Query         T0585 APC62366.1, Bartonella henselae, 234 residues
Match_columns 234
No_of_seqs    114 out of 1820
Neff          8.1 
Searched_HMMs 11830
Date          Sun Jun 13 15:26:57 2010
Command       /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0585.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0585.hhr 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PF01520 Amidase_3:  N-acetylmu 100.0       0       0  306.1  10.4  174    7-222     1-175 (175)
  2 PF07454 SpoIIP:  Stage II spor  97.8  0.0011 9.4E-08   39.3  16.0  171    3-217    72-267 (268)
  3 PF04414 tRNA_deacylase:  D-ami  92.2    0.27 2.3E-05   24.5   8.7   40  181-225    88-127 (215)
  4 PF04007 DUF354:  Protein of un  81.0     1.3 0.00011   20.3   5.2   65    5-85      1-94  (335)
  5 PF02879 PGM_PMM_II:  Phosphogl  70.6     2.4 0.00021   18.6   7.8   66    2-86     20-96  (105)
  6 PF04952 AstE_AspA:  Succinylgl  66.0       3 0.00026   18.0   4.2   42  179-231   158-199 (292)
  7 PF05681 Fumerase:  Fumarate hy  36.4     9.2 0.00078   15.0   5.8   23  183-205   173-195 (271)
  8 PF11684 DUF3280:  Protein of u  27.3      13  0.0011   14.0   6.9   64   17-80     13-86  (140)
  9 PF03129 HGTP_anticodon:  Antic  22.3      16  0.0014   13.5   6.3   54   29-86     11-64  (94)
 10 PF01750 HycI:  Hydrogenase mat  22.1      16  0.0014   13.4   2.0   10   75-84     36-45  (130)
 11 PF00561 Abhydrolase_1:  alpha/  20.1      18  0.0015   13.2   5.1   44    6-53      3-48  (231)

No 1  
>PF01520 Amidase_3:  N-acetylmuramoyl-L-alanine amidase;  InterPro: IPR002508   The cell wall envelope of Gram-positive bacteria is a macromolecular, exoskeletal organelle that is assembled and turned over at designated sites. The cell wall also functions as a surface organelle that allows Gram-positive pathogens to interact with their environment, in particular the tissues of the infected host. All of these functions require that surface proteins and enzymes be properly targeted to the cell wall envelope. Two basic mechanisms, cell wall sorting and targeting, have been identified. Cell well sorting is the covalent attachment of surface proteins to the peptidoglycan via a C-terminal sorting signal that contains a consensus LPXTG sequence. More than 100 proteins that possess cell wall-sorting signals, including the M proteins of Streptococcus pyogenes, protein A of Staphylococcus aureus, and several internalins of Listeria monocytogenes, have been identified. Cell wall targeting involves the noncovalent attachment of proteins to the cell surface via specialised binding domains. Several of these wall-binding domains appear to interact with secondary wall polymers that are associated with the peptidoglycan, for example teichoic acids and polysaccharides. Proteins that are targeted to the cell surface include muralytic enzymes such as autolysins, lysostaphin, and phage lytic enzymes. Other examples for targeted proteins are the surface S-layer proteins of bacilli and clostridia, as well as virulence factors required for the pathogenesis of L. monocytogenes (internalin B) and Streptococcus pneumoniae (PspA) infections .   Autolysin 3.5.1.28 from EC hydrolyses the link between N-acetylmuramoyl residues and L-amino acid residues in certain bacterial cell wall glycopeptides.; GO: 0008745 N-acetylmuramoyl-L-alanine amidase activity, 0009253 peptidoglycan catabolic process; PDB: 1jwq_A 3czx_C 1xov_A.
Probab=100.00  E-value=0  Score=306.11  Aligned_cols=174  Identities=40%  Similarity=0.618  Sum_probs=156.2

Q ss_pred             EEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCHHHHHHHHHHCCCCEEEEEECCCC
Q ss_conf             99827877889975088884068889999999999999569919998738887479899999998449978998603567
Q T0585             7 VVLDPGHGGIDGGARGVTGILEKDVTLAFARALRDELQKGSHTIVALTRDSDIFLRLSERVKKAQEFDADLFISIHADTI   86 (234)
Q Consensus         7 IvIDpGHGG~D~Ga~g~~G~~E~~~~l~iA~~l~~~L~~~g~~vv~~tr~~D~~~sl~~R~~~A~~~~adl~iSiH~ns~   86 (234)
                      |||||||||.||||++.+|+.|+++||++|++|+++|++.| ..|++||++|.+++|.+|+..||+.+||+|||||+|++
T Consensus         1 I~iDpGHgg~d~Ga~~~~g~~E~~~~l~ia~~l~~~L~~~G-~~V~ltr~~d~~~~l~~R~~~an~~~adl~iSiH~ns~   79 (175)
T PF01520_consen    1 IVIDPGHGGSDPGAIGPNGLKEKDVNLDIAKRLKKYLEKAG-ANVILTRDDDEDVSLQERVNLANSNGADLFISIHANSS   79 (175)
T ss_dssp             EEEE--EETTB---BSSSS-BHHHHHHHHHHHHHHHHHHCT-EEEEECSSSSHHHHHHHHHHHHHHTT-SEEEEEEEE--
T ss_pred             CEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCC-CEEEEECCCCCCCCHHHHHHHHHHHCCCEEEEEECCCC
T ss_conf             98969899798996689998668999999999999998789-88999589898899999999999809969999724778


Q ss_pred             CCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             78874258998527888707899999741023331133321036789999998874107889999999999887511664
Q T0585            87 DVHSLRGATVYTISDEASDAIAKSLAESENKVDLLDGLPKEESLELTDILLDLTRRETHAFSINFANNVVSNLSKSHINL  166 (234)
Q Consensus        87 ~~~~~~G~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~s~~la~~i~~~l~~~~~~~  166 (234)
                      +++.++|+++||.....                                        ....+..||+.|++++.+.. +.
T Consensus        80 ~~~~~~G~ev~~~~~~~----------------------------------------~~~~s~~lA~~i~~~l~~~~-~~  118 (175)
T PF01520_consen   80 NNGAARGTEVYYSYNNS----------------------------------------NSPKSKRLAERIQKELVKKG-GL  118 (175)
T ss_dssp             SSTT----EEEE---CG----------------------------------------GCHHHHHHHHHHHHHHHHH----
T ss_pred             CCCCCCCEEEEEECCCC----------------------------------------CCHHHHHHHHHHHHHHHHHC-CC
T ss_conf             99998961899850323----------------------------------------50889999999999999870-87


Q ss_pred             CCCCEECCC-CEEEECCCCCEEEEEEECCCCHHHHHHHCCHHHHHHHHHHHHHHHHH
Q ss_conf             568500486-02640698977766540388989998723988999999999999999
Q T0585           167 INNPHRYAD-FQVLKAPDVPSVLIEIGYLSNKEDEKLLNNPQWRKQMAASIAYSIRQ  222 (234)
Q Consensus       167 ~~~~~~~~~-l~vlr~~~~PaVLiE~gFisN~~D~~~l~~~~~~~~lA~aia~gI~~  222 (234)
                      +++|++.++ |++|+.+.||+||||+|||||++|+++|.++.+|+++|++|++||.+
T Consensus       119 ~~rg~~~~~~l~vlr~t~~PavliE~gfisN~~D~~~l~~~~~~~~iA~aia~gI~~  175 (175)
T PF01520_consen  119 PNRGVKPRNNLYVLRNTNMPAVLIELGFISNPEDAARLNDPEYQQKIAKAIAEGIKK  175 (175)
T ss_dssp             -----EECT--HHHHHHCS-EEEEEECETTSHHHHHHHTHHHHCCCHHHCCCHHHH-
T ss_pred             CCCCCEECCHHHHHHCCCCCEEEEEECCCCCHHHHHHHCCHHHHHHHHHHHHHHHHC
T ss_conf             778830230124420589887999744769989999866989999999999998609


No 2  
>PF07454 SpoIIP:  Stage II sporulation protein P (SpoIIP);  InterPro: IPR010897   This family contains the bacterial stage II sporulation protein P (SpoIIP) (approximately 350 residues long). It has been shown that a block in polar cytokinesis in Bacillus subtilis is mediated partly by transcription of spoIID, spoIIM and spoIIP. This inhibition of polar division is involved in the locking in of asymmetry after the formation of a polar septum during sporulation .   SpoIIP is one of the three genes (spoIID, spoIIM and spoIIP, , , ), under the control of sigma E, that have been shown to be essential for the engulfment of the forespore by the mother cell. Their products are involved in degradation of the septal peptidoglycan and mutations in spoIID, spoIIM or spoIIP block sporulation at morphological stage II, prior to the stage of engulfment. These three genes are absolutely conserved (sometimes even duplicated) in all endospore formers .
Probab=97.75  E-value=0.0011  Score=39.34  Aligned_cols=171  Identities=20%  Similarity=0.203  Sum_probs=96.5

Q ss_pred             CCEEEEEECCCCCCC----CC---CCCCCC-CCHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCC---CCCHH---HHHH
Q ss_conf             965899827877889----97---508888-4068889999999999999569919998738887---47989---9999
Q T0585             3 ASFRVVLDPGHGGID----GG---ARGVTG-ILEKDVTLAFARALRDELQKGSHTIVALTRDSDI---FLRLS---ERVK   68 (234)
Q Consensus         3 ~~~~IvIDpGHGG~D----~G---a~g~~G-~~E~~~~l~iA~~l~~~L~~~g~~vv~~tr~~D~---~~sl~---~R~~   68 (234)
                      ++-.|+|=--|+...    .|   ..+..| ..+..=...++.+|++.|+++|+.|+.-+...|.   .-+..   +-++
T Consensus        72 ~~p~V~IYHTHt~EsY~p~~~~~~~~~~~~~~~~~~nV~~VG~~L~~~Le~~Gi~v~hd~t~hd~~~y~~sY~~Sr~tv~  151 (268)
T PF07454_consen   72 GKPQVLIYHTHTTESYLPSDGLESIPGPGGATDEEYNVVGVGDYLAEELEKYGIGVIHDKTVHDYPSYNQSYKRSRETVK  151 (268)
T ss_pred             CCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCEEEEECCCCCCCHHHHHHHHHHHHHH
T ss_conf             99889999289844246876763111224555554118999999999998769228986887886007889999999999


Q ss_pred             HHHHCCC--CEEEEEECCCCCCCCC-----CE---EEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH
Q ss_conf             9984499--7899860356778874-----25---899852788870789999974102333113332103678999999
Q T0585            69 KAQEFDA--DLFISIHADTIDVHSL-----RG---ATVYTISDEASDAIAKSLAESENKVDLLDGLPKEESLELTDILLD  138 (234)
Q Consensus        69 ~A~~~~a--dl~iSiH~ns~~~~~~-----~G---~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d  138 (234)
                      .+=+..+  +++|-||-|+.++...     .|   +.++......                                   
T Consensus       152 ~~L~~~p~i~~viDiHRD~~~~~~~~t~~InGk~~Aki~fVvG~~-----------------------------------  196 (268)
T PF07454_consen  152 KILKENPDIKVVIDIHRDSVPDRKKTTTEINGKNYAKIMFVVGRD-----------------------------------  196 (268)
T ss_pred             HHHHHCCCCEEEEECCCCCCCCCCCEEEEECCEEEEEEEEEECCC-----------------------------------
T ss_conf             999878996199981578998777248999999857899997889-----------------------------------


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCEEEECCCCC-EEEEEEECCCCHHHHHHHCCHHHHHHHHHHHH
Q ss_conf             88741078899999999998875116645685004860264069897-77665403889899987239889999999999
Q T0585           139 LTRRETHAFSINFANNVVSNLSKSHINLINNPHRYADFQVLKAPDVP-SVLIEIGYLSNKEDEKLLNNPQWRKQMAASIA  217 (234)
Q Consensus       139 ~~~~~~~~~s~~la~~i~~~l~~~~~~~~~~~~~~~~l~vlr~~~~P-aVLiE~gFisN~~D~~~l~~~~~~~~lA~aia  217 (234)
                         ...+..-..||..+...+.+..+++.++......  .-+.--+| |+|||+|=.+|..|...-.    -+-+|++++
T Consensus       197 ---np~~~~Nl~fA~~l~~~~~~~yPGl~rgI~~~~~--~YNQdL~~~alLiEvG~~~Nt~eEa~~s----~~~lA~vl~  267 (268)
T PF07454_consen  197 ---NPNWEKNLAFAEQLHAKAEKKYPGLSRGIFIKDG--RYNQDLSPNALLIEVGGQDNTLEEAKRS----AEYLADVLA  267 (268)
T ss_pred             ---CCCHHHHHHHHHHHHHHHHHHCCCCCEEEEECCC--EECCCCCCCEEEEEECCCCCCHHHHHHH----HHHHHHHHC
T ss_conf             ---9789999999999999999678895201466575--1377578981899958987879999999----999999853


No 3  
>PF04414 tRNA_deacylase:  D-aminoacyl-tRNA deacylase;  InterPro: IPR007508 This is a family of hypothetical proteins. It is present in prokaryotes and Arabidopsis.; PDB: 2gfq_C 1yqe_A.
Probab=92.23  E-value=0.27  Score=24.51  Aligned_cols=40  Identities=28%  Similarity=0.444  Sum_probs=30.8

Q ss_pred             CCCCCEEEEEEECCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             698977766540388989998723988999999999999999998
Q T0585           181 APDVPSVLIEIGYLSNKEDEKLLNNPQWRKQMAASIAYSIRQFAE  225 (234)
Q Consensus       181 ~~~~PaVLiE~gFisN~~D~~~l~~~~~~~~lA~aia~gI~~y~~  225 (234)
                      ..+.|++.||+|     ...+.|.++...+.+|++|.+++.....
T Consensus        88 ~~~~Ps~FvEIG-----Ste~eW~d~~a~~~vA~avl~~~~~~~~  127 (215)
T PF04414_consen   88 DLNVPSLFVEIG-----STEEEWNDPDAAEAVAEAVLEVLDKDEE  127 (215)
T ss_dssp             ---SBEEEEEE--------HHHHT-CHHHHHHHHHHHHHHHHST-
T ss_pred             CCCCCCEEEEEC-----CCHHHHCCHHHHHHHHHHHHHHHCCCCC
T ss_conf             789972899966-----9889957918999999999998526554


No 4  
>PF04007 DUF354:  Protein of unknown function (DUF354);  InterPro: IPR007152 Members of this family are around 350 amino acids in length. They are found in archaea and some bacteria and have no known function.
Probab=80.97  E-value=1.3  Score=20.31  Aligned_cols=65  Identities=26%  Similarity=0.398  Sum_probs=43.1

Q ss_pred             EEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCC------------------CH---
Q ss_conf             589982787788997508888406888999999999999956991999873888747------------------98---
Q T0585             5 FRVVLDPGHGGIDGGARGVTGILEKDVTLAFARALRDELQKGSHTIVALTRDSDIFL------------------RL---   63 (234)
Q Consensus         5 ~~IvIDpGHGG~D~Ga~g~~G~~E~~~~l~iA~~l~~~L~~~g~~vv~~tr~~D~~~------------------sl---   63 (234)
                      ++|.||-+|-..                .-+-+-+-++|++.|+.|.+++|+.+...                  ++   
T Consensus         1 m~IwiDi~~p~h----------------vhfFk~iI~eLe~~Ghev~itaR~~~~~~~LL~~ygi~y~~vG~~g~s~~~K   64 (335)
T PF04007_consen    1 MRIWIDIGNPAH----------------VHFFKPIIRELEKRGHEVLITARDYDETIELLDMYGIEYIVVGKHGKSLYGK   64 (335)
T ss_pred             CEEEEECCCCHH----------------HHHHHHHHHHHHHCCCEEEEEEECCCCHHHHHHHCCCCEEEEECCCCCHHHH
T ss_conf             949997799516----------------7899999999973897999999445538999998299759980688988999


Q ss_pred             --------HHHHHHHHHCCCCEEEEEECCC
Q ss_conf             --------9999999844997899860356
Q T0585            64 --------SERVKKAQEFDADLFISIHADT   85 (234)
Q Consensus        64 --------~~R~~~A~~~~adl~iSiH~ns   85 (234)
                              .+-.+++.+.++|++||.|--.
T Consensus        65 l~~~~~R~~~l~k~~~~~~pDv~i~~~s~~   94 (335)
T PF04007_consen   65 LLESIERQYKLYKLIKKFKPDVAISFGSPD   94 (335)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCEEEECCCHH
T ss_conf             998999999999998750998899658889


No 5  
>PF02879 PGM_PMM_II:  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II;  InterPro: IPR005845   The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) . PGM (5.4.2.2 from EC) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose . PGM/PMM (5.4.2.2 from EC; 5.4.2.8 from EC) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate , . Both PNGM (5.4.2.3 from EC) and PAGM (5.4.2.10 from EC) are involved in the biosynthesis of UDP-N-acetylglucosamine , .    Despite differences in substrate specificity, these enzymes share a similar catalytic mechanism, converting 1-phospho-sugars to 6-phospho-sugars via a biphosphorylated 1,6-phospho-sugar. The active enzyme is phosphorylated at a conserved serine residue and binds one magnesium ion; residues around the active site serine are well conserved among family members. The reaction mechanism involves phosphoryl transfer from the phosphoserine to the substrate to create a biophosphorylated sugar, followed by a phosphoryl transfer from the substrate back to the enzyme .   The structures of PGM and PGM/PMM have been determined, and were found to be very similar in topology. These enzymes are both composed of four domains and a large central active site cleft, where each domain contains residues essential for catalysis and/or substrate recognition. Domain I contains the catalytic phosphoserine, domain II contains a metal-binding loop to coordinate the magnesium ion, domain III contains the sugar-binding loop that recognises the two different binding orientations of the 1- and 6-phospho-sugars, and domain IV contains a phosphate-binding site required for orienting the incoming phospho-sugar substrate.   This entry represents domain II found in alpha-D-phosphohexomutase enzymes. This domain has a 3-layer alpha/beta/alpha topology.; GO: 0016868 intramolecular transferase activity, phosphotransferases, 0005975 carbohydrate metabolic process; PDB: 1kfi_B 1kfq_A 3pmg_A 1c47_B 1jdy_B 1vkl_B 1c4g_B 1lxt_B 2z0f_A 2fuv_B ....
Probab=70.59  E-value=2.4  Score=18.58  Aligned_cols=66  Identities=26%  Similarity=0.314  Sum_probs=45.6

Q ss_pred             CCCEEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCC-C----------CCHHHHHHHH
Q ss_conf             9965899827877889975088884068889999999999999569919998738887-4----------7989999999
Q T0585             2 NASFRVVLDPGHGGIDGGARGVTGILEKDVTLAFARALRDELQKGSHTIVALTRDSDI-F----------LRLSERVKKA   70 (234)
Q Consensus         2 ~~~~~IvIDpGHGG~D~Ga~g~~G~~E~~~~l~iA~~l~~~L~~~g~~vv~~tr~~D~-~----------~sl~~R~~~A   70 (234)
                      .+.|+|++|+.||-.                   +..+...|++.|..++.+....|. +          .++..-.+.+
T Consensus        20 ~~~lkIvvD~~~G~~-------------------~~~~~~ll~~lg~~~~~~n~~~d~~f~~~~~p~p~~~~l~~~~~~v   80 (105)
T PF02879_consen   20 KSGLKIVVDCMNGVG-------------------GGVLPELLERLGCDVVELNCEPDPDFPGCHNPNPEEESLQQLIKIV   80 (105)
T ss_dssp             HCTEEEEEE-TT----------------------HHHHHHHHHHCTTECEEESSS--TTHTTTSSSTTSTTTTHHHHHHH
T ss_pred             CCCCEEEEECCCCHH-------------------HHHHHHHHHHCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHH
T ss_conf             599879998998979-------------------9999999998399679877712998566543343278999999998


Q ss_pred             HHCCCCEEEEEECCCC
Q ss_conf             8449978998603567
Q T0585            71 QEFDADLFISIHADTI   86 (234)
Q Consensus        71 ~~~~adl~iSiH~ns~   86 (234)
                      .+.++|+.+++--|+-
T Consensus        81 ~~~~ad~g~~~DgDaD   96 (105)
T PF02879_consen   81 KESGADLGIAFDGDAD   96 (105)
T ss_dssp             HHTTTSEEEEE-TTSS
T ss_pred             HCCCCEEEEEECCCCC
T ss_conf             5649809999778677


No 6  
>PF04952 AstE_AspA:  Succinylglutamate desuccinylase / Aspartoacylase family;  InterPro: IPR007036   This family describes both succinylglutamate desuccinylase that catalyses the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway and also includes aspartoacylase 3.5.1.15 from EC which cleaves acylaspartate into a fatty acid and aspartate. Mutations in P45381 from SWISSPROT lead to Canavan disease .; GO: 0016788 hydrolase activity, acting on ester bonds, 0008152 metabolic process; PDB: 2qvp_A 3b2y_A 3fmc_C 2q51_A 2i3c_B 2o53_B 2o4h_B 2q4z_A 2gu2_A 1yw6_B ....
Probab=65.99  E-value=3  Score=17.99  Aligned_cols=42  Identities=14%  Similarity=0.135  Sum_probs=27.8

Q ss_pred             EECCCCCEEEEEEECCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             40698977766540388989998723988999999999999999998400024
Q T0585           179 LKAPDVPSVLIEIGYLSNKEDEKLLNNPQWRKQMAASIAYSIRQFAEYRQKIM  231 (234)
Q Consensus       179 lr~~~~PaVLiE~gFisN~~D~~~l~~~~~~~~lA~aia~gI~~y~~~~~k~~  231 (234)
                      +.....|++.+|+|=.           ..+....++..++||.+++....-+.
T Consensus       158 ~~~~g~~a~tvE~G~~-----------~~~~~~~~~~~~~gi~~~L~~~g~~~  199 (292)
T PF04952_consen  158 AESAGIPAVTVELGGQ-----------GDFDPEDVERGADGILNVLRHLGMLD  199 (292)
T ss_dssp             HHHHSSEEEEEEE-E------------C---HHHHHHHHHHHHHHHHHHHCCH
T ss_pred             HHHCCCEEEEEEECCC-----------CCCCHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             9875974999996898-----------76499999999999999999846857


No 7  
>PF05681 Fumerase:  Fumarate hydratase (Fumerase);  InterPro: IPR004646   A number of Fe-S cluster-containing hydro-lyases share a conserved motif, including argininosuccinate lyase, adenylosuccinate lyase, aspartase, class I fumarate hydratase (fumarase), and tartrate dehydratase (see IPR000362 from INTERPRO). Proteins in this group represent a subset of closely related proteins or modules, including the Escherichia coli tartrate dehydratase alpha chain and the N-terminal region of the class I fumarase (where the C-terminal region is homologous to the tartrate dehydratase beta chain). The activity of archaeal proteins in this group is unknown.; GO: 0016829 lyase activity
Probab=36.40  E-value=9.2  Score=14.99  Aligned_cols=23  Identities=17%  Similarity=0.421  Sum_probs=14.1

Q ss_pred             CCCEEEEEEECCCCHHHHHHHCC
Q ss_conf             89777665403889899987239
Q T0585           183 DVPSVLIEIGYLSNKEDEKLLNN  205 (234)
Q Consensus       183 ~~PaVLiE~gFisN~~D~~~l~~  205 (234)
                      .||-++|=+|.=.+.+.+..|.-
T Consensus       173 ~CPP~ivGVGIGGt~d~aa~LaK  195 (271)
T PF05681_consen  173 PCPPIIVGVGIGGTFDKAALLAK  195 (271)
T ss_pred             CCCCCEEEEEECCCHHHHHHHHH
T ss_conf             99988579997886999999999


No 8  
>PF11684 DUF3280:  Protein of unknown function (DUF2380)
Probab=27.35  E-value=13  Score=14.05  Aligned_cols=64  Identities=22%  Similarity=0.249  Sum_probs=38.5

Q ss_pred             CCCCCCCCCCCHHH--HHHHHHHHHHHHHHHCC-CEEEEEEC-------CCCCCCCHHHHHHHHHHCCCCEEEE
Q ss_conf             99750888840688--89999999999999569-91999873-------8887479899999998449978998
Q T0585            17 DGGARGVTGILEKD--VTLAFARALRDELQKGS-HTIVALTR-------DSDIFLRLSERVKKAQEFDADLFIS   80 (234)
Q Consensus        17 D~Ga~g~~G~~E~~--~~l~iA~~l~~~L~~~g-~~vv~~tr-------~~D~~~sl~~R~~~A~~~~adl~iS   80 (234)
                      |+++.+..|..+.+  ---.++..|++.|...| +.+|-+..       ..+-+-|..-..++|.+.+||+.|-
T Consensus        13 Dts~~~~~~~~~~e~~RL~~~~~~lr~~l~~~G~y~~vd~ap~aa~i~~~~~l~~C~gC~~~~Ar~lGAd~~i~   86 (140)
T PF11684_consen   13 DTSAEGAPGPRAAEQARLALVTDQLREDLAESGRYRVVDLAPVAAEIAKISNLRKCNGCAARIARKLGADYAIT   86 (140)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEECCCHHHHHHCCCCCCCCCCCHHHHHHHHHCCCEEEE
T ss_conf             38876678989899999999999999999865983773550666764136895548537999999819987999


No 9  
>PF03129 HGTP_anticodon:  Anticodon binding domain;  InterPro: IPR004154 tRNA synthetases, or tRNA ligases are involved in protein synthesis. This domain is found in histidyl, glycyl, threonyl and prolyl tRNA synthetases  it is probably the anticodon binding domain .; GO: 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006412 translation; PDB: 1nyq_B 1nyr_B 1h4q_B 1hc7_B 1h4t_C 1h4s_A 1nj5_A 1nj1_A 1nj2_A 1nj6_A ....
Probab=22.26  E-value=16  Score=13.45  Aligned_cols=54  Identities=19%  Similarity=0.265  Sum_probs=41.5

Q ss_pred             HHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCHHHHHHHHHHCCCCEEEEEECCCC
Q ss_conf             8889999999999999569919998738887479899999998449978998603567
Q T0585            29 KDVTLAFARALRDELQKGSHTIVALTRDSDIFLRLSERVKKAQEFDADLFISIHADTI   86 (234)
Q Consensus        29 ~~~~l~iA~~l~~~L~~~g~~vv~~tr~~D~~~sl~~R~~~A~~~~adl~iSiH~ns~   86 (234)
                      .+-..+.|..+...|...|+.+.+ -   +...++..+.+.|...++.+.|-|=.+..
T Consensus        11 ~~~~~~~a~~l~~~L~~~gi~v~~-d---~~~~~l~kk~~~a~~~g~p~~iiiG~~e~   64 (94)
T PF03129_consen   11 DEELLEYAEKLAQKLRSAGIRVEL-D---DRNKSLGKKIKYADKIGIPYVIIIGEKEL   64 (94)
T ss_dssp             HHHHHHHHHHHHHHHHTT-SEEEE-E---SSSS-SHHHHHHHHHTTESEEEEE-HHHH
T ss_pred             HHHHHHHHHHHHHHHHHCCCEEEE-E---CCCCCHHHHHHHHHHCCCCEEEEECCHHH
T ss_conf             399999999999999878998999-8---89998779999999839989999998478


No 10 
>PF01750 HycI:  Hydrogenase maturation protease;  InterPro: IPR000671   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.    Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised . More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin  and archaean preflagellin have been described , .   Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure.   Metalloproteases are the most diverse of the four main types of protease, with more than 30 families identified to date . In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as abXHEbbHbc, where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases .   The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesized as a precursor devoid of the metalloenzyme active site. This precursor undergoes a complex post-translational maturation process that requires a number of accessory proteins , , . At one step of this process, after nickel incorporation, each hydrogenase isoenzyme is processed by proteolytic cleavage at the C-terminal end by the corresponding hydrogenase maturation endopeptidase . For example, Escherichia coli HycI is involved in processing of pre-HycE (the large subunit of hydrogenase 3) , ; HybD is involved in processing of pre-HybC (the large subunit of hydrogenase 2) ; and HyaD is assumed to be involved in processing of the large subunit of hydrogenase 1. This group represents metallopeptidases of the MEROPS peptidase family A31 (HybD endopeptidase family, clan AE).   The cleavage site is after a His or an Arg, liberating a short peptide , . This cleavage occurs only in the presence of nickel, and the endopeptidase probably uses the metal in the large subunit of [NiFe]-hydrogenases as a recognition motif . There is no direct evidence for the active site or substrate-binding site, but there are predictions based on an available structure .   Nomenclature note: the following names are used in different organisms for members of this group: HycI, HybD, HyaD, HoxM, HoxW, HupD, HynC, HupM, VhoD, VhtD . Gene/protein names are sometimes used interchangeably to designate various "hydrogenase cluster" proteins unrelated to each other in various organisms. For example, the following names are used for members of this group, but also for unrelated proteins: HupD is used in Azotobacter chroococcum and Anabaena sp. to designate an unrelated hydrogenase maturation factor; HydD is used to designate hydrogenase structural genes in Thermococcus litoralis, Pyrococcus abyssi, and other species.; GO: 0008047 enzyme activator activity, 0008233 peptidase activity; PDB: 1cfz_B 2e85_A 2i8l_A.
Probab=22.09  E-value=16  Score=13.43  Aligned_cols=10  Identities=30%  Similarity=0.189  Sum_probs=5.1

Q ss_pred             CCEEEEEECC
Q ss_conf             9789986035
Q T0585            75 ADLFISIHAD   84 (234)
Q Consensus        75 adl~iSiH~n   84 (234)
                      +|..|=+.+=
T Consensus        36 ~d~vIiVDAv   45 (130)
T PF01750_consen   36 YDRVIIVDAV   45 (130)
T ss_dssp             -SEEEEEE--
T ss_pred             CCEEEEEECC
T ss_conf             9989999757


No 11 
>PF00561 Abhydrolase_1:  alpha/beta hydrolase fold A web page of Esterases and alpha/beta hydrolases.;  InterPro: IPR000073 The alpha/beta hydrolase fold  is common to a number of hydrolytic enzymes of widely differing phylogenetic origin and catalytic function. The core of each enzyme is an alpha/beta-sheet (rather than a barrel), containing 8 strands connected by helices . The enzymes are believed to have diverged from a common ancestor, preserving the arrangement of the catalytic residues. All have a catalytic triad, the elements of which are borne on loops, which are the best conserved structural features of the fold.; PDB: 1ede_A 2eda_A 1edb_A 2edc_A 1edd_A 1bee_A 2yxp_X 2dhe_A 1bez_A 1hde_B ....
Probab=20.09  E-value=18  Score=13.17  Aligned_cols=44  Identities=25%  Similarity=0.169  Sum_probs=25.9

Q ss_pred             EEEEEC-CCCCCCCC-CCCCCCCCHHHHHHHHHHHHHHHHHHCCCEEEEE
Q ss_conf             899827-87788997-5088884068889999999999999569919998
Q T0585             6 RVVLDP-GHGGIDGG-ARGVTGILEKDVTLAFARALRDELQKGSHTIVAL   53 (234)
Q Consensus         6 ~IvIDp-GHGG~D~G-a~g~~G~~E~~~~l~iA~~l~~~L~~~g~~vv~~   53 (234)
                      +|++|. |||..++. ...    .+..-..+++..+...++..|...+.+
T Consensus         3 vi~~D~~G~G~S~~~~~~~----~~~~~~~~~~~~~~~~~~~l~~~~~~l   48 (231)
T PF00561_consen    3 VIAPDLRGHGQSDPSYPPD----DEDYTLEDLAADLEALLDHLGIEKVHL   48 (231)
T ss_dssp             EEEEECTTTTTSBSCSTSS----GGGGSHHHHHHHHHHHHHHTTTSSEEE
T ss_pred             EEEEECCCCCCCCCCCCCC----CCCCCHHHHHHHHHHHHHHCCCCCCEE
T ss_conf             9998099999999987888----788689999999999999809997269


Done!