Query T0587 3NDV, , 373 residues
Match_columns 373
No_of_seqs 159 out of 465
Neff 5.3
Searched_HMMs 11830
Date Sun Jun 13 15:29:37 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0587.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0587.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03576 Peptidase_S58: Peptid 100.0 0 0 727.8 18.7 324 18-357 1-326 (326)
2 PF01960 ArgJ: ArgJ family; I 95.0 0.032 2.7E-06 29.4 6.6 55 246-300 171-226 (388)
3 PF01955 CbiZ: Adenosylcobinam 48.3 6.2 0.00052 16.2 6.6 74 249-336 107-191 (191)
4 PF03584 Herpes_ICP4_N: Herpes 17.3 21 0.0018 13.1 1.4 23 350-372 128-150 (173)
5 PF12043 DUF3527: Domain of un 16.8 23 0.0019 12.9 2.5 16 179-194 209-224 (332)
6 PF10095 DUF2333: Uncharacteri 12.5 30 0.0025 12.3 2.1 15 106-120 67-81 (336)
7 PF07944 DUF1680: Putative gly 10.1 36 0.0031 11.8 2.0 32 326-359 321-352 (520)
8 PF04312 DUF460: Protein of un 8.4 42 0.0036 11.4 2.8 21 253-273 79-99 (138)
9 PF11332 DUF3134: Protein of u 8.1 44 0.0037 11.3 1.0 28 65-92 8-35 (73)
10 PF10813 DUF2733: Protein of u 7.4 47 0.004 11.1 0.7 10 17-26 11-20 (32)
No 1
>PF03576 Peptidase_S58: Peptidase family S58 ; InterPro: IPR005321 Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases . Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , . 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. This group of serine peptidases belong to MEROPS peptidase family S58 (DmpA aminopeptidase family, clan PB(S)). The protein fold of the peptidase unit for members of this family resembles that of archaean proteasome subunit B, the type example of clan PB. The type example is aminopeptidase DmpA from OOchrobactrum anthropi. This family also contains proteins that have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity of peptidases in the family. L-aminopeptidase D-Ala-esterase/amidase (DmpA) from O. anthropi releases the N-terminal L and/or D-Ala residues from peptide substrates. This is the only known enzyme to liberate N-terminal amino acids with both D and L stereospecificity. DmpA active form is an alphabeta heterodimer, which results from a putative autocatalytic cleavage of an inactive precursor polypeptide. DmpA shows structural homology to N-terminal nucleophile (Ntn) hydrolase family members, and may work by a similar catalytic mechanism, however their secondary structure elements differ significantly .; PDB: 1b65_A 2drh_B.
Probab=100.00 E-value=0 Score=727.80 Aligned_cols=324 Identities=42% Similarity=0.627 Sum_probs=301.3
Q ss_pred CCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCCEEEECC-CCCCCCCCEECCCCCCCCCCCCCHHHHHHHCCCCCCEE
Q ss_conf 74524557625334575276544445677434653688748-87444643201226787654441027876200115465
Q T0587 18 LNAITDVAGVEVGHTTVISGDGAMVIGKGPYRTGVTIIHPL-GKTSLDGVAAGRAVINGTGEWTGMHLVDEVGQFLGPIA 96 (373)
Q Consensus 18 ~N~ITDV~GV~VGh~t~~~gd~~l~~~~~~~~TGvTvIlP~-g~~~~~~v~ag~~~~~Gt~e~~~l~~v~e~g~~~~aIv 96 (373)
+|+|||||||+|||+|+.++ +++||||||+|| ++++..++++++++.||++|+.+++|++|++++++||+
T Consensus 1 ~N~ITDV~GV~VGh~t~~~~---------~~~TGvTvI~p~~~~~~~~~~~agv~v~nG~p~t~gt~~l~~~g~v~~~I~ 71 (326)
T PF03576_consen 1 RNAITDVPGVRVGHATDDDG---------PVRTGVTVILPHGGNLFPEGATAGVDVRNGAPGTRGTDLLDELGTVETPIV 71 (326)
T ss_dssp -SSGGG----BB----EEES----------EEE--EEEBTTTT-TTTEEE----EE------BB--HHHHH---B-S-EE
T ss_pred CCCCCCCCCCEEECEECCCC---------CCCCEEEEEEECCCCCCCCCCEEEEEECCCCCCCCCHHHCCCCCCCCCCEE
T ss_conf 98644579876845598789---------968506999957987677884689994379864336211364872042889
Q ss_pred EECCCHHHHHHHHHHHHHHHCCCC-CCCCCCCCCEEEEEEECCCCCCCCCCCCHHHHHHHHHHCCCCCHHCCCCCCCCCE
Q ss_conf 665224889999999999981878-6767711004014200343885566788899999998405875001654211000
Q T0587 97 LTGTGNVGLVHQSMMDWSVGKVPE-EALFSRLLPVVAETLDNRLNDVFGHGLTRDHVFAALDGAKGGPVAEGNVGGGTGM 175 (373)
Q Consensus 97 LTggsa~Glaa~gv~~~l~~~~~g-~~~~~~~vPIVa~~~Dl~lnd~~~~~~~~~~~~~A~~~A~~~~v~eG~vGAGtGa 175 (373)
|||||+||||++|+|+||+|++++ +....++||||+||||.+|||++..+++++|+|+|+++|+.++|+||||||||||
T Consensus 72 LTggsa~Glaa~gv~~~l~e~~~~~~~~~~~~~PIV~e~~Da~L~Dl~~~~~~~~~g~~A~~~A~~~~v~eG~VGAGtGa 151 (326)
T PF03576_consen 72 LTGGSAFGLAADGVMRWLEERGIGIGDTGGTVVPIVPECNDAVLNDLRGGHVKAEHGYAALEAASSGPVAEGNVGAGTGA 151 (326)
T ss_dssp EEEGGG---HHHHHHHHHHHHHCCSSSS------EEEEE--TTTS--------HHHHHHHHHC-BSS-------------
T ss_pred EECCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCEEEECCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCC
T ss_conf 87842899999999999997199877888826779706685598857689998999999998613375345683613581
Q ss_pred EEECCCCCCCEEEEEEECCCCEEEEEEEEEECCCCCCCCCCCCCCHHHHCCCCCCCCHHHHHCCCCCCCCCCCCCEEEEE
Q ss_conf 01004788420468872178517999998735676566521670022330433565001210134456665678589999
Q T0587 176 IAYTFKGGIGTSSRVVSAGDTRYTVGVLVQANHGDRNDLRIAGVQIGKEIKGAWPEVNGIVAAGPDAGKPQDKNSLLIVI 255 (373)
Q Consensus 176 ~~g~~KGGiGsAS~~v~~g~~~~tVgaLV~~N~G~~~d~~~~g~p~G~~~~~~~~~~~~~~~~~~~~~~~~~~nTtI~VV 255 (373)
+||+||||||||||+++.+.++|||||||++|||++.|++++++++|+++....+...... ....+.+||||+||
T Consensus 152 ~~~~~KGGiGtaSr~v~~~~~~~tVGaLV~~N~G~~~~l~~~g~~~g~~~~~~~~~~~~~~-----~~~~~~~nTtI~vV 226 (326)
T PF03576_consen 152 TCGGFKGGIGTASRVVGDGGGGYTVGALVQVNFGDVGDLWIAGVPVGRELGGERPPEELAA-----EAAPPGDNTTIGVV 226 (326)
T ss_dssp -BTTB--------EEEE----EEEE--EEEE----GGG----------TTTT--HHHH-----------------EEEEE
T ss_pred EECCCCCCCCCEEEEECCCCCCEEEEEEEEECCCCCCCCEECCCCCCHHHCCCCCCCCCCC-----CCCCCCCCCEEEEE
T ss_conf 6154567464068996248976899999997899877635866036532245676432211-----35678999899999
Q ss_pred EECCCCCHHHHHHHHHHHCCCCEECCCCCCCCCCCEEEEEECCCCCCCCCCCCCCHHHHHCCHHHHCHHHHHHHHHHHHH
Q ss_conf 65687898999999986402411014778778763799863377566764322200121125123148999999999999
Q T0587 256 ATDAPLMPHQLERMARRAALGVGRNGSTAGALSGEFALAFSTSHVIPLGGKPRLPAIINDTDSETMNALFRGVVQATEEA 335 (373)
Q Consensus 256 ATDApL~~~Ql~RlA~~A~~GlAR~~~~~~~~dGD~vfA~STg~~~~~~~~~~~~~~~~~~~~~~l~~lf~AaaeaveeA 335 (373)
||||||+|+||||||+|||+||||+|++|+|+||||+|||||+++.++....... .+.+++..||.||+|++|+||||
T Consensus 227 ATDApL~~~Ql~RlA~~A~~GlAR~gp~~~~~dGD~vfa~ST~~~~~~~~~~~~~--~~~~~~~~l~~l~~aaaea~eeA 304 (326)
T PF03576_consen 227 ATDAPLTKRQLKRLAKRAHDGLARTGPVHTNGDGDIVFAFSTGNRPAHDPDADSG--IEQLPDDALDPLFAAAAEAVEEA 304 (326)
T ss_dssp EE-S---HHHHHHHHHHCC---TT-----------EEEEEESSSEEETCGGS-CE--EEEE-CGGGHHHHHHHHHHHHHH
T ss_pred EECCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCCCCCCCCC--CCCCCHHHHHHHHHHHHHHHHHH
T ss_conf 9799289999999999875214321567779987889999778877886432231--02256678999999999999999
Q ss_pred HHHHHHHCCCCCCCCCCEEEEC
Q ss_conf 9988751464207988672008
Q T0587 336 LVNQLVASETMTGANNAKVYGI 357 (373)
Q Consensus 336 Ilnal~~A~~~~G~~g~~~~al 357 (373)
|+|||++|++|+|++||++|+|
T Consensus 305 I~nav~~A~~~~G~~g~~~~al 326 (326)
T PF03576_consen 305 ILNAVLAAETMTGRDGHTVPAL 326 (326)
T ss_dssp HHHHHHC---B---TT--B---
T ss_pred HHHHHHHCCCCCCCCCCEEECC
T ss_conf 9999974667637998774179
No 2
>PF01960 ArgJ: ArgJ family; InterPro: IPR002813 ArgJ is a bifunctional protein that catalyses the first 2.3.1.35 from EC and fifth steps 2.3.1.1 from EC in arginine biosynthesis . The structure has been determined for glutamate N-acetyltransferase 2 (ornithine acetyltransferase; 2.3.1.35 from EC), an ArgJ-like protein from Streptomyces clavuligerus .; GO: 0004358 glutamate N-acetyltransferase activity, 0006526 arginine biosynthetic process; PDB: 2vzk_H 1vz8_A 1vz7_C 2v4i_G 1vz6_B 1vra_B.
Probab=94.99 E-value=0.032 Score=29.42 Aligned_cols=55 Identities=22% Similarity=0.273 Sum_probs=45.5
Q ss_pred CCCCCEEEEEEECCCCCHHHHHHHHHHHCCCCEECCCCCC-CCCCCEEEEEECCCC
Q ss_conf 5678589999656878989999999864024110147787-787637998633775
Q T0587 246 QDKNSLLIVIATDAPLMPHQLERMARRAALGVGRNGSTAG-ALSGEFALAFSTSHV 300 (373)
Q Consensus 246 ~~~nTtI~VVATDApL~~~Ql~RlA~~A~~GlAR~~~~~~-~~dGD~vfA~STg~~ 300 (373)
|.+-|.++.|.|||++++.+|+++=+.+.+-==-.|..-+ ++--|+++.|++|..
T Consensus 171 PnMATML~fi~TDA~i~~~~L~~~L~~av~~SFN~IsVDGDtSTNDtv~~lAnG~a 226 (388)
T PF01960_consen 171 PNMATMLAFITTDAAISPDLLQKALREAVDRSFNRISVDGDTSTNDTVLLLANGAA 226 (388)
T ss_dssp --EE--EEEEEESS---HHHHHHHHHHHHHHTGGGB-SSS---SS-EEEEEE----
T ss_pred CCHHCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEECCCCCHHHHHHHHHCCCC
T ss_conf 35031030022188689999999999999844888657798867889999858898
No 3
>PF01955 CbiZ: Adenosylcobinamide amidohydrolase; InterPro: IPR002808 This prokaryotic protein that includes CbiZ which converts adenosylcobinamide (AdoCbi) to adenosylcobyric acid (AdoCby), an intermediate of the de novo coenzyme B12 biosynthetic route .
Probab=48.31 E-value=6.2 Score=16.23 Aligned_cols=74 Identities=20% Similarity=0.196 Sum_probs=43.3
Q ss_pred CCEEEEEEECCCCCHHHHHHHHHHH---------CCCCEEC--CCCCCCCCCCEEEEEECCCCCCCCCCCCCCHHHHHCC
Q ss_conf 8589999656878989999999864---------0241101--4778778763799863377566764322200121125
Q T0587 249 NSLLIVIATDAPLMPHQLERMARRA---------ALGVGRN--GSTAGALSGEFALAFSTSHVIPLGGKPRLPAIINDTD 317 (373)
Q Consensus 249 nTtI~VVATDApL~~~Ql~RlA~~A---------~~GlAR~--~~~~~~~dGD~vfA~STg~~~~~~~~~~~~~~~~~~~ 317 (373)
|||=++|.+|++|++.-+-+.=+-| ..++-.. ..+.+..|.=+|++..++...+.
T Consensus 107 GTINi~v~~~~~Ls~~Alv~ai~TaTEAKt~AL~el~i~~~~~~aTGT~TDaV~Va~~~~g~~~~y-------------- 172 (191)
T PF01955_consen 107 GTINIIVFINAPLSDAALVNAIMTATEAKTAALQELGIRSPYSQATGTGTDAVAVASPQSGGPIPY-------------- 172 (191)
T ss_pred CEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEECCCCCCCCC--------------
T ss_conf 808999997998997899999999999999999982654445667787655489982699985340--------------
Q ss_pred HHHHCHHHHHHHHHHHHHH
Q ss_conf 1231489999999999999
Q T0587 318 SETMNALFRGVVQATEEAL 336 (373)
Q Consensus 318 ~~~l~~lf~AaaeaveeAI 336 (373)
......|.+..+++|.|||
T Consensus 173 aG~~T~lG~~i~~aV~~av 191 (191)
T PF01955_consen 173 AGPHTELGELIGRAVYEAV 191 (191)
T ss_pred CCCCCHHHHHHHHHHHHHC
T ss_conf 6730589999999999659
No 4
>PF03584 Herpes_ICP4_N: Herpesvirus ICP4-like protein N-terminal region; InterPro: IPR005206 The immediate-early protein ICP4 (infected-cell polypeptide 4) is required for efficient transcription of early and late viral genes and is thus essential for productive infection. ICP4 is a large phosphoprotein that binds DNA in a sequence specific manner as a homodimer. ICP4 represses transcription from LAT, ICP4 and ORF-P that have high-affinity a ICP4 binding site that spans the transcription initiation site. ICP4 proteins have two highly conserved regions, this family contains the N-terminal region that contains sites for DNA binding and homodimerisation .; GO: 0016563 transcription activator activity, 0045941 positive regulation of transcription, 0042025 host cell nucleus
Probab=17.29 E-value=21 Score=13.14 Aligned_cols=23 Identities=26% Similarity=0.543 Sum_probs=18.5
Q ss_pred CCCEEEECCHHHHHHHHHHHCCC
Q ss_conf 88672008989999999974379
Q T0587 350 NNAKVYGIPHDQLARIMKARFPR 372 (373)
Q Consensus 350 ~g~~~~alp~~~~~~~~~~~~~r 372 (373)
.|+..++|||-.-.-.|.+||+|
T Consensus 128 ~g~~lwaLPH~aaaVaMsRRYDr 150 (173)
T PF03584_consen 128 AGRALWALPHAAAAVAMSRRYDR 150 (173)
T ss_pred CCCHHHCCHHHHHHHHHHHHCCC
T ss_conf 56464311579999999874040
No 5
>PF12043 DUF3527: Domain of unknown function (DUF3527)
Probab=16.78 E-value=23 Score=12.95 Aligned_cols=16 Identities=6% Similarity=0.158 Sum_probs=7.7
Q ss_pred CCCCCCCEEEEEEECC
Q ss_conf 0478842046887217
Q T0587 179 TFKGGIGTSSRVVSAG 194 (373)
Q Consensus 179 ~~KGGiGsAS~~v~~g 194 (373)
.-+..-.+.++++|.|
T Consensus 209 ~~~~s~~s~tVilP~G 224 (332)
T PF12043_consen 209 GSSESSCSTTVILPSG 224 (332)
T ss_pred CCCCCCCCEEEEECCC
T ss_conf 5778875179995776
No 6
>PF10095 DUF2333: Uncharacterized protein conserved in bacteria (DUF2333)
Probab=12.54 E-value=30 Score=12.26 Aligned_cols=15 Identities=13% Similarity=-0.062 Sum_probs=6.3
Q ss_pred HHHHHHHHHHHCCCC
Q ss_conf 999999999981878
Q T0587 106 VHQSMMDWSVGKVPE 120 (373)
Q Consensus 106 aa~gv~~~l~~~~~g 120 (373)
..-.++..|+++..|
T Consensus 67 tli~v~~tLL~K~GG 81 (336)
T PF10095_consen 67 TLIWVMETLLNKPGG 81 (336)
T ss_pred HHHHHHHHHHCCCCC
T ss_conf 999999998536887
No 7
>PF07944 DUF1680: Putative glycosyl hydrolase of unknown function (DUF1680); InterPro: IPR012878 The members of this family are sequences derived from hypothetical bacterial and eukaryotic proteins of unknown function. One member of this family is annotated as a possible arabinosidase, but no references were found to back this.
Probab=10.14 E-value=36 Score=11.79 Aligned_cols=32 Identities=25% Similarity=0.268 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCH
Q ss_conf 9999999999998875146420798867200898
Q T0587 326 RGVVQATEEALVNQLVASETMTGANNAKVYGIPH 359 (373)
Q Consensus 326 ~AaaeaveeAIlnal~~A~~~~G~~g~~~~alp~ 359 (373)
..-+|..|++.+|+++++-+..| +...|-.|+
T Consensus 321 ~~yaD~~Er~lyN~ila~~~~d~--~~~~Y~~pl 352 (520)
T PF07944_consen 321 AKYADYYERALYNAILAGQSPDG--GSFFYFNPL 352 (520)
T ss_pred CHHHHHHHHHHHCCCCCCCCCCC--CEEEECCCC
T ss_conf 17999999999643444548988--837840587
No 8
>PF04312 DUF460: Protein of unknown function (DUF460); InterPro: IPR007408 This is an archaeal protein of unknown function.
Probab=8.41 E-value=42 Score=11.39 Aligned_cols=21 Identities=29% Similarity=0.543 Sum_probs=12.7
Q ss_pred EEEEECCCCCHHHHHHHHHHH
Q ss_conf 999656878989999999864
Q T0587 253 IVIATDAPLMPHQLERMARRA 273 (373)
Q Consensus 253 ~VVATDApL~~~Ql~RlA~~A 273 (373)
++||||..=.|.-.+|||++-
T Consensus 79 viVAtDV~p~P~~VkKia~~f 99 (138)
T PF04312_consen 79 VIVATDVNPPPETVKKIARSF 99 (138)
T ss_pred EEEEECCCCCCHHHHHHHHHH
T ss_conf 899806988958999999981
No 9
>PF11332 DUF3134: Protein of unknown function (DUF3134)
Probab=8.13 E-value=44 Score=11.31 Aligned_cols=28 Identities=14% Similarity=0.107 Sum_probs=20.7
Q ss_pred CCEECCCCCCCCCCCCCHHHHHHHCCCC
Q ss_conf 4320122678765444102787620011
Q T0587 65 GVAAGRAVINGTGEWTGMHLVDEVGQFL 92 (373)
Q Consensus 65 ~v~ag~~~~~Gt~e~~~l~~v~e~g~~~ 92 (373)
+-.--++|+|...+..+|+|++..|.+.
T Consensus 8 pR~q~a~Vip~~~e~SlLdWLe~tGRLi 35 (73)
T PF11332_consen 8 PRYQPAPVIPLRQEPSLLDWLESTGRLI 35 (73)
T ss_pred CCCCCCCEECCCCCCHHHHHHHHCCCCC
T ss_conf 6568887504888437999999819701
No 10
>PF10813 DUF2733: Protein of unknown function (DUF2733)
Probab=7.42 E-value=47 Score=11.12 Aligned_cols=10 Identities=40% Similarity=0.630 Sum_probs=0.0
Q ss_pred CCCCCCCCCC
Q ss_conf 8745245576
Q T0587 17 ALNAITDVAG 26 (373)
Q Consensus 17 ~~N~ITDV~G 26 (373)
+.|.|.||.|
T Consensus 11 r~n~l~Dv~G 20 (32)
T PF10813_consen 11 RHNPLKDVDG 20 (32)
T ss_pred CCCCCCCCCC
T ss_conf 6785244689
Done!