Query psy12894
Match_columns 124
No_of_seqs 214 out of 1380
Neff 9.0
Searched_HMMs 46136
Date Fri Aug 16 22:29:53 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12894.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12894hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00190 Tryp_SPc Trypsin-like 99.8 7.6E-18 1.7E-22 116.5 9.2 77 47-123 1-84 (232)
2 smart00020 Tryp_SPc Trypsin-li 99.7 2.2E-17 4.8E-22 114.4 7.8 78 46-123 1-84 (229)
3 PF00089 Trypsin: Trypsin; In 99.7 3.5E-16 7.7E-21 107.4 8.2 75 47-123 1-82 (220)
4 KOG3627|consensus 99.6 1.3E-14 2.7E-19 102.8 9.0 79 44-123 10-100 (256)
5 COG5640 Secreted trypsin-like 99.2 4E-12 8.7E-17 93.0 3.1 79 44-122 30-118 (413)
6 PF09342 DUF1986: Domain of un 98.5 3.3E-07 7.1E-12 64.5 6.9 50 56-105 14-65 (267)
7 PF03761 DUF316: Domain of unk 98.4 4.4E-07 9.6E-12 65.4 4.8 55 37-91 30-90 (282)
8 COG3591 V8-like Glu-specific e 96.2 0.009 1.9E-07 42.8 4.4 39 54-92 45-86 (251)
9 PF13365 Trypsin_2: Trypsin-li 95.7 0.016 3.4E-07 35.8 3.5 20 72-91 1-21 (120)
10 TIGR02037 degP_htrA_DO peripla 68.1 8.9 0.00019 29.5 4.0 31 69-101 57-88 (428)
11 TIGR02038 protease_degS peripl 61.3 35 0.00075 25.7 5.9 30 70-101 78-108 (351)
12 PRK10942 serine endoprotease; 50.8 30 0.00066 27.2 4.2 31 70-102 111-143 (473)
13 PRK10898 serine endoprotease; 50.6 53 0.0011 24.7 5.4 30 70-101 78-108 (353)
14 PRK10139 serine endoprotease; 50.1 28 0.0006 27.3 3.9 31 70-102 90-122 (455)
15 PF10459 Peptidase_S46: Peptid 28.6 43 0.00094 27.9 2.0 21 71-91 48-69 (698)
16 COG2401 ABC-type ATPase fused 21.6 56 0.0012 26.0 1.4 12 113-124 245-256 (593)
No 1
>cd00190 Tryp_SPc Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues.
Probab=99.75 E-value=7.6e-18 Score=116.45 Aligned_cols=77 Identities=42% Similarity=0.761 Sum_probs=65.0
Q ss_pred eeCCEEcCCCCCceEEEEEeC-CceeEEEEEecCCEEEecccccCCCCCceEEEEEceeecCCC---C---CeecEEECC
Q psy12894 47 IVGGNVTKLHEFPWIAALTKK-GKFYCGATLIAKRHVLTAAHCIEGVNPKEIKVTLGEHDRLSK---N---ESVPVIIHF 119 (124)
Q Consensus 47 i~gg~~~~~~~~Pw~v~l~~~-~~~~CgGsLi~~~~vlTaahC~~~~~~~~~~V~~G~~~~~~~---~---~~~~vi~Hp 119 (124)
|+||..+..++|||+|.+... ..+.|+|+||+++||||||||+.......+.|++|..+.... . ...++++||
T Consensus 1 i~~G~~~~~~~~Pw~v~i~~~~~~~~C~GtlIs~~~VLTaAhC~~~~~~~~~~v~~g~~~~~~~~~~~~~~~v~~~~~hp 80 (232)
T cd00190 1 IVGGSEAKIGSFPWQVSLQYTGGRHFCGGSLISPRWVLTAAHCVYSSAPSNYTVRLGSHDLSSNEGGGQVIKVKKVIVHP 80 (232)
T ss_pred CcCCeECCCCCCCCEEEEEccCCcEEEEEEEeeCCEEEECHHhcCCCCCccEEEEeCcccccCCCCceEEEEEEEEEECC
Confidence 579999999999999999876 678999999999999999999986556789999998876542 1 134599999
Q ss_pred CCCC
Q psy12894 120 SVSN 123 (124)
Q Consensus 120 ~y~~ 123 (124)
+|+.
T Consensus 81 ~y~~ 84 (232)
T cd00190 81 NYNP 84 (232)
T ss_pred CCCC
Confidence 9974
No 2
>smart00020 Tryp_SPc Trypsin-like serine protease. Many of these are synthesised as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. A few, however, are active as single chain molecules, and others are inactive due to substitutions of the catalytic triad residues.
Probab=99.72 E-value=2.2e-17 Score=114.42 Aligned_cols=78 Identities=45% Similarity=0.841 Sum_probs=66.1
Q ss_pred ceeCCEEcCCCCCceEEEEEeCC-ceeEEEEEecCCEEEecccccCCCCCceEEEEEceeecCCCC-----CeecEEECC
Q psy12894 46 RIVGGNVTKLHEFPWIAALTKKG-KFYCGATLIAKRHVLTAAHCIEGVNPKEIKVTLGEHDRLSKN-----ESVPVIIHF 119 (124)
Q Consensus 46 ri~gg~~~~~~~~Pw~v~l~~~~-~~~CgGsLi~~~~vlTaahC~~~~~~~~~~V~~G~~~~~~~~-----~~~~vi~Hp 119 (124)
|++||..+.+++|||++.+.... .+.|+|+||++++|||||||+.......+.|++|.++..... ...++++||
T Consensus 1 ~~~~G~~~~~~~~Pw~~~i~~~~~~~~C~GtlIs~~~VLTaahC~~~~~~~~~~v~~g~~~~~~~~~~~~~~v~~~~~~p 80 (229)
T smart00020 1 RIVGGSEANIGSFPWQVSLQYRGGRHFCGGSLISPRWVLTAAHCVYGSDPSNIRVRLGSHDLSSGEEGQVIKVSKVIIHP 80 (229)
T ss_pred CccCCCcCCCCCCCcEEEEEEcCCCcEEEEEEecCCEEEECHHHcCCCCCcceEEEeCcccCCCCCCceEEeeEEEEECC
Confidence 58899999999999999998876 789999999999999999999865456899999988765443 244599999
Q ss_pred CCCC
Q psy12894 120 SVSN 123 (124)
Q Consensus 120 ~y~~ 123 (124)
+|+.
T Consensus 81 ~~~~ 84 (229)
T smart00020 81 NYNP 84 (229)
T ss_pred CCCC
Confidence 9973
No 3
>PF00089 Trypsin: Trypsin; InterPro: IPR001254 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: 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-, N-, 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. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; 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. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. 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) [, ]. This group of serine proteases belong to the MEROPS peptidase family S1 (chymotrypsin family, clan PA(S))and to peptidase family S6 (Hap serine peptidases). The chymotrypsin family is almost totally confined to animals, although trypsin-like enzymes are found in actinomycetes of the genera Streptomyces and Saccharopolyspora, and in the fungus Fusarium oxysporum []. The enzymes are inherently secreted, being synthesised with a signal peptide that targets them to the secretory pathway. Animal enzymes are either secreted directly, packaged into vesicles for regulated secretion, or are retained in leukocyte granules []. The Hap family, 'Haemophilus adhesion and penetration', are proteins that play a role in the interaction with human epithelial cells. The serine protease activity is localized at the N-terminal domain, whereas the binding domain is in the C-terminal region. ; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1SPJ_A 1A5I_A 2ZGH_A 2ZKS_A 2ZGJ_A 2ZGC_A 2ODP_A 2I6Q_A 2I6S_A 2ODQ_A ....
Probab=99.66 E-value=3.5e-16 Score=107.44 Aligned_cols=75 Identities=40% Similarity=0.757 Sum_probs=62.4
Q ss_pred eeCCEEcCCCCCceEEEEEeCC-ceeEEEEEecCCEEEecccccCCCCCceEEEEEceeecCCCCC------eecEEECC
Q psy12894 47 IVGGNVTKLHEFPWIAALTKKG-KFYCGATLIAKRHVLTAAHCIEGVNPKEIKVTLGEHDRLSKNE------SVPVIIHF 119 (124)
Q Consensus 47 i~gg~~~~~~~~Pw~v~l~~~~-~~~CgGsLi~~~~vlTaahC~~~~~~~~~~V~~G~~~~~~~~~------~~~vi~Hp 119 (124)
|.||..+.+++|||++.+.... .++|+|+||+++||||||||+.. ...+.+++|......... ..+++.||
T Consensus 1 i~~g~~~~~~~~p~~v~i~~~~~~~~C~G~li~~~~vLTaahC~~~--~~~~~v~~g~~~~~~~~~~~~~~~v~~~~~h~ 78 (220)
T PF00089_consen 1 IVGGDPASPGEFPWVVSIRYSNGRFFCTGTLISPRWVLTAAHCVDG--ASDIKVRLGTYSIRNSDGSEQTIKVSKIIIHP 78 (220)
T ss_dssp SBSSEECGTTSSTTEEEEEETTTEEEEEEEEEETTEEEEEGGGHTS--GGSEEEEESESBTTSTTTTSEEEEEEEEEEET
T ss_pred CCCCEECCCCCCCeEEEEeeCCCCeeEeEEeccccccccccccccc--cccccccccccccccccccccccccccccccc
Confidence 6899999999999999999977 89999999999999999999985 467889999843332222 33489999
Q ss_pred CCCC
Q psy12894 120 SVSN 123 (124)
Q Consensus 120 ~y~~ 123 (124)
+|+.
T Consensus 79 ~~~~ 82 (220)
T PF00089_consen 79 KYDP 82 (220)
T ss_dssp TSBT
T ss_pred cccc
Confidence 9985
No 4
>KOG3627|consensus
Probab=99.58 E-value=1.3e-14 Score=102.84 Aligned_cols=79 Identities=39% Similarity=0.697 Sum_probs=64.0
Q ss_pred CCceeCCEEcCCCCCceEEEEEeCC--ceeEEEEEecCCEEEecccccCCC-CCceEEEEEceeecCCC---------CC
Q psy12894 44 NQRIVGGNVTKLHEFPWIAALTKKG--KFYCGATLIAKRHVLTAAHCIEGV-NPKEIKVTLGEHDRLSK---------NE 111 (124)
Q Consensus 44 ~~ri~gg~~~~~~~~Pw~v~l~~~~--~~~CgGsLi~~~~vlTaahC~~~~-~~~~~~V~~G~~~~~~~---------~~ 111 (124)
..||+||..+.++++||++++.... .+.|||+||+++||||||||+... .. .+.|++|.++.... ..
T Consensus 10 ~~~i~~g~~~~~~~~Pw~~~l~~~~~~~~~Cggsli~~~~vltaaHC~~~~~~~-~~~V~~G~~~~~~~~~~~~~~~~~~ 88 (256)
T KOG3627|consen 10 EGRIVGGTEAEPGSFPWQVSLQYGGNGRHLCGGSLISPRWVLTAAHCVKGASAS-LYTVRLGEHDINLSVSEGEEQLVGD 88 (256)
T ss_pred cCCEeCCccCCCCCCCCEEEEEECCCcceeeeeEEeeCCEEEEChhhCCCCCCc-ceEEEECccccccccccCchhhhce
Confidence 5799999999999999999998875 689999999999999999999753 22 78999997643322 11
Q ss_pred eecEEECCCCCC
Q psy12894 112 SVPVIIHFSVSN 123 (124)
Q Consensus 112 ~~~vi~Hp~y~~ 123 (124)
..++++||+|+.
T Consensus 89 v~~~i~H~~y~~ 100 (256)
T KOG3627|consen 89 VEKIIVHPNYNP 100 (256)
T ss_pred eeEEEECCCCCC
Confidence 334889999985
No 5
>COG5640 Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=99.24 E-value=4e-12 Score=93.02 Aligned_cols=79 Identities=28% Similarity=0.495 Sum_probs=60.9
Q ss_pred CCceeCCEEcCCCCCceEEEEEeC-----CceeEEEEEecCCEEEecccccCCCC---CceEEEEEceeecCCC--CCee
Q psy12894 44 NQRIVGGNVTKLHEFPWIAALTKK-----GKFYCGATLIAKRHVLTAAHCIEGVN---PKEIKVTLGEHDRLSK--NESV 113 (124)
Q Consensus 44 ~~ri~gg~~~~~~~~Pw~v~l~~~-----~~~~CgGsLi~~~~vlTaahC~~~~~---~~~~~V~~G~~~~~~~--~~~~ 113 (124)
..||+||..+..++||++|++..+ ...+|||+++..|||||||||+.... ....+|..+..+.... ...+
T Consensus 30 s~rIigGs~Anag~~P~~VaLv~~isd~~s~tfCGgs~l~~RYvLTAAHC~~~~s~is~d~~~vv~~l~d~Sq~~rg~vr 109 (413)
T COG5640 30 SSRIIGGSNANAGEYPSLVALVDRISDYVSGTFCGGSKLGGRYVLTAAHCADASSPISSDVNRVVVDLNDSSQAERGHVR 109 (413)
T ss_pred ceeEecCcccccccCchHHHHHhhcccccceeEeccceecceEEeeehhhccCCCCccccceEEEecccccccccCcceE
Confidence 679999999999999999998653 34689999999999999999997643 2345555555444332 2456
Q ss_pred cEEECCCCC
Q psy12894 114 PVIIHFSVS 122 (124)
Q Consensus 114 ~vi~Hp~y~ 122 (124)
+++.|..|.
T Consensus 110 ~i~~~efY~ 118 (413)
T COG5640 110 TIYVHEFYS 118 (413)
T ss_pred EEeeecccc
Confidence 699999886
No 6
>PF09342 DUF1986: Domain of unknown function (DUF1986); InterPro: IPR015420 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: 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-, N-, 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. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; 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. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. 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) [, ]. This domain is found in serine endopeptidases belonging to MEROPS peptidase family S1A (clan PA). It is found in unusual mosaic proteins, which are encoded by the Drosophila nudel gene (see P98159 from SWISSPROT). Nudel is involved in defining embryonic dorsoventral polarity. Three proteases; ndl, gd and snk process easter to create active easter. Active easter defines cell identities along the dorsal-ventral continuum by activating the spz ligand for the Tl receptor in the ventral region of the embryo. Nudel, pipe and windbeutel together trigger the protease cascade within the extraembryonic perivitelline compartment which induces dorsoventral polarity of the Drosophila embryo [].
Probab=98.55 E-value=3.3e-07 Score=64.49 Aligned_cols=50 Identities=22% Similarity=0.704 Sum_probs=43.5
Q ss_pred CCCceEEEEEeCCceeEEEEEecCCEEEecccccCCC--CCceEEEEEceee
Q psy12894 56 HEFPWIAALTKKGKFYCGATLIAKRHVLTAAHCIEGV--NPKEIKVTLGEHD 105 (124)
Q Consensus 56 ~~~Pw~v~l~~~~~~~CgGsLi~~~~vlTaahC~~~~--~~~~~~V~~G~~~ 105 (124)
..|||.+.++..+.+.|.|.||.+.|+|++..|+.+. ......|.+|...
T Consensus 14 y~WPWlA~IYvdG~~~CsgvLlD~~WlLvsssCl~~I~L~~~YvsallG~~K 65 (267)
T PF09342_consen 14 YHWPWLADIYVDGRYWCSGVLLDPHWLLVSSSCLRGISLSHHYVSALLGGGK 65 (267)
T ss_pred ccCcceeeEEEcCeEEEEEEEeccceEEEeccccCCcccccceEEEEecCcc
Confidence 3599999999999999999999999999999999863 3467789999754
No 7
>PF03761 DUF316: Domain of unknown function (DUF316) ; InterPro: IPR005514 This is a family of uncharacterised proteins from Caenorhabditis elegans.
Probab=98.40 E-value=4.4e-07 Score=65.43 Aligned_cols=55 Identities=29% Similarity=0.709 Sum_probs=44.5
Q ss_pred CCCCcc--CCCceeCCEEcCCCCCceEEEEEeCCc----eeEEEEEecCCEEEecccccCC
Q psy12894 37 ACGQVE--RNQRIVGGNVTKLHEFPWIAALTKKGK----FYCGATLIAKRHVLTAAHCIEG 91 (124)
Q Consensus 37 ~cg~~~--~~~ri~gg~~~~~~~~Pw~v~l~~~~~----~~CgGsLi~~~~vlTaahC~~~ 91 (124)
.||... ...++..|..+...+.||.+.+..... ..++|+|||+|||||++||+..
T Consensus 30 ~CG~~~~~~~~~~~~g~~~~~~~~pW~v~v~~~~~~~~~~~~~gtlIS~RHiLtss~~~~~ 90 (282)
T PF03761_consen 30 TCGKKKLPYPSKVFNGTPAESGEAPWAVSVYTKNHNEGNYFSTGTLISPRHILTSSHCVMN 90 (282)
T ss_pred hcCCCCCCCcccccCCcccccCCCCCEEEEEeccCcccceecceEEeccCeEEEeeeEEEe
Confidence 799543 244578888888899999999977532 4579999999999999999974
No 8
>COG3591 V8-like Glu-specific endopeptidase [Amino acid transport and metabolism]
Probab=96.21 E-value=0.009 Score=42.75 Aligned_cols=39 Identities=38% Similarity=0.629 Sum_probs=29.0
Q ss_pred CCCCCceEEEEEeC---CceeEEEEEecCCEEEecccccCCC
Q psy12894 54 KLHEFPWIAALTKK---GKFYCGATLIAKRHVLTAAHCIEGV 92 (124)
Q Consensus 54 ~~~~~Pw~v~l~~~---~~~~CgGsLi~~~~vlTaahC~~~~ 92 (124)
....|||-+-.... +..-|+++||+++-+||++||+...
T Consensus 45 dt~~~Py~av~~~~~~tG~~~~~~~lI~pntvLTa~Hc~~s~ 86 (251)
T COG3591 45 DTTQFPYSAVVQFEAATGRLCTAATLIGPNTVLTAGHCIYSP 86 (251)
T ss_pred cCCCCCcceeEEeecCCCcceeeEEEEcCceEEEeeeEEecC
Confidence 34568988766542 3345666999999999999999753
No 9
>PF13365 Trypsin_2: Trypsin-like peptidase domain; PDB: 1Y8T_A 2Z9I_A 3QO6_A 1L1J_A 1QY6_A 2O8L_A 3OTP_E 2ZLE_I 1KY9_A 3CS0_A ....
Probab=95.71 E-value=0.016 Score=35.75 Aligned_cols=20 Identities=40% Similarity=0.464 Sum_probs=18.5
Q ss_pred EEEEEecCC-EEEecccccCC
Q psy12894 72 CGATLIAKR-HVLTAAHCIEG 91 (124)
Q Consensus 72 CgGsLi~~~-~vlTaahC~~~ 91 (124)
|.|.+|.++ ++||++||+..
T Consensus 1 GTGf~i~~~g~ilT~~Hvv~~ 21 (120)
T PF13365_consen 1 GTGFLIGPDGYILTAAHVVED 21 (120)
T ss_dssp EEEEEEETTTEEEEEHHHHTC
T ss_pred CEEEEEcCCceEEEchhheec
Confidence 689999999 99999999975
No 10
>TIGR02037 degP_htrA_DO periplasmic serine protease, Do/DeqQ family. This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures.
Probab=68.12 E-value=8.9 Score=29.48 Aligned_cols=31 Identities=32% Similarity=0.508 Sum_probs=23.4
Q ss_pred ceeEEEEEecCC-EEEecccccCCCCCceEEEEE
Q psy12894 69 KFYCGATLIAKR-HVLTAAHCIEGVNPKEIKVTL 101 (124)
Q Consensus 69 ~~~CgGsLi~~~-~vlTaahC~~~~~~~~~~V~~ 101 (124)
...+.|.+|++. +|||.+|.+.+ ...+.|.+
T Consensus 57 ~~~GSGfii~~~G~IlTn~Hvv~~--~~~i~V~~ 88 (428)
T TIGR02037 57 RGLGSGVIISADGYILTNNHVVDG--ADEITVTL 88 (428)
T ss_pred cceeeEEEECCCCEEEEcHHHcCC--CCeEEEEe
Confidence 357999999875 99999999974 34455554
No 11
>TIGR02038 protease_degS periplasmic serine pepetdase DegS. This family consists of the periplasmic serine protease DegS (HhoB), a shorter paralog of protease DO (HtrA, DegP) and DegQ (HhoA). It is found in E. coli and several other Proteobacteria of the gamma subdivision. It contains a trypsin domain and a single copy of PDZ domain (in contrast to DegP with two copies). A critical role of this DegS is to sense stress in the periplasm and partially degrade an inhibitor of sigma(E).
Probab=61.26 E-value=35 Score=25.66 Aligned_cols=30 Identities=27% Similarity=0.351 Sum_probs=22.1
Q ss_pred eeEEEEEecCC-EEEecccccCCCCCceEEEEE
Q psy12894 70 FYCGATLIAKR-HVLTAAHCIEGVNPKEIKVTL 101 (124)
Q Consensus 70 ~~CgGsLi~~~-~vlTaahC~~~~~~~~~~V~~ 101 (124)
....|.+|++. +|||.+|.+.. ...+.|.+
T Consensus 78 ~~GSG~vi~~~G~IlTn~HVV~~--~~~i~V~~ 108 (351)
T TIGR02038 78 GLGSGVIMSKEGYILTNYHVIKK--ADQIVVAL 108 (351)
T ss_pred ceEEEEEEeCCeEEEecccEeCC--CCEEEEEE
Confidence 35889999865 99999999974 23455554
No 12
>PRK10942 serine endoprotease; Provisional
Probab=50.84 E-value=30 Score=27.19 Aligned_cols=31 Identities=26% Similarity=0.382 Sum_probs=23.2
Q ss_pred eeEEEEEecC--CEEEecccccCCCCCceEEEEEc
Q psy12894 70 FYCGATLIAK--RHVLTAAHCIEGVNPKEIKVTLG 102 (124)
Q Consensus 70 ~~CgGsLi~~--~~vlTaahC~~~~~~~~~~V~~G 102 (124)
....|.+|+. .+|||.+|.+.+ ...+.|.+.
T Consensus 111 ~~GSG~ii~~~~G~IlTn~HVv~~--a~~i~V~~~ 143 (473)
T PRK10942 111 ALGSGVIIDADKGYVVTNNHVVDN--ATKIKVQLS 143 (473)
T ss_pred ceEEEEEEECCCCEEEeChhhcCC--CCEEEEEEC
Confidence 4688999984 699999999874 345666554
No 13
>PRK10898 serine endoprotease; Provisional
Probab=50.64 E-value=53 Score=24.74 Aligned_cols=30 Identities=27% Similarity=0.423 Sum_probs=22.0
Q ss_pred eeEEEEEecCC-EEEecccccCCCCCceEEEEE
Q psy12894 70 FYCGATLIAKR-HVLTAAHCIEGVNPKEIKVTL 101 (124)
Q Consensus 70 ~~CgGsLi~~~-~vlTaahC~~~~~~~~~~V~~ 101 (124)
....|.+|++. +|||.+|-+.+ ...+.|.+
T Consensus 78 ~~GSGfvi~~~G~IlTn~HVv~~--a~~i~V~~ 108 (353)
T PRK10898 78 TLGSGVIMDQRGYILTNKHVIND--ADQIIVAL 108 (353)
T ss_pred ceeeEEEEeCCeEEEecccEeCC--CCEEEEEe
Confidence 46889999865 99999999863 34455554
No 14
>PRK10139 serine endoprotease; Provisional
Probab=50.11 E-value=28 Score=27.28 Aligned_cols=31 Identities=29% Similarity=0.367 Sum_probs=23.5
Q ss_pred eeEEEEEec--CCEEEecccccCCCCCceEEEEEc
Q psy12894 70 FYCGATLIA--KRHVLTAAHCIEGVNPKEIKVTLG 102 (124)
Q Consensus 70 ~~CgGsLi~--~~~vlTaahC~~~~~~~~~~V~~G 102 (124)
....|.+|+ +.+|||.+|.+.+ ...+.|.+.
T Consensus 90 ~~GSG~ii~~~~g~IlTn~HVv~~--a~~i~V~~~ 122 (455)
T PRK10139 90 GLGSGVIIDAAKGYVLTNNHVINQ--AQKISIQLN 122 (455)
T ss_pred ceEEEEEEECCCCEEEeChHHhCC--CCEEEEEEC
Confidence 468899997 4799999999974 345666653
No 15
>PF10459 Peptidase_S46: Peptidase S46; InterPro: IPR019500 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: 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-, N-, 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. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; 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. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. 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) [, ]. This entry represents S46 peptidases, where dipeptidyl-peptidase 7 (DPP-7) is the best-characterised member of this family. It is a serine peptidase that is located on the cell surface and is predicted to have two N-terminal transmembrane domains.
Probab=28.60 E-value=43 Score=27.87 Aligned_cols=21 Identities=33% Similarity=0.619 Sum_probs=17.4
Q ss_pred eEEEEEecCC-EEEecccccCC
Q psy12894 71 YCGATLIAKR-HVLTAAHCIEG 91 (124)
Q Consensus 71 ~CgGsLi~~~-~vlTaahC~~~ 91 (124)
.|+|++||+. .|+|=-||..+
T Consensus 48 GCSgsfVS~~GLvlTNHHC~~~ 69 (698)
T PF10459_consen 48 GCSGSFVSPDGLVLTNHHCGYG 69 (698)
T ss_pred ceeEEEEcCCceEEecchhhhh
Confidence 4999999976 67888999864
No 16
>COG2401 ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only]
Probab=21.63 E-value=56 Score=25.98 Aligned_cols=12 Identities=17% Similarity=0.277 Sum_probs=9.5
Q ss_pred ecEEECCCCCCC
Q psy12894 113 VPVIIHFSVSNT 124 (124)
Q Consensus 113 ~~vi~Hp~y~~~ 124 (124)
.+|++||+|.++
T Consensus 245 arvvvhpdyr~d 256 (593)
T COG2401 245 ARVVVHPDYRAD 256 (593)
T ss_pred eEEEeccccccC
Confidence 359999999764
Done!