Query psy15292
Match_columns 132
No_of_seqs 134 out of 1414
Neff 11.1
Searched_HMMs 46136
Date Fri Aug 16 17:21:34 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15292.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15292hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3627|consensus 99.7 6.9E-16 1.5E-20 99.7 10.2 123 3-125 86-230 (256)
2 cd00190 Tryp_SPc Trypsin-like 99.6 2E-14 4.3E-19 91.2 8.6 122 2-124 69-209 (232)
3 smart00020 Tryp_SPc Trypsin-li 99.5 2.6E-13 5.7E-18 86.1 10.6 122 2-123 69-208 (229)
4 PF00089 Trypsin: Trypsin; In 99.3 5.6E-12 1.2E-16 79.4 6.0 119 2-122 67-198 (220)
5 KOG3627|consensus 97.7 7.2E-05 1.6E-09 48.5 4.7 55 73-127 94-154 (256)
6 cd00190 Tryp_SPc Trypsin-like 97.7 0.00011 2.3E-09 46.5 5.0 48 80-127 87-135 (232)
7 smart00020 Tryp_SPc Trypsin-li 97.2 0.0009 2E-08 42.4 4.9 47 80-126 87-134 (229)
8 PF00089 Trypsin: Trypsin; In 97.1 0.0022 4.7E-08 40.3 5.4 49 80-128 85-134 (220)
9 COG5640 Secreted trypsin-like 96.9 0.0064 1.4E-07 41.3 6.4 33 2-34 104-136 (413)
10 PF09342 DUF1986: Domain of un 95.4 0.046 1E-06 35.3 4.5 44 20-63 87-131 (267)
11 PF03761 DUF316: Domain of unk 94.3 0.85 1.8E-05 30.2 8.7 43 17-61 156-199 (282)
12 PF09342 DUF1986: Domain of un 78.5 17 0.00036 24.1 6.3 44 80-123 87-131 (267)
13 TIGR02037 degP_htrA_DO peripla 68.2 15 0.00032 26.2 4.6 39 20-62 103-141 (428)
14 PRK10139 serine endoprotease; 52.0 36 0.00077 24.7 4.3 39 19-61 135-173 (455)
15 PF14903 WG_beta_rep: WG conta 50.7 21 0.00045 15.0 2.4 23 8-30 9-32 (35)
16 PRK10898 serine endoprotease; 45.6 52 0.0011 22.9 4.2 37 20-61 123-159 (353)
17 TIGR02038 protease_degS peripl 39.7 71 0.0015 22.3 4.1 38 20-62 123-160 (351)
18 PRK10372 PTS system L-ascorbat 38.6 62 0.0014 19.3 3.4 29 8-36 64-92 (154)
19 KOG1749|consensus 35.4 53 0.0011 19.1 2.5 14 112-125 96-109 (143)
20 PRK10942 serine endoprotease; 35.1 86 0.0019 23.0 4.1 39 19-61 156-194 (473)
21 PF13365 Trypsin_2: Trypsin-li 33.9 33 0.00072 18.9 1.6 10 21-30 56-65 (120)
22 PRK09854 cmtB putative PTS sys 33.5 1E+02 0.0023 18.1 4.1 29 8-36 63-91 (147)
23 COG1762 PtsN Phosphotransferas 28.0 60 0.0013 19.3 2.1 28 9-37 62-89 (152)
24 PF00818 Ice_nucleation: Ice n 26.5 41 0.00089 12.0 0.7 9 120-128 1-9 (16)
25 PRK09913 putative fructose-lik 25.6 92 0.002 18.3 2.6 27 9-36 61-87 (148)
26 COG2401 ABC-type ATPase fused 25.3 53 0.0012 24.0 1.7 16 4-19 242-257 (593)
27 cd07268 Glo_EDI_BRP_like_4 Thi 23.9 1.5E+02 0.0032 18.1 3.1 27 20-46 35-62 (149)
28 PF09173 eIF2_C: Initiation fa 22.7 1.3E+02 0.0028 16.5 2.5 11 53-63 77-87 (88)
29 PF14781 BBS2_N: Ciliary BBSom 22.4 1.8E+02 0.0038 17.5 3.2 29 6-34 19-51 (136)
30 PF08206 OB_RNB: Ribonuclease 21.8 43 0.00094 16.4 0.6 25 7-31 20-44 (58)
31 cd00211 PTS_IIA_fru PTS_IIA, P 21.6 1.7E+02 0.0037 16.6 3.2 28 9-37 56-83 (136)
32 PRK10896 PTS system sugar tran 21.4 1.7E+02 0.0038 17.2 3.2 28 9-36 69-96 (154)
No 1
>KOG3627|consensus
Probab=99.68 E-value=6.9e-16 Score=99.72 Aligned_cols=123 Identities=27% Similarity=0.450 Sum_probs=91.0
Q ss_pred EEeeeEEEeCCCCCCCCCC-CceEEEEeCCCeeeCCCeeeeeecCCCC---cccCCcEEEeccCccccCCCcccccceee
Q psy15292 3 KLNTRQSFVHPQYSPSDFR-NDVALIKIDKDVVFKQHIIPVCLPDQTV---KLVGKSATVAGWGRTRHASSLSSAIPTYV 78 (132)
Q Consensus 3 ~~~v~~~~~h~~y~~~~~~-~diall~l~~~~~~~~~~~~~cl~~~~~---~~~g~~~~~~GwG~~~~~~~~~~~~l~~~ 78 (132)
...+.++++||+|+..... ||||||+|.+++.|++.++|+|||.... ...+..|.++|||.+..........++++
T Consensus 86 ~~~v~~~i~H~~y~~~~~~~nDiall~l~~~v~~~~~i~piclp~~~~~~~~~~~~~~~v~GWG~~~~~~~~~~~~L~~~ 165 (256)
T KOG3627|consen 86 VGDVEKIIVHPNYNPRTLENNDIALLRLSEPVTFSSHIQPICLPSSADPYFPPGGTTCLVSGWGRTESGGGPLPDTLQEV 165 (256)
T ss_pred hceeeEEEECCCCCCCCCCCCCEEEEEECCCcccCCcccccCCCCCcccCCCCCCCEEEEEeCCCcCCCCCCCCceeEEE
Confidence 3447788899999998877 9999999999999999999999985543 22457899999999876533446667754
Q ss_pred e---ccCCeEEEEeccc--e----ee-c--cCeeeeecCCCCCCC--C----CceEEEEeecccC
Q psy15292 79 S---ISNDVALIKIDKD--V----VF-K--QHIIPVCLPDQTVKL--V----GKSATVAGWGRTR 125 (132)
Q Consensus 79 ~---~~~d~c~~~~~~~--~----~~-~--~~v~~icl~~~~~~~--~----g~~~~v~gwg~~~ 125 (132)
. ++++.|...+... + .. . ......|.++++.++ . ...+.|..||...
T Consensus 166 ~v~i~~~~~C~~~~~~~~~~~~~~~Ca~~~~~~~~~C~GDSGGPLv~~~~~~~~~~GivS~G~~~ 230 (256)
T KOG3627|consen 166 DVPIISNSECRRAYGGLGTITDTMLCAGGPEGGKDACQGDSGGPLVCEDNGRWVLVGIVSWGSGG 230 (256)
T ss_pred EEeEcChhHhcccccCccccCCCEEeeCccCCCCccccCCCCCeEEEeeCCcEEEEEEEEecCCC
Confidence 4 7778898776542 1 11 1 122336888888777 3 4889999999863
No 2
>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=99.57 E-value=2e-14 Score=91.20 Aligned_cols=122 Identities=27% Similarity=0.507 Sum_probs=84.9
Q ss_pred eEEeeeEEEeCCCCCCCCCCCceEEEEeCCCeeeCCCeeeeeecCCCC-cccCCcEEEeccCccccCCCcccccceeee-
Q psy15292 2 FKLNTRQSFVHPQYSPSDFRNDVALIKIDKDVVFKQHIIPVCLPDQTV-KLVGKSATVAGWGRTRHASSLSSAIPTYVS- 79 (132)
Q Consensus 2 ~~~~v~~~~~h~~y~~~~~~~diall~l~~~~~~~~~~~~~cl~~~~~-~~~g~~~~~~GwG~~~~~~~~~~~~l~~~~- 79 (132)
+.+.|.++++||+|+.....+|||||+|+.++.++..++|+||+.... ...+..+.+.|||...... .....++...
T Consensus 69 ~~~~v~~~~~hp~y~~~~~~~DiAll~L~~~~~~~~~v~picl~~~~~~~~~~~~~~~~G~g~~~~~~-~~~~~~~~~~~ 147 (232)
T cd00190 69 QVIKVKKVIVHPNYNPSTYDNDIALLKLKRPVTLSDNVRPICLPSSGYNLPAGTTCTVSGWGRTSEGG-PLPDVLQEVNV 147 (232)
T ss_pred EEEEEEEEEECCCCCCCCCcCCEEEEEECCcccCCCcccceECCCccccCCCCCEEEEEeCCcCCCCC-CCCceeeEEEe
Confidence 356789999999999988999999999999999999999999998742 2267889999999875542 2233444433
Q ss_pred --ccCCeEEEEeccceee-ccC--------eeeeecCCCCCCC--C----CceEEEEeeccc
Q psy15292 80 --ISNDVALIKIDKDVVF-KQH--------IIPVCLPDQTVKL--V----GKSATVAGWGRT 124 (132)
Q Consensus 80 --~~~d~c~~~~~~~~~~-~~~--------v~~icl~~~~~~~--~----g~~~~v~gwg~~ 124 (132)
++.+.|...+...... ... ....|.++++.++ . ...+.|..||..
T Consensus 148 ~~~~~~~C~~~~~~~~~~~~~~~C~~~~~~~~~~c~gdsGgpl~~~~~~~~~lvGI~s~g~~ 209 (232)
T cd00190 148 PIVSNAECKRAYSYGGTITDNMLCAGGLEGGKDACQGDSGGPLVCNDNGRGVLVGIVSWGSG 209 (232)
T ss_pred eeECHHHhhhhccCcccCCCceEeeCCCCCCCccccCCCCCcEEEEeCCEEEEEEEEehhhc
Confidence 5666776554420000 111 2346777777666 3 456677777653
No 3
>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=99.52 E-value=2.6e-13 Score=86.09 Aligned_cols=122 Identities=25% Similarity=0.492 Sum_probs=85.0
Q ss_pred eEEeeeEEEeCCCCCCCCCCCceEEEEeCCCeeeCCCeeeeeecCCCC-cccCCcEEEeccCccccCCCcccccceeee-
Q psy15292 2 FKLNTRQSFVHPQYSPSDFRNDVALIKIDKDVVFKQHIIPVCLPDQTV-KLVGKSATVAGWGRTRHASSLSSAIPTYVS- 79 (132)
Q Consensus 2 ~~~~v~~~~~h~~y~~~~~~~diall~l~~~~~~~~~~~~~cl~~~~~-~~~g~~~~~~GwG~~~~~~~~~~~~l~~~~- 79 (132)
+.+.|..++.||+|+.....+|||||+|+.++.+++.++|+||+.... ...+..+.+.|||............++...
T Consensus 69 ~~~~v~~~~~~p~~~~~~~~~DiAll~L~~~i~~~~~~~pi~l~~~~~~~~~~~~~~~~g~g~~~~~~~~~~~~~~~~~~ 148 (229)
T smart00020 69 QVIKVSKVIIHPNYNPSTYDNDIALLKLKSPVTLSDNVRPICLPSSNYNVPAGTTCTVSGWGRTSEGAGSLPDTLQEVNV 148 (229)
T ss_pred eEEeeEEEEECCCCCCCCCcCCEEEEEECcccCCCCceeeccCCCcccccCCCCEEEEEeCCCCCCCCCcCCCEeeEEEE
Confidence 457899999999999888999999999999999999999999997632 226788999999987542222233444433
Q ss_pred --ccCCeEEEEeccc-eeeccC--------eeeeecCCCCCCC--CC---ceEEEEeecc
Q psy15292 80 --ISNDVALIKIDKD-VVFKQH--------IIPVCLPDQTVKL--VG---KSATVAGWGR 123 (132)
Q Consensus 80 --~~~d~c~~~~~~~-~~~~~~--------v~~icl~~~~~~~--~g---~~~~v~gwg~ 123 (132)
+..+.|...+... ...... ....|.++++.++ .+ ..+.|..||.
T Consensus 149 ~~~~~~~C~~~~~~~~~~~~~~~C~~~~~~~~~~c~gdsG~pl~~~~~~~~l~Gi~s~g~ 208 (229)
T smart00020 149 PIVSNATCRRAYSGGGAITDNMLCAGGLEGGKDACQGDSGGPLVCNDGRWVLVGIVSWGS 208 (229)
T ss_pred EEeCHHHhhhhhccccccCCCcEeecCCCCCCcccCCCCCCeeEEECCCEEEEEEEEECC
Confidence 5666677544321 111111 2346777877776 34 5777777886
No 4
>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=99.31 E-value=5.6e-12 Score=79.41 Aligned_cols=119 Identities=28% Similarity=0.539 Sum_probs=81.6
Q ss_pred eEEeeeEEEeCCCCCCCCCCCceEEEEeCCCeeeCCCeeeeeecCCCCc-ccCCcEEEeccCccccCCCcccccceeee-
Q psy15292 2 FKLNTRQSFVHPQYSPSDFRNDVALIKIDKDVVFKQHIIPVCLPDQTVK-LVGKSATVAGWGRTRHASSLSSAIPTYVS- 79 (132)
Q Consensus 2 ~~~~v~~~~~h~~y~~~~~~~diall~l~~~~~~~~~~~~~cl~~~~~~-~~g~~~~~~GwG~~~~~~~~~~~~l~~~~- 79 (132)
+.+.|.+++.||+|+.....+|||||+|++++.+.+.+.|+|++..... ..+..+.+.|||...... ....++...
T Consensus 67 ~~~~v~~~~~h~~~~~~~~~~DiAll~L~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~G~~~~~~~~--~~~~~~~~~~ 144 (220)
T PF00089_consen 67 QTIKVSKIIIHPKYDPSTYDNDIALLKLDRPITFGDNIQPICLPSAGSDPNVGTSCIVVGWGRTSDNG--YSSNLQSVTV 144 (220)
T ss_dssp EEEEEEEEEEETTSBTTTTTTSEEEEEESSSSEHBSSBEESBBTSTTHTTTTTSEEEEEESSBSSTTS--BTSBEEEEEE
T ss_pred cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc--cccccccccc
Confidence 4678999999999999889999999999999999999999999985432 368889999999865543 223333322
Q ss_pred --ccCCeEEEEecc----ceee-cc-CeeeeecCCCCCCC--CCc-eEEEEeec
Q psy15292 80 --ISNDVALIKIDK----DVVF-KQ-HIIPVCLPDQTVKL--VGK-SATVAGWG 122 (132)
Q Consensus 80 --~~~d~c~~~~~~----~~~~-~~-~v~~icl~~~~~~~--~g~-~~~v~gwg 122 (132)
++++.|...+.. .... .. .-...|-++++.++ .+. ...|..+|
T Consensus 145 ~~~~~~~c~~~~~~~~~~~~~c~~~~~~~~~~~g~sG~pl~~~~~~lvGI~s~~ 198 (220)
T PF00089_consen 145 PVVSRKTCRSSYNDNLTPNMICAGSSGSGDACQGDSGGPLICNNNYLVGIVSFG 198 (220)
T ss_dssp EEEEHHHHHHHTTTTSTTTEEEEETTSSSBGGTTTTTSEEEETTEEEEEEEEEE
T ss_pred ccccccccccccccccccccccccccccccccccccccccccceeeecceeeec
Confidence 444455443211 1110 11 11356778887777 455 67777776
No 5
>KOG3627|consensus
Probab=97.73 E-value=7.2e-05 Score=48.49 Aligned_cols=55 Identities=38% Similarity=0.814 Sum_probs=43.3
Q ss_pred ccceeee--cc-CCeEEEEeccceeeccCeeeeecCCCCC---CCCCceEEEEeecccCcC
Q psy15292 73 AIPTYVS--IS-NDVALIKIDKDVVFKQHIIPVCLPDQTV---KLVGKSATVAGWGRTRHA 127 (132)
Q Consensus 73 ~~l~~~~--~~-~d~c~~~~~~~~~~~~~v~~icl~~~~~---~~~g~~~~v~gwg~~~~~ 127 (132)
.|..|.. .. +|++++++..++.+++.+.++|||.... ...+..|.++|||++...
T Consensus 94 ~H~~y~~~~~~~nDiall~l~~~v~~~~~i~piclp~~~~~~~~~~~~~~~v~GWG~~~~~ 154 (256)
T KOG3627|consen 94 VHPNYNPRTLENNDIALLRLSEPVTFSSHIQPICLPSSADPYFPPGGTTCLVSGWGRTESG 154 (256)
T ss_pred ECCCCCCCCCCCCCEEEEEECCCcccCCcccccCCCCCcccCCCCCCCEEEEEeCCCcCCC
Confidence 3445544 34 9999999999999999999999985433 225699999999998765
No 6
>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=97.69 E-value=0.00011 Score=46.54 Aligned_cols=48 Identities=40% Similarity=0.872 Sum_probs=41.4
Q ss_pred ccCCeEEEEeccceeeccCeeeeecCCCCCCC-CCceEEEEeecccCcC
Q psy15292 80 ISNDVALIKIDKDVVFKQHIIPVCLPDQTVKL-VGKSATVAGWGRTRHA 127 (132)
Q Consensus 80 ~~~d~c~~~~~~~~~~~~~v~~icl~~~~~~~-~g~~~~v~gwg~~~~~ 127 (132)
..+|++++++..++.++..+.++||+...... .+..+.+.|||.....
T Consensus 87 ~~~DiAll~L~~~~~~~~~v~picl~~~~~~~~~~~~~~~~G~g~~~~~ 135 (232)
T cd00190 87 YDNDIALLKLKRPVTLSDNVRPICLPSSGYNLPAGTTCTVSGWGRTSEG 135 (232)
T ss_pred CcCCEEEEEECCcccCCCcccceECCCccccCCCCCEEEEEeCCcCCCC
Confidence 57899999999999999999999999885333 7899999999997654
No 7
>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=97.21 E-value=0.0009 Score=42.38 Aligned_cols=47 Identities=38% Similarity=0.864 Sum_probs=40.2
Q ss_pred ccCCeEEEEeccceeeccCeeeeecCCCCCCC-CCceEEEEeecccCc
Q psy15292 80 ISNDVALIKIDKDVVFKQHIIPVCLPDQTVKL-VGKSATVAGWGRTRH 126 (132)
Q Consensus 80 ~~~d~c~~~~~~~~~~~~~v~~icl~~~~~~~-~g~~~~v~gwg~~~~ 126 (132)
..+|++++++..++.+++.+.++|++...... .+..+.+.|||....
T Consensus 87 ~~~DiAll~L~~~i~~~~~~~pi~l~~~~~~~~~~~~~~~~g~g~~~~ 134 (229)
T smart00020 87 YDNDIALLKLKSPVTLSDNVRPICLPSSNYNVPAGTTCTVSGWGRTSE 134 (229)
T ss_pred CcCCEEEEEECcccCCCCceeeccCCCcccccCCCCEEEEEeCCCCCC
Confidence 67899999999999999999999999863222 789999999998764
No 8
>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=97.05 E-value=0.0022 Score=40.26 Aligned_cols=49 Identities=45% Similarity=0.908 Sum_probs=41.8
Q ss_pred ccCCeEEEEeccceeeccCeeeeecCCCCCCC-CCceEEEEeecccCcCC
Q psy15292 80 ISNDVALIKIDKDVVFKQHIIPVCLPDQTVKL-VGKSATVAGWGRTRHAG 128 (132)
Q Consensus 80 ~~~d~c~~~~~~~~~~~~~v~~icl~~~~~~~-~g~~~~v~gwg~~~~~~ 128 (132)
..+|++++++..++.+.+.+.++|++.....+ .+..|.+.|||.....+
T Consensus 85 ~~~DiAll~L~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~G~~~~~~~~ 134 (220)
T PF00089_consen 85 YDNDIALLKLDRPITFGDNIQPICLPSAGSDPNVGTSCIVVGWGRTSDNG 134 (220)
T ss_dssp TTTSEEEEEESSSSEHBSSBEESBBTSTTHTTTTTSEEEEEESSBSSTTS
T ss_pred cccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence 46899999999999999999999999965433 78999999999976554
No 9
>COG5640 Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=96.85 E-value=0.0064 Score=41.25 Aligned_cols=33 Identities=27% Similarity=0.555 Sum_probs=29.0
Q ss_pred eEEeeeEEEeCCCCCCCCCCCceEEEEeCCCee
Q psy15292 2 FKLNTRQSFVHPQYSPSDFRNDVALIKIDKDVV 34 (132)
Q Consensus 2 ~~~~v~~~~~h~~y~~~~~~~diall~l~~~~~ 34 (132)
++..|..++.|+-|.+.++.||||+++|.++..
T Consensus 104 ~rg~vr~i~~~efY~~~n~~ND~Av~~l~~~a~ 136 (413)
T COG5640 104 ERGHVRTIYVHEFYSPGNLGNDIAVLELARAAS 136 (413)
T ss_pred cCcceEEEeeecccccccccCcceeeccccccc
Confidence 356788999999999999999999999998654
No 10
>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=95.37 E-value=0.046 Score=35.34 Aligned_cols=44 Identities=16% Similarity=0.384 Sum_probs=33.8
Q ss_pred CCCceEEEEeCCCeeeCCCeeeeeecCCCCcc-cCCcEEEeccCc
Q psy15292 20 FRNDVALIKIDKDVVFKQHIIPVCLPDQTVKL-VGKSATVAGWGR 63 (132)
Q Consensus 20 ~~~diall~l~~~~~~~~~~~~~cl~~~~~~~-~g~~~~~~GwG~ 63 (132)
.+.+++|+.|++|+.|+++++|..||...... ....|...|-..
T Consensus 87 ~~S~v~LLHL~~~~~fTr~VlP~flp~~~~~~~~~~~CVAVg~d~ 131 (267)
T PF09342_consen 87 PESNVLLLHLEQPANFTRYVLPTFLPETSNENESDDECVAVGHDD 131 (267)
T ss_pred cccceeeeeecCcccceeeecccccccccCCCCCCCceEEEEccc
Confidence 36799999999999999999999998633222 344787777544
No 11
>PF03761 DUF316: Domain of unknown function (DUF316) ; InterPro: IPR005514 This is a family of uncharacterised proteins from Caenorhabditis elegans.
Probab=94.35 E-value=0.85 Score=30.22 Aligned_cols=43 Identities=21% Similarity=0.509 Sum_probs=32.3
Q ss_pred CCCCCCceEEEEeCCCeeeCCCeeeeeecCCCCcc-cCCcEEEecc
Q psy15292 17 PSDFRNDVALIKIDKDVVFKQHIIPVCLPDQTVKL-VGKSATVAGW 61 (132)
Q Consensus 17 ~~~~~~diall~l~~~~~~~~~~~~~cl~~~~~~~-~g~~~~~~Gw 61 (132)
.....++.+|++|+.+ +.....|+||+.+.... .++...+.|+
T Consensus 156 ~~~~~~~~mIlEl~~~--~~~~~~~~Cl~~~~~~~~~~~~~~~yg~ 199 (282)
T PF03761_consen 156 NFNRPYSPMILELEED--FSKNVSPPCLADSSTNWEKGDEVDVYGF 199 (282)
T ss_pred ccccccceEEEEEccc--ccccCCCEEeCCCccccccCceEEEeec
Confidence 4456789999999998 67889999999766543 4555556665
No 12
>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=78.52 E-value=17 Score=24.11 Aligned_cols=44 Identities=16% Similarity=0.385 Sum_probs=33.6
Q ss_pred ccCCeEEEEeccceeeccCeeeeecCCC-CCCCCCceEEEEeecc
Q psy15292 80 ISNDVALIKIDKDVVFKQHIIPVCLPDQ-TVKLVGKSATVAGWGR 123 (132)
Q Consensus 80 ~~~d~c~~~~~~~~~~~~~v~~icl~~~-~~~~~g~~~~v~gwg~ 123 (132)
...+..++.+.++..|+.++.|+.+++. ........|...|--.
T Consensus 87 ~~S~v~LLHL~~~~~fTr~VlP~flp~~~~~~~~~~~CVAVg~d~ 131 (267)
T PF09342_consen 87 PESNVLLLHLEQPANFTRYVLPTFLPETSNENESDDECVAVGHDD 131 (267)
T ss_pred cccceeeeeecCcccceeeecccccccccCCCCCCCceEEEEccc
Confidence 3467788889999999999999999984 3333556888777544
No 13
>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=68.20 E-value=15 Score=26.22 Aligned_cols=39 Identities=28% Similarity=0.323 Sum_probs=26.7
Q ss_pred CCCceEEEEeCCCeeeCCCeeeeeecCCCCcccCCcEEEeccC
Q psy15292 20 FRNDVALIKIDKDVVFKQHIIPVCLPDQTVKLVGKSATVAGWG 62 (132)
Q Consensus 20 ~~~diall~l~~~~~~~~~~~~~cl~~~~~~~~g~~~~~~GwG 62 (132)
...|+|||++..+ ..+.++.+........|+...+.|+-
T Consensus 103 ~~~DlAllkv~~~----~~~~~~~l~~~~~~~~G~~v~aiG~p 141 (428)
T TIGR02037 103 PRTDIAVLKIDAK----KNLPVIKLGDSDKLRVGDWVLAIGNP 141 (428)
T ss_pred CCCCEEEEEecCC----CCceEEEccCCCCCCCCCEEEEEECC
Confidence 4689999999864 23456666544443478888888864
No 14
>PRK10139 serine endoprotease; Provisional
Probab=52.05 E-value=36 Score=24.70 Aligned_cols=39 Identities=26% Similarity=0.400 Sum_probs=25.0
Q ss_pred CCCCceEEEEeCCCeeeCCCeeeeeecCCCCcccCCcEEEecc
Q psy15292 19 DFRNDVALIKIDKDVVFKQHIIPVCLPDQTVKLVGKSATVAGW 61 (132)
Q Consensus 19 ~~~~diall~l~~~~~~~~~~~~~cl~~~~~~~~g~~~~~~Gw 61 (132)
+...|||||+++.+- ...++.+........|+...+.|.
T Consensus 135 D~~~DlAvlkv~~~~----~l~~~~lg~s~~~~~G~~V~aiG~ 173 (455)
T PRK10139 135 DDQSDIALLQIQNPS----KLTQIAIADSDKLRVGDFAVAVGN 173 (455)
T ss_pred cCCCCEEEEEecCCC----CCceeEecCccccCCCCEEEEEec
Confidence 347899999997532 234555554433336888877775
No 15
>PF14903 WG_beta_rep: WG containing repeat
Probab=50.74 E-value=21 Score=14.96 Aligned_cols=23 Identities=30% Similarity=0.577 Sum_probs=15.5
Q ss_pred EEEeCCCCCC-CCCCCceEEEEeC
Q psy15292 8 QSFVHPQYSP-SDFRNDVALIKID 30 (132)
Q Consensus 8 ~~~~h~~y~~-~~~~~diall~l~ 30 (132)
++++.|+|+. ..+.++.|.++..
T Consensus 9 ~~vi~~~yd~i~~~~~g~~~v~~~ 32 (35)
T PF14903_consen 9 KIVIPPKYDEIYPFSNGYAIVKKD 32 (35)
T ss_pred CEEEEccccCccccCCCEEEEEEC
Confidence 4567778866 3467788877654
No 16
>PRK10898 serine endoprotease; Provisional
Probab=45.62 E-value=52 Score=22.93 Aligned_cols=37 Identities=19% Similarity=0.284 Sum_probs=22.7
Q ss_pred CCCceEEEEeCCCeeeCCCeeeeeecCCCCcccCCcEEEecc
Q psy15292 20 FRNDVALIKIDKDVVFKQHIIPVCLPDQTVKLVGKSATVAGW 61 (132)
Q Consensus 20 ~~~diall~l~~~~~~~~~~~~~cl~~~~~~~~g~~~~~~Gw 61 (132)
...|+|||++... ...++.+........|+...+.|+
T Consensus 123 ~~~DlAvl~v~~~-----~l~~~~l~~~~~~~~G~~V~aiG~ 159 (353)
T PRK10898 123 SLTDLAVLKINAT-----NLPVIPINPKRVPHIGDVVLAIGN 159 (353)
T ss_pred CCCCEEEEEEcCC-----CCCeeeccCcCcCCCCCEEEEEeC
Confidence 4689999999753 123334433322237888877776
No 17
>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=39.75 E-value=71 Score=22.26 Aligned_cols=38 Identities=21% Similarity=0.194 Sum_probs=23.9
Q ss_pred CCCceEEEEeCCCeeeCCCeeeeeecCCCCcccCCcEEEeccC
Q psy15292 20 FRNDVALIKIDKDVVFKQHIIPVCLPDQTVKLVGKSATVAGWG 62 (132)
Q Consensus 20 ~~~diall~l~~~~~~~~~~~~~cl~~~~~~~~g~~~~~~GwG 62 (132)
...|+|||++...- +.++.+........|+...+.|+-
T Consensus 123 ~~~DlAvlkv~~~~-----~~~~~l~~s~~~~~G~~V~aiG~P 160 (351)
T TIGR02038 123 PLTDLAVLKIEGDN-----LPTIPVNLDRPPHVGDVVLAIGNP 160 (351)
T ss_pred CCCCEEEEEecCCC-----CceEeccCcCccCCCCEEEEEeCC
Confidence 47899999998532 233344333333378888888864
No 18
>PRK10372 PTS system L-ascorbate-specific transporter subunit IIA; Provisional
Probab=38.58 E-value=62 Score=19.32 Aligned_cols=29 Identities=17% Similarity=0.260 Sum_probs=22.5
Q ss_pred EEEeCCCCCCCCCCCceEEEEeCCCeeeC
Q psy15292 8 QSFVHPQYSPSDFRNDVALIKIDKDVVFK 36 (132)
Q Consensus 8 ~~~~h~~y~~~~~~~diall~l~~~~~~~ 36 (132)
-+++|+.........-++++++..|+.|.
T Consensus 64 iAIPH~~~~~~v~~~~i~v~~l~~pI~~~ 92 (154)
T PRK10372 64 LAMPHGRPEEGVKKTGFALVTLKKPLEFN 92 (154)
T ss_pred EEEecCChhcCCccceEEEEEeCCCEEeC
Confidence 46788876533557889999999999985
No 19
>KOG1749|consensus
Probab=35.39 E-value=53 Score=19.09 Aligned_cols=14 Identities=36% Similarity=0.582 Sum_probs=9.2
Q ss_pred CCceEEEEeecccC
Q psy15292 112 VGKSATVAGWGRTR 125 (132)
Q Consensus 112 ~g~~~~v~gwg~~~ 125 (132)
.++.+.++|+|+..
T Consensus 96 endevlv~gfgrkg 109 (143)
T KOG1749|consen 96 ENDEVLVAGFGRKG 109 (143)
T ss_pred cCCeeeeeccCccC
Confidence 46667777777654
No 20
>PRK10942 serine endoprotease; Provisional
Probab=35.09 E-value=86 Score=22.97 Aligned_cols=39 Identities=26% Similarity=0.379 Sum_probs=24.2
Q ss_pred CCCCceEEEEeCCCeeeCCCeeeeeecCCCCcccCCcEEEecc
Q psy15292 19 DFRNDVALIKIDKDVVFKQHIIPVCLPDQTVKLVGKSATVAGW 61 (132)
Q Consensus 19 ~~~~diall~l~~~~~~~~~~~~~cl~~~~~~~~g~~~~~~Gw 61 (132)
+...|+|||++..+-. +.++.+........|+...+.|.
T Consensus 156 D~~~DlAvlki~~~~~----l~~~~lg~s~~l~~G~~V~aiG~ 194 (473)
T PRK10942 156 DPRSDIALIQLQNPKN----LTAIKMADSDALRVGDYTVAIGN 194 (473)
T ss_pred cCCCCEEEEEecCCCC----CceeEecCccccCCCCEEEEEcC
Confidence 3468999999864322 34455544333347888777775
No 21
>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=33.94 E-value=33 Score=18.86 Aligned_cols=10 Identities=50% Similarity=0.833 Sum_probs=8.7
Q ss_pred CCceEEEEeC
Q psy15292 21 RNDVALIKID 30 (132)
Q Consensus 21 ~~diall~l~ 30 (132)
..|+|||++.
T Consensus 56 ~~D~All~v~ 65 (120)
T PF13365_consen 56 DYDLALLKVD 65 (120)
T ss_dssp -TTEEEEEES
T ss_pred cccEEEEEEe
Confidence 4899999999
No 22
>PRK09854 cmtB putative PTS system mannitol-specific transporter subunit IIA; Provisional
Probab=33.50 E-value=1e+02 Score=18.09 Aligned_cols=29 Identities=14% Similarity=0.305 Sum_probs=21.6
Q ss_pred EEEeCCCCCCCCCCCceEEEEeCCCeeeC
Q psy15292 8 QSFVHPQYSPSDFRNDVALIKIDKDVVFK 36 (132)
Q Consensus 8 ~~~~h~~y~~~~~~~diall~l~~~~~~~ 36 (132)
-++.|+.....-.+.-|+++.+..|+.|.
T Consensus 63 iAIPHa~~~~~v~~~~i~v~~~~~~I~~~ 91 (147)
T PRK09854 63 VAMPHARPECGALKTGMSLTLLEQGVYFP 91 (147)
T ss_pred EEecCCCcccCccccceEEEEeCCCEEcC
Confidence 46788865442356789999999999985
No 23
>COG1762 PtsN Phosphotransferase system mannitol/fructose-specific IIA domain (Ntr-type) [Carbohydrate transport and metabolism / Signal transduction mechanisms]
Probab=28.04 E-value=60 Score=19.33 Aligned_cols=28 Identities=14% Similarity=0.242 Sum_probs=20.5
Q ss_pred EEeCCCCCCCCCCCceEEEEeCCCeeeCC
Q psy15292 9 SFVHPQYSPSDFRNDVALIKIDKDVVFKQ 37 (132)
Q Consensus 9 ~~~h~~y~~~~~~~diall~l~~~~~~~~ 37 (132)
+++|.+-.. -...-++++++..|+.|..
T Consensus 62 AIPHa~~~~-v~~~~i~~~~l~~pv~f~~ 89 (152)
T COG1762 62 AIPHAKSEH-VKKPAIAVARLKEPVDFGS 89 (152)
T ss_pred ecCCCChhh-hccCEEEEEEeCCCcCCCC
Confidence 456765433 5677899999999999864
No 24
>PF00818 Ice_nucleation: Ice nucleation protein repeat; InterPro: IPR000258 Certain Gram-negative bacteria express proteins that enable them to promote nucleation of ice at relatively high temperatures (above -5C) [, ]. These proteins are localised at the outer membrane surface and can cause frost damage to many plants. The primary structure of the proteins contains a highly repetitive domain that dominates the sequence. The domain comprises a number of 48-residue repeats, which themselves contain 3 blocks of 16 residues, the first 8 of which are identical. It is thought that the repetitive domain may be responsible for aligning water molecules in the seed crystal. [.........48.residues.repeated.domain..........] / / | | \ \ AGYGSTxTagxxssli AGYGSTxTagxxsxlt AGYGSTxTaqxxsxlt [16.residues...] [16.residues...] [16.residues...] ; GO: 0009279 cell outer membrane
Probab=26.54 E-value=41 Score=11.96 Aligned_cols=9 Identities=56% Similarity=1.103 Sum_probs=4.1
Q ss_pred eecccCcCC
Q psy15292 120 GWGRTRHAG 128 (132)
Q Consensus 120 gwg~~~~~~ 128 (132)
|+|.+...+
T Consensus 1 GYGSTqTA~ 9 (16)
T PF00818_consen 1 GYGSTQTAG 9 (16)
T ss_pred CCCcccccC
Confidence 445554433
No 25
>PRK09913 putative fructose-like phosphotransferase system subunit EIIA; Provisional
Probab=25.58 E-value=92 Score=18.31 Aligned_cols=27 Identities=7% Similarity=0.060 Sum_probs=19.4
Q ss_pred EEeCCCCCCCCCCCceEEEEeCCCeeeC
Q psy15292 9 SFVHPQYSPSDFRNDVALIKIDKDVVFK 36 (132)
Q Consensus 9 ~~~h~~y~~~~~~~diall~l~~~~~~~ 36 (132)
++.|+... .....-++++++..|+.|+
T Consensus 61 AiPH~~~~-~v~~~~i~i~~l~~pi~~~ 87 (148)
T PRK09913 61 AVPHGKSA-CVKQPFVLFARKAQAIDWQ 87 (148)
T ss_pred ecCcCCch-hcCCCEEEEEEeCCCcCCC
Confidence 56777433 2456788899999998885
No 26
>COG2401 ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only]
Probab=25.32 E-value=53 Score=24.04 Aligned_cols=16 Identities=25% Similarity=0.520 Sum_probs=12.9
Q ss_pred EeeeEEEeCCCCCCCC
Q psy15292 4 LNTRQSFVHPQYSPSD 19 (132)
Q Consensus 4 ~~v~~~~~h~~y~~~~ 19 (132)
.+|.++.+||+|..+.
T Consensus 242 ariarvvvhpdyr~dg 257 (593)
T COG2401 242 ARIARVVVHPDYRADG 257 (593)
T ss_pred hheeEEEeccccccCc
Confidence 3688999999998644
No 27
>cd07268 Glo_EDI_BRP_like_4 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.
Probab=23.92 E-value=1.5e+02 Score=18.11 Aligned_cols=27 Identities=33% Similarity=0.330 Sum_probs=20.2
Q ss_pred CCCceEEEEeCCCeeeCCCe-eeeeecC
Q psy15292 20 FRNDVALIKIDKDVVFKQHI-IPVCLPD 46 (132)
Q Consensus 20 ~~~diall~l~~~~~~~~~~-~~~cl~~ 46 (132)
...-|+|++|.+|+.+..+. .-+-||.
T Consensus 35 NGRPI~l~~L~qPl~~~~~~I~cvELP~ 62 (149)
T cd07268 35 NGRPIALIKLEKPLQFAGWSISIVELPF 62 (149)
T ss_pred CCeeEEEEEcCCCceeCCcEEEEEEeCC
Confidence 45689999999999988764 4445653
No 28
>PF09173 eIF2_C: Initiation factor eIF2 gamma, C terminal; InterPro: IPR015256 This entry represents a domain which is found in the initiation factors eIF2 and EF-Tu, adopting a beta barrel structure with Greek key topology. It is required for formation of the ternary complex with GTP and initiator tRNA []. ; PDB: 1S0U_A 1KK1_A 1KK0_A 1KK2_A 1KJZ_A 1KK3_A 2D74_A 2DCU_A 3P3M_A 3V11_A ....
Probab=22.69 E-value=1.3e+02 Score=16.50 Aligned_cols=11 Identities=36% Similarity=0.891 Sum_probs=7.1
Q ss_pred CCcEEEeccCc
Q psy15292 53 GKSATVAGWGR 63 (132)
Q Consensus 53 g~~~~~~GwG~ 63 (132)
+.+=.+.|||.
T Consensus 77 ~~rWRLIG~G~ 87 (88)
T PF09173_consen 77 GNRWRLIGWGI 87 (88)
T ss_dssp TTSEEEEEEEE
T ss_pred cCeEEEEEEEe
Confidence 44556778874
No 29
>PF14781 BBS2_N: Ciliary BBSome complex subunit 2, N-terminal
Probab=22.44 E-value=1.8e+02 Score=17.48 Aligned_cols=29 Identities=14% Similarity=0.422 Sum_probs=19.1
Q ss_pred eeEEEeCCCCCC----CCCCCceEEEEeCCCee
Q psy15292 6 TRQSFVHPQYSP----SDFRNDVALIKIDKDVV 34 (132)
Q Consensus 6 v~~~~~h~~y~~----~~~~~diall~l~~~~~ 34 (132)
..+|++|.-... ....++|++|.+.+.++
T Consensus 19 ~gKV~IH~ph~~~~~~~~~~~~i~~LNin~~it 51 (136)
T PF14781_consen 19 GGKVFIHNPHERGQRTGRQDSDISFLNINQEIT 51 (136)
T ss_pred CCEEEEECCCccccccccccCceeEEECCCceE
Confidence 356788743322 12678999999887775
No 30
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=21.83 E-value=43 Score=16.39 Aligned_cols=25 Identities=20% Similarity=0.418 Sum_probs=14.3
Q ss_pred eEEEeCCCCCCCCCCCceEEEEeCC
Q psy15292 7 RQSFVHPQYSPSDFRNDVALIKIDK 31 (132)
Q Consensus 7 ~~~~~h~~y~~~~~~~diall~l~~ 31 (132)
..++++++.-....+.|..++++..
T Consensus 20 ~DifIp~~~l~~A~~gD~V~v~i~~ 44 (58)
T PF08206_consen 20 EDIFIPPRNLNGAMDGDKVLVRITP 44 (58)
T ss_dssp EEEEE-HHHHTTS-TT-EEEEEEEE
T ss_pred CCEEECHHHHCCCCCCCEEEEEEec
Confidence 3466666555566778888777654
No 31
>cd00211 PTS_IIA_fru PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation.
Probab=21.59 E-value=1.7e+02 Score=16.58 Aligned_cols=28 Identities=14% Similarity=0.306 Sum_probs=19.6
Q ss_pred EEeCCCCCCCCCCCceEEEEeCCCeeeCC
Q psy15292 9 SFVHPQYSPSDFRNDVALIKIDKDVVFKQ 37 (132)
Q Consensus 9 ~~~h~~y~~~~~~~diall~l~~~~~~~~ 37 (132)
++.|+.-.. ....-++++++..|+.+..
T Consensus 56 AlPH~~~~~-~~~~~i~v~~l~~~i~~~~ 83 (136)
T cd00211 56 AIPHAKSEA-VKKPGIAVLRLKEPVDFGS 83 (136)
T ss_pred ecCCCCchh-hcccEEEEEEeCCCccCCC
Confidence 456665332 4577889999999998753
No 32
>PRK10896 PTS system sugar transporter subunit IIA; Provisional
Probab=21.38 E-value=1.7e+02 Score=17.24 Aligned_cols=28 Identities=11% Similarity=0.362 Sum_probs=15.5
Q ss_pred EEeCCCCCCCCCCCceEEEEeCCCeeeC
Q psy15292 9 SFVHPQYSPSDFRNDVALIKIDKDVVFK 36 (132)
Q Consensus 9 ~~~h~~y~~~~~~~diall~l~~~~~~~ 36 (132)
++.|+.........-+++++|..|+.|.
T Consensus 69 AiPH~~~~~~~~~~~~~~~~l~~pi~~~ 96 (154)
T PRK10896 69 AIPHGKLEEDTLRAVGVFVQLEQPIAFD 96 (154)
T ss_pred eeceecchhccccceEEEEEeCCCccCC
Confidence 4566654322223334556788887774
Done!