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!