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!