Consensus 191 devt~~RLkrADrrTrimt~eqYvefsE~RqaSFt~Rkgkr-FRdwld~s 239 (352)
T KOG3902|consen 191 DEVTMRRLKRADRRTRIMTGEQYVEFSECRQASFTCRKGKR-FRDWLDLS 239 (352)
T ss_pred HHHHHHHHHHHHHHHhhccHHHHHHHHHHhhhhhhhhcchh-HHhhhCCc
Confidence 3444555543 7788999999999999999999888777 56666665
No 9
>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=43.40 E-value=20 Score=25.86 Aligned_cols=23 Identities=30% Similarity=0.641 Sum_probs=16.2
Q ss_pred HHHHHHHhcCCHHHH----HHHHHHHh
Q 031510 103 AKMQAILNQFTEDQM----NRYESFRR 125 (158)
Q Consensus 103 ~km~~Lls~FSeEQl----dRYE~yRR 125 (158)
..+..+..+||++|. +||+.||.
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 10
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=40.08 E-value=20 Score=22.92 Aligned_cols=27 Identities=15% Similarity=0.384 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHhccCChHHHHHHHHHH
Q 031510 114 EDQMNRYESFRRSALQKSNMRRVFIAS 140 (158)
Q Consensus 114 eEQldRYE~yRRS~f~Ka~IKRLinsv 140 (158)
+-.+.+++..|++++++++|.++++.-
T Consensus 8 ~~~it~~~La~~~gis~~tl~~~~~~~ 34 (63)
T PF13443_consen 8 ERGITQKDLARKTGISRSTLSRILNGK 34 (63)
T ss_dssp HTT--HHHHHHHHT--HHHHHHHHTTT
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHhcc
Confidence 445688899999999999999999843
No 11
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=38.12 E-value=31 Score=25.80 Aligned_cols=28 Identities=21% Similarity=0.350 Sum_probs=24.6
Q ss_pred HHHHHHHHHHhccCChHHHHHHHHHHhh
Q 031510 115 DQMNRYESFRRSALQKSNMRRVFIASLN 142 (158)
Q Consensus 115 EQldRYE~yRRS~f~Ka~IKRLinsv~g 142 (158)
-+..||..|-.-.||++.|+||+....-
T Consensus 7 ~~~r~~~~~~~~~Lp~apv~Ri~r~~~~ 34 (91)
T COG2036 7 KEIRRYQRSTDLLLPKAPVRRILRKAGA 34 (91)
T ss_pred HHHHhhhhhhhhhcCchHHHHHHHHHhH
Confidence 4678999999999999999999998764
No 12
>PF13495 Phage_int_SAM_4: Phage integrase, N-terminal SAM-like domain; PDB: 2A3V_A.
Probab=35.83 E-value=66 Score=21.25 Aligned_cols=33 Identities=15% Similarity=0.320 Sum_probs=23.2
Q ss_pred HhcCCHHHHHHHHHHHh--ccCChHHHHHHHHHHh
Q 031510 109 LNQFTEDQMNRYESFRR--SALQKSNMRRVFIASL 141 (158)
Q Consensus 109 ls~FSeEQldRYE~yRR--S~f~Ka~IKRLinsv~ 141 (158)
+..+++++..+|-.|-+ -++..++|+..++++-
T Consensus 38 ~~~it~~~i~~y~~~l~~~~~~s~~T~~~~~~~l~ 72 (85)
T PF13495_consen 38 PDEITPEDIEQYLNYLQNERGLSPSTINQYLSALR 72 (85)
T ss_dssp GGG--HHHHHHHHHHHHTTT---HHHHHHHHHHHH
T ss_pred cchhHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHH
Confidence 35677999999999988 6789999998887653
No 13
>PRK13291 metal-dependent hydrolase; Provisional
Probab=35.09 E-value=43 Score=26.46 Aligned_cols=39 Identities=15% Similarity=0.220 Sum_probs=31.2
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHhccCChHHHHHHHHHHhhc
Q 031510 103 AKMQAILNQFTEDQMNRYESFRRSALQKSNMRRVFIASLNS 143 (158)
Q Consensus 103 ~km~~Lls~FSeEQldRYE~yRRS~f~Ka~IKRLinsv~gq 143 (158)
+++-.|+.+|++++++|. +..+.+.+-+++-++..+++.
T Consensus 118 ~~~i~ll~~l~~e~l~r~--~~~~~~~~~Tl~~~l~~~~~H 156 (173)
T PRK13291 118 KRWVALLESLTEEDLERT--FNHPDGGETTLDEAIGLYAWH 156 (173)
T ss_pred HHHHHHHHcCCHHHHHcc--cCCCCCCeeeHHHHHHHHHHH
Confidence 445559999999999987 566678888999988887764
No 14
>PRK10878 hypothetical protein; Provisional
Probab=28.87 E-value=1.1e+02 Score=21.75 Aligned_cols=36 Identities=6% Similarity=0.151 Sum_probs=25.6
Q ss_pred HhcCCHHHHHHHHH-------------HHhccCChHHHHHHHHHHhhcC
Q 031510 109 LNQFTEDQMNRYES-------------FRRSALQKSNMRRVFIASLNSL 144 (158)
Q Consensus 109 ls~FSeEQldRYE~-------------yRRS~f~Ka~IKRLinsv~gqS 144 (158)
+..+|++|+++||. ..++.-+++.++++|..|.+..
T Consensus 16 ~~~l~~~e~~~Fe~LL~~~D~dL~~W~~g~~~p~d~~l~~iV~~Ir~~~ 64 (72)
T PRK10878 16 YDSLSDDEKRIFIRLLECDDPDLFNWLMNHGKPADAELERMVRLIQTRN 64 (72)
T ss_pred HhhCCHHHHHHHHHHHcCCCHHHHHHHhCCCCCCCHHHHHHHHHHHHhc
Confidence 44556666666653 4678888999999999888743
No 15
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=28.06 E-value=1.7e+02 Score=19.83 Aligned_cols=30 Identities=10% Similarity=-0.025 Sum_probs=27.7
Q ss_pred cCCHHHHHHHHHHHhccCChHHHHHHHHHH
Q 031510 111 QFTEDQMNRYESFRRSALQKSNMRRVFIAS 140 (158)
Q Consensus 111 ~FSeEQldRYE~yRRS~f~Ka~IKRLinsv 140 (158)
.|++++...+-......++...++++.+.+
T Consensus 66 ~~~~~e~~~l~~~l~~~~~~~~~~~~~~~~ 95 (96)
T smart00529 66 GVDEEEVHEEAERLEHVLSDELEDRLDRFL 95 (96)
T ss_pred CCCHHHHHHHHHHHHccCCHHHHHHHHHHh
Confidence 899999999999999999999999998854
No 16
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.93 E-value=90 Score=24.24 Aligned_cols=33 Identities=21% Similarity=0.321 Sum_probs=23.7
Q ss_pred HhcCCHHHHHHHHHHHhccCChHHHHHHHHHHhhcCCCCCce
Q 031510 109 LNQFTEDQMNRYESFRRSALQKSNMRRVFIASLNSLNLVRLF 150 (158)
Q Consensus 109 ls~FSeEQldRYE~yRRS~f~Ka~IKRLinsv~gqS~V~qnV 150 (158)
+.++|++|.+|+|+ ++.|||+...--.| =-|||
T Consensus 3 ~~~ls~~q~~~leA--------AaFRrLv~HL~~rs-dvQNI 35 (104)
T COG3492 3 MQELSEEQRDRLEA--------AAFRRLVEHLQERS-DVQNI 35 (104)
T ss_pred hHhcCHHHHHHHHH--------HHHHHHHHHHHHhc-ccchh
Confidence 45789999999885 56677887766665 44554
No 17
>PRK02922 glycogen synthesis protein GlgS; Provisional
Probab=26.52 E-value=82 Score=22.83 Aligned_cols=27 Identities=22% Similarity=0.455 Sum_probs=20.6
Q ss_pred HHHHHHHhcCCHHHH----HHHHHHHhccCC
Q 031510 103 AKMQAILNQFTEDQM----NRYESFRRSALQ 129 (158)
Q Consensus 103 ~km~~Lls~FSeEQl----dRYE~yRRS~f~ 129 (158)
.....+..+||++|. +||.-||.-..+
T Consensus 29 Idvd~V~gnmsee~r~~F~eRla~Yr~~~~~ 59 (67)
T PRK02922 29 VDIQAVTGNMDEEHRTWFCARYAWYCQQMMQ 59 (67)
T ss_pred ccHHHHHhcCCHHHHHHHHHHHHHHHHHHHH
Confidence 345668899999996 689999975543
No 18
>COG5123 TOA2 Transcription initiation factor IIA, gamma subunit [Transcription]
Probab=26.26 E-value=50 Score=25.97 Aligned_cols=30 Identities=20% Similarity=0.163 Sum_probs=18.0
Q ss_pred HHHHHHhccCChHHHHHHHHHHhhcCCCCCc
Q 031510 119 RYESFRRSALQKSNMRRVFIASLNSLNLVRL 149 (158)
Q Consensus 119 RYE~yRRS~f~Ka~IKRLinsv~gqS~V~qn 149 (158)
-||.||||.+-|.-.+ .+...+++-.+.++
T Consensus 4 yYElYRrs~ig~~L~d-alD~lis~g~isp~ 33 (113)
T COG5123 4 YYELYRRSMIGKVLED-ALDELISAGVISPN 33 (113)
T ss_pred HHHHHHHHHHHHHHHH-HHHHHHhcCCcCHH
Confidence 3999999988765443 33444444434443
No 19
>cd02432 Nodulin-21_like_1 Nodulin-21 and CCC1-related protein family. Nodulin-21_like_1: This is a family of proteins closely related to nodulin-21, a plant nodule-specific protein that may be involved in symbiotic nitrogen fixation. This family is also related to CCC1, a yeast vacuole transmembrane protein that functions as an iron and manganese transporter.
Probab=23.70 E-value=2.2e+02 Score=23.73 Aligned_cols=41 Identities=7% Similarity=0.059 Sum_probs=34.4
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHhccCChHHHHHHHHHHhhc
Q 031510 103 AKMQAILNQFTEDQMNRYESFRRSALQKSNMRRVFIASLNS 143 (158)
Q Consensus 103 ~km~~Lls~FSeEQldRYE~yRRS~f~Ka~IKRLinsv~gq 143 (158)
+..+.|-.+...|..+=++.|++.+|++...+++.+.+...
T Consensus 75 ~e~~~i~~~p~~e~~el~~~~~~~G~~~~~a~~~a~~l~~~ 115 (218)
T cd02432 75 KERRELAEDPEAELEELADIYEERGLSPELARQVADELMAK 115 (218)
T ss_pred HHHHHHHhCcHHHHHHHHHHHHHcCCCHHHHHHHHHHHhhc
Confidence 44555778888888888999999999999999999988743
No 20
>PF11521 TFIIE-A_C-term: C-terminal general transcription factor TFIIE alpha; InterPro: IPR021600 TFIIE is compiled of two subunits, alpha and beta. This family of proteins are the C-terminal domain of the alpha subunit of the protein which is the largest subunit and contains several functional domains which are important for basal transcription and cell growth. The C-terminal end of the protein binds directly to the amino-terminal PH domain of p62/Tfb1 (of IIH) which is involved in the recruitment of the general transcription factor IIH to the transcription preinitiation complex. P53 competes for the same binding site as TFIIE alpha which shows their structural similarity. Like p53, TFIIE alpha 336-439 can activate transcription in vivo []. ; PDB: 2RNR_A 2RNQ_A 2JTX_A.
Probab=22.76 E-value=75 Score=23.54 Aligned_cols=23 Identities=13% Similarity=0.339 Sum_probs=16.2
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHH
Q 031510 100 AKMAKMQAILNQFTEDQMNRYES 122 (158)
Q Consensus 100 ee~~km~~Lls~FSeEQldRYE~ 122 (158)
.+....-.||+.||++..+.|-.
T Consensus 53 ~eVtq~p~LV~qMT~~EKEaYi~ 75 (86)
T PF11521_consen 53 SEVTQRPELVAQMTPEEKEAYIQ 75 (86)
T ss_dssp HHHHH-HHHHHHS-HHHHHHHHH
T ss_pred hhcCcchHHHHHcCHHHHHHHHH
Confidence 44455567999999999999954
No 21
>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=21.88 E-value=1.1e+02 Score=19.23 Aligned_cols=26 Identities=23% Similarity=0.236 Sum_probs=20.6
Q ss_pred HHHHHHHhccCChHHHHHHHHHHhhc
Q 031510 118 NRYESFRRSALQKSNMRRVFIASLNS 143 (158)
Q Consensus 118 dRYE~yRRS~f~Ka~IKRLinsv~gq 143 (158)
.-=|.=++.+++|+++.|+++.....
T Consensus 20 t~~eia~~~gl~~stv~r~L~tL~~~ 45 (52)
T PF09339_consen 20 TLSEIARALGLPKSTVHRLLQTLVEE 45 (52)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 45567789999999999999987654
No 22
>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=21.71 E-value=63 Score=20.88 Aligned_cols=14 Identities=21% Similarity=0.574 Sum_probs=11.2
Q ss_pred HHHHHHHHHhcCCH
Q 031510 101 KMAKMQAILNQFTE 114 (158)
Q Consensus 101 e~~km~~Lls~FSe 114 (158)
+..|.++|++|||.
T Consensus 12 k~ikrrilidnfsn 25 (37)
T PF08199_consen 12 KFIKRRILIDNFSN 25 (37)
T ss_pred HHHHHHHhhhcccc
Confidence 45788999999984
No 23
>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=21.60 E-value=1.1e+02 Score=29.98 Aligned_cols=8 Identities=13% Similarity=0.094 Sum_probs=3.6
Q ss_pred HHHHhcCC
Q 031510 106 QAILNQFT 113 (158)
Q Consensus 106 ~~Lls~FS 113 (158)
..||..|.
T Consensus 363 e~Iv~~~~ 370 (574)
T PF07462_consen 363 ENIVPEGI 370 (574)
T ss_pred hhhhcCcC
Confidence 34444444
No 24
>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=20.53 E-value=1.9e+02 Score=17.82 Aligned_cols=34 Identities=15% Similarity=0.163 Sum_probs=21.0
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHhccCChHHHHHH
Q 031510 103 AKMQAILNQFTEDQMNRYESFRRSALQKSNMRRV 136 (158)
Q Consensus 103 ~km~~Lls~FSeEQldRYE~yRRS~f~Ka~IKRL 136 (158)
+.++..|..|++.|..-+..+.--+++-..|-+.
T Consensus 2 ~~l~~~l~~L~~~~r~i~~l~~~~g~s~~eIa~~ 35 (54)
T PF08281_consen 2 EALQQALAQLPERQREIFLLRYFQGMSYAEIAEI 35 (54)
T ss_dssp HHHHHHHHCS-HHHHHHHHHHHTS---HHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCcCHHHHHHH
Confidence 4566788888888888888776666655554443
Done!