Query T0592 3NHV, Bacillus halodurans, 144 residues Match_columns 144 No_of_seqs 125 out of 3918 Neff 7.4 Searched_HMMs 11830 Date Mon Jul 5 09:03:22 2010 Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0592.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0592.hhr No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PF00581 Rhodanese: Rhodanese- 99.7 1.8E-17 1.5E-21 121.6 6.8 92 19-114 1-113 (113) 2 PF04273 DUF442: Putative phos 92.8 0.11 9.4E-06 27.5 5.8 75 15-96 12-107 (110) 3 PF05706 CDKN3: Cyclin-depende 74.5 1.1 8.9E-05 21.7 3.2 35 65-99 126-160 (207) 4 PF03853 YjeF_N: YjeF-related 61.1 4.1 0.00034 18.2 3.9 37 67-103 22-61 (173) 5 PF04722 Ssu72: Ssu72-like pro 54.5 5 0.00042 17.7 3.5 29 20-53 15-43 (195) 6 PF07755 DUF1611: Protein of u 52.4 5.9 0.0005 17.3 3.5 79 21-116 77-159 (301) 7 PF00202 Aminotran_3: Aminotra 41.9 8.8 0.00075 16.2 3.5 63 55-119 58-129 (339) 8 PF05430 DUF752: Protein of un 33.4 12 0.001 15.4 3.4 40 61-106 72-111 (124) 9 PF09992 DUF2233: Predicted pe 31.1 13 0.0011 15.2 4.2 39 69-108 147-188 (211) 10 PF02572 CobA_CobO_BtuR: ATP:c 30.0 13 0.0011 15.1 2.5 25 75-99 6-30 (172) 11 PF02780 Transketolase_C: Tran 28.9 14 0.0012 14.9 3.6 66 20-100 24-90 (124) 12 PF00782 DSPc: Dual specificit 26.3 16 0.0014 14.7 3.4 32 69-100 70-102 (133) 13 PF07879 PHB_acc_N: PHB/PHA ac 25.0 17 0.0014 14.5 3.0 31 14-45 16-46 (64) 14 PF10623 PilI: Plasmid conjuga 21.1 20 0.0017 14.0 2.3 35 19-53 30-64 (83) No 1 >PF00581 Rhodanese: Rhodanese-like domain This Prosite entry represents a subset of this family.; InterPro: IPR001763 Rhodanese, a sulphurtransferase involved in cyanide detoxification (see) shares evolutionary relationship with a large family of proteins , including Cdc25 phosphatase catalytic domain. non-catalytic domains of eukaryotic dual-specificity MAPK-phosphatases. non-catalytic domains of yeast PTP-type MAPK-phosphatases. non-catalytic domains of yeast Ubp4, Ubp5, Ubp7. non-catalytic domains of mammalian Ubp-Y. Drosophila heat shock protein HSP-67BB. several bacterial cold-shock and phage shock proteins. plant senescence associated proteins. catalytic and non-catalytic domains of rhodanese (see ). Rhodanese has an internal duplication. This domain is found as a single copy in other proteins, including phosphatases and ubiquitin C-terminal hydrolases .; PDB: 3d1p_A 2jtr_A 2jtq_A 2jts_A 2fsx_A 1tq1_A 3fnj_F 3flh_B 1yt8_A 2eg4_A .... Probab=99.68 E-value=1.8e-17 Score=121.58 Aligned_cols=92 Identities=35% Similarity=0.589 Sum_probs=72.1 Q ss_pred CHHHHHHHHHCCCCCEEEEECCCCCCCCCCCCCCCCCCCHHHH---------------HHHHHHCCCCCCCEEEEECCCC Q ss_conf 7999999996189888998645222322323454333372565---------------5654200035753588852887 Q T0592 19 DIADLSIDIKKGYEGIIVVDVRDAEAYKECHIPTAISIPGNKI---------------NEDTTKRLSKEKVIITYCWGPA 83 (144) Q Consensus 19 ~~~el~~~l~~g~~~~vlIDvR~~~ey~~ghIpGAi~ip~~~l---------------~~~~~~~l~~d~~iVvyC~~~~ 83 (144) +|.++.+++ ++++++|||||++.+|..+|||||+|+|...+ .......++++++||+||.++ T Consensus 1 s~~el~~~~--~~~~~~liDvR~~~e~~~ghI~gsv~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iv~yc~~g- 77 (113) T PF00581_consen 1 SAEELKQLL--EDPNVVLIDVRPPEEYEEGHIPGSVNIPWDSLDPSEDAIFPEKLAEELEELGAGLDKDKPIVFYCSGG- 77 (113) T ss_dssp -HHHHHHHH--TTTTEEEEEESSHHHHHHSBBTTEEEEEGGGGSSSSTCHHHHHHHHHHHHHHHHSTTTSEEEEESSSS- T ss_pred CHHHHHHHH--CCCCEEEEEECCHHHHHCCCCCCCEEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCC- T ss_conf 989998663--08896999918989996493889898440322345432201344454311001246898699996787- Q ss_pred CCHHHHHHHH-----HHHCCC-CEEEECCCHHHHHHC Q ss_conf 3056789999-----997189-806652795999873 Q T0592 84 CNGATKAAAK-----FAQLGF-RVKELIGGIEYWRKE 114 (144) Q Consensus 84 ~~~s~~aa~~-----L~~~G~-~v~~l~GG~~aW~~~ 114 (144) .++..++.. |...|| +|++|+||+.+|.++ T Consensus 78 -~~~~~~~~~~~~~~l~~~G~~~v~~l~GG~~~w~~~ 113 (113) T PF00581_consen 78 -WRSSFAAAALAAWILRALGYKNVYILDGGFEAWQEE 113 (113) T ss_dssp -SHHHHHHHHHHHHHHHHHHHTEEEEEE--HHHHHHH T ss_pred -CCCCCHHHHHHHHHHHHCCCCCEEEECCHHHHHHCC T ss_conf -555403778999999986999889978849998449 No 2 >PF04273 DUF442: Putative phosphatase (DUF442); InterPro: IPR005939 This is a family of largely hypothetical proteins of unknown function. ; PDB: 3gxh_A. Probab=92.78 E-value=0.11 Score=27.51 Aligned_cols=75 Identities=12% Similarity=0.172 Sum_probs=41.8 Q ss_pred CCCCCHHHHHHHHHCCCCCEEEEECCCCCCCCC-C---CCCC--------CCCCCHH-------HHHH--HHHHCCCCCC Q ss_conf 700179999999961898889986452223223-2---3454--------3333725-------6556--5420003575 Q T0592 15 SYETDIADLSIDIKKGYEGIIVVDVRDAEAYKE-C---HIPT--------AISIPGN-------KINE--DTTKRLSKEK 73 (144) Q Consensus 15 ~~~i~~~el~~~l~~g~~~~vlIDvR~~~ey~~-g---hIpG--------Ai~ip~~-------~l~~--~~~~~l~~d~ 73 (144) +-.+++.++.+.-.+|=+ .||..|+..|-.. . .+.. -+|+|.. .+.. ..+.. ..+ T Consensus 12 a~Q~~~~di~~la~~Gfk--tVIn~Rpd~E~~~qp~~~~~~~~a~~~GL~y~~iPv~~~~~~~~~v~~f~~~l~~--~~~ 87 (110) T PF04273_consen 12 AGQPSPEDIAQLAAQGFK--TVINNRPDGEDPGQPSSAEEREAAEAAGLEYVHIPVDSGQITPEDVEAFAAALEE--LPG 87 (110) T ss_dssp E----HHHHHHHHH------EEEE-S-TTSTTS-T---T---HHHH---EEEE----TTS--HHHHHHHHHHHHH--T-- T ss_pred CCCCCHHHHHHHHHCCCC--EEEECCCCCCCCCCCCHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHHH--CCC T ss_conf 589899999999978973--9998998988889974199999999869928995137888999999999999984--899 Q ss_pred CEEEEECCCCCCHHHHHHHHHHH Q ss_conf 35888528873056789999997 Q T0592 74 VIITYCWGPACNGATKAAAKFAQ 96 (144) Q Consensus 74 ~iVvyC~~~~~~~s~~aa~~L~~ 96 (144) +|.+||.+| .||...+ .|.+ T Consensus 88 PVL~hCrsG--~Rs~~l~-~l~~ 107 (110) T PF04273_consen 88 PVLAHCRSG--TRSSALW-ALAQ 107 (110) T ss_dssp -EEEE-SSS--HHHHHHH-HH-- T ss_pred CEEEECCCC--HHHHHHH-HHHC T ss_conf 999989998--0299999-8860 No 3 >PF05706 CDKN3: Cyclin-dependent kinase inhibitor 3 (CDKN3); InterPro: IPR008425 This family consists of cyclin-dependent kinase inhibitor 3 or kinase associated phosphatase proteins from several mammalian species. The cyclin-dependent kinase (Cdk)-associated protein phosphatase (KAP) is a Homo sapiens dual specificity protein phosphatase that dephosphorylates Cdk2 on threonine 160 in a cyclin-dependent manner ,.; PDB: 1fpz_C 1fq1_A. Probab=74.47 E-value=1.1 Score=21.70 Aligned_cols=35 Identities=23% Similarity=0.329 Sum_probs=25.3 Q ss_pred HHHCCCCCCCEEEEECCCCCCHHHHHHHHHHHCCC Q ss_conf 42000357535888528873056789999997189 Q T0592 65 TTKRLSKEKVIITYCWGPACNGATKAAAKFAQLGF 99 (144) Q Consensus 65 ~~~~l~~d~~iVvyC~~~~~~~s~~aa~~L~~~G~ 99 (144) ....+..++.||++|.+|-++....||-.|..+|. T Consensus 126 L~~~L~~gkkvvIHC~GGlGRTGlvAAcLL~~Lg~ 160 (207) T PF05706_consen 126 LKACLENGKKVVIHCYGGLGRTGLVAACLLVELGQ 160 (207) T ss_dssp HHHHHHTT--EEEE-------HHHHHHHHHHHH-S T ss_pred HHHHHHCCCEEEEEECCCCCHHHHHHHHHHHHCCC T ss_conf 99999769989999168875156789999864278 No 4 >PF03853 YjeF_N: YjeF-related protein N-terminus; InterPro: IPR004443 The C-terminal region of yjeF from Escherichia coli shows similarity to hydroxyethylthiazole kinase (thiM) and other enzymes involved in thiamine biosynthesis. Saccharomyces cerevisiae YKL151C and Bacillus subtilis yxkO match the yjeF C-terminal domain but lack this region. The proteins in this group are of unknown function.; PDB: 3d3k_B 3d3j_A 2dg2_F 2o8n_A 1jzt_A 2ax3_A. Probab=61.10 E-value=4.1 Score=18.21 Aligned_cols=37 Identities=24% Similarity=0.377 Sum_probs=25.1 Q ss_pred HCC--CCCCCEEEEECCCCC-CHHHHHHHHHHHCCCCEEE Q ss_conf 000--357535888528873-0567899999971898066 Q T0592 67 KRL--SKEKVIITYCWGPAC-NGATKAAAKFAQLGFRVKE 103 (144) Q Consensus 67 ~~l--~~d~~iVvyC~~~~~-~~s~~aa~~L~~~G~~v~~ 103 (144) ..+ ++.+.|+++|..|+- ...--+++.|...||+|.+ T Consensus 22 ~~~~~~~~~~v~vl~G~GNNGGDglv~AR~L~~~G~~V~v 61 (173) T PF03853_consen 22 RRFPDPKPPRVLVLCGPGNNGGDGLVAARHLAQRGYKVTV 61 (173) T ss_dssp HHS-TTTT-EEEEEE----------HHHHHHHHTTSEEEE T ss_pred HHCCCCCCCEEEEEECCCCCHHHHHHHHHHHHHCCCCEEE T ss_conf 8746467997999989998769999999999987993399 No 5 >PF04722 Ssu72: Ssu72-like protein; InterPro: IPR006811 The yeast Ssu72 is an essential protein that may be involved in transcription start site specification .; PDB: 3fmv_H 3fdf_B. Probab=54.47 E-value=5 Score=17.68 Aligned_cols=29 Identities=17% Similarity=0.247 Sum_probs=12.9 Q ss_pred HHHHHHHHHCCCCCEEEEECCCCCCCCCCCCCCC Q ss_conf 9999999961898889986452223223234543 Q T0592 20 IADLSIDIKKGYEGIIVVDVRDAEAYKECHIPTA 53 (144) Q Consensus 20 ~~el~~~l~~g~~~~vlIDvR~~~ey~~ghIpGA 53 (144) +.|....|++. .+ ||++-..=..-.+||. T Consensus 15 SMEaH~~L~~~--G~---~V~SyGTGs~VkLPGp 43 (195) T PF04722_consen 15 SMEAHKVLKKA--GF---NVSSYGTGSHVKLPGP 43 (195) T ss_dssp HHHHHHHHHH--------EEEEE-----EEEE-E T ss_pred CHHHHHHHHHC--CC---CEEECCCCCCEECCCC T ss_conf 76999999987--99---6164058872148899 No 6 >PF07755 DUF1611: Protein of unknown function (DUF1611); InterPro: IPR011669 This entry contains a number of hypothetical bacterial and archaeal proteins. The region is approximately 350 residues long. A member of this family (Q6M063 from SWISSPROT) is thought to associate with another subunit to form an H^+-transporting ATPase, but no evidence has been found to support this.; PDB: 2obn_B 2g0t_B. Probab=52.36 E-value=5.9 Score=17.25 Aligned_cols=79 Identities=16% Similarity=0.087 Sum_probs=40.8 Q ss_pred HHHHHHHHCCCCCEEEEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCEEEE----ECCCCCCHHHHHHHHHHH Q ss_conf 9999999618988899864522232232345433337256556542000357535888----528873056789999997 Q T0592 21 ADLSIDIKKGYEGIIVVDVRDAEAYKECHIPTAISIPGNKINEDTTKRLSKEKVIITY----CWGPACNGATKAAAKFAQ 96 (144) Q Consensus 21 ~el~~~l~~g~~~~vlIDvR~~~ey~~ghIpGAi~ip~~~l~~~~~~~l~~d~~iVvy----C~~~~~~~s~~aa~~L~~ 96 (144) .++.+..++ .+..|+|||.+ .+....-.|... .+ +.++|+. |+.|....+......|++ T Consensus 77 pel~~~A~~--~g~~i~DvR~p-~~~~~~~~g~~~------------~v--~~~ri~vvGTDcavGK~tTal~L~~~~~~ 139 (301) T PF07755_consen 77 PELAALAKK--HGVQIWDVRKP-PKDLPVASGKIR------------EV--KCKRILVVGTDCAVGKMTTALELRRALRE 139 (301) T ss_dssp HHHHCCHHC------EEETTS---SS-------GC------------C---SSEEEEEE---S----HHHHHHHHHHHHH T ss_pred HHHHHHHHH--HCCEEEECCCC-CCCCCCCCCCCC------------CC--CCCEEEEECCCCCCCHHHHHHHHHHHHHH T ss_conf 999999998--19926563479-875420345113------------68--99889996168552389999999999997 Q ss_pred CCCCEEEECCCHHHHHHCCC Q ss_conf 18980665279599987389 Q T0592 97 LGFRVKELIGGIEYWRKENG 116 (144) Q Consensus 97 ~G~~v~~l~GG~~aW~~~G~ 116 (144) .|+++..+--|-.+|..+|+ T Consensus 140 ~G~~a~fvaTGQTGimi~~~ 159 (301) T PF07755_consen 140 RGIKAGFVATGQTGIMIAGY 159 (301) T ss_dssp ----EEEE-----------B T ss_pred CCCCEEEEECCCEEEEEECC T ss_conf 69971699728726787468 No 7 >PF00202 Aminotran_3: Aminotransferase class-III; InterPro: IPR005814 Aminotransferases share certain mechanistic features with other pyridoxalphosphate-dependent enzymes, such as the covalent binding of the pyridoxalphosphate group to a lysine residue. On the basis of sequence similarity, these various enzymes can be grouped into subfamilies. One of these, called class-III, includes acetylornithine aminotransferase (2.6.1.11 from EC), which catalyzes the transfer of an amino group from acetylornithine to alpha-ketoglutarate, yielding N-acetyl-glutamic-5-semi-aldehyde and glutamic acid; ornithine aminotransferase (2.6.1.13 from EC), which catalyzes the transfer of an amino group from ornithine to alpha-ketoglutarate, yielding glutamic-5-semi-aldehyde and glutamic acid; omega-amino acid--pyruvate aminotransferase (2.6.1.18 from EC), which catalyzes transamination between a variety of omega-amino acids, mono- and diamines, and pyruvate; 4-aminobutyrate aminotransferase (2.6.1.19 from EC) (GABA transaminase), which catalyzes the transfer of an amino group from GABA to alpha-ketoglutarate, yielding succinate semialdehyde and glutamic acid; DAPA aminotransferase (2.6.1.62 from EC), a bacterial enzyme (bioA), which catalyzes an intermediate step in the biosynthesis of biotin, the transamination of 7-keto-8-aminopelargonic acid to form 7,8-diaminopelargonic acid; 2,2-dialkylglycine decarboxylase (4.1.1.64 from EC), a Burkholderia cepacia (Pseudomonas cepacia) enzyme (dgdA) that catalyzes the decarboxylating amino transfer of 2,2-dialkylglycine and pyruvate to dialkyl ketone, alanine and carbon dioxide; glutamate-1-semialdehyde aminotransferase (5.4.3.8 from EC) (GSA); Bacillus subtilis aminotransferases yhxA and yodT; Haemophilus influenzae aminotransferase HI0949; and Caenorhabditis elegans aminotransferase T01B11.2.; GO: 0008483 transaminase activity, 0030170 pyridoxal phosphate binding; PDB: 2pb2_A 2pb0_B 1wkg_A 1wkh_B 1vef_B 2can_A 1gbn_B 1oat_C 2byj_A 2byl_B .... Probab=41.94 E-value=8.8 Score=16.21 Aligned_cols=63 Identities=16% Similarity=0.109 Sum_probs=38.6 Q ss_pred CCCHHHHHHHHHHCCCCCCCEEEEECCCCCCHHHHHHHHHHH--------CCC-CEEEECCCHHHHHHCCCCCC Q ss_conf 337256556542000357535888528873056789999997--------189-80665279599987389413 Q T0592 55 SIPGNKINEDTTKRLSKEKVIITYCWGPACNGATKAAAKFAQ--------LGF-RVKELIGGIEYWRKENGEVE 119 (144) Q Consensus 55 ~ip~~~l~~~~~~~l~~d~~iVvyC~~~~~~~s~~aa~~L~~--------~G~-~v~~l~GG~~aW~~~G~pve 119 (144) +-+..++.+...+.+|....-|++|.+| .-+..+|.++.+ -|- ++..+.||+.+|....+.+. T Consensus 58 ~~~~~~lae~L~~~~p~~~~~v~f~~SG--seAve~AiklAr~y~~~~~~tgr~~ii~~~~~yHG~t~~~~s~~ 129 (339) T PF00202_consen 58 HPPAVELAEKLAELAPPGLDRVFFANSG--SEAVEAAIKLARQYHKKRGYTGRSKIISFEGSYHGRTLGALSVT 129 (339) T ss_dssp EHHHHHHHHHHHHHS-TTESEEEEE------HHHHHHHHHHHHHHHHHHHTT--EEEEECT------HHHCTTT T ss_pred CHHHHHHHHHHHHHCCCCCCEEEEECCC--CHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCCCCCCEEECC T ss_conf 6799999999971089975679875688--57999999998664002478887479993686577874615655 No 8 >PF05430 DUF752: Protein of unknown function (DUF752); InterPro: IPR008471 This family contains several uncharacterised bacterial proteins with no known function.; PDB: 2qy6_B 2e58_D. Probab=33.37 E-value=12 Score=15.39 Aligned_cols=40 Identities=20% Similarity=0.297 Sum_probs=27.3 Q ss_pred HHHHHHHCCCCCCCEEEEECCCCCCHHHHHHHHHHHCCCCEEEECC Q ss_conf 5565420003575358885288730567899999971898066527 Q T0592 61 INEDTTKRLSKEKVIITYCWGPACNGATKAAAKFAQLGFRVKELIG 106 (144) Q Consensus 61 l~~~~~~~l~~d~~iVvyC~~~~~~~s~~aa~~L~~~G~~v~~l~G 106 (144) +.........++.++++||. +..+...|...||+|.-..| T Consensus 72 ~~~~la~~~~~g~~l~Tys~------a~~VR~~L~~aGF~V~~~~g 111 (124) T PF05430_consen 72 FFKQLARLLKPGGTLATYSA------AGAVRRALKAAGFEVEKVPG 111 (124) T ss_dssp HHHHHHHCB-----EEES---------HHHHHHHHH---B-EEE-- T ss_pred HHHHHHHHHCCCCEEEEEEC------CHHHHHHHHHCCCEEEECCC T ss_conf 99999998479978999856------09999999986997982589 No 9 >PF09992 DUF2233: Predicted periplasmic protein (DUF2233) Probab=31.14 E-value=13 Score=15.17 Aligned_cols=39 Identities=18% Similarity=0.181 Sum_probs=25.3 Q ss_pred CCCCCC-EEEEECCCCCCHHHHHHHHHH-HCCC-CEEEECCCH Q ss_conf 035753-588852887305678999999-7189-806652795 Q T0592 69 LSKEKV-IITYCWGPACNGATKAAAKFA-QLGF-RVKELIGGI 108 (144) Q Consensus 69 l~~d~~-iVvyC~~~~~~~s~~aa~~L~-~~G~-~v~~l~GG~ 108 (144) ++++.. +++.+++.+ ..-...+..|. .+|. ++.+|+||- T Consensus 147 ~~~~G~~~~~v~~~~g-~tl~ela~~~~~~lg~~~A~nLDGGg 188 (211) T PF09992_consen 147 IDADGRVLLLVVDGAG-MTLYELAQIMKDELGAVNALNLDGGG 188 (211) T ss_pred ECCCCCEEEEEEECCC-CCHHHHHHHHHHHCCCCEEEECCCCC T ss_conf 8479989999996998-69999999999857998899837863 No 10 >PF02572 CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase BtuR/CobO/CobP; InterPro: IPR003724 ATP:cob(I)alamin (or ATP:corrinoid) adenosyltransferases (2.5.1.17 from EC), catalyse the conversion of cobalamin (vitamin B12) into its coenzyme form, adenosylcobalamin (coenzyme B12) . Adenosylcobalamin (AdoCbl) is required for the ativity of certain enzymes. AdoCbl contains an adenosyl moiety liganded to the cobalt ion of cobalamin via a covalent Co-C bond, and its synthesis is unique to certain prokaryotes. ATP:cob(I)alamin adenosyltransferases are classed into three groups: CobA-type , EutT-type and PduO-type . Each of the three enzyme types appears to be specialised for particular AdoCbl-dependent enzymes or for the de novo synthesis AdoCbl. PduO and EutT are distantly related, sharing short conserved motifs, while CobA is evolutionarily unrelated and is an example of convergent evolution. This entry represnts the ATP:cob(I)alamin adenosyltransferases CobA (Salmonella typhimurium), CobO (Pseudomonas denitrificans), and ButR (Escherichia coli). There is a high degree of sequence identity between these proteins . CobA is responsible for attaching the adenosyl moiety from ATP to the cobalt ion of the corrin ring, necessary for the convertion of cobalamin to adenosylcobalamin , . ; GO: 0005524 ATP binding, 0008817 cob(I)yrinic acid a,c-diamide adenosyltransferase activity, 0009236 cobalamin biosynthetic process; PDB: 1g64_B 1g5t_A 1g5r_A. Probab=29.98 E-value=13 Score=15.12 Aligned_cols=25 Identities=12% Similarity=0.085 Sum_probs=10.0 Q ss_pred EEEEECCCCCCHHHHHHHHHHHCCC Q ss_conf 5888528873056789999997189 Q T0592 75 IITYCWGPACNGATKAAAKFAQLGF 99 (144) Q Consensus 75 iVvyC~~~~~~~s~~aa~~L~~~G~ 99 (144) |.+||..|.+..++.....|+++|. T Consensus 6 i~vytG~GKGKTTAAlG~alRA~G~ 30 (172) T PF02572_consen 6 IQVYTGDGKGKTTAALGLALRAAGH 30 (172) T ss_dssp EEEEE------HHHH---HHHH--- T ss_pred EEEEECCCCCCHHHHHHHHHHHHCC T ss_conf 9999679998178999999998448 No 11 >PF02780 Transketolase_C: Transketolase, C-terminal domain; InterPro: IPR005476 Transketolase 2.2.1.1 from EC (TK) catalyzes the reversible transfer of a two-carbon ketol unit from xylulose 5-phosphate to an aldose receptor, such as ribose 5-phosphate, to form sedoheptulose 7-phosphate and glyceraldehyde 3- phosphate. This enzyme, together with transaldolase, provides a link between the glycolytic and pentose-phosphate pathways. TK requires thiamine pyrophosphate as a cofactor. In most sources where TK has been purified, it is a homodimer of approximately 70 Kd subunits. TK sequences from a variety of eukaryotic and prokaryotic sources , show that the enzyme has been evolutionarily conserved. In the peroxisomes of methylotrophic yeast Hansenula polymorpha, there is a highly related enzyme, dihydroxy-acetone synthase (DHAS) 2.2.1.3 from EC (also known as formaldehyde transketolase), which exhibits a very unusual specificity by including formaldehyde amongst its substrates. 1-deoxyxylulose-5-phosphate synthase (DXP synthase) is an enzyme so far found in bacteria (gene dxs) and plants (gene CLA1) which catalyzes the thiamine pyrophosphoate-dependent acyloin condensation reaction between carbon atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D- xylulose-5-phosphate (dxp), a precursor in the biosynthetic pathway to isoprenoids, thiamine (vitamin B1), and pyridoxol (vitamin B6). DXP synthase is evolutionary related to TK. The N-terminal section, contains a histidine residue which appears to function in proton transfer during catalysis . In the central section there are conserved acidic residues that are part of the active cleft and may participate in substrate-binding . This family includes transketolase enzymes 2.2.1.1 from EC and also partially matches to 2-oxoisovalerate dehydrogenase beta subunit P37941 from SWISSPROT 1.2.4.4 from EC. Both these enzymes utilise thiamine pyrophosphate as a cofactor, suggesting there may be common aspects in their mechanism of catalysis.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 1r9j_A 1ay0_A 1tkb_B 1trk_A 1ngs_A 1tkc_A 1gpu_B 1tka_B 3hyl_A 1qgd_B .... Probab=28.92 E-value=14 Score=14.94 Aligned_cols=66 Identities=17% Similarity=0.145 Sum_probs=33.5 Q ss_pred HHHHHHHHHCCCCCEEEEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCEEEEECCC-CCCHHHHHHHHHHHCC Q ss_conf 999999996189888998645222322323454333372565565420003575358885288-7305678999999718 Q T0592 20 IADLSIDIKKGYEGIIVVDVRDAEAYKECHIPTAISIPGNKINEDTTKRLSKEKVIITYCWGP-ACNGATKAAAKFAQLG 98 (144) Q Consensus 20 ~~el~~~l~~g~~~~vlIDvR~~~ey~~ghIpGAi~ip~~~l~~~~~~~l~~d~~iVvyC~~~-~~~~s~~aa~~L~~~G 98 (144) +.++.+.|.+..-++-+||+|... ++|.+.+. ..+.+.+.++++-.+. .+.-+...+..+...| T Consensus 24 a~~aa~~L~~~gi~~~vi~~~~l~-----------P~d~~~i~----~~~~~~~~ivvvEe~~~~gG~g~~v~~~l~~~~ 88 (124) T PF02780_consen 24 ALEAADELREEGISVGVIDLRSLK-----------PFDEEAIL----ESAKKTKRIVVVEEHYKIGGLGSEVAEFLAENG 88 (124) T ss_dssp HHHHHHHHHHC-S-EEEEEEEEEE-----------SSBHHHHH----HHCHHHHHEEEEESSCSEEEEHHHHHHHHHHHC T ss_pred HHHHHHHHHHCCCCEEEEEEEEEE-----------CCCHHHHH----HHHHHCCEEEECCCCCCCCCHHHHHHHHHHHHC T ss_conf 999999988759872578743986-----------17578999----998427819992599744428999999999848 Q ss_pred CC Q ss_conf 98 Q T0592 99 FR 100 (144) Q Consensus 99 ~~ 100 (144) +. T Consensus 89 ~~ 90 (124) T PF02780_consen 89 FN 90 (124) T ss_dssp GG T ss_pred CC T ss_conf 66 No 12 >PF00782 DSPc: Dual specificity phosphatase, catalytic domain; InterPro: IPR000340 Protein tyrosine (pTyr) phosphorylation is a common post-translational modification which can create novel recognition motifs for protein interactions and cellular localisation, affect protein stability, and regulate enzyme activity. Consequently, maintaining an appropriate level of protein tyrosine phosphorylation is essential for many cellular functions. Tyrosine-specific protein phosphatases (PTPase; 3.1.3.48 from EC) catalyse the removal of a phosphate group attached to a tyrosine residue, using a cysteinyl-phosphate enzyme intermediate. These enzymes are key regulatory components in signal transduction pathways (such as the MAP kinase pathway) and cell cycle control, and are important in the control of cell growth, proliferation, differentiation and transformation , . The PTP superfamily can be divided into four subfamilies : (1) pTyr-specific phosphatases (2) dual specificity phosphatases (dTyr and dSer/dThr) (3) Cdc25 phosphatases (dTyr and/or dThr) (4) LMW (low molecular weight) phosphatases Based on their cellular localization, PTPases are also classified as: Receptor-like, which are transmembrane receptors that contain PTPase domains Non-receptor (intracellular) PTPases All PTPases carry the highly conserved active site motif C(X)5R (PTP signature motif), employ a common catalytic mechanism, and share a similar core structure made of a central parallel beta-sheet with flanking alpha-helices containing a beta-loop-alpha-loop that encompasses the PTP signature motif . Functional diversity between PTPases is endowed by regulatory domains and subunits. This entry represents dual specificity protein-tyrosine phosphatases. Ser/Thr and Tyr dual specificity phosphatases are a group of enzymes with both Ser/Thr (3.1.3.16 from EC) and tyrosine specific protein phosphatase (3.1.3.48 from EC) activity able to remove both the serine/threonine or tyrosine-bound phosphate group from a wide range of phosphoproteins, including a number of enzymes which have been phosphorylated under the action of a kinase. Dual specificity protein phosphatases (DSPs) regulate mitogenic signal transduction and control the cell cycle. The crystal structure of a human DSP, vaccinia H1-related phosphatase (or VHR), has been determined at 2.1 angstrom resolution . A shallow active site pocket in VHR allows for the hydrolysis of phosphorylated serine, threonine, or tyrosine protein residues, whereas the deeper active site of protein tyrosine phosphatases (PTPs) restricts substrate specificity to only phosphotyrosine. Positively charged crevices near the active site may explain the enzyme's preference for substrates with two phosphorylated residues. The VHR structure defines a conserved structural scaffold for both DSPs and PTPs. A "recognition region" connecting helix alpha1 to strand beta1, may determine differences in substrate specificity between VHR, the PTPs, and other DSPs. These proteins may also have inactive phosphatase domains, and dependent on the domain composition this loss of catalytic activity has different effects on protein function. Inactive single domain phosphatases can still specifically bind substrates, and protect again dephosphorylation, while the inactive domains of tandem phosphatases can be further subdivided into two classes. Those which bind phosphorylated tyrosine residues may recruit multi-phosphorylated substrates for the adjacent active domains and are more conserved, while the other class have accumulated several variable amino acid substitutions and have a complete loss of tyrosine binding capability. The second class shows a release of evolutionary constraint for the sites around the catalytic centre, which emphasises a difference in function from the first group. There is a region of higher conservation common to both classes, suggesting a new regulatory centre.; GO: 0008138 protein tyrosine/serine/threonine phosphatase activity, 0006470 protein amino acid dephosphorylation; PDB: 1d5r_A 2img_A 1i9t_A 1i9s_A 2c46_D 1yn9_C 2q05_C 3cm3_A 2rf6_A 2p4d_A .... Probab=26.33 E-value=16 Score=14.66 Aligned_cols=32 Identities=13% Similarity=0.153 Sum_probs=19.6 Q ss_pred CCCCCCEEEEECCCCCCHHHHHH-HHHHHCCCC Q ss_conf 03575358885288730567899-999971898 Q T0592 69 LSKEKVIITYCWGPACNGATKAA-AKFAQLGFR 100 (144) Q Consensus 69 l~~d~~iVvyC~~~~~~~s~~aa-~~L~~~G~~ 100 (144) ......|.|.|..|.+++...++ +.+...|++ T Consensus 70 ~~~~~~VlVHC~~G~~RS~~v~~ayLm~~~~~~ 102 (133) T PF00782_consen 70 RQQGGKVLVHCQAGISRSGTVVAAYLMRKEGMS 102 (133) T ss_dssp HHTTCEEEEEE----HHHHHHHHHHHHHHSTSS T ss_pred HCCCCEEEEECCCCCCHHHHHHHHHHHHHCCCC T ss_conf 656847999838877769999999999943999 No 13 >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=25.03 E-value=17 Score=14.51 Aligned_cols=31 Identities=23% Similarity=0.298 Sum_probs=23.8 Q ss_pred CCCCCCHHHHHHHHHCCCCCEEEEECCCCCCC Q ss_conf 57001799999999618988899864522232 Q T0592 14 LSYETDIADLSIDIKKGYEGIIVVDVRDAEAY 45 (144) Q Consensus 14 ~~~~i~~~el~~~l~~g~~~~vlIDvR~~~ey 45 (144) .+--|+-.++++++.+|. ++.++|..+-++. T Consensus 16 ~S~YITL~di~~lV~~g~-~~~V~DakTgeDi 46 (64) T PF07879_consen 16 TSSYITLEDIAQLVREGE-EFKVVDAKTGEDI 46 (64) T ss_pred CCEEEEHHHHHHHHHCCC-EEEEEECCCCCHH T ss_conf 753777999999997898-4899977887531 No 14 >PF10623 PilI: Plasmid conjugative transfer protein PilI Probab=21.11 E-value=20 Score=14.05 Aligned_cols=35 Identities=14% Similarity=0.190 Sum_probs=11.9 Q ss_pred CHHHHHHHHHCCCCCEEEEECCCCCCCCCCCCCCC Q ss_conf 79999999961898889986452223223234543 Q T0592 19 DIADLSIDIKKGYEGIIVVDVRDAEAYKECHIPTA 53 (144) Q Consensus 19 ~~~el~~~l~~g~~~~vlIDvR~~~ey~~ghIpGA 53 (144) |+.++.......+..+++|=..+..-+....|||| T Consensus 30 D~~~~~~~F~T~DN~LvvV~~N~R~i~R~ER~PGS 64 (83) T PF10623_consen 30 DPDELARRFCTPDNCLVVVCCNNRFIFRKERAPGS 64 (83) T ss_pred CHHHHHHCCCCCCCEEEEEEECCHHHHHHHCCCCC T ss_conf 97898612347887389998265554212308998 Done!