Query T0547 BR53, unknown, 611 residues
Match_columns 611
No_of_seqs 261 out of 901
Neff 5.4
Searched_HMMs 11830
Date Fri May 21 18:09:28 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/hhm/T0547.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/hhm/T0547.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02784 Orn_Arg_deC_N: Pyrido 100.0 2.8E-45 0 357.7 24.5 247 51-328 1-251 (251)
2 PF00278 Orn_DAP_Arg_deC: Pyri 99.1 7.3E-12 6.2E-16 105.5 1.4 92 439-538 24-116 (116)
3 PF01168 Ala_racemase_N: Alani 98.5 1.4E-05 1.2E-09 58.2 16.7 184 51-274 2-188 (214)
4 PF00576 Transthyretin: HIUase 53.7 4.7 0.0004 16.4 4.9 75 465-550 23-101 (112)
5 PF00331 Glyco_hydro_10: Glyco 49.3 5.4 0.00046 15.9 4.6 58 208-274 187-246 (319)
6 PF07279 DUF1442: Protein of u 46.1 6 0.00051 15.6 6.9 155 109-280 25-186 (218)
7 PF04227 Indigoidine_A: Indigo 45.3 6 0.00051 15.6 2.7 11 258-268 164-174 (293)
8 PF04958 AstA: Arginine N-succ 44.5 6.4 0.00054 15.4 3.5 65 21-87 2-66 (338)
9 PF08002 DUF1697: Protein of u 37.8 7.9 0.00067 14.7 4.1 21 148-168 67-87 (137)
10 PF02738 Ald_Xan_dh_C2: Molybd 35.5 8.6 0.00073 14.4 2.5 47 138-192 109-155 (543)
11 PF02353 CMAS: Cyclopropane-fa 32.1 8.6 0.00073 14.4 1.8 18 382-399 253-270 (273)
12 PF12224 Amidoligase_2: Putati 31.0 10 0.00085 13.9 6.7 58 208-265 88-149 (252)
13 PF00809 Pterin_bind: Pterin b 29.4 11 0.0009 13.7 6.7 93 211-321 105-204 (210)
14 PF00351 Biopterin_H: Biopteri 27.9 11 0.00095 13.5 5.2 11 316-326 246-256 (332)
15 PF01715 IPPT: IPP transferase 27.4 8.3 0.00071 14.5 1.0 39 287-327 33-71 (252)
16 PF00682 HMGL-like: HMGL-like 27.3 11 0.00097 13.5 7.8 33 206-239 163-195 (237)
17 PF02049 FliE: Flagellar hook- 25.6 7.5 0.00063 14.9 0.5 30 374-403 33-63 (95)
18 PF01262 AlaDh_PNT_C: Alanine 23.6 10 0.00086 13.8 0.9 40 122-165 16-58 (168)
19 PF07997 DUF1694: Protein of u 23.3 13 0.0011 12.9 1.6 85 34-156 6-94 (120)
20 PF03945 Endotoxin_N: delta en 21.8 4.6 0.00039 16.4 -1.2 46 374-419 100-148 (226)
21 PF08123 DOT1: Histone methyla 20.9 15 0.0013 12.6 3.8 35 292-326 78-112 (205)
22 PF01698 FLO_LFY: Floricaula / 20.6 8.4 0.00071 14.5 -0.0 15 309-323 226-240 (386)
23 PF08368 FAST_2: FAST kinase-l 20.5 11 0.00093 13.6 0.5 42 514-555 45-87 (93)
No 1
>PF02784 Orn_Arg_deC_N: Pyridoxal-dependent decarboxylase, pyridoxal binding domain; InterPro: IPR000183 These enzymes are collectively known as group IV decarboxylases . Pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates can be classified into two different families on the basis of sequence similarities , . Members of this family while most probably evolutionary related, do not share extensive regions of sequence similarities. The proteins contain a conserved lysine residue which is known, in mouse ODC , to be the site of attachment of the pyridoxal-phosphate group. The proteins also contain a stretch of three consecutive glycine residues and has been proposed to be part of a substrate- binding region .; GO: 0003824 catalytic activity; PDB: 2nv9_A 2nva_H 1szr_B 1qu4_B 2tod_C 1f3t_D 3btn_B 7odc_A 1d7k_B 2oo0_A ....
Probab=100.00 E-value=2.8e-45 Score=357.73 Aligned_cols=247 Identities=31% Similarity=0.483 Sum_probs=215.3
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEECCCHHHHHHHHHHCCCCCCEEEECCHHHHHHHHHCCCCCCCEE
Q ss_conf 47999999999999999999970889872378745337878999999984666785166228899999996489988178
Q T0547 51 FPHLIQKQIENIYGNFNKARKEFGYKGGFNAVYPLKVNQYPGFVKNLVKLGKDYNYGLEAGSKAELLLAMAYNNEGAPIT 130 (611)
Q Consensus 51 f~dil~~ri~~l~~aF~~A~~~~~Y~g~y~~vYaiKaN~~~~Vv~~i~~~G~~~~~GlEv~Sk~EL~~ala~g~~~~~Ii 130 (611)
+.+.++.|++++.++|.. .+++++||+|||+++.|++.+.+.| +|+||+|.+|+.+|+++|+++.+|+
T Consensus 1 d~~~~~~~~~~~~~~~~~--------~~~~~~YA~KaN~~~~il~~l~~~g----~g~dv~S~~El~~al~~g~~~~~ii 68 (251)
T PF02784_consen 1 DEDTIIERIRELLRAFLP--------YNVQVFYAVKANPNPAILKLLAEEG----CGFDVASPGELELALAAGFPPDRII 68 (251)
T ss_dssp EHHHHHHHHHHHHHHHST--------T-EEEEEBGGGS--HHHHHHHHHTT-----EEEESSHHHHHHHHHTTT-GGGEE
T ss_pred CCHHHHHHHHHHHHHCCC--------CCEEEEEEEECCCCHHHHHHHHHCC----CCEEECCHHHHHHHHHCCCCCHHEE
T ss_conf 937999999999986286--------7548999970289899999999839----9869868999999997699920367
Q ss_pred ECC-CCCHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHCCCCCEEEEEEEECC-CCCCCCCCCCCCCCCCCCCH
Q ss_conf 788-9899999999854235710489866889999999999984698622688885078-87764220466656478898
Q T0547 131 VNG-FKDRELINIGFIAAEMGHNITLTIEGLNELEAIIDIAKERFKPKPNIGLRVRLHS-AGVGIWAKSGGINSKFGLTS 208 (611)
Q Consensus 131 ~nG-~Kd~e~I~lAl~a~~lG~~v~IViDs~~EL~~I~~ia~~~l~v~p~IgiRv~l~~-~~~g~~~~Tgg~~SKFGl~~ 208 (611)
|+| +|++++|+.|+.. |. .+|++||++||++|.++++.+ +|+|||+|.. .++..+..|||..||||++.
T Consensus 69 ~~gp~k~~~~l~~a~~~---~~-~~i~iDs~~el~~l~~~~~~~-----~v~lRin~~~~~~~~~~~~~g~~~skFGi~~ 139 (251)
T PF02784_consen 69 FTGPAKSDEELEEAIEY---GV-ATINIDSLDELERLAALAPGA-----RVGLRINPGVGIGAHSKLSTGGKESKFGIDI 139 (251)
T ss_dssp EE-SS--HHHHHHHHHT---T--SEEEESSHHHHHHHHHHHTTH-----EEEEB-B-S-STTTSCHCCCSSTSST---BG
T ss_pred ECCCCCCHHHHHHHHHC---CC-CEEEECCHHHHHHHHHHCCCC-----CEEEEEECCCCCCCCCCCCCCCHHHCCCCCH
T ss_conf 62899999999999984---99-989947989999999974706-----3789981487766776421331121057672
Q ss_pred HH-HHHHHHHHHHCCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHH-HCCCCCEEEEECCCCCCCCCCCCCCCC
Q ss_conf 99-9999999986689873478886338876788999999999999999999-717994058724556554777777777
Q T0547 209 TE-LIEAVNLLKENKLLEQFTMIHFHLGSQITEIHPLKKALNEAGNIYTELR-KMGAKNLKAINLGGGLAVEYSQFKNEK 286 (611)
Q Consensus 209 ~e-i~~~i~~l~~~~~l~~L~gLHfHIGSQI~di~~~~~ai~ea~~ly~eL~-~~g~~~l~~LDIGGGlgV~Y~~~~~~~ 286 (611)
++ +.++++.+++.+ + .+.|||||+|||+.+...|..+++.+.+++.++. +.|..++++||+||||||+|..
T Consensus 140 ~~~~~~~~~~~~~~~-l-~l~GlH~H~GS~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~l~~idiGGG~~v~y~~----- 212 (251)
T PF02784_consen 140 EEEAEEALDRAKELG-L-RLVGLHFHIGSQIRDPEAFREAIARLLDLIDELRRELGFEDLEWIDIGGGFGVPYDD----- 212 (251)
T ss_dssp GG-HHHHHHHHHHTT-E-EEEEEB----TTBSSTHHHHHHHHHHHHHHHHHHHH---TT-SEEE--------SSS-----
T ss_pred HHHHHHHHHHHHCCC-C-EEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCCCC-----
T ss_conf 588999998640148-5-189999876878888799999999999999987661198768789854997888887-----
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCHHHHHC
Q ss_conf 778888999999999999999964899877887075677750
Q T0547 287 SRNYTLREYANDVVFILKNIAEQKKDLEPDIFIESGRFVAAN 328 (611)
Q Consensus 287 s~ny~l~eya~~Iv~~i~~~c~~~~vp~P~Ii~EpGRaivA~ 328 (611)
++++++|+..+...+++.|.. +.+.|+|++|||||+||+
T Consensus 213 --~~~~~~~~~~~~~~~~~~~~~-~~~~~~l~~EpGR~lva~ 251 (251)
T PF02784_consen 213 --DYDFEDYADLIRAALKEFFPS-GFPGPKLIIEPGRYLVAN 251 (251)
T ss_dssp --SSCHHHHHHHHHHHHHHHCTT-TTTTSEEEEEE--TTTGG
T ss_pred --CCCCHHHHHHHHHHHHHHHHC-CCCCCEEEEECCHHHHCC
T ss_conf --556445999999999998740-489958999707898679
No 2
>PF00278 Orn_DAP_Arg_deC: Pyridoxal-dependent decarboxylase, C-terminal sheet domain; InterPro: IPR000183 These enzymes are collectively known as group IV decarboxylases . Pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates can be classified into two different families on the basis of sequence similarities , . Members of this family while most probably evolutionary related, do not share extensive regions of sequence similarities. The proteins contain a conserved lysine residue which is known, in mouse ODC , to be the site of attachment of the pyridoxal-phosphate group. The proteins also contain a stretch of three consecutive glycine residues and has been proposed to be part of a substrate- binding region .; GO: 0003824 catalytic activity; PDB: 2qgh_A 3c5q_A 2yxx_A 1knw_A 1ko0_A 1hkw_B 1hkv_B 2o0t_B 1f3t_A 1szr_B ....
Probab=99.09 E-value=7.3e-12 Score=105.51 Aligned_cols=92 Identities=35% Similarity=0.621 Sum_probs=80.6
Q ss_pred HHHHHHHHHHCCHHHHCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCC-CCCCCCCCEEEEEEECC
Q ss_conf 65330324422310100066312013546788865104873364374663014677765567-78887896078886020
Q T0547 439 RYLVNFSLFQSMPDFWGLEQNFPIMPLDRLDEEPTRSASIWDITCDSDGEISYSKDKPLFLH-DVDVEKENYFLGFFLVG 517 (611)
Q Consensus 439 ~y~~NfS~FqslPD~Wai~Q~Fpi~Pl~rl~e~P~~~~~l~DiTCDSDG~i~~~~~~~l~lh-~~~~~~e~y~lG~FlvG 517 (611)
+|++|.|++++ |+.|..++.||+.++.+-++.|.+...|++-||||.++|.. ..+|+ +++ ..-+|.|+.+|
T Consensus 24 ~~~vd~G~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~v~G~tC~~~D~i~~----~~~lP~~l~---~GD~l~f~~~G 95 (116)
T PF00278_consen 24 WYYVDDGIYGS-PDPWLYDQYFPILPLNRDNEGPEEPYTVWGPTCDSGDVIAR----DVPLPKELE---VGDWLVFENMG 95 (116)
T ss_dssp EEEES----SS-THHHHHS----EEEESS-TTSSEEEEEEE---SSTT--SEE----EEEEETT--------EEEES---
T ss_pred EEEECCCHHHC-HHHHHHCCCCCEEECCCCCCCCCEEEEEEECCCCCCCEEEE----ECCCCCCCC---CCCEEEEEECC
T ss_conf 99993794669-78796198751687245677785789999467689999926----536788889---99899999256
Q ss_pred HHHHHHCCCCCCCCCCCEEEE
Q ss_conf 699974775156789857999
Q T0547 518 AYQEVLGMKHNLFTHPTEAII 538 (611)
Q Consensus 518 AYQeiLGd~HNLfg~t~~v~v 538 (611)
||+-.++..||.|+.+.+|.|
T Consensus 96 AYt~~~s~~Fn~~~~p~~v~v 116 (116)
T PF00278_consen 96 AYTMSLSSNFNGFPPPAEVYV 116 (116)
T ss_dssp --SGTTSBCCCTT--EEEEEE
T ss_pred CCHHHHCCCCCCCCCCCEEEC
T ss_conf 031655674669899879979
No 3
>PF01168 Ala_racemase_N: Alanine racemase, N-terminal domain; InterPro: IPR001608 Alanine racemase plays a role in providing the D-alanine required for cell wall biosynthesis by isomerising L-alanine to D-alanine. Proteins containing this domain are found in both prokaryotes and eukaryotes ,. The molecular structure of alanine racemase from Bacillus stearothermophilus was determined by X-ray crystallography to a resolution of 1.9 A . The alanine racemase monomer is composed of two domains, an eight-stranded alpha/beta barrel at the N-terminus, and a C-terminal domain essentially composed of beta-strands. The pyridoxal 5'-phosphate (PLP) cofactor lies in and above the mouth of the alpha/beta barrel and is covalently linked via an aldimine linkage to a lysine residue, which is at the C-terminus of the first beta-strand of the alpha/beta barrel. This domain is also found in the PROSC (proline synthetase co-transcribed bacterial homolog) family of proteins, which are not known to have alenine racemase activity.; PDB: 3cpg_A 1b54_A 1ct5_A 1w8g_A 3gwq_B 1rcq_A 2odo_D 2rjg_B 3b8u_D 2rjh_A ....
Probab=98.46 E-value=1.4e-05 Score=58.16 Aligned_cols=184 Identities=17% Similarity=0.156 Sum_probs=127.5
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEECCC-HHHHHHHH-HH-CCCCCCEEEECCHHHHHHHHHCCCCCC
Q ss_conf 4799999999999999999997088987237874533787-89999999-84-666785166228899999996489988
Q T0547 51 FPHLIQKQIENIYGNFNKARKEFGYKGGFNAVYPLKVNQY-PGFVKNLV-KL-GKDYNYGLEAGSKAELLLAMAYNNEGA 127 (611)
Q Consensus 51 f~dil~~ri~~l~~aF~~A~~~~~Y~g~y~~vYaiKaN~~-~~Vv~~i~-~~-G~~~~~GlEv~Sk~EL~~ala~g~~~~ 127 (611)
+.+.++++++.+++.. . . +..=-+|+|.. ..+++.+. .. |. -++=|++..|....... .
T Consensus 2 dl~~l~~Ni~~~~~~~-~---------~-~i~~vvK~~a~g~g~~~~~~~~~~g~---~~~~va~~~Ea~~l~~~----~ 63 (214)
T PF01168_consen 2 DLDALRHNIKKIRQRA-P---------K-KIRAVVKANAYGHGIVRVAKALAEGV---DGFGVATLQEAEELREA----P 63 (214)
T ss_dssp EHHHHHHHHHHHHHHS-T---------S-EEEEB-HHHHSCHHHHHHHHHHHHTS---SEEEESSHHHHHHHHHG----G
T ss_pred CHHHHHHHHHHHHHHC-C---------C-CEEEEECCCCCCCCHHHHHHHHHHCC---CCHHCCCHHHHHHHHHC----C
T ss_conf 8899999999999865-8---------8-68999868877822999999999759---76240849899999838----5
Q ss_pred CEEECCCCCHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCC
Q ss_conf 17878898999999998542357104898668899999999999846986226888850788776422046665647889
Q T0547 128 PITVNGFKDRELINIGFIAAEMGHNITLTIEGLNELEAIIDIAKERFKPKPNIGLRVRLHSAGVGIWAKSGGINSKFGLT 207 (611)
Q Consensus 128 ~Ii~nG~Kd~e~I~lAl~a~~lG~~v~IViDs~~EL~~I~~ia~~~l~v~p~IgiRv~l~~~~~g~~~~Tgg~~SKFGl~ 207 (611)
.+++++. ..+.++.++. ++++++||+++.++.+.+.++. .+.+..+.|.|+.+ . .+.|+.
T Consensus 64 il~~~~~-~~~~~~~~~~-----~~~~~~v~s~~~~~~l~~~~~~-~~~~~~v~l~idtG-----------~--~R~G~~ 123 (214)
T PF01168_consen 64 ILVLGPP-PPEELEELVE-----YNIIPTVDSPEQLEALNKAARK-QGKPLPVHLKIDTG-----------M--GRLGVR 123 (214)
T ss_dssp EEE-C---SGGGHHHHHH-----TTEEEEE-SHHHHHHHHHHHHH-TSS-EEEEEBE--S-----------S--T-----
T ss_pred EEEECCC-CHHHHHHHHH-----CCEEEEECCHHHHHHHHHHHHH-CCCCCEEEEEECCC-----------C--CCCCCC
T ss_conf 8546388-8889999873-----9899999989999999999898-59973499999986-----------8--868879
Q ss_pred HHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCC
Q ss_conf 8999999999986689873478886338876788999999999999999999717994058724556
Q T0547 208 STELIEAVNLLKENKLLEQFTMIHFHLGSQITEIHPLKKALNEAGNIYTELRKMGAKNLKAINLGGG 274 (611)
Q Consensus 208 ~~ei~~~i~~l~~~~~l~~L~gLHfHIGSQI~di~~~~~ai~ea~~ly~eL~~~g~~~l~~LDIGGG 274 (611)
.+++.++++.+++.+.+ .+.|+..|.|+--..-..-+..++...++...+++.| .....+.+|+-
T Consensus 124 ~~~~~~l~~~i~~~~~l-~l~Gi~th~~~~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~~~~s~g~S 188 (214)
T PF01168_consen 124 PEELEELARAIKALPGL-RLEGIMTHFGHADDPDATRRAQFERFRRLVEALEKAG-IKPPIVSMGNS 188 (214)
T ss_dssp HHHHHHHHHHHHCTTTE-EEEEEBE--SSTTSSCHHHHHHHHHHHHHHHHHHHTT-TTSSCEBEEBH
T ss_pred HHHHHHHHHHHHHCCCC-CEEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHCC-CCCCEEECCCC
T ss_conf 99999999999857998-6678996316778801779999999999999998608-99988965698
No 4
>PF00576 Transthyretin: HIUase/Transthyretin family; InterPro: IPR000895 Transthyretin (formerly prealbumin) is one of 3 thyroid hormone-binding proteins found in the blood of vertebrates . It is produced in the liver and circulates in the bloodstream, where it binds retinol and thyroxine (T4) . It differs from the other 2 hormone-binding proteins (T4-binding globulin and albumin) in 3 distinct ways: (1) the gene is expressed at a high rate in the brain choroid plexus; (2) it is enriched in cerebrospinal fluid; and (3) no genetically caused absence has been observed, suggesting an essential role in brain function, distinct from that played in the bloodstream . The protein consists of around 130 amino acids, which assemble as a homotetramer that contains an internal channel in which T4 is bound. Within this complex, T4 appears to be transported across the blood-brain barrier, where, in the choroid plexus, the hormone stimulates further synthesis of transthyretin. The protein then diffuses back into the bloodstream, where it binds T4 for transport back to the brain .; GO: 0005496 steroid binding, 0006810 transport; PDB: 2gpz_C 2igl_D 2g2n_B 2g2p_D 2h6u_G 2h1x_C 2qel_C 2g5u_A 2fbr_A 1ttb_B ....
Probab=53.68 E-value=4.7 Score=16.40 Aligned_cols=75 Identities=25% Similarity=0.251 Sum_probs=46.6
Q ss_pred CCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCHHHHHHCCCCCCCCCCCEEEEEE--CC
Q ss_conf 5467888651048733643746630146777655677888789607888602069997477515678985799998--89
Q T0547 465 LDRLDEEPTRSASIWDITCDSDGEISYSKDKPLFLHDVDVEKENYFLGFFLVGAYQEVLGMKHNLFTHPTEAIISI--NE 542 (611)
Q Consensus 465 l~rl~e~P~~~~~l~DiTCDSDG~i~~~~~~~l~lh~~~~~~e~y~lG~FlvGAYQeiLGd~HNLfg~t~~v~v~~--~~ 542 (611)
|.|+++ +...-.|+.-+.|+||+++... +.-..+. +| -|-=.|.||+|-.-+|. .-| -.+|.|.+ ++
T Consensus 23 L~~~~~-~~~~~~i~~~~T~~DGR~~~~l---~~~~~~~-~G--~Y~l~F~~g~Yf~~~g~--~~F--~p~V~v~F~i~d 91 (112)
T PF00576_consen 23 LYRLDE-DGSWELIASGRTNADGRIDHPL---LPGEDFQ-PG--VYELRFDTGDYFAAQGV--PSF--YPEVPVRFTIDD 91 (112)
T ss_dssp EEEEET-TSSEEEEEEEEB--BTTBSSTS---SETTTS-------EEEEEEHHHHHHHTT---STS--ESEEEEEE-TSS
T ss_pred EEECCC-CCCCEEEEEEEECCCCCCCCCC---CCCCCCC-CE--EEEEEEEHHHHHHHCCC--CCC--CCCEEEEEEECC
T ss_conf 998248-9984899999968992685475---6854447-78--89999991572665499--957--303409999888
Q ss_pred C-C-EEEEEE
Q ss_conf 9-6-288751
Q T0547 543 K-G-YEVEGI 550 (611)
Q Consensus 543 ~-g-~~i~~~ 550 (611)
. . |.|--+
T Consensus 92 ~~~HYHvPlL 101 (112)
T PF00576_consen 92 PGEHYHVPLL 101 (112)
T ss_dssp TTSEEEEEEE
T ss_pred CCCCEEEEEE
T ss_conf 9981798599
No 5
>PF00331 Glyco_hydro_10: Glycosyl hydrolase family 10; InterPro: IPR001000 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families , , . This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site . Because the fold of proteins is better conserved than their sequences, some of the families can be grouped in 'clans'. Glycoside hydrolase family 10 GH10 from CAZY comprises enzymes with a number of known activities; xylanase (3.2.1.8 from EC); endo-1,3-beta-xylanase (3.2.1.32 from EC); cellobiohydrolase (3.2.1.91 from EC). These enzymes were formerly known as cellulase family F. The microbial degradation of cellulose and xylans requires several types of enzymes such as endoglucanases (), cellobiohydrolases () (exoglucanases), or xylanases () , . Fungi and bacteria produces a spectrum of cellulolytic enzymes (cellulases) and xylanases which, on the basis of sequence similarities, can be classified into families. One of these families is known as the cellulase family F or as the glycosyl hydrolases family 10 . ; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 1vbr_A 1vbu_A 1ta3_B 1b3x_A 1b3z_A 1b3v_A 1b3y_A 1bg4_A 1b30_A 1b31_A ....
Probab=49.32 E-value=5.4 Score=15.92 Aligned_cols=58 Identities=16% Similarity=0.320 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHHCCC-CCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHCCCC-CEEEEECCCC
Q ss_conf 8999999999986689-87347888633887678899999999999999999971799-4058724556
Q T0547 208 STELIEAVNLLKENKL-LEQFTMIHFHLGSQITEIHPLKKALNEAGNIYTELRKMGAK-NLKAINLGGG 274 (611)
Q Consensus 208 ~~ei~~~i~~l~~~~~-l~~L~gLHfHIGSQI~di~~~~~ai~ea~~ly~eL~~~g~~-~l~~LDIGGG 274 (611)
...+.+.++.+++.+. ++ -.|+.+|+++... +..++..++ ++.+.|.+ .+..+||...
T Consensus 187 ~~~~~~lv~~l~~~gvpId-gIG~Q~H~~~~~~-~~~i~~~l~-------~~a~~Gl~i~ITElDv~~~ 246 (319)
T PF00331_consen 187 RDAYLELVKELKARGVPID-GIGLQSHFGAGYP-PEEIRAALD-------RFADLGLPIHITELDVRDP 246 (319)
T ss_dssp HHHHHHHHHHHHHTT-----EE----EEESSSS-HHHHHHHHH-------HHHTT--EEEEESBEEESS
T ss_pred HHHHHHHHHHHHHCCCCCC-EEEEEEECCCCCC-HHHHHHHHH-------HHHHCCCCEEEEEEEECCC
T ss_conf 9999999999987898743-2666551168899-999999999-------9997499538987441578
No 6
>PF07279 DUF1442: Protein of unknown function (DUF1442); InterPro: IPR009902 This family consists of several hypothetical Arabidopsis thaliana proteins of around 225 residues in length. The function of this family is unknown.
Probab=46.08 E-value=6 Score=15.57 Aligned_cols=155 Identities=15% Similarity=0.084 Sum_probs=77.7
Q ss_pred EECCHHHHHHHHHCCCCCCCEE--E-CCCCCHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHCCCCCEEEEEEE
Q ss_conf 6228899999996489988178--7-889899999999854235710489866889999999999984698622688885
Q T0547 109 EAGSKAELLLAMAYNNEGAPIT--V-NGFKDRELINIGFIAAEMGHNITLTIEGLNELEAIIDIAKERFKPKPNIGLRVR 185 (611)
Q Consensus 109 Ev~Sk~EL~~ala~g~~~~~Ii--~-nG~Kd~e~I~lAl~a~~lG~~v~IViDs~~EL~~I~~ia~~~l~v~p~IgiRv~ 185 (611)
.--+-.|+..|||+|.....|+ | +|.-..--|-||..|++-|-+.+-+++..+++....+..++ .+..-.+-+.+
T Consensus 25 ~ep~~aEfISALAAG~nAkLiVe~~s~~~~~~ttiaLaaAA~~TgGR~VCIlp~~~~~~~~~~~l~~-~~~~~~vEfiv- 102 (218)
T PF07279_consen 25 KEPDVAEFISALAAGNNAKLIVEAWSSGGAIATTIALAAAARHTGGRHVCILPDEQSLSEYKKALGE-AGLSDVVEFIV- 102 (218)
T ss_pred CCCCHHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCEEEEEECCHHHHHHHHHHHCC-CCCCCCCEEEE-
T ss_conf 7987899999985654540799971467733669999999987098199990785779999998531-45113525996-
Q ss_pred ECCCCCCCCCCCCCCCCCC---CCCHHHHH-HHHHHHHHCCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 0788776422046665647---88989999-9999998668987347888633887678899999999999999999971
Q T0547 186 LHSAGVGIWAKSGGINSKF---GLTSTELI-EAVNLLKENKLLEQFTMIHFHLGSQITEIHPLKKALNEAGNIYTELRKM 261 (611)
Q Consensus 186 l~~~~~g~~~~Tgg~~SKF---Gl~~~ei~-~~i~~l~~~~~l~~L~gLHfHIGSQI~di~~~~~ai~ea~~ly~eL~~~ 261 (611)
+- .... ...+-..--| -....+.. ++++.++-.+.- .+ .+--+.-+.-.+-..|...+ +..
T Consensus 103 -Ge-~~~~-~~~~~~~vDF~vVDck~~~~~~~vl~~a~~~~rG-AV-VV~~Na~~~~~~g~sw~~~~----------~~~ 167 (218)
T PF07279_consen 103 -GE-SPEE-VMPGLKGVDFLVVDCKREDFAARVLRAAKLSPRG-AV-VVCYNAFSRSRNGFSWRSVL----------RGR 167 (218)
T ss_pred -CC-CHHH-HHHHCCCCCEEEEECCHHHHHHHHHHHHCCCCCC-EE-EEEECCCCCCCCCCCHHHHC----------CCC
T ss_conf -58-9999-9841468878998065788899999860438983-49-99865655676876266651----------689
Q ss_pred CCCCEEEEECCCCCCCCCC
Q ss_conf 7994058724556554777
Q T0547 262 GAKNLKAINLGGGLAVEYS 280 (611)
Q Consensus 262 g~~~l~~LDIGGGlgV~Y~ 280 (611)
.+..-.+|-||+|+-|---
T Consensus 168 ~~Vrsv~LPIG~GleVt~I 186 (218)
T PF07279_consen 168 RVVRSVFLPIGEGLEVTRI 186 (218)
T ss_pred CCEEEEEEECCCCEEEEEE
T ss_conf 7337899624787699998
No 7
>PF04227 Indigoidine_A: Indigoidine synthase A like protein; InterPro: IPR007342 Indigoidine is a blue pigment synthesised by Erwinia chrysanthemi implicated in pathogenicity and protection from oxidative stress. IdgA is involved in indigoidine biosynthesis, but its specific function is unknown .; PDB: 1vkm_F.
Probab=45.29 E-value=6 Score=15.57 Aligned_cols=11 Identities=18% Similarity=0.181 Sum_probs=5.1
Q ss_pred HHHCCCCCEEE
Q ss_conf 99717994058
Q T0547 258 LRKMGAKNLKA 268 (611)
Q Consensus 258 L~~~g~~~l~~ 268 (611)
|...|.+.+.|
T Consensus 164 LET~GV~Vvgy 174 (293)
T PF04227_consen 164 LETQGVPVVGY 174 (293)
T ss_dssp HHHTT--EE--
T ss_pred HHCCCCEEEEE
T ss_conf 73179469995
No 8
>PF04958 AstA: Arginine N-succinyltransferase beta subunit; InterPro: IPR007041 Arginine N-succinyltransferase 2.3.1.109 from EC catalyzes the transfer of succinyl-CoA to arginine to produce succinylarginine. This is the first step in arginine catabolism by the arginine succinyltransferase pathway.; GO: 0008791 arginine N-succinyltransferase activity, 0006527 arginine catabolic process; PDB: 1yle_A.
Probab=44.50 E-value=6.4 Score=15.40 Aligned_cols=65 Identities=14% Similarity=0.076 Sum_probs=46.3
Q ss_pred EEECCCCCCCHHHHHHHHHHCCCCCCEEEECHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEE
Q ss_conf 6872788888899999998557998589874799999999999999999997088987237874533
Q T0547 21 VCINYEKKPAIIDIVKELRDDGYKGPLLLRFPHLIQKQIENIYGNFNKARKEFGYKGGFNAVYPLKV 87 (611)
Q Consensus 21 l~v~p~~~~~l~dlv~~l~~~~~~tPllvrf~dil~~ri~~l~~aF~~A~~~~~Y~g~y~~vYaiKa 87 (611)
+.|+|...-||..|.+-.++.|.|.--|-.+.+.|++||.+-.++|..... ..+|.-.++|-.--
T Consensus 2 lviRPv~~~Dl~aL~~lA~~sg~G~TsLP~d~~~L~~rI~~S~~sFa~~~~--~~~~~~~YlFVLED 66 (338)
T PF04958_consen 2 LVIRPVRPSDLDALYELARESGPGFTSLPADRERLAARIERSERSFAGEAV--DQPGDEGYLFVLED 66 (338)
T ss_dssp EEEEE--GGGHHHHHHHHHHS----TTS-S-HHHHHHHHHHHHHHHH-TT---------EEEEEEEE
T ss_pred EEEECCCCCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC--CCCCCCCEEEEEEE
T ss_conf 478348513699999999982998636999989999999999998623224--78776426999995
No 9
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2hiy_C.
Probab=37.75 E-value=7.9 Score=14.67 Aligned_cols=21 Identities=24% Similarity=0.526 Sum_probs=9.7
Q ss_pred HCCCCEEEEECCHHHHHHHHH
Q ss_conf 357104898668899999999
Q T0547 148 EMGHNITLTIEGLNELEAIID 168 (611)
Q Consensus 148 ~lG~~v~IViDs~~EL~~I~~ 168 (611)
..|+.+-+.+=+.+||..+.+
T Consensus 67 ~fg~~~~v~vrt~~el~~~~~ 87 (137)
T PF08002_consen 67 RFGFEVPVIVRTAEELRAIVA 87 (137)
T ss_dssp H-TT---EEEEEHHHHHHHHT
T ss_pred HCCCCCCEEEECHHHHHHHHH
T ss_conf 619987889972999999999
No 10
>PF02738 Ald_Xan_dh_C2: Molybdopterin-binding domain of aldehyde dehydrogenase; InterPro: IPR008274 Aldehyde oxidase () catalyzes the conversion of an aldehyde in the presence of oxygen and water to an acid and hydrogen peroxide. The enzyme is a homodimer, and requires FAD, molybdenum and two 2FE-2S clusters as cofactors. Xanthine dehydrogenase () catalyzes the hydrogenation of xanthine to urate, and also requires FAD, molybdenum and two 2FE-2S clusters as cofactors. This activity is often found in a bifunctional enzyme with xanthine oxidase () activity too. The enzyme can be converted from the dehydrogenase form to the oxidase form irreversibly by proteolysis or reversibly through oxidation of sulphhydryl groups.; GO: 0016491 oxidoreductase activity, 0006118 electron transport; PDB: 3hrd_B 1rm6_D 1sb3_D 1t3q_E 1ffu_B 1ffv_B 1n63_E 1n61_E 1zxi_E 1n5w_E ....
Probab=35.48 E-value=8.6 Score=14.42 Aligned_cols=47 Identities=19% Similarity=0.237 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCC
Q ss_conf 9999998542357104898668899999999999846986226888850788776
Q T0547 138 ELINIGFIAAEMGHNITLTIEGLNELEAIIDIAKERFKPKPNIGLRVRLHSAGVG 192 (611)
Q Consensus 138 e~I~lAl~a~~lG~~v~IViDs~~EL~~I~~ia~~~l~v~p~IgiRv~l~~~~~g 192 (611)
.....|+.+++.|+-|.++.+-.+++.. ...+|..-+|++.+.+..|
T Consensus 109 ~~~~aa~~A~~~grPVk~~~sR~E~~~~--------~~~r~~~~~~~~~g~~~dG 155 (543)
T PF02738_consen 109 FEVAAALAARKTGRPVKLVWSREEDFQA--------GPKRPAAKIRVRAGVDKDG 155 (543)
T ss_dssp HHHHHHHHHHHH-S-EEEE--HHHHHHH--------S--B-EEEEEEEEEE----
T ss_pred HHHHHHHHHHHHCCCEEEEECHHHHCCC--------CCCCCHHHEEEEEEECCCC
T ss_conf 9999999999849989999616984766--------7897554578889998999
No 11
>PF02353 CMAS: Cyclopropane-fatty-acyl-phospholipid synthase; InterPro: IPR003333 Methyl transfer from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalyzed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. This entry represents cyclopropane-fatty-acyl-phospholipid synthase that is slosely related to methyltransferases. Cyclopropane-fatty-acyl-phospholipid synthase or CFA synthase 2.1.1.79 from EC catalyses the reaction: S-adenosyl-L-methionine + phospholipid olefinic fatty acid -> S-adenosyl-L-homocysteine + phospholipid cyclopropane fatty acid. The major mycolic acid produced by Mycobacterium tuberculosis contains two cis-cyclopropanes in the meromycolate chain. Cyclopropanation may contribute to the structural integrity of the cell wall complex .; GO: 0008825 cyclopropane-fatty-acyl-phospholipid synthase activity, 0008610 lipid biosynthetic process; PDB: 3hem_A 1kpi_A 1kph_A 1kpg_D 1kp9_A 1tpy_A 2fk7_A 3ha5_A 3ha3_A 3ha7_A ....
Probab=32.11 E-value=8.6 Score=14.41 Aligned_cols=18 Identities=22% Similarity=0.183 Sum_probs=8.6
Q ss_pred HHHHHHHHHHHHCCCCCH
Q ss_conf 999999999973696678
Q T0547 382 IDHLESILTLFDLGYVDL 399 (611)
Q Consensus 382 ~~~~~~~~~~f~~G~l~L 399 (611)
..|+.-+-..|..|.+++
T Consensus 253 ~~yl~~~~~~F~~g~~~~ 270 (273)
T PF02353_consen 253 RYYLAYCAAAFRSGDIDV 270 (273)
T ss_dssp HHHH---HHHHHTTSSEE
T ss_pred HHHHHHHHHHHHCCCCEE
T ss_conf 999999999997799869
No 12
>PF12224 Amidoligase_2: Putative amidoligase enzyme
Probab=30.98 E-value=10 Score=13.90 Aligned_cols=58 Identities=14% Similarity=0.121 Sum_probs=40.8
Q ss_pred HHHHHHHHHHHHHCCCCC--CEEEEEEECCCCCCC--HHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 899999999998668987--347888633887678--8999999999999999999717994
Q T0547 208 STELIEAVNLLKENKLLE--QFTMIHFHLGSQITE--IHPLKKALNEAGNIYTELRKMGAKN 265 (611)
Q Consensus 208 ~~ei~~~i~~l~~~~~l~--~L~gLHfHIGSQI~d--i~~~~~ai~ea~~ly~eL~~~g~~~ 265 (611)
..++.++++.|++++... .-.|+|.|||-.... ...+++-++-+.-+-..|.++..++
T Consensus 88 ~~~i~~v~~~L~~~~~~~t~~scg~HVHv~~~~~~~~~~~l~~l~~~~~~~E~~L~~~~p~~ 149 (252)
T PF12224_consen 88 LEEIDEVLRALRRAGAVGTNDSCGFHVHVNPEPPGFSADTLRNLAKAIWLFEDWLRELLPPD 149 (252)
T ss_pred HHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 79999999999976992247771679995585678689999999999999899999866997
No 13
>PF00809 Pterin_bind: Pterin binding enzyme This Prosite entry is a subset of the Pfam family; InterPro: IPR000489 All organisms require reduced folate cofactors for the synthesis of a variety of metabolites. Most microorganisms must synthesize folate de novo because they lack the active transport system of higher vertebrate cells that allows these organisms to use dietary folates. Proteins containing this domain include dihydropteroate synthase (2.5.1.15 from EC) as well as a group of methyltransferase enzymes including methyltetrahydrofolate, corrinoid iron-sulphur protein methyltransferase (MeTr) Q46389 from SWISSPROT that catalyses a key step in the Wood-Ljungdahl pathway of carbon dioxide fixation. Dihydropteroate synthase (2.5.1.15 from EC) (DHPS) catalyses the condensation of 6-hydroxymethyl-7,8-dihydropteridine pyrophosphate to para-aminobenzoic acid to form 7,8-dihydropteroate. This is the second step in the three-step pathway leading from 6-hydroxymethyl-7,8-dihydropterin to 7,8-dihydrofolate. DHPS is the target of sulphonamides, which are substrate analogues that compete with para-aminobenzoic acid. Bacterial DHPS (gene sul or folP) is a protein of about 275 to 315 amino acid residues that is either chromosomally encoded or found on various antibiotic resistance plasmids. In the lower eukaryote Pneumocystis carinii, DHPS is the C-terminal domain of a multifunctional folate synthesis enzyme (gene fas) .; GO: 0004156 dihydropteroate synthase activity, 0009396 folic acid and derivative biosynthetic process; PDB: 2vef_B 2veg_A 1ad4_A 1ad1_A 2bmb_A 1twz_B 1tws_A 1tx2_A 1tx0_B 1tww_B ....
Probab=29.37 E-value=11 Score=13.71 Aligned_cols=93 Identities=18% Similarity=0.137 Sum_probs=48.9
Q ss_pred HHHHHHHHHHCCCCCCEEEEEEEC-CCCCCCHHHHH-HHHHHHHHHHHH----HHHCCCC-CEEEEECCCCCCCCCCCCC
Q ss_conf 999999998668987347888633-88767889999-999999999999----9971799-4058724556554777777
Q T0547 211 LIEAVNLLKENKLLEQFTMIHFHL-GSQITEIHPLK-KALNEAGNIYTE----LRKMGAK-NLKAINLGGGLAVEYSQFK 283 (611)
Q Consensus 211 i~~~i~~l~~~~~l~~L~gLHfHI-GSQI~di~~~~-~ai~ea~~ly~e----L~~~g~~-~l~~LDIGGGlgV~Y~~~~ 283 (611)
..+.+..+++++. .+.++|..- ...+.....++ ..+.++.+++.+ +.+.|.+ .==++|-|=||+-.
T Consensus 105 ~~~~~~l~a~~~~--~~V~m~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~Gi~~~~IiiDPgigf~~~----- 177 (210)
T PF00809_consen 105 DPEMLPLAAEYGA--PVVLMHSDGKPKGMPKTAEYRLDVAEEIIEFFEERIEALLKAGIPRERIIIDPGIGFGKT----- 177 (210)
T ss_dssp HTTHHHHHHHHTS--EEEEE--CTCTTTGSTSHHHSHCHHHHHHHHHHHHHHHHHH-T--GGGEEEETTTT-TTS-----
T ss_pred CHHHHHHHHHHCC--EEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHEEEECCCCCCCC-----
T ss_conf 5899999998399--799995267766665554223209999999999999999986999778999789888888-----
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEC
Q ss_conf 77777888899999999999999996489987788707
Q T0547 284 NEKSRNYTLREYANDVVFILKNIAEQKKDLEPDIFIES 321 (611)
Q Consensus 284 ~~~s~ny~l~eya~~Iv~~i~~~c~~~~vp~P~Ii~Ep 321 (611)
.+..-.++..++.+... .+.|.++.=+
T Consensus 178 ---------~~~~~~~l~~i~~~~~~--~~~p~l~g~s 204 (210)
T PF00809_consen 178 ---------QEQNLELLRNIKELREL--LGLPILVGGS 204 (210)
T ss_dssp ---------HHHHHHHHHTHHHHHTC--TTSEBEEEET
T ss_pred ---------HHHHHHHHHHHHHHHHH--CCCCEEEEEE
T ss_conf ---------89999999999999986--8999899985
No 14
>PF00351 Biopterin_H: Biopterin-dependent aromatic amino acid hydroxylase; InterPro: IPR001273 Phenylalanine, tyrosine and tryptophan hydroxylases constitute a family of tetrahydrobiopterin-dependent aromatic amino acid hydroxylases, all of which are rate-limiting catalysts for important metabolic pathways . The proteins are structurally and functionally related, each containing iron, and catalysing ring hydroxylation of aromatic amino acids, using tetra-hydrobiopterin (BH4) as a substrate. All are regulated by phosphorylation at serines in their N-termini. It has been suggested that the proteins each contain a conserved C-terminal catalytic (C) domain and an unrelated N-terminal regulatory (R) domain. It is possible that the R domains arose from genes that were recruited from different sources to combine with the common gene for the catalytic core. Thus, by combining with the same C domain, the proteins acquired the unique regulatory properties of the separate R domains. A variety of enzymes belong to this family that includes, phenylalanine-4-hydroxylase from Chromobacterium violaceum where it is copper-dependent; it is iron-dependent in Pseudomonas aeruginosa, phenylalanine-4-hydroxylase catalyzes the conversion of phenylalanine to tyrosine. In humans, deficiencies are the cause of phenylketonuria, the most common inborn error of amino acid metabolism , tryptophan 5-hydroxylase catalyzes the rate-limiting step in serotonin biosynthesis: the conversion of tryptophan to 3-hydroxy-anthranilate and tyrosine 3-hydroxylase catalyzes the rate limiting step in catecholamine biosynthesis: the conversion of tyrosine to 3,4-dihydroxy-L-phenylalanine.; GO: 0004497 monooxygenase activity, 0005506 iron ion binding, 0009072 aromatic amino acid family metabolic process; PDB: 3e2t_A 1mlw_A 1ltu_A 1ltz_A 1ltv_A 2phm_A 1phz_A 1mmt_A 4pah_A 3pah_A ....
Probab=27.91 E-value=11 Score=13.53 Aligned_cols=11 Identities=9% Similarity=0.081 Sum_probs=4.7
Q ss_pred EEEEECCHHHH
Q ss_conf 78870756777
Q T0547 316 DIFIESGRFVA 326 (611)
Q Consensus 316 ~Ii~EpGRaiv 326 (611)
.+-++|-+.+.
T Consensus 246 ~~pfdp~~~~~ 256 (332)
T PF00351_consen 246 RRPFDPERVMR 256 (332)
T ss_dssp EEE--HHHHTT
T ss_pred CCCCCHHHHHC
T ss_conf 11698999826
No 15
>PF01715 IPPT: IPP transferase; InterPro: IPR002627 tRNA isopentenyltransferases 2.5.1.8 from EC also known as tRNA delta(2)-isopentenylpyrophosphate transferases or IPP transferases. These enzymes modify both cytoplasmic and mitochondrial tRNAs at A(37) to give isopentenyl A(37) .; GO: 0004811 tRNA isopentenyltransferase activity, 0005524 ATP binding, 0008033 tRNA processing; PDB: 3crq_A 3crm_A 3crr_A 2zm5_A 3foz_B 2zxu_B 3eph_B 3epk_A 3epl_A 3epj_A ....
Probab=27.36 E-value=8.3 Score=14.51 Aligned_cols=39 Identities=18% Similarity=0.374 Sum_probs=26.2
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCHHHHH
Q ss_conf 77888899999999999999996489987788707567775
Q T0547 287 SRNYTLREYANDVVFILKNIAEQKKDLEPDIFIESGRFVAA 327 (611)
Q Consensus 287 s~ny~l~eya~~Iv~~i~~~c~~~~vp~P~Ii~EpGRaivA 327 (611)
+-+|++..|.++....+++++.+..+ |.|+-=+|=|+=|
T Consensus 33 ~e~~sv~~f~~~a~~~i~~i~~~gk~--pivvGGTglYi~a 71 (252)
T PF01715_consen 33 DEEYSVGDFQRDAREAIEEIHARGKI--PIVVGGTGLYIKA 71 (252)
T ss_dssp TS---HHHHHHHHHHHHHHHHH---E--EEEE---HHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHCCCC--EEEEECHHHHHHH
T ss_conf 88878999999999999999867996--5998172999999
No 16
>PF00682 HMGL-like: HMGL-like of this family is not conserved in other members. are a sub-families of this Pfam.; InterPro: IPR000891 Pyruvate carboxylase (6.4.1.1 from EC) (PC), a member of the biotin-dependent enzyme family, is involved in the gluconeogenesis by mediating the carboxylation of pyruvate to oxaloacetate. Biotin-dependent carboxylase enzymes perform a two step reaction. Enzyme-bound biotin is first carboxylated by bicarbonate and ATP and the carboxyl group temporarily bound to biotin is subsequently transferred to an acceptor substrate such as pyruvate . PC has three functional domains: a biotin carboxylase (BC) domain, a carboxyltransferase (CT) domain which perform the second part of the reaction and a biotinyl domain , . The mechanism by which the carboxyl group is transferred from the carboxybiotin to the pyruvate is not well understood. The pyruvate carboxyltransferase domain is also found in other pyruvate binding enzymes and acetyl-CoA dependent enzymes suggesting that this domain can be associated with different enzymatic activities. This domain is found towards the N-terminal region of various aldolase enzymes. This N-terminal TIM barrel domain interacts with the C-terminal domain. The C-terminal DmpG_comm domain (IPR012425 from INTERPRO) is thought to promote heterodimerisation with members of IPR003361 from INTERPRO to form a bifunctional aldolase-dehydrogenase . ; GO: 0003824 catalytic activity; PDB: 3ewb_X 3fig_A 1sr9_A 1nvm_C 3dxi_B 2cw6_E 2ftp_A 1ydn_A 1ydo_C 3bg3_B ....
Probab=27.31 E-value=11 Score=13.46 Aligned_cols=33 Identities=18% Similarity=0.145 Sum_probs=20.8
Q ss_pred CCHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCC
Q ss_conf 8989999999999866898734788863388767
Q T0547 206 LTSTELIEAVNLLKENKLLEQFTMIHFHLGSQIT 239 (611)
Q Consensus 206 l~~~ei~~~i~~l~~~~~l~~L~gLHfHIGSQI~ 239 (611)
+++.++.+.++.+++.-.- ...++|+|=.-+..
T Consensus 163 ~~P~~~~~li~~l~~~~~~-~~l~~H~Hnd~Gla 195 (237)
T PF00682_consen 163 LTPEDVAELIRALRRRLPN-IPLGFHCHNDLGLA 195 (237)
T ss_dssp S-HHHHHHHHHHHHHHSTT-SGEEEEE-TTTS-H
T ss_pred CCHHHHHHHHHHHHHHCCC-CEEEEEECCCCCHH
T ss_conf 4999999999999987699-46999963785749
No 17
>PF02049 FliE: Flagellar hook-basal body complex protein FliE; InterPro: IPR001624 Four genes from the major Bacillus subtilis chemotaxis locus have been shown to encode proteins that are similar to the Salmonella typhimurium FlgB, FlgC, FlgG and FliF proteins; a further gene product is similar to the Escherichia coli FliE protein . All of these proteins are thought to form part of the hook-basal body complex of the bacterial flagella . The FlgB, FlgC and FlgG proteins are components of the proximal and distal rods; FliF forms the M-ring that anchors the rod assembly to the membrane; but the role of FliE has not yet been determined . The similarity between the proteins in these two organisms suggests that the structures of the M-ring and the rod may be similar . Nevertheless, some differences in size and amino acid composition between some of the homologues suggest the basal body proteins may be organised slightly differently within B. subtilis . From gel electrophoresis and autoradiography of 35S-labelled S. typhimurium hook-basal body complexes and the deduced number of sulphur-containing residues in FliE, the stoichiometry of the protein in the hook-basal body complex has been estimated to be about nine subunits . FliE does not undergo cleavage of a signal peptide, nor does it show any similarity to the axial components like the rod or hook proteins, which are thought to be exported by the flagellum-specific export pathway . On this evidence, it has been suggested that FliE may be in the vicinity of the MS ring, perhaps acting as an adaptor protein between ring and rod substructures .; GO: 0003774 motor activity, 0005198 structural molecule activity, 0001539 ciliary or flagellar motility, 0009288 flagellin-based flagellum
Probab=25.56 E-value=7.5 Score=14.85 Aligned_cols=30 Identities=20% Similarity=0.369 Sum_probs=17.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHCCC-CCHHHHH
Q ss_conf 68899999999999999973696-6789998
Q T0547 374 ALEYLHDSIDHLESILTLFDLGY-VDLQDRS 403 (611)
Q Consensus 374 ~~E~~~da~~~~~~~~~~f~~G~-l~L~~ra 403 (611)
..+-.++.+.--++....|..|- .+|.+--
T Consensus 33 ai~~vn~~q~~a~~~~~~~~~G~~~~l~evm 63 (95)
T PF02049_consen 33 AINSVNQQQQQADQLAQAFATGKSVDLHEVM 63 (95)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHH
T ss_conf 9999999999999999999828999899999
No 18
>PF01262 AlaDh_PNT_C: Alanine dehydrogenase/PNT, C-terminal domain; InterPro: IPR007698 Alanine dehydrogenases () and pyridine nucleotide transhydrogenase () have been shown to share regions of similarity . Alanine dehydrogenase catalyzes the NAD-dependent reversible reductive amination of pyruvate into alanine. Pyridine nucleotide transhydrogenase catalyzes the reduction of NADP^+ to NADPH with the concomitant oxidation of NADH to NAD^+. This enzyme is located in the plasma membrane of prokaryotes and in the inner membrane of the mitochondria of eukaryotes. The transhydrogenation between NADH and NADP is coupled with the translocation of a proton across the membrane. In prokaryotes the enzyme is composed of two different subunits, an alpha chain (gene pntA) and a beta chain (gene pntB), while in eukaryotes it is a single chain protein. The sequence of alanine dehydrogenase from several bacterial species are related with those of the alpha subunit of bacterial pyridine nucleotide transhydrogenase and of the N-terminal half of the eukaryotic enzyme. The two most conserved regions correspond respectively to the N-terminal extremity of these proteins and to a central glycine-rich region which is part of the NAD(H)-binding site. This is a C-terminal domain of alanine dehydrogenases (1.4.1.1 from EC). This domain is also found in the lysine 2-oxoglutarate reductases. ; GO: 0016491 oxidoreductase activity, 0006118 electron transport; PDB: 2vhx_F 2vhz_B 2voe_F 2vhw_B 2vhy_B 2voj_A 2vhv_B 1pjb_A 1say_A 1pjc_A ....
Probab=23.58 E-value=10 Score=13.85 Aligned_cols=40 Identities=18% Similarity=0.127 Sum_probs=20.2
Q ss_pred CCCCCCCEEECC--CCCHHHHHHHHHHHHCCCCEEEEECC-HHHHHH
Q ss_conf 489988178788--98999999998542357104898668-899999
Q T0547 122 YNNEGAPITVNG--FKDRELINIGFIAAEMGHNITLTIEG-LNELEA 165 (611)
Q Consensus 122 ~g~~~~~Ii~nG--~Kd~e~I~lAl~a~~lG~~v~IViDs-~~EL~~ 165 (611)
-+.++.+++.-| .=...-+++ +..+|.+++ ++|. +..++.
T Consensus 16 ~~v~pakvvViGaG~vG~~A~~~---a~~LGa~v~-~~D~~~~~~~~ 58 (168)
T PF01262_consen 16 GGVPPAKVVVIGAGVVGLGAAET---AKGLGAEVV-VPDVRPERLEQ 58 (168)
T ss_dssp --B---EEEEE-------HHHHH---HHH---EEE-EEESSHHHHHH
T ss_pred CCCCCEEEEEECCCHHHHHHHHH---HHHCCCEEE-EECCCHHHHHH
T ss_conf 99788699997987899999999---987799799-70379899976
No 19
>PF07997 DUF1694: Protein of unknown function (DUF1694); InterPro: IPR012543 This family contains many hypothetical proteins.; PDB: 2ohw_A.
Probab=23.32 E-value=13 Score=12.94 Aligned_cols=85 Identities=19% Similarity=0.277 Sum_probs=45.2
Q ss_pred HHHHHHHCCCCCCEEEECHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEECCCHHHHHHHHHHCCCCCCEEEECCH
Q ss_conf 99999855799858987479999999999999999999708898723787453378789999999846667851662288
Q T0547 34 IVKELRDDGYKGPLLLRFPHLIQKQIENIYGNFNKARKEFGYKGGFNAVYPLKVNQYPGFVKNLVKLGKDYNYGLEAGSK 113 (611)
Q Consensus 34 lv~~l~~~~~~tPllvrf~dil~~ri~~l~~aF~~A~~~~~Y~g~y~~vYaiKaN~~~~Vv~~i~~~G~~~~~GlEv~Sk 113 (611)
+-+.+.+.-+|+|-+=-++ =|++-..|++ |++-++.- .+.. +-...
T Consensus 6 l~~~l~~~~~G~p~~kPDE------qr~yLGtfrE-----------RV~lalt~----------~q~~-------~~~~~ 51 (120)
T PF07997_consen 6 LEKRLQQGAYGTPQLKPDE------QRKYLGTFRE-----------RVILALTI----------EQVE-------EPKIY 51 (120)
T ss_dssp HHHHHH-------SSHHHH------HHH-----GG-----------GEEEE---------------TT-------SSS--
T ss_pred HHHHHHHHCCCCCCCCHHH------HHHHCCCHHH-----------HHHEEEEH----------HHHH-------CHHHH
T ss_conf 9999998667998899899------9884552775-----------75303429----------9982-------82479
Q ss_pred HHHHHHHHCCCCCCCEEECCCCC----HHHHHHHHHHHHCCCCEEEE
Q ss_conf 99999996489988178788989----99999998542357104898
Q T0547 114 AELLLAMAYNNEGAPITVNGFKD----RELINIGFIAAEMGHNITLT 156 (611)
Q Consensus 114 ~EL~~ala~g~~~~~Ii~nG~Kd----~e~I~lAl~a~~lG~~v~IV 156 (611)
.|+..+|+- .++..+..||.=+ ..||++| .+.|+.-+||
T Consensus 52 ~~~~~~l~~-~~~~~l~ing~l~~~~~~~YiklA---~~~~~~ftiV 94 (120)
T PF07997_consen 52 PEFEQALKD-YPNYQLLINGNLDYSFQSKYIKLA---NKHNIPFTIV 94 (120)
T ss_dssp HHHHHHHHC--SSEEEEE-----HHHHHHHHHHH---HH----EEE-
T ss_pred HHHHHHHHH-CCCCEEEECCCCCHHHHHHHHHHH---HHCCCCEEEE
T ss_conf 999999964-989789984889878899999999---9859986996
No 20
>PF03945 Endotoxin_N: delta endotoxin, N-terminal domain; InterPro: IPR005639 This family contains insecticidal toxins produced by Bacillus species of bacteria. During spore formation the bacteria produce crystals of this protein. When an insect ingests these proteins, they are activated by proteolytic cleavage. The N-terminus is cleaved in all of the proteins and a C-terminal extension is cleaved in some members. Once activated, the endotoxin binds to the gut epithelium and causes cell lysis by the formation of cation-selective channels, which leads to death. The activated region of the delta toxin is composed of three distinct structural domains: an N-terminal helical bundle domain involved in membrane insertion and pore formation; a beta-sheet central domain (IPR001178 from INTERPRO) involved in receptor binding; and a C-terminal beta-sandwich domain (IPR005638 from INTERPRO) that interacts with the N-terminal domain to form a channel , . This entry represents the conserved N-terminal domain.; GO: 0009405 pathogenesis; PDB: 2c9k_A 1i5p_A 1ciy_A 3eb7_A 1ji6_A 1dlc_A 1w99_A.
Probab=21.84 E-value=4.6 Score=16.45 Aligned_cols=46 Identities=17% Similarity=0.203 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHC---CCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 688999999999999999736---9667899989999999999999985
Q T0547 374 ALEYLHDSIDHLESILTLFDL---GYVDLQDRSNAEILTHLITKKAILL 419 (611)
Q Consensus 374 ~~E~~~da~~~~~~~~~~f~~---G~l~L~~ra~~E~l~~~i~~~~~~~ 419 (611)
.++.|.++..........|.. -.+.|.--|+|-.|+..+.+.....
T Consensus 100 v~~~f~~~~~~f~~~l~~f~~~~~e~~lLp~YaqaAnLhLlLLrd~i~~ 148 (226)
T PF03945_consen 100 VRSRFNDLNSKFTNALPQFQVPGYEVLLLPLYAQAANLHLLLLRDGIIY 148 (226)
T ss_dssp HHHHHHHHHHHHHHHGGGGSCTTSHHTTHHHHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9999999999999988987117723549999999999999999999999
No 21
>PF08123 DOT1: Histone methylation protein DOT1 ; InterPro: IPR013110 The DOT1 domain regulates gene expression by methylating histone H3 . H3 methylation by DOT1 has been shown to be required for the DNA damage checkpoint in yeast .; PDB: 1nw3_A 1u2z_B.
Probab=20.86 E-value=15 Score=12.59 Aligned_cols=35 Identities=17% Similarity=0.115 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCEEEEECCHHHH
Q ss_conf 89999999999999999648998778870756777
Q T0547 292 LREYANDVVFILKNIAEQKKDLEPDIFIESGRFVA 326 (611)
Q Consensus 292 l~eya~~Iv~~i~~~c~~~~vp~P~Ii~EpGRaiv 326 (611)
..++|......++..|+..|...+.+-++.|-++.
T Consensus 78 ~~~~A~~~~~~~~~~~~~~G~~~~~~~l~~gDF~~ 112 (205)
T PF08123_consen 78 LADLAEKQWEELKKRMKIFGKKPGEVELIRGDFLD 112 (205)
T ss_dssp HHHHHHHHHHHHHHHHHH-------B---SS-TTT
T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCC
T ss_conf 99999999999999999838777654885545335
No 22
>PF01698 FLO_LFY: Floricaula / Leafy protein; InterPro: IPR002910 This family consists of various plant development proteins which are homologues of Floricaula (FLO) and leafy (LFY) proteins which are floral meristem identity proteins. Mutations in the sequences of these proteins affect flower and leaf development.; GO: 0003677 DNA binding, 0045449 regulation of transcription; PDB: 2vy2_A 2vy1_A.
Probab=20.65 E-value=8.4 Score=14.47 Aligned_cols=15 Identities=27% Similarity=0.463 Sum_probs=11.4
Q ss_pred HCCCCCCEEEEECCH
Q ss_conf 648998778870756
Q T0547 309 QKKDLEPDIFIESGR 323 (611)
Q Consensus 309 ~~~vp~P~Ii~EpGR 323 (611)
+..-.||-|+||||-
T Consensus 226 ERQREHPFIVTEPGE 240 (386)
T PF01698_consen 226 ERQREHPFIVTEPGE 240 (386)
T ss_dssp -------B-------
T ss_pred CCCCCCCEEECCCCH
T ss_conf 421458726557306
No 23
>PF08368 FAST_2: FAST kinase-like protein, subdomain 2; InterPro: IPR013579 This domain represents a conserved region of eukaryotic Fas-activated serine/threonine (FAST) kinases (2.7.1 from EC) that contains several conserved leucine residues. FAST kinase is rapidly activated during Fas-mediated apoptosis, when it phosphorylates TIA-1, a nuclear RNA-binding protein that has been implicated as an effector of apoptosis . Note that many family members are hypothetical proteins. This subdomain is often found associated with the FAST kinase-like protein, subdomain 2.
Probab=20.47 E-value=11 Score=13.62 Aligned_cols=42 Identities=14% Similarity=0.003 Sum_probs=31.8
Q ss_pred EECCHHHHHHCCCCCCCCCCCEEEEEEC-CCCEEEEEECCCCC
Q ss_conf 6020699974775156789857999988-99628875137887
Q T0547 514 FLVGAYQEVLGMKHNLFTHPTEAIISIN-EKGYEVEGIIEAQS 555 (611)
Q Consensus 514 FlvGAYQeiLGd~HNLfg~t~~v~v~~~-~~g~~i~~~~~gdt 555 (611)
.....++++.-.+.+|||..+.+...+. +-||.|+.++.=|+
T Consensus 45 ~~~~~~~~v~~~L~~llg~~~~~~~~v~tpygy~iD~e~~lD~ 87 (93)
T PF08368_consen 45 RPSPLQQEVQEALEQLLGGENYFRSNVTTPYGYSIDFECVLDK 87 (93)
T ss_pred CCCHHHHHHHHHHHHHHCCCCEEEECCCCCCCEEEEEEEEECC
T ss_conf 8667899999999998098673676155899507979999889
Done!