Query T0521 pf110239_CAD, Plasmodium Falciparum, 179 residues
Match_columns 179
No_of_seqs 127 out of 3519
Neff 8.7
Searched_HMMs 11830
Date Fri May 21 18:05:17 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/hhm/T0521.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/hhm/T0521.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10591 SPARC_Ca_bdg: Secrete 98.6 4.6E-09 3.9E-13 68.5 1.9 62 34-95 50-111 (113)
2 PF10591 SPARC_Ca_bdg: Secrete 98.3 2.1E-07 1.8E-11 58.9 3.8 63 103-173 50-112 (113)
3 PF00036 efhand: EF hand; Int 97.2 1E-04 8.4E-09 43.6 3.2 27 40-66 2-28 (29)
4 PF00036 efhand: EF hand; Int 96.7 0.00039 3.3E-08 40.2 2.7 26 109-134 2-27 (29)
5 PF05042 Caleosin: Caleosin re 95.4 0.049 4.2E-06 28.2 8.7 124 39-165 8-162 (174)
6 PF09279 efhand_like: Phosphoi 92.7 0.03 2.5E-06 29.4 2.8 65 109-178 2-70 (83)
7 PF08726 efhand_Ca_insen: Ca2+ 88.3 0.039 3.3E-06 28.8 0.1 64 105-175 4-67 (69)
8 PF05099 TerB: Tellurite resis 85.6 0.15 1.2E-05 25.5 1.9 93 50-144 35-136 (140)
9 PF05517 p25-alpha: p25-alpha 81.3 0.96 8.2E-05 20.8 4.6 60 40-99 4-68 (154)
10 PF03979 Sigma70_r1_1: Sigma-7 53.0 5.1 0.00043 16.6 5.1 46 38-85 7-52 (82)
11 PF07879 PHB_acc_N: PHB/PHA ac 46.4 6.6 0.00055 16.0 3.2 21 114-134 10-30 (64)
12 PF00046 Homeobox: Homeobox do 46.2 6.6 0.00056 16.0 5.2 45 31-80 6-50 (57)
13 PF08976 DUF1880: Domain of un 33.6 5.1 0.00044 16.6 0.8 27 70-96 5-31 (118)
14 PF09069 efhand_2: EF-hand; I 31.8 11 0.00095 14.7 4.3 25 40-65 5-29 (90)
15 PF07499 RuvA_C: RuvA, C-termi 25.5 15 0.0012 14.0 3.7 38 57-96 3-40 (47)
16 PF01397 Terpene_synth: Terpen 21.7 17 0.0015 13.6 5.6 94 36-133 28-135 (184)
17 PF09068 efhand_1: EF hand; I 21.1 18 0.0015 13.5 7.6 95 25-134 28-124 (127)
No 1
>PF10591 SPARC_Ca_bdg: Secreted protein acidic and rich in cysteine Ca binding region; PDB: 1sra_A 1bmo_B 2v53_A 1nub_A.
Probab=98.60 E-value=4.6e-09 Score=68.45 Aligned_cols=62 Identities=26% Similarity=0.395 Sum_probs=42.5
Q ss_pred HHHHHHHHHHHHHHCCCCCCEEEHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCHHHHHHHH
Q ss_conf 88999999999983879898070889998773179998899999998643200001112333
Q T0521 34 NNHIKYINELFYKLDTNHNGSLSHREIYTVLASVGIKKWDINRILQALDINDRGNITYTEFM 95 (179)
Q Consensus 34 ~e~i~~l~~~F~~~D~d~dG~Is~~El~~~l~~~g~~~~ei~~i~~~~D~d~~g~I~f~EFi 95 (179)
++....+...|..+|.|+||.|+.+|+..+...+..++.-+..++..+|.|++|.|++.||+
T Consensus 50 ~~~~~~~~~~F~~lD~n~Dg~L~~~El~~~~~~l~~~e~c~~~f~~~cD~n~Dg~Is~~E~~ 111 (113)
T PF10591_consen 50 QECKEELHWMFKQLDKNGDGVLSRSELKPLRAPLVPMEHCIEKFLKECDVNKDGKISLEEWC 111 (113)
T ss_dssp GGGHHHHHHH------T----B-TTTTGGGGSTTSTTGGGHHHHHHHH-TT-SSSB-HHHH-
T ss_pred HHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHH
T ss_conf 88899999999986888889818999999999863349999999998189899989999783
No 2
>PF10591 SPARC_Ca_bdg: Secreted protein acidic and rich in cysteine Ca binding region; PDB: 1sra_A 1bmo_B 2v53_A 1nub_A.
Probab=98.28 E-value=2.1e-07 Score=58.94 Aligned_cols=63 Identities=27% Similarity=0.354 Sum_probs=52.0
Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHH
Q ss_conf 00001234444432148996147899999985179998999999998364889865443335548899999
Q T0521 103 NIESTFLKAAFNKIDKDEDGYISKSDIVSLVHDKVLDNNDIDNFFLSVHSIKKGIPREHIINKISFQEFKD 173 (179)
Q Consensus 103 ~~~~~~l~~aF~~~D~d~~G~I~~~el~~~l~~~~~~~~~~~~~~~~~d~~~dg~~~~~~~~~i~~~EF~~ 173 (179)
....+.+...|..+|.|++|+|+.+||+.+..........+..++..+|.|+||. ||+.||..
T Consensus 50 ~~~~~~~~~~F~~lD~n~Dg~L~~~El~~~~~~l~~~e~c~~~f~~~cD~n~Dg~--------Is~~E~~~ 112 (113)
T PF10591_consen 50 QECKEELHWMFKQLDKNGDGVLSRSELKPLRAPLVPMEHCIEKFLKECDVNKDGK--------ISLEEWCK 112 (113)
T ss_dssp GGGHHHHHHH------T----B-TTTTGGGGSTTSTTGGGHHHHHHHH-TT-SSS--------B-HHHH--
T ss_pred HHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC--------CCHHHHHC
T ss_conf 8889999999998688888981899999999986334999999999818989998--------99997835
No 3
>PF00036 efhand: EF hand; InterPro: IPR002048 Many calcium-binding proteins belong to the same evolutionary family and share a type of calcium-binding domain known as the EF-hand. This type of domain consists of a twelve residue loop flanked on both side by a twelve residue alpha-helical domain. In an EF-hand loop the calcium ion is coordinated in a pentagonal bipyramidal configuration. The six residues involved in the binding are in positions 1, 3, 5, 7, 9 and 12; these residues are denoted by X, Y, Z, -Y, -X and -Z. The invariant Glu or Asp at position 12 provides two oxygens for liganding Ca (bidentate ligand).; GO: 0005509 calcium ion binding; PDB: 1rsw_A 1cb1_A 1rsx_A 3icb_A 1rt0_A 1d1o_A 1cdn_A 4icb_A 2bcb_A 1ksm_A ....
Probab=97.17 E-value=1e-04 Score=43.61 Aligned_cols=27 Identities=30% Similarity=0.584 Sum_probs=17.0
Q ss_pred HHHHHHHHCCCCCCEEEHHHHHHHHHC
Q ss_conf 999999838798980708899987731
Q T0521 40 INELFYKLDTNHNGSLSHREIYTVLAS 66 (179)
Q Consensus 40 l~~~F~~~D~d~dG~Is~~El~~~l~~ 66 (179)
++++|..+|+|+||+|+++||..+++.
T Consensus 2 ~~~~f~~~D~d~dG~I~~~Ef~~~l~~ 28 (29)
T PF00036_consen 2 LKEMFREFDKDGDGKISFDEFKEMLKS 28 (29)
T ss_dssp HHHHHHHHSTTTSSCBEHHHHHHHHHH
T ss_pred HHHHHHHHCCCCCCCCCHHHHHHHHHH
T ss_conf 889999878999996969999999984
No 4
>PF00036 efhand: EF hand; InterPro: IPR002048 Many calcium-binding proteins belong to the same evolutionary family and share a type of calcium-binding domain known as the EF-hand. This type of domain consists of a twelve residue loop flanked on both side by a twelve residue alpha-helical domain. In an EF-hand loop the calcium ion is coordinated in a pentagonal bipyramidal configuration. The six residues involved in the binding are in positions 1, 3, 5, 7, 9 and 12; these residues are denoted by X, Y, Z, -Y, -X and -Z. The invariant Glu or Asp at position 12 provides two oxygens for liganding Ca (bidentate ligand).; GO: 0005509 calcium ion binding; PDB: 1rsw_A 1cb1_A 1rsx_A 3icb_A 1rt0_A 1d1o_A 1cdn_A 4icb_A 2bcb_A 1ksm_A ....
Probab=96.66 E-value=0.00039 Score=40.22 Aligned_cols=26 Identities=38% Similarity=0.613 Sum_probs=13.9
Q ss_pred HHHHHHHHCCCCCCCCCHHHHHHHHH
Q ss_conf 34444432148996147899999985
Q T0521 109 LKAAFNKIDKDEDGYISKSDIVSLVH 134 (179)
Q Consensus 109 l~~aF~~~D~d~~G~I~~~el~~~l~ 134 (179)
++.+|+.+|+||+|+|+.+|++.+++
T Consensus 2 ~~~~f~~~D~d~dG~I~~~Ef~~~l~ 27 (29)
T PF00036_consen 2 LKEMFREFDKDGDGKISFDEFKEMLK 27 (29)
T ss_dssp HHHHHHHHSTTTSSCBEHHHHHHHHH
T ss_pred HHHHHHHHCCCCCCCCCHHHHHHHHH
T ss_conf 88999987899999696999999998
No 5
>PF05042 Caleosin: Caleosin related protein; InterPro: IPR007736 This family contains plant proteins related to caleosin. Caleosins contain calcium-binding domains and have an oleosin-like association with lipid bodies. Caleosins are present at relatively low levels and are mainly bound to microsomal membrane fractions at the early stages of seed development. As the seeds mature, overall levels of caleosins increased dramatically and they were associated almost exclusively with storage lipid bodies . The calcium binding domain is probably related to the calcium-binding EF-hands motif IPR002048 from INTERPRO.
Probab=95.45 E-value=0.049 Score=28.17 Aligned_cols=124 Identities=12% Similarity=0.140 Sum_probs=72.9
Q ss_pred HHHHHHHHHCCCCCCEEEHHHHHHHHHCCCCCHHHHHHHHHHHHHHH-CCHHHHHHHH-----HHHH----HH-------
Q ss_conf 99999998387989807088999877317999889999999864320-0001112333-----3221----00-------
Q T0521 39 YINELFYKLDTNHNGSLSHREIYTVLASVGIKKWDINRILQALDIND-RGNITYTEFM-----AGCY----RW------- 101 (179)
Q Consensus 39 ~l~~~F~~~D~d~dG~Is~~El~~~l~~~g~~~~ei~~i~~~~D~d~-~g~I~f~EFi-----~~~~----~~------- 101 (179)
.|.+...-+|+|+||.|...|-...++.+|...--. ++..+=.+. -++.+...++ .+-+ .-
T Consensus 8 vLQqHvaFFDrd~DGiIyP~eTy~GfralGf~~~~S--~~~a~~In~~lSy~T~p~w~P~p~f~Iyv~nIhk~kHGSDsg 85 (174)
T PF05042_consen 8 VLQQHVAFFDRDKDGIIYPWETYQGFRALGFNILLS--LLAAIIINGALSYPTRPSWLPSPFFPIYVKNIHKAKHGSDSG 85 (174)
T ss_pred HHHHHHHHCCCCCCCEECHHHHHHHHHHHCCCHHHH--HHHHHHHHCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCC
T ss_conf 888767523789994687589877999918669999--999999854668877788899983068624000045368765
Q ss_pred -----HHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHCCC--C-------HHHHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf -----0000012344444321489961478999999851799--9-------89999999983648898654433355
Q T0521 102 -----KNIESTFLKAAFNKIDKDEDGYISKSDIVSLVHDKVL--D-------NNDIDNFFLSVHSIKKGIPREHIINK 165 (179)
Q Consensus 102 -----~~~~~~~l~~aF~~~D~d~~G~I~~~el~~~l~~~~~--~-------~~~~~~~~~~~d~~~dg~~~~~~~~~ 165 (179)
...-.++...+|.+++..+.+.+|..|+.+++++... + ..++.-+ -.+-.+.||.........
T Consensus 86 ~YD~eGRFvp~kFEeIFsKya~~~pd~LT~~El~~ml~~nR~~~D~~GW~aa~~EW~~l-y~L~~d~dG~l~Ke~vR~ 162 (174)
T PF05042_consen 86 TYDTEGRFVPQKFEEIFSKYARTRPDALTFDELWEMLKGNRNPNDPFGWFAAFFEWGLL-YILAKDKDGFLHKEDVRG 162 (174)
T ss_pred CCCCCCCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHHH-HHHHCCCCCCCCHHHHHH
T ss_conf 34677868679999999984778987548999999999656867732112678589999-998607058751888877
No 6
>PF09279 efhand_like: Phosphoinositide-specific phospholipase C, efhand-like; InterPro: IPR015359 This domain is predominantly found in the enzyme phosphoinositol-specific phospholipase C. It adopts a structure consisting of a core of four alpha helices, in an EF like fold, and is required for functioning of the enzyme . ; PDB: 2fju_B 2zkm_X 1djg_B 1djy_B 2isd_A 1qat_B 1djz_B 1dji_B 1djh_B 1djx_A ....
Probab=92.67 E-value=0.03 Score=29.44 Aligned_cols=65 Identities=14% Similarity=0.382 Sum_probs=31.4
Q ss_pred HHHHHHHHCCCCCCCCCHHHHHHHHHHC----CCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf 3444443214899614789999998517----999899999999836488986544333554889999998620
Q T0521 109 LKAAFNKIDKDEDGYISKSDIVSLVHDK----VLDNNDIDNFFLSVHSIKKGIPREHIINKISFQEFKDYMLST 178 (179)
Q Consensus 109 l~~aF~~~D~d~~G~I~~~el~~~l~~~----~~~~~~~~~~~~~~d~~~dg~~~~~~~~~i~~~EF~~~m~~~ 178 (179)
|..+|..+.. +.+++|.++|...+... ..+...+.+++.....+.. ....+.++.++|..+|.|.
T Consensus 2 i~~if~~ys~-~~~~mt~~~l~~FL~~~Q~e~~~~~~~~~~ii~~~e~~~~----~~~~~~ls~dgF~~yL~S~ 70 (83)
T PF09279_consen 2 IEEIFKKYSS-NKEYMTAEELRRFLREEQGEPRLDEEQAKEIIEKYEPNEE----NKQRGQLSLDGFTRYLFSD 70 (83)
T ss_dssp HHCCHHHH-----SSEEHHHHHHHHHHTS--ST---HHHHHHHHHH---HH----HHHTTEEE----HHHHHS-
T ss_pred HHHHHHHHCC-CCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCHH----HHHCCCCCHHHHHHHHCCC
T ss_conf 8999999818-9995689999999999745731529999999999811275----6654782999999997798
No 7
>PF08726 efhand_Ca_insen: Ca2+ insensitive EF hand; InterPro: IPR014837 EF hands are helix-loop-helix binding motifs involved in the regulation of many cellular processes. EF hands usually bind to Ca2+ ions, which cause a major conformational change that allows the protein to interact with its designated targets. This protein corresponds to an EF hand which has partially or entirely lost its calcium-binding properties. The calcium insensitive EF hand is still able to mediate protein-protein recognition . ; PDB: 1h8b_A 1sjj_B.
Probab=88.31 E-value=0.039 Score=28.78 Aligned_cols=64 Identities=13% Similarity=0.229 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf 00123444443214899614789999998517999899999999836488986544333554889999998
Q T0521 105 ESTFLKAAFNKIDKDEDGYISKSDIVSLVHDKVLDNNDIDNFFLSVHSIKKGIPREHIINKISFQEFKDYM 175 (179)
Q Consensus 105 ~~~~l~~aF~~~D~d~~G~I~~~el~~~l~~~~~~~~~~~~~~~~~d~~~dg~~~~~~~~~i~~~EF~~~m 175 (179)
+.+.+..||+.+ .++.++||.+||++.+.. +..+-+...+..-. |.-.....+..+|..|..-|
T Consensus 4 TaEqv~~aFr~l-A~~KpYIT~~dL~~~L~p-----e~aey~~~~M~~~~-g~~~~~~~~~~DY~sf~~~l 67 (69)
T PF08726_consen 4 TAEQVIEAFRAL-AGGKPYITEEDLRRSLTP-----EQAEYCIQRMPPYE-GPDGDAIPGAYDYISFMRSL 67 (69)
T ss_dssp TCHHHHHHHHCC-TTS-SCE-HHHHHHHS-C-----CCHHHHHCCSEC-------------EECHHHHCCH
T ss_pred CHHHHHHHHHHH-HCCCCCCCHHHHHHHCCC-----HHHHHHHHHCCCCC-CCCCCCCCCCCCHHHHHHHH
T ss_conf 799999999999-779980169999987080-----88999999884768-98767898874899999998
No 8
>PF05099 TerB: Tellurite resistance protein TerB; InterPro: IPR007791 This family contains the TerB tellurite resistance proteins from a number of bacteria.; PDB: 2h5n_A 2jxu_A.
Probab=85.64 E-value=0.15 Score=25.45 Aligned_cols=93 Identities=15% Similarity=0.243 Sum_probs=58.1
Q ss_pred CCCCEEEHHHHHHHHH----CCCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHH-H-HHHHHHHHHHHHHHCCCCCCC
Q ss_conf 9898070889998773----179998899999998643200001112333322100-0-000012344444321489961
Q T0521 50 NHNGSLSHREIYTVLA----SVGIKKWDINRILQALDINDRGNITYTEFMAGCYRW-K-NIESTFLKAAFNKIDKDEDGY 123 (179)
Q Consensus 50 d~dG~Is~~El~~~l~----~~g~~~~ei~~i~~~~D~d~~g~I~f~EFi~~~~~~-~-~~~~~~l~~aF~~~D~d~~G~ 123 (179)
--||.|+.+|...+.. ..++++.+...++..+..-.....++.+++...... . .....-+..++.+... ||.
T Consensus 35 ~aDG~v~~~E~~~i~~~l~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~~~r~~ll~~l~~ia~A--DG~ 112 (140)
T PF05099_consen 35 KADGEVSEEEIEAIRRLLRERFGLDDEEAQELIEAFNELKQEPIDLEELLRELAEALSPEEREELLEALWAIAYA--DGE 112 (140)
T ss_dssp H------CHHHHHHHHHHGCTGGGSCHHHHHHHHHHCHHHHHTS-HHHHHHHHCTS--HHHHHHHHHH--TTTT------
T ss_pred HCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHC--CCC
T ss_conf 867999999999999999984199999999999999998741547999999998626899999999999999854--789
Q ss_pred CCHHHHH---HHHHHCCCCHHHHH
Q ss_conf 4789999---99851799989999
Q T0521 124 ISKSDIV---SLVHDKVLDNNDID 144 (179)
Q Consensus 124 I~~~el~---~~l~~~~~~~~~~~ 144 (179)
++..|-. .+....++++....
T Consensus 113 ~~~~E~~~l~~ia~~Lgl~~~~~~ 136 (140)
T PF05099_consen 113 IDPEEQEFLRRIAEALGLSEEEFE 136 (140)
T ss_dssp -SCCHHHHHHHHHHH----SS---
T ss_pred CCHHHHHHHHHHHHHCCCCHHHHH
T ss_conf 999999999999999399999972
No 9
>PF05517 p25-alpha: p25-alpha ; InterPro: IPR008907 This family encodes a 25 kDa protein that is phosphorylated by a Ser/Thr-Pro kinase . It has been described as a brain specific protein, but it is found in Tetrahymena thermophila.; PDB: 1pul_A 2jrf_A 1wlm_A.
Probab=81.33 E-value=0.96 Score=20.77 Aligned_cols=60 Identities=12% Similarity=0.290 Sum_probs=43.8
Q ss_pred HHHHHHHHCCCCCCEEEHHHHHHHHHCCCC-----CHHHHHHHHHHHHHHHCCHHHHHHHHHHHH
Q ss_conf 999999838798980708899987731799-----988999999986432000011123333221
Q T0521 40 INELFYKLDTNHNGSLSHREIYTVLASVGI-----KKWDINRILQALDINDRGNITYTEFMAGCY 99 (179)
Q Consensus 40 l~~~F~~~D~d~dG~Is~~El~~~l~~~g~-----~~~ei~~i~~~~D~d~~g~I~f~EFi~~~~ 99 (179)
+-+.|..+-++....++..-|..+++..++ +...++-+|..+-..+..+|+|++|..++.
T Consensus 4 ~F~~Fa~fG~~~~~~M~~~~f~K~~kD~~lid~kiT~td~DIiF~KvK~k~~r~I~f~~F~~aL~ 68 (154)
T PF05517_consen 4 AFKAFASFGKKNGKEMDSKQFAKLCKDCGLIDKKITSTDVDIIFAKVKAKSARRITFEQFLEALA 68 (154)
T ss_dssp HHHHHHC--T-SSSEE---HHHHHHHHTT---SS----HHHHHHHHHS-SS-SSEEHHHHHHHHH
T ss_pred HHHHHHHHCCCCCCCCCHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHCCCCCEECHHHHHHHHH
T ss_conf 99999972678634355889999999868868887626777888986047772522999999999
No 10
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 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 recognized by the major sigma factors , . This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase , . Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0030528 transcription regulator activity, 0045449 regulation of transcription; PDB: 2k6x_A.
Probab=53.01 E-value=5.1 Score=16.62 Aligned_cols=46 Identities=22% Similarity=0.241 Sum_probs=26.7
Q ss_pred HHHHHHHHHHCCCCCCEEEHHHHHHHHHCCCCCHHHHHHHHHHHHHHH
Q ss_conf 999999998387989807088999877317999889999999864320
Q T0521 38 KYINELFYKLDTNHNGSLSHREIYTVLASVGIKKWDINRILQALDIND 85 (179)
Q Consensus 38 ~~l~~~F~~~D~d~dG~Is~~El~~~l~~~g~~~~ei~~i~~~~D~d~ 85 (179)
..++.+...- -+.|+|++.|+..+|....+++..+..++..+...|
T Consensus 7 ~~i~~Li~~g--K~~G~lT~~EI~~~Lp~~~~~~d~id~i~~~L~~~G 52 (82)
T PF03979_consen 7 EKIKKLIALG--KKKGYLTYDEINDALPDDDLDPDQIDEIYEFLEEEG 52 (82)
T ss_dssp HHHHHHHH----------BHHHHHHH-S-S---HHHHHHHHHHHHH--
T ss_pred HHHHHHHHHH--HHCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHCC
T ss_conf 9999999987--566868699999877777899999999999999889
No 11
>PF07879 PHB_acc_N: PHB/PHA accumulation regulator DNA-binding domain; InterPro: IPR012909 This domain is found at the N-terminus of the polyhydroxyalkanoate (PHA) synthesis regulators. These regulators have been shown to directly bind DNA and PHA . The invariant nature of this domain compared to the C-terminal IPR007897 from INTERPRO domain(s) suggests that it contains the DNA-binding function.
Probab=46.36 E-value=6.6 Score=16.00 Aligned_cols=21 Identities=33% Similarity=0.544 Sum_probs=17.9
Q ss_pred HHHCCCCCCCCCHHHHHHHHH
Q ss_conf 432148996147899999985
Q T0521 114 NKIDKDEDGYISKSDIVSLVH 134 (179)
Q Consensus 114 ~~~D~d~~G~I~~~el~~~l~ 134 (179)
+.||+..+.|||.++++++..
T Consensus 10 RLYDT~~S~YITL~di~~lV~ 30 (64)
T PF07879_consen 10 RLYDTETSSYITLEDIAQLVR 30 (64)
T ss_pred CCCCCCCCEEEEHHHHHHHHH
T ss_conf 551688753777999999997
No 12
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates , , . Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies . The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA . The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1ftz_A 1jgg_B 1hdd_D 1p7i_D 3hdd_B 2hot_A 1du0_B 2hdd_A 1enh_A 1ztr_A ....
Probab=46.18 E-value=6.6 Score=15.99 Aligned_cols=45 Identities=20% Similarity=0.322 Sum_probs=36.9
Q ss_pred CCCHHHHHHHHHHHHHHCCCCCCEEEHHHHHHHHHCCCCCHHHHHHHHHH
Q ss_conf 99888999999999983879898070889998773179998899999998
Q T0521 31 SVINNHIKYINELFYKLDTNHNGSLSHREIYTVLASVGIKKWDINRILQA 80 (179)
Q Consensus 31 ~~~~e~i~~l~~~F~~~D~d~dG~Is~~El~~~l~~~g~~~~ei~~i~~~ 80 (179)
..+++++..|.+.|.. +...+.++...+...+|++...|...|..
T Consensus 6 ~~t~~q~~~Le~~f~~-----~~~P~~~~~~~La~~~~l~~~~V~~WF~n 50 (57)
T PF00046_consen 6 RFTKEQLEILEEYFEK-----NPYPSEEEIEELAKELGLSEKQVKNWFQN 50 (57)
T ss_dssp SSSHHHHHHHHHHHHH-----SSSCCHHHHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHH-----CCCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9999999999999987-----57565005565423343200455124998
No 13
>PF08976 DUF1880: Domain of unknown function (DUF1880); InterPro: IPR015070 This protein is found predominantly in DJ binding protein. It has no known function. ; PDB: 1wlz_B.
Probab=33.61 E-value=5.1 Score=16.61 Aligned_cols=27 Identities=26% Similarity=0.674 Sum_probs=14.6
Q ss_pred CHHHHHHHHHHHHHHHCCHHHHHHHHH
Q ss_conf 988999999986432000011123333
Q T0521 70 KKWDINRILQALDINDRGNITYTEFMA 96 (179)
Q Consensus 70 ~~~ei~~i~~~~D~d~~g~I~f~EFi~ 96 (179)
++++.+.+|..+-.|.-|.+-|.||+.
T Consensus 5 tDeQFd~LW~~mPvN~~G~lkY~eFLs 31 (118)
T PF08976_consen 5 TDEQFDRLWNEMPVNAKGNLKYHEFLS 31 (118)
T ss_dssp -HHHHHHHHTTS-B-----EEHHHHHH
T ss_pred CHHHHHHHHHHCCCCCCCCCCHHHHHH
T ss_conf 288999999858778556650799998
No 14
>PF09069 efhand_2: EF-hand; InterPro: IPR015154 Like other EF hand domains, this domain forms a helix-loop-helix motif, though since it does not contain the canonical pattern of calcium binding residues found in many EF hand domains, it does not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain (IPR001202 from INTERPRO), enhancing dystroglycan binding . ; PDB: 1eg3_A 1eg4_A.
Probab=31.85 E-value=11 Score=14.65 Aligned_cols=25 Identities=24% Similarity=0.477 Sum_probs=11.8
Q ss_pred HHHHHHHHCCCCCCEEEHHHHHHHHH
Q ss_conf 99999983879898070889998773
Q T0521 40 INELFYKLDTNHNGSLSHREIYTVLA 65 (179)
Q Consensus 40 l~~~F~~~D~d~dG~Is~~El~~~l~ 65 (179)
+|=+|..+ .|.+|.++..-|...|+
T Consensus 5 yRYlF~~i-sd~~g~~~~~~l~~lL~ 29 (90)
T PF09069_consen 5 YRYLFSQI-SDSNGMMDQRKLGLLLH 29 (90)
T ss_dssp HHHHHHHH-S-----B-TTT---HHH
T ss_pred HHHHHHHH-HCCCCCCCHHHHHHHHH
T ss_conf 99999897-38998762999999999
No 15
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure . In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB . Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 Holliday junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1ixr_B 1ixs_A 1cuk_A 1hjp_A 1c7y_A 1bvs_B 2ztc_B 2h5x_B 2ztd_B.
Probab=25.48 E-value=15 Score=14.00 Aligned_cols=38 Identities=13% Similarity=0.269 Sum_probs=26.9
Q ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCHHHHHHHHH
Q ss_conf 8899987731799988999999986432000011123333
Q T0521 57 HREIYTVLASVGIKKWDINRILQALDINDRGNITYTEFMA 96 (179)
Q Consensus 57 ~~El~~~l~~~g~~~~ei~~i~~~~D~d~~g~I~f~EFi~ 96 (179)
.+|...+|..+|.++.++.+..+.+.. ....+.++.|.
T Consensus 3 ~~ea~~AL~~LGy~~~ea~~a~~~~~~--~~~~~~e~~ir 40 (47)
T PF07499_consen 3 LEEAVSALLALGYSRKEAEKALKKVLK--NEDLSVEELIR 40 (47)
T ss_dssp HHHHHHHHHH----HHHHHHHHHHHHH--STTS-HHHHHH
T ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHC--CCCCCHHHHHH
T ss_conf 899999999939999999999999760--79999999999
No 16
>PF01397 Terpene_synth: Terpene synthase, N-terminal domain; InterPro: IPR001906 Sequences containing this domain belong to the terpene synthase family. It has been suggested that this gene family be designated tps (for terpene synthase). Sequence comparisons reveal similarities between the monoterpene (C_10) synthases, sesquiterpene (C_15) synthases and the diterpene (C_20) synthases. It has been split into six subgroups on the basis of phylogeny, called Tpsa-Tpsf . Tpsa includes vetispiridiene synthase Q39979 from SWISSPROT, 5-epi- aristolochene synthase, Q40577 from SWISSPROT and (+)-delta-cadinene synthase P93665 from SWISSPROT. Tpsb includes (-)-limonene synthase, Q40322 from SWISSPROT. Tpsc includes copalyl diphosphate synthase (kaurene synthase A), O04408 from SWISSPROT. Tpsd includes taxadiene synthase, Q41594 from SWISSPROT, pinene synthase, O24475 from SWISSPROT and myrcene synthase, O24474 from SWISSPROT. Tpse includes ent-kaurene synthase B Q39548 from SWISSPROT. Tpsf includes linalool synthase Q9ZPN5 from SWISSPROT. In the fungus Phaeosphaeria sp.L487 the synthesis of ent-kaurene from geranylgeranyl dophosphate is promoted by a single bifunctional protein .; GO: 0016829 lyase activity, 0008152 metabolic process; PDB: 1n24_A 1n23_A 1n1b_B 1n22_B 1n20_B 1n1z_A 1n21_A 2j5c_A 2ong_B 2onh_A ....
Probab=21.74 E-value=17 Score=13.57 Aligned_cols=94 Identities=22% Similarity=0.379 Sum_probs=47.3
Q ss_pred HHHHHHHHHHHHCCCC-CCEEEHHHHHHHHHCCCCC---HHHHHHHHHHHHH----HHCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999999838798-9807088999877317999---8899999998643----200001112333322100000001
Q T0521 36 HIKYINELFYKLDTNH-NGSLSHREIYTVLASVGIK---KWDINRILQALDI----NDRGNITYTEFMAGCYRWKNIEST 107 (179)
Q Consensus 36 ~i~~l~~~F~~~D~d~-dG~Is~~El~~~l~~~g~~---~~ei~~i~~~~D~----d~~g~I~f~EFi~~~~~~~~~~~~ 107 (179)
++..|++.+..+=... +..+..=++...++++|++ +.||..++..+-. ++.+..| .-+.++..+...+.
T Consensus 28 ~~~~Lk~~v~~~l~~~~~d~~~~L~lID~lqRLGi~yhFe~EI~~~L~~i~~~~~~~~~~~~D---L~~~AL~FRLLRqh 104 (184)
T PF01397_consen 28 RLEELKEEVRNMLPSSYPDPLEKLELIDTLQRLGISYHFEDEIKEILDQIYSNWDDNGEGEDD---LYTTALRFRLLRQH 104 (184)
T ss_dssp HHHHHHHHHHHHHHC-SSSHHHHHHHHHHHHH---GGGGHHHHHHHHHHHHHCSTTTCCSTTS---HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCC---HHHHHHHHHHHHHC
T ss_conf 999999999998870488999999999999986865778999999999999761335765676---88989999999981
Q ss_pred ---HHHHHHHHHCCCCCCCCCH---HHHHHHH
Q ss_conf ---2344444321489961478---9999998
Q T0521 108 ---FLKAAFNKIDKDEDGYISK---SDIVSLV 133 (179)
Q Consensus 108 ---~l~~aF~~~D~d~~G~I~~---~el~~~l 133 (179)
.-..+|..| +|.+|.... ++++-++
T Consensus 105 Gy~VS~dvF~~F-~d~~G~F~~~l~~D~~glL 135 (184)
T PF01397_consen 105 GYNVSSDVFNKF-KDENGKFKESLSKDVKGLL 135 (184)
T ss_dssp T----GGGGGGG-B-----B-GGGGG-----H
T ss_pred CCCCCHHHHHHH-HCCCCCCCHHHHHHHHHHH
T ss_conf 852468888541-1489971164788889999
No 17
>PF09068 efhand_1: EF hand; InterPro: IPR015153 Like other EF hand domains, this domain forms a helix-loop-helix motif, though since it does not contain the canonical pattern of calcium binding residues found in many EF hand domains, it does not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain (IPR001202 from INTERPRO), enhancing dystroglycan binding . ; PDB: 1eg3_A 1eg4_A.
Probab=21.14 E-value=18 Score=13.50 Aligned_cols=95 Identities=16% Similarity=0.099 Sum_probs=44.6
Q ss_pred HHHHHCCCCHHHHHHHHHHHHHHCCCC--CCEEEHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHH
Q ss_conf 999863998889999999999838798--980708899987731799988999999986432000011123333221000
Q T0521 25 IMAHELSVINNHIKYINELFYKLDTNH--NGSLSHREIYTVLASVGIKKWDINRILQALDINDRGNITYTEFMAGCYRWK 102 (179)
Q Consensus 25 ~i~~~~~~~~e~i~~l~~~F~~~D~d~--dG~Is~~El~~~l~~~g~~~~ei~~i~~~~D~d~~g~I~f~EFi~~~~~~~ 102 (179)
.+-+.+...-=.+..+.++|....-+. |-.|+..++..+|.. ++..+.....+..+-+.. ...
T Consensus 28 ~lQK~l~l~lv~~~~~~~~f~~~~l~~~~d~~l~v~~l~~~L~~----------ly~~l~~~~p~~~~i~~~-----~v~ 92 (127)
T PF09068_consen 28 ALQKALCLDLVDLWNVIEAFRRHGLNQSNDQLLSVSQLITCLSS----------LYDQLNERLPTLVQIPSD-----NVE 92 (127)
T ss_dssp HHHHHTTGGG--HHHHHHHHHHTT---T-TSEE-HHHHHHHHHH----------HHHHHHHHSTTS--HH----------
T ss_pred HHHHHHHCCCCCHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHH----------HHHHHHHHCCCCCCCCHH-----HHH
T ss_conf 99999871764399999999976987545557899999999999----------999999878896678705-----898
Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHH
Q ss_conf 00001234444432148996147899999985
Q T0521 103 NIESTFLKAAFNKIDKDEDGYISKSDIVSLVH 134 (179)
Q Consensus 103 ~~~~~~l~~aF~~~D~d~~G~I~~~el~~~l~ 134 (179)
.-.+--+.....+||..++|.|++-.++..+.
T Consensus 93 ~~vdL~LNwLlnvYD~~R~G~Irvls~Ki~L~ 124 (127)
T PF09068_consen 93 LCVDLLLNWLLNVYDPGRTGKIRVLSFKIALA 124 (127)
T ss_dssp HHHHHHHHHHHHHH-------EEHHHHH----
T ss_pred HHHHHHHHHHHHHHCCCCCCEEEEHHHHHHHH
T ss_conf 89999999999984878887454249999999
Done!