Query psy8704
Match_columns 74
No_of_seqs 136 out of 1062
Neff 8.1
Searched_HMMs 46136
Date Fri Aug 16 17:07:23 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8704.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8704hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1542|consensus 100.0 3.9E-30 8.5E-35 171.7 6.0 71 1-74 173-244 (372)
2 KOG1543|consensus 100.0 2.5E-28 5.4E-33 163.4 7.9 73 1-74 126-199 (325)
3 cd02620 Peptidase_C1A_Cathepsi 99.9 1.9E-27 4.1E-32 152.9 8.0 74 1-74 20-93 (236)
4 PTZ00203 cathepsin L protease; 99.9 6.8E-27 1.5E-31 157.7 7.9 71 1-74 142-215 (348)
5 PTZ00200 cysteine proteinase; 99.9 7.1E-27 1.5E-31 161.6 7.7 71 1-74 250-321 (448)
6 cd02621 Peptidase_C1A_Cathepsi 99.9 1.6E-26 3.5E-31 148.8 8.1 73 1-74 21-97 (243)
7 PTZ00021 falcipain-2; Provisio 99.9 1.3E-26 2.9E-31 161.3 7.2 71 1-74 282-353 (489)
8 smart00645 Pept_C1 Papain fami 99.9 7.9E-26 1.7E-30 140.0 8.0 72 1-74 17-89 (174)
9 cd02698 Peptidase_C1A_Cathepsi 99.9 1.1E-25 2.3E-30 145.1 7.7 72 1-74 20-95 (239)
10 PTZ00364 dipeptidyl-peptidase 99.9 2.2E-25 4.7E-30 156.8 7.8 72 1-73 224-302 (548)
11 cd02248 Peptidase_C1A Peptidas 99.9 6.6E-25 1.4E-29 137.6 8.0 72 1-74 16-87 (210)
12 PTZ00049 cathepsin C-like prot 99.9 6.2E-25 1.3E-29 157.0 7.9 73 1-74 401-481 (693)
13 PF00112 Peptidase_C1: Papain 99.9 2.9E-23 6.3E-28 130.0 6.5 73 1-74 18-91 (219)
14 cd02619 Peptidase_C1 C1 Peptid 99.9 2.8E-22 6.1E-27 125.6 8.4 74 1-74 13-91 (223)
15 PTZ00462 Serine-repeat antigen 99.9 1.1E-21 2.4E-26 144.0 8.2 72 1-74 548-622 (1004)
16 KOG1544|consensus 99.8 2.7E-20 5.9E-25 124.8 -2.3 73 2-74 228-300 (470)
17 cd00585 Peptidase_C1B Peptidas 98.3 6E-06 1.3E-10 57.9 7.4 73 1-74 58-157 (437)
18 PF03051 Peptidase_C1_2: Pepti 97.9 2E-05 4.3E-10 55.3 4.4 73 1-74 59-158 (438)
19 COG4870 Cysteine protease [Pos 97.8 3.5E-06 7.7E-11 57.6 -1.1 26 1-26 115-140 (372)
20 COG3579 PepC Aminopeptidase C 90.2 1.1 2.4E-05 31.4 5.3 72 2-74 62-160 (444)
21 KOG4128|consensus 66.2 6.4 0.00014 27.7 2.5 72 2-74 67-167 (457)
22 KOG2735|consensus 63.5 8.7 0.00019 27.5 2.8 22 8-29 374-395 (466)
23 PF12301 CD99L2: CD99 antigen 53.6 15 0.00033 23.0 2.4 29 9-40 123-151 (169)
24 PF04060 FeS: Putative Fe-S cl 41.2 22 0.00048 16.2 1.4 7 8-14 14-20 (35)
25 PF12368 DUF3650: Protein of u 38.9 8.3 0.00018 17.1 -0.3 11 60-70 9-19 (28)
26 PRK15364 pathogenicity island 37.9 23 0.00049 22.7 1.4 19 51-69 96-114 (196)
27 PF00648 Peptidase_C2: Calpain 33.3 32 0.0007 22.7 1.7 19 2-20 49-67 (298)
28 PF08723 Gag_p15: Gag protein 33.1 24 0.00052 20.9 0.9 15 7-21 27-42 (123)
29 PF12854 PPR_1: PPR repeat 32.2 34 0.00073 15.1 1.2 15 50-64 18-32 (34)
30 COG4871 Uncharacterized protei 30.7 35 0.00076 21.6 1.4 10 4-13 140-151 (193)
31 cd00044 CysPc Calpains, domain 28.7 51 0.0011 22.1 2.1 20 2-21 70-89 (315)
32 PF07249 Cerato-platanin: Cera 27.4 12 0.00026 22.1 -0.9 9 4-12 57-65 (119)
33 smart00230 CysPc Calpain-like 26.7 60 0.0013 21.9 2.1 20 2-21 62-81 (318)
34 smart00151 SWIB SWI complex, B 24.5 59 0.0013 17.3 1.5 15 57-71 28-42 (77)
35 PF09641 DUF2026: Protein of u 24.4 63 0.0014 21.0 1.8 18 8-25 26-45 (204)
36 KOG0632|consensus 24.4 85 0.0019 21.9 2.5 32 13-44 58-91 (388)
37 PF14445 Prok-RING_2: Prokaryo 23.5 30 0.00064 17.6 0.1 7 5-11 32-38 (57)
38 COG4422 Bacteriophage protein 23.2 81 0.0017 20.6 2.1 19 5-23 26-44 (250)
39 PF05543 Peptidase_C47: Stapho 23.1 1.6E+02 0.0034 18.7 3.4 56 3-67 19-80 (175)
40 COG0264 Tsf Translation elonga 22.4 63 0.0014 22.2 1.6 29 39-69 20-48 (296)
41 CHL00098 tsf elongation factor 22.3 68 0.0015 20.6 1.7 29 39-69 16-44 (200)
42 PF14502 HTH_41: Helix-turn-he 21.7 71 0.0015 15.9 1.3 19 49-67 17-35 (48)
43 TIGR00116 tsf translation elon 21.5 78 0.0017 21.5 1.9 18 52-69 30-47 (290)
44 PF02201 SWIB: SWIB/MDM2 domai 21.2 85 0.0018 16.6 1.7 15 57-71 28-42 (76)
45 cd04407 RhoGAP_myosin_IXB RhoG 21.2 92 0.002 19.3 2.1 20 55-74 19-38 (186)
46 PF03380 DUF282: Caenorhabditi 21.1 28 0.00061 16.6 -0.2 19 42-60 5-23 (39)
47 PRK09377 tsf elongation factor 21.0 82 0.0018 21.4 1.9 29 39-69 20-48 (290)
48 PRK11713 16S ribosomal RNA met 20.7 1E+02 0.0022 19.8 2.3 19 49-67 185-203 (234)
49 PF11058 Ral: Antirestriction 20.6 1.4E+02 0.0031 15.3 2.4 19 9-27 45-63 (66)
50 PF00317 Ribonuc_red_lgN: Ribo 20.5 1E+02 0.0022 16.5 1.9 31 12-43 5-35 (83)
51 COG1854 LuxS LuxS protein invo 20.0 37 0.0008 21.2 0.1 35 13-55 51-87 (161)
No 1
>KOG1542|consensus
Probab=99.96 E-value=3.9e-30 Score=171.68 Aligned_cols=71 Identities=37% Similarity=0.559 Sum_probs=66.8
Q ss_pred CCCCCCchHHHHHHHHHHHHHHHHHcCCCcceecCHHHHhhhcCCCCCCCCCCCHHHHHHHHHh-cCCCCCCCCC
Q psy8704 1 MNRAEMSSDEAFGAVEAMSDRVCIASGGKKHVRLSSDDLVSCCRLCGFGCNGGFPGMAWRYWVK-NGINTYKPVK 74 (74)
Q Consensus 1 rdQ~~Cgscwafa~~~~~e~~~~i~~~~~~~~~lS~q~lidC~~~~~~gC~GG~~~~a~~y~~~-~Gi~~e~~Y~ 74 (74)
||||.||||||||+++++|..+.|+++ +++.||+||||||+. +++||+||.+..||+|+++ .||..|++||
T Consensus 173 KnQG~CGSCWAFS~tG~vEga~~i~~g--~LvsLSEQeLvDCD~-~d~gC~GGl~~nA~~~~~~~gGL~~E~dYP 244 (372)
T KOG1542|consen 173 KNQGMCGSCWAFSTTGAVEGAWAIATG--KLVSLSEQELVDCDS-CDNGCNGGLMDNAFKYIKKAGGLEKEKDYP 244 (372)
T ss_pred ccCCcCcchhhhhhhhhhhhHHHhhcC--cccccchhhhhcccC-cCCcCCCCChhHHHHHHHHhCCccccccCC
Confidence 799999999999999999999999999 899999999999986 4789999999999999665 4999999997
No 2
>KOG1543|consensus
Probab=99.95 E-value=2.5e-28 Score=163.42 Aligned_cols=73 Identities=44% Similarity=0.687 Sum_probs=68.7
Q ss_pred CCCCCCchHHHHHHHHHHHHHHHHHcCCCcceecCHHHHhhhcCCCCCCCCCCCHHHHHHHHHhcCCCC-CCCCC
Q psy8704 1 MNRAEMSSDEAFGAVEAMSDRVCIASGGKKHVRLSSDDLVSCCRLCGFGCNGGFPGMAWRYWVKNGINT-YKPVK 74 (74)
Q Consensus 1 rdQ~~Cgscwafa~~~~~e~~~~i~~~~~~~~~lS~q~lidC~~~~~~gC~GG~~~~a~~y~~~~Gi~~-e~~Y~ 74 (74)
|||+.|||||||+++++||++++|++++ .++.||+||||||+..++.||.||++..||+|++++|+++ +++||
T Consensus 126 kdQg~CgsCWAFaa~~aie~~~~i~~g~-~l~sLSeq~lvdC~~~~~~GC~GG~~~~A~~yi~~~G~~t~~~~Yp 199 (325)
T KOG1543|consen 126 KDQGSCGSCWAFAATGALEDRYNIKTGG-KLLSLSEQDLVDCCGECGDGCNGGEPKNAFKYIKKNGGVTECENYP 199 (325)
T ss_pred CCCCcCcchHHHHHHHHHHHHHHHHhCC-ccCccChhhhhhccCCCCCCcCCCCHHHHHHHHHHhCCCCCCcCCC
Confidence 7999999999999999999999999997 6899999999999986678999999999999999998888 99986
No 3
>cd02620 Peptidase_C1A_CathepsinB Cathepsin B group; composed of cathepsin B and similar proteins, including tubulointerstitial nephritis antigen (TIN-Ag). Cathepsin B is a lysosomal papain-like cysteine peptidase which is expressed in all tissues and functions primarily as an exopeptidase through its carboxydipeptidyl activity. Together with other cathepsins, it is involved in the degradation of proteins, proenzyme activation, Ag processing, metabolism and apoptosis. Cathepsin B has been implicated in a number of human diseases such as cancer, rheumatoid arthritis, osteoporosis and Alzheimer's disease. The unique carboxydipeptidyl activity of cathepsin B is attributed to the presence of an occluding loop in its active site which favors the binding of the C-termini of substrate proteins. Some members of this group do not possess the occluding loop. TIN-Ag is an extracellular matrix basement protein which was originally identified as a target Ag involved in anti-tubular basement membrane
Probab=99.95 E-value=1.9e-27 Score=152.92 Aligned_cols=74 Identities=49% Similarity=0.866 Sum_probs=67.7
Q ss_pred CCCCCCchHHHHHHHHHHHHHHHHHcCCCcceecCHHHHhhhcCCCCCCCCCCCHHHHHHHHHhcCCCCCCCCC
Q psy8704 1 MNRAEMSSDEAFGAVEAMSDRVCIASGGKKHVRLSSDDLVSCCRLCGFGCNGGFPGMAWRYWVKNGINTYKPVK 74 (74)
Q Consensus 1 rdQ~~Cgscwafa~~~~~e~~~~i~~~~~~~~~lS~q~lidC~~~~~~gC~GG~~~~a~~y~~~~Gi~~e~~Y~ 74 (74)
|||+.||+||||+++++||+++.|++++.+.+.||+|+||||+...+.||+||++..+|+|++++||++|++||
T Consensus 20 ~dQg~CGsCwAfa~~~~le~~~~i~~~~~~~~~LS~Q~lidC~~~~~~gC~GG~~~~a~~~i~~~G~~~e~~yP 93 (236)
T cd02620 20 RDQGNCGSCWAFSAVEAFSDRLCIQSNGKENVLLSAQDLLSCCSGCGDGCNGGYPDAAWKYLTTTGVVTGGCQP 93 (236)
T ss_pred CCcccchhHHHHHHHHHHhhHHHHhcCCCCccccCHHHHHhhcCCCCCCCCCCCHHHHHHHHHhcCCCcCCEec
Confidence 69999999999999999999999988755678999999999986435799999999999999999999999986
No 4
>PTZ00203 cathepsin L protease; Provisional
Probab=99.94 E-value=6.8e-27 Score=157.69 Aligned_cols=71 Identities=34% Similarity=0.460 Sum_probs=65.2
Q ss_pred CCCCCCchHHHHHHHHHHHHHHHHHcCCCcceecCHHHHhhhcCCCCCCCCCCCHHHHHHHHHhc---CCCCCCCCC
Q psy8704 1 MNRAEMSSDEAFGAVEAMSDRVCIASGGKKHVRLSSDDLVSCCRLCGFGCNGGFPGMAWRYWVKN---GINTYKPVK 74 (74)
Q Consensus 1 rdQ~~Cgscwafa~~~~~e~~~~i~~~~~~~~~lS~q~lidC~~~~~~gC~GG~~~~a~~y~~~~---Gi~~e~~Y~ 74 (74)
|||+.|||||||+++++||++++|+++ +++.||+|+||||+.. +.||+||++..||+|++++ ||++|++||
T Consensus 142 kdQg~CGSCWAfa~~~aiEs~~~i~~~--~~~~LSeQqLvdC~~~-~~GC~GG~~~~a~~yi~~~~~ggi~~e~~YP 215 (348)
T PTZ00203 142 KNQGACGSCWAFSAVGNIESQWAVAGH--KLVRLSEQQLVSCDHV-DNGCGGGLMLQAFEWVLRNMNGTVFTEKSYP 215 (348)
T ss_pred cccCCCccHHHHhhHHHHHHHHHHhcC--CCccCCHHHHHhccCC-CCCCCCCCHHHHHHHHHHhcCCCCCccccCC
Confidence 799999999999999999999999988 6789999999999864 5799999999999999864 588999996
No 5
>PTZ00200 cysteine proteinase; Provisional
Probab=99.94 E-value=7.1e-27 Score=161.56 Aligned_cols=71 Identities=30% Similarity=0.481 Sum_probs=66.5
Q ss_pred CCCC-CCchHHHHHHHHHHHHHHHHHcCCCcceecCHHHHhhhcCCCCCCCCCCCHHHHHHHHHhcCCCCCCCCC
Q psy8704 1 MNRA-EMSSDEAFGAVEAMSDRVCIASGGKKHVRLSSDDLVSCCRLCGFGCNGGFPGMAWRYWVKNGINTYKPVK 74 (74)
Q Consensus 1 rdQ~-~Cgscwafa~~~~~e~~~~i~~~~~~~~~lS~q~lidC~~~~~~gC~GG~~~~a~~y~~~~Gi~~e~~Y~ 74 (74)
|||| .||||||||+++++|++++|+++ ..+.||+|+||||+.. +.||+||++..||+|++++||++|++||
T Consensus 250 kdQG~~CGSCWAFat~~aiEs~~~i~~~--~~~~LSeQqLvDC~~~-~~GC~GG~~~~A~~yi~~~Gi~~e~~YP 321 (448)
T PTZ00200 250 KDQGLNCGSCWAFSSVGSVESLYKIYRD--KSVDLSEQELVNCDTK-SQGCSGGYPDTALEYVKNKGLSSSSDVP 321 (448)
T ss_pred ccCCCccchHHHHhHHHHHHHHHHHhcC--CCeecCHHHHhhccCc-cCCCCCCcHHHHHHHHhhcCccccccCC
Confidence 7999 99999999999999999999877 6789999999999864 5799999999999999999999999997
No 6
>cd02621 Peptidase_C1A_CathepsinC Cathepsin C; also known as Dipeptidyl Peptidase I (DPPI), an atypical papain-like cysteine peptidase with chloride dependency and dipeptidyl aminopeptidase activity, resulting from its tetrameric structure which limits substrate access. Each subunit of the tetramer is composed of three peptides: the heavy and light chains, which together adopts the papain fold and forms the catalytic domain; and the residual propeptide region, which forms a beta barrel and points towards the substrate's N-terminus. The subunit composition is the result of the unique characteristic of procathepsin C maturation involving the cleavage of the catalytic domain and the non-autocatalytic excision of an activation peptide within its propeptide region. By removing N-terminal dipeptide extensions, cathepsin C activates granule serine peptidases (granzymes) involved in cell-mediated apoptosis, inflammation and tissue remodelling. Loss-of-function mutations in cathepsin C are assoc
Probab=99.94 E-value=1.6e-26 Score=148.84 Aligned_cols=73 Identities=32% Similarity=0.454 Sum_probs=66.7
Q ss_pred CCCCCCchHHHHHHHHHHHHHHHHHcCC----CcceecCHHHHhhhcCCCCCCCCCCCHHHHHHHHHhcCCCCCCCCC
Q psy8704 1 MNRAEMSSDEAFGAVEAMSDRVCIASGG----KKHVRLSSDDLVSCCRLCGFGCNGGFPGMAWRYWVKNGINTYKPVK 74 (74)
Q Consensus 1 rdQ~~Cgscwafa~~~~~e~~~~i~~~~----~~~~~lS~q~lidC~~~~~~gC~GG~~~~a~~y~~~~Gi~~e~~Y~ 74 (74)
|||+.||+||||+++++||++++|++++ ...+.||+|+|+||+.. +.||+||++..+++|++++||++|++||
T Consensus 21 ~dQg~CGsCwAfa~~~~ies~~~i~~~~~~~~~~~~~lS~q~l~dC~~~-~~GC~GG~~~~a~~~~~~~Gi~~e~~yP 97 (243)
T cd02621 21 RNQGGCGSCYAFASVYALEARIMIASNKTDPLGQQPILSPQHVLSCSQY-SQGCDGGFPFLVGKFAEDFGIVTEDYFP 97 (243)
T ss_pred CCCCcCccHHHHHHHHHHHHHHHHHhCCCCccccCcccCHHHhhhhcCC-CCCCCCCCHHHHHHHHHhcCcCCCceeC
Confidence 7999999999999999999999998874 23689999999999863 5799999999999999999999999986
No 7
>PTZ00021 falcipain-2; Provisional
Probab=99.93 E-value=1.3e-26 Score=161.32 Aligned_cols=71 Identities=24% Similarity=0.354 Sum_probs=66.3
Q ss_pred CCCCCCchHHHHHHHHHHHHHHHHHcCCCcceecCHHHHhhhcCCCCCCCCCCCHHHHHHHHHhc-CCCCCCCCC
Q psy8704 1 MNRAEMSSDEAFGAVEAMSDRVCIASGGKKHVRLSSDDLVSCCRLCGFGCNGGFPGMAWRYWVKN-GINTYKPVK 74 (74)
Q Consensus 1 rdQ~~Cgscwafa~~~~~e~~~~i~~~~~~~~~lS~q~lidC~~~~~~gC~GG~~~~a~~y~~~~-Gi~~e~~Y~ 74 (74)
||||.||||||||++++||++++|+++ .++.||+|+||||+.. +.||+||++..||+|+.++ ||++|++||
T Consensus 282 KdQG~CGSCWAFAa~~alEs~~~I~~g--~~v~LSeQqLVDCs~~-n~GC~GG~~~~Af~yi~~~gGl~tE~~YP 353 (489)
T PTZ00021 282 KDQKNCGSCWAFSTVGVVESQYAIRKN--ELVSLSEQELVDCSFK-NNGCYGGLIPNAFEDMIELGGLCSEDDYP 353 (489)
T ss_pred ccccccccHHHHHHHHHHHHHHHHHcC--CCcccCHHHHhhhccC-CCCCCCcchHhhhhhhhhccccCcccccC
Confidence 799999999999999999999999988 6789999999999864 6799999999999999776 999999997
No 8
>smart00645 Pept_C1 Papain family cysteine protease.
Probab=99.93 E-value=7.9e-26 Score=140.02 Aligned_cols=72 Identities=39% Similarity=0.607 Sum_probs=66.5
Q ss_pred CCCCCCchHHHHHHHHHHHHHHHHHcCCCcceecCHHHHhhhcCCCCCCCCCCCHHHHHHHHHhc-CCCCCCCCC
Q psy8704 1 MNRAEMSSDEAFGAVEAMSDRVCIASGGKKHVRLSSDDLVSCCRLCGFGCNGGFPGMAWRYWVKN-GINTYKPVK 74 (74)
Q Consensus 1 rdQ~~Cgscwafa~~~~~e~~~~i~~~~~~~~~lS~q~lidC~~~~~~gC~GG~~~~a~~y~~~~-Gi~~e~~Y~ 74 (74)
|||+.||+||||+++++||++++|+++ +.+.||+|+|++|....+.||+||++..|++|++++ ||++|++||
T Consensus 17 ~dQg~CGsCwAfa~~~~ie~~~~i~~~--~~~~lS~q~l~~C~~~~~~gC~GG~~~~a~~~~~~~~Gi~~e~~~P 89 (174)
T smart00645 17 KDQGQCGSCWAFSATGALEGRYCIKTG--KLVSLSEQQLVDCSTGGNNGCNGGLPDNAFEYIKKNGGLETESCYP 89 (174)
T ss_pred ccCcccchHHHHHHHHHHHHHHHHhcC--CccccCHHHHhhhcCCCCCCCCCcCHHHHHHHHHHcCCcccccccC
Confidence 799999999999999999999999988 578999999999986434599999999999999998 999999986
No 9
>cd02698 Peptidase_C1A_CathepsinX Cathepsin X; the only papain-like lysosomal cysteine peptidase exhibiting carboxymonopeptidase activity. It can also act as a carboxydipeptidase, like cathepsin B, but has been shown to preferentially cleave substrates through a monopeptidyl carboxypeptidase pathway. The propeptide region of cathepsin X, the shortest among papain-like peptidases, is covalently attached to the active site cysteine in the inactive form of the enzyme. Little is known about the biological function of cathepsin X. Some studies point to a role in early tumorigenesis. A more recent study indicates that cathepsin X expression is restricted to immune cells suggesting a role in phagocytosis and the regulation of the immune response.
Probab=99.93 E-value=1.1e-25 Score=145.05 Aligned_cols=72 Identities=33% Similarity=0.462 Sum_probs=65.7
Q ss_pred CCCC---CCchHHHHHHHHHHHHHHHHHcCCC-cceecCHHHHhhhcCCCCCCCCCCCHHHHHHHHHhcCCCCCCCCC
Q psy8704 1 MNRA---EMSSDEAFGAVEAMSDRVCIASGGK-KHVRLSSDDLVSCCRLCGFGCNGGFPGMAWRYWVKNGINTYKPVK 74 (74)
Q Consensus 1 rdQ~---~Cgscwafa~~~~~e~~~~i~~~~~-~~~~lS~q~lidC~~~~~~gC~GG~~~~a~~y~~~~Gi~~e~~Y~ 74 (74)
|||+ .||||||||++++||+++.|+++++ ..+.||+|+||||+. +.||+||++..+++|++++||++|++||
T Consensus 20 k~Qg~~~~CGsCwAfa~~~aies~~~i~~~~~~~~~~lS~Q~lldC~~--~~gC~GG~~~~a~~~~~~~Gl~~e~~yP 95 (239)
T cd02698 20 RNQHIPQYCGSCWAHGSTSALADRINIARKGAWPSVYLSVQVVIDCAG--GGSCHGGDPGGVYEYAHKHGIPDETCNP 95 (239)
T ss_pred ccCCCCCCCCcchHHHhHHHHHHHHHHHHCCCCCCcccCHHHHHhCCC--CCCccCcCHHHHHHHHHHcCcCCCCeeC
Confidence 7898 8999999999999999999987643 357899999999986 5799999999999999999999999986
No 10
>PTZ00364 dipeptidyl-peptidase I precursor; Provisional
Probab=99.92 E-value=2.2e-25 Score=156.84 Aligned_cols=72 Identities=29% Similarity=0.421 Sum_probs=66.0
Q ss_pred CCCCC---CchHHHHHHHHHHHHHHHHHcCCC----cceecCHHHHhhhcCCCCCCCCCCCHHHHHHHHHhcCCCCCCCC
Q psy8704 1 MNRAE---MSSDEAFGAVEAMSDRVCIASGGK----KHVRLSSDDLVSCCRLCGFGCNGGFPGMAWRYWVKNGINTYKPV 73 (74)
Q Consensus 1 rdQ~~---Cgscwafa~~~~~e~~~~i~~~~~----~~~~lS~q~lidC~~~~~~gC~GG~~~~a~~y~~~~Gi~~e~~Y 73 (74)
|||+. ||||||||++++||+|++|+++++ ..+.||+|+||||+. ++.||+||++..|++|++++||++|++|
T Consensus 224 rdQg~~~~CGSCWAFAav~alEsr~~I~tn~~~~~g~~~~LS~QqLVDCs~-~n~GCdGG~p~~A~~yi~~~GI~tE~dY 302 (548)
T PTZ00364 224 PPASPGRGCNSSYVEAALAAMMARVMVASNRTDPLGQQTFLSARHVLDCSQ-YGQGCAGGFPEEVGKFAETFGILTTDSY 302 (548)
T ss_pred cCCCCCCCCcCHHHHHHHHHHHHHHHHHhCCCcccCcccCcCHHHHhcccC-CCCCCCCCcHHHHHHHHHhCCccccccc
Confidence 79999 999999999999999999998642 368899999999985 3689999999999999999999999998
No 11
>cd02248 Peptidase_C1A Peptidase C1A subfamily (MEROPS database nomenclature); composed of cysteine peptidases (CPs) similar to papain, including the mammalian CPs (cathepsins B, C, F, H, L, K, O, S, V, X and W). Papain is an endopeptidase with specific substrate preferences, primarily for bulky hydrophobic or aromatic residues at the S2 subsite, a hydrophobic pocket in papain that accommodates the P2 sidechain of the substrate (the second residue away from the scissile bond). Most members of the papain subfamily are endopeptidases. Some exceptions to this rule can be explained by specific details of the catalytic domains like the occluding loop in cathepsin B which confers an additional carboxydipeptidyl activity and the mini-chain of cathepsin H resulting in an N-terminal exopeptidase activity. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage proteins in seeds. Parasitic CPs act extracellularly to help invade tissues and cells, to h
Probab=99.92 E-value=6.6e-25 Score=137.62 Aligned_cols=72 Identities=32% Similarity=0.490 Sum_probs=66.6
Q ss_pred CCCCCCchHHHHHHHHHHHHHHHHHcCCCcceecCHHHHhhhcCCCCCCCCCCCHHHHHHHHHhcCCCCCCCCC
Q psy8704 1 MNRAEMSSDEAFGAVEAMSDRVCIASGGKKHVRLSSDDLVSCCRLCGFGCNGGFPGMAWRYWVKNGINTYKPVK 74 (74)
Q Consensus 1 rdQ~~Cgscwafa~~~~~e~~~~i~~~~~~~~~lS~q~lidC~~~~~~gC~GG~~~~a~~y~~~~Gi~~e~~Y~ 74 (74)
|||+.||+|||||++++||++++|+++ ..+.||+|+|++|....+.+|.||++..+++|++++|+++|++||
T Consensus 16 ~dQg~cgsCwAfa~~~~le~~~~i~~~--~~~~lS~q~l~~c~~~~~~gC~GG~~~~a~~~~~~~Gi~~e~~yP 87 (210)
T cd02248 16 KDQGSCGSCWAFSTVGALEGAYAIKTG--KLVSLSEQQLVDCSTSGNNGCNGGNPDNAFEYVKNGGLASESDYP 87 (210)
T ss_pred ccCCCCcchHHhHHHHHHHHHHHHHcC--CCcccCHHHHhccCCCCCCCCCCCCHHHhHHHHHHCCcCccccCC
Confidence 799999999999999999999999988 678899999999986435799999999999999999999999986
No 12
>PTZ00049 cathepsin C-like protein; Provisional
Probab=99.92 E-value=6.2e-25 Score=156.98 Aligned_cols=73 Identities=27% Similarity=0.278 Sum_probs=65.0
Q ss_pred CCCCCCchHHHHHHHHHHHHHHHHHcCCC--------cceecCHHHHhhhcCCCCCCCCCCCHHHHHHHHHhcCCCCCCC
Q psy8704 1 MNRAEMSSDEAFGAVEAMSDRVCIASGGK--------KHVRLSSDDLVSCCRLCGFGCNGGFPGMAWRYWVKNGINTYKP 72 (74)
Q Consensus 1 rdQ~~Cgscwafa~~~~~e~~~~i~~~~~--------~~~~lS~q~lidC~~~~~~gC~GG~~~~a~~y~~~~Gi~~e~~ 72 (74)
|||+.||||||||++++||+|++|++++. ....||+|+||||+.. +.||+||++..|++|++++||++|.+
T Consensus 401 kdQG~CGSCWAFAat~alEsR~~Ia~~~~l~~~~~~~~~~~LS~QqLLDCs~~-nqGC~GG~~~~A~kya~~~GI~tEsc 479 (693)
T PTZ00049 401 TNQLLCGSCYIASQMYAFKRRIEIALTKNLDKKYLNNFDDLLSIQTVLSCSFY-DQGCNGGFPYLVSKMAKLQGIPLDKV 479 (693)
T ss_pred CCCccCcHHHHHHHHHHHHHHHHHHhccccccccccccccCcCHHHhcccCCC-CCCcCCCcHHHHHHHHHHCCCCcCCc
Confidence 69999999999999999999999987521 1237999999999863 68999999999999999999999999
Q ss_pred CC
Q psy8704 73 VK 74 (74)
Q Consensus 73 Y~ 74 (74)
||
T Consensus 480 YP 481 (693)
T PTZ00049 480 FP 481 (693)
T ss_pred cC
Confidence 86
No 13
>PF00112 Peptidase_C1: Papain family cysteine protease This is family C1 in the peptidase classification. ; InterPro: IPR000668 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. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of proteins belong to the peptidase family C1, sub-family C1A (papain family, clan CA). It includes proteins classed as non-peptidase homologs. These are have either been shown experimentally to lack peptidase activity or lack one or more of the active site residues. The papain family has a wide variety of activities, including broad-range (papain) and narrow-range endo-peptidases, aminopeptidases, dipeptidyl peptidases and enzymes with both exo- and endo-peptidase activity []. Members of the papain family are widespread, found in baculovirus [], eubacteria, yeast, and practically all protozoa, plants and mammals []. The proteins are typically lysosomal or secreted, and proteolytic cleavage of the propeptide is required for enzyme activation, although bleomycin hydrolase is cytosolic in fungi and mammals []. Papain-like cysteine proteinases are essentially synthesised as inactive proenzymes (zymogens) with N-terminal propeptide regions. The activation process of these enzymes includes the removal of propeptide regions. The propeptide regions serve a variety of functions in vivo and in vitro. The pro-region is required for the proper folding of the newly synthesised enzyme, the inactivation of the peptidase domain and stabilisation of the enzyme against denaturing at neutral to alkaline pH conditions. Amino acid residues within the pro-region mediate their membrane association, and play a role in the transport of the proenzyme to lysosomes. Among the most notable features of propeptides is their ability to inhibit the activity of their cognate enzymes and that certain propeptides exhibit high selectivity for inhibition of the peptidases from which they originate []. The catalytic residues of papain are Cys-25 and His-159, other important residues being Gln-19, which helps form the 'oxyanion hole', and Asn-175, which orientates the imidazole ring of His-159. ; GO: 0008234 cysteine-type peptidase activity, 0006508 proteolysis; PDB: 3MOR_B 3HHI_B 1S4V_A 3F75_A 1MEG_A 1PCI_C 1PPO_A 3HD3_B 1F29_A 1EWL_A ....
Probab=99.89 E-value=2.9e-23 Score=129.96 Aligned_cols=73 Identities=33% Similarity=0.469 Sum_probs=64.6
Q ss_pred CCCCCCchHHHHHHHHHHHHHHHHHcCCCcceecCHHHHhhhcCCCCCCCCCCCHHHHHHHHHh-cCCCCCCCCC
Q psy8704 1 MNRAEMSSDEAFGAVEAMSDRVCIASGGKKHVRLSSDDLVSCCRLCGFGCNGGFPGMAWRYWVK-NGINTYKPVK 74 (74)
Q Consensus 1 rdQ~~Cgscwafa~~~~~e~~~~i~~~~~~~~~lS~q~lidC~~~~~~gC~GG~~~~a~~y~~~-~Gi~~e~~Y~ 74 (74)
|||+.||+|||||+++++|.+++++.. ...+.||+|+|++|....+.+|+||++..+++|+++ +||++|++||
T Consensus 18 ~dQg~~gsCwafa~~~~~e~~~~~~~~-~~~~~lS~q~l~~~~~~~~~~c~gg~~~~a~~~~~~~~Gi~~e~~~p 91 (219)
T PF00112_consen 18 RDQGSCGSCWAFAAAAALESRLAIQNN-GKNVDLSEQYLIDCSNKYNKGCDGGSPFDALKYIKNNNGIVTEEDYP 91 (219)
T ss_dssp -BTTSSBTHHHHHHHHHHHHHHHHHHT-SSCEEB-HHHHHHHSTGTSSTTBBBEHHHHHHHHHHHTSBEBTTTS-
T ss_pred ccCCcccccccchhccceecccccccc-ccccccccccccccccccccccccCcccccceeecccCccccccccc
Confidence 799999999999999999999999984 378999999999998733579999999999999999 8999999985
No 14
>cd02619 Peptidase_C1 C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some exceptions like cathepsins B, C, H and X, which are exopeptidases. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage proteins in seeds while mammalian CPs are primarily lysosomal enzymes responsible for protein degradation in the lysosome. Papain-like CPs are synthesized as inactive proenzymes with N-terminal propeptide regions, which are removed upon activation. Bleomycin hydrolase (BH) is a CP that detoxifies bleomycin by hydrolysis of an amide group. It acts as a carboxypeptidase on its C-terminus to convert itself into an aminopeptidase and peptide ligase. BH is found in all tissues in mammals as well as in many other eukaryotes. It forms a hexameric ring barrel str
Probab=99.88 E-value=2.8e-22 Score=125.60 Aligned_cols=74 Identities=26% Similarity=0.239 Sum_probs=66.0
Q ss_pred CCCCCCchHHHHHHHHHHHHHHHHHcCCCcceecCHHHHhhhcCCC----CCCCCCCCHHHHHH-HHHhcCCCCCCCCC
Q psy8704 1 MNRAEMSSDEAFGAVEAMSDRVCIASGGKKHVRLSSDDLVSCCRLC----GFGCNGGFPGMAWR-YWVKNGINTYKPVK 74 (74)
Q Consensus 1 rdQ~~Cgscwafa~~~~~e~~~~i~~~~~~~~~lS~q~lidC~~~~----~~gC~GG~~~~a~~-y~~~~Gi~~e~~Y~ 74 (74)
|||+.||+|||||+++++|+++.++......+.||+|+|++|.... ..+|.||.+..++. +++.+||++|++||
T Consensus 13 ~dQg~~gsCwafa~~~~les~~~~~~~~~~~~~lS~q~l~~c~~~~~~~~~~~c~gG~~~~~~~~~~~~~Gi~~e~~~P 91 (223)
T cd02619 13 KNQGSRGSCWAFASAYALESAYRIKGGEDEYVDLSPQYLYICANDECLGINGSCDGGGPLSALLKLVALKGIPPEEDYP 91 (223)
T ss_pred ccCCCCcCcHHHHHHHHHHHHHHHhcCCcccccCCHHHHHHhccccccccCCCCCCCcHHHHHHHHHHHcCCCccccCC
Confidence 7999999999999999999999998764456899999999998652 25899999999998 88889999999986
No 15
>PTZ00462 Serine-repeat antigen protein; Provisional
Probab=99.86 E-value=1.1e-21 Score=144.01 Aligned_cols=72 Identities=11% Similarity=0.088 Sum_probs=62.9
Q ss_pred CCCCCCchHHHHHHHHHHHHHHHHHcCCCcceecCHHHHhhhcCC-CCCCCCCCC-HHHHHHHHHhc-CCCCCCCCC
Q psy8704 1 MNRAEMSSDEAFGAVEAMSDRVCIASGGKKHVRLSSDDLVSCCRL-CGFGCNGGF-PGMAWRYWVKN-GINTYKPVK 74 (74)
Q Consensus 1 rdQ~~Cgscwafa~~~~~e~~~~i~~~~~~~~~lS~q~lidC~~~-~~~gC~GG~-~~~a~~y~~~~-Gi~~e~~Y~ 74 (74)
||||.||+|||||++++||++++|+++ ..+.||+|+|+||+.. .+.||.||+ +..++.|++++ ||++|++||
T Consensus 548 KDQG~CGSCWAFASaaaLES~~cIkgg--~~v~LSeQqLVDCs~~~gn~GC~GG~~~~efl~yI~e~GgLptESdYP 622 (1004)
T PTZ00462 548 EDQGNCAISWIFASKYHLETIKCMKGY--EPHAISALYIANCSKGEHKDRCDEGSNPLEFLQIIEDNGFLPADSNYL 622 (1004)
T ss_pred ccCCcchHHHHHHHHHHHHHHHHHhcC--CCcccCHHHHHhcccccCCCCCCCCCcHHHHHHHHHHcCCCcccccCC
Confidence 799999999999999999999999987 6789999999999864 247999997 55566999888 589999986
No 16
>KOG1544|consensus
Probab=99.76 E-value=2.7e-20 Score=124.76 Aligned_cols=73 Identities=32% Similarity=0.458 Sum_probs=69.2
Q ss_pred CCCCCchHHHHHHHHHHHHHHHHHcCCCcceecCHHHHhhhcCCCCCCCCCCCHHHHHHHHHhcCCCCCCCCC
Q psy8704 2 NRAEMSSDEAFGAVEAMSDRVCIASGGKKHVRLSSDDLVSCCRLCGFGCNGGFPGMAWRYWVKNGINTYKPVK 74 (74)
Q Consensus 2 dQ~~Cgscwafa~~~~~e~~~~i~~~~~~~~~lS~q~lidC~~~~~~gC~GG~~~~a~~y~~~~Gi~~e~~Y~ 74 (74)
||++|++.|||+++++..+|++|++.+..+..||+|+||+|+.....||.||.++.||-||++.|++++.+||
T Consensus 228 DQgnCa~SWafSTaavasDRiAI~S~GR~t~~LSpQnLlSC~~h~q~GC~gG~lDRAWWYlRKrGvVsdhCYP 300 (470)
T KOG1544|consen 228 DQGNCAGSWAFSTAAVASDRVAIHSLGRMTPVLSPQNLLSCDTHQQQGCRGGRLDRAWWYLRKRGVVSDHCYP 300 (470)
T ss_pred ccCCcccceeeeeehhccceeEEeeccccccccChHHhcchhhhhhccCccCcccchheeeeccccccccccc
Confidence 8999999999999999999999999988889999999999987655899999999999999999999999996
No 17
>cd00585 Peptidase_C1B Peptidase C1B subfamily (MEROPS database nomenclature); composed of eukaryotic bleomycin hydrolases (BH) and bacterial aminopeptidases C (pepC). The proteins of this subfamily contain a large insert relative to the C1A peptidase (papain) subfamily. BH is a cysteine peptidase that detoxifies bleomycin by hydrolysis of an amide group. It acts as a carboxypeptidase on its C-terminus to convert itself into an aminopeptidase and peptide ligase. BH is found in all tissues in mammals as well as in many other eukaryotes. Bleomycin, a glycopeptide derived from the fungus Streptomyces verticullus, is an effective anticancer drug due to its ability to induce DNA strand breaks. Human BH is the major cause of tumor cell resistance to bleomycin chemotherapy, and is also genetically linked to Alzheimer's disease. In addition to its peptidase activity, the yeast BH (Gal6) binds DNA and acts as a repressor in the Gal4 regulatory system. BH forms a hexameric ring barrel structure w
Probab=98.25 E-value=6e-06 Score=57.85 Aligned_cols=73 Identities=16% Similarity=0.084 Sum_probs=58.5
Q ss_pred CCCCCCchHHHHHHHHHHHHHHHHHcCCCcceecCHHHHhhhcC------------------C---------CCCCCCCC
Q psy8704 1 MNRAEMSSDEAFGAVEAMSDRVCIASGGKKHVRLSSDDLVSCCR------------------L---------CGFGCNGG 53 (74)
Q Consensus 1 rdQ~~Cgscwafa~~~~~e~~~~i~~~~~~~~~lS~q~lidC~~------------------~---------~~~gC~GG 53 (74)
+||+.-|-||.||++.+|+..+..+.+. ..+.||+.++..=+. . ...--+||
T Consensus 58 tnQ~~SGrCW~FA~Ln~lr~~~~k~~~~-~~felSq~Yl~f~dklEkaN~fle~ii~~~~~~~~~R~v~~ll~~~~~DGG 136 (437)
T cd00585 58 TNQKSSGRCWLFAALNVLRHQFMKKLNL-KEFEFSQSYLFFWDKLEKANYFLENIIETADEPLDDRLVQFLLANPQNDGG 136 (437)
T ss_pred ccCCCCchhHHHHCHHHHHHHHHHHcCC-CCEEeCcHHHHHHHHHHHHHHHHHHHHHHhcCCCccHHHHHHHhCCcCCCC
Confidence 5899999999999999999998876553 468999988776111 0 12356899
Q ss_pred CHHHHHHHHHhcCCCCCCCCC
Q psy8704 54 FPGMAWRYWVKNGINTYKPVK 74 (74)
Q Consensus 54 ~~~~a~~y~~~~Gi~~e~~Y~ 74 (74)
.-..+...|++.|+++.+.|+
T Consensus 137 qw~m~~~li~KYGvVPk~~~p 157 (437)
T cd00585 137 QWDMLVNLIEKYGLVPKSVMP 157 (437)
T ss_pred chHHHHHHHHHcCCCcccccC
Confidence 999999999999999998875
No 18
>PF03051 Peptidase_C1_2: Peptidase C1-like family This family is a subfamily of the Prosite entry; InterPro: IPR004134 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. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of proteins belong to MEROPS peptidase family C1, sub-family C1B (bleomycin hydrolase, clan CA). This family contains prokaryotic and eukaryotic aminopeptidases and bleomycin hydrolases.; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis; PDB: 3PW3_F 2CB5_A 1CB5_C 2DZZ_A 2E02_A 2E01_A 2E03_A 1A6R_A 1GCB_A 3GCB_A ....
Probab=97.89 E-value=2e-05 Score=55.32 Aligned_cols=73 Identities=16% Similarity=0.091 Sum_probs=46.4
Q ss_pred CCCCCCchHHHHHHHHHHHHHHHHHcCCCcceecCHHHHh----------------hhcCC-----------CCCCCCCC
Q psy8704 1 MNRAEMSSDEAFGAVEAMSDRVCIASGGKKHVRLSSDDLV----------------SCCRL-----------CGFGCNGG 53 (74)
Q Consensus 1 rdQ~~Cgscwafa~~~~~e~~~~i~~~~~~~~~lS~q~li----------------dC~~~-----------~~~gC~GG 53 (74)
.||..-|-||.||++.+++..+..+.+. ..+.||+.++. +.... ...--+||
T Consensus 59 tnQk~SGRCW~FA~lN~lR~~~~kk~~l-~~felSq~Yl~F~DKlEKaN~fLe~ii~~~~~~~d~R~v~~ll~~~~~DGG 137 (438)
T PF03051_consen 59 TNQKSSGRCWLFAALNVLRHEIMKKLNL-KDFELSQNYLFFWDKLEKANYFLENIIDTADEPLDDRLVRFLLKNPVSDGG 137 (438)
T ss_dssp -B--BSSTHHHHHHHHHHHHHHHHHCT--SS--B-HHHHHHHHHHHHHHHHHHHHHHCCTS-TTSHHHHHHHHSTT-S-B
T ss_pred CCCCCCCCcchhhchHHHHHHHHHHcCC-CceEeechHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHHhcCCCCCC
Confidence 4899999999999999999998887663 46899998865 22110 01246899
Q ss_pred CHHHHHHHHHhcCCCCCCCCC
Q psy8704 54 FPGMAWRYWVKNGINTYKPVK 74 (74)
Q Consensus 54 ~~~~a~~y~~~~Gi~~e~~Y~ 74 (74)
.-+.+..-|++.||++.+.||
T Consensus 138 qw~~~~nli~KYGvVPk~~mp 158 (438)
T PF03051_consen 138 QWDMVVNLIKKYGVVPKSVMP 158 (438)
T ss_dssp -HHHHHHHHHHH---BGGGST
T ss_pred chHHHHHHHHHcCcCcHhhCC
Confidence 999999899989999988875
No 19
>COG4870 Cysteine protease [Posttranslational modification, protein turnover, chaperones]
Probab=97.75 E-value=3.5e-06 Score=57.64 Aligned_cols=26 Identities=15% Similarity=0.104 Sum_probs=23.2
Q ss_pred CCCCCCchHHHHHHHHHHHHHHHHHc
Q psy8704 1 MNRAEMSSDEAFGAVEAMSDRVCIAS 26 (74)
Q Consensus 1 rdQ~~Cgscwafa~~~~~e~~~~i~~ 26 (74)
|||+.||+||||+++.++|+.+....
T Consensus 115 ~dQg~~Gscwaf~t~~sles~l~~~~ 140 (372)
T COG4870 115 KDQGSGGSCWAFATTRSLESYLNPES 140 (372)
T ss_pred cccCcccceEeeeehhhhhheecccc
Confidence 69999999999999999998877654
No 20
>COG3579 PepC Aminopeptidase C [Amino acid transport and metabolism]
Probab=90.22 E-value=1.1 Score=31.36 Aligned_cols=72 Identities=14% Similarity=0.057 Sum_probs=45.8
Q ss_pred CCCCCchHHHHHHHHHHHHHHHHHcCCCcceecCHHHHhhhcC----------------C-----------CCCCCCCCC
Q psy8704 2 NRAEMSSDEAFGAVEAMSDRVCIASGGKKHVRLSSDDLVSCCR----------------L-----------CGFGCNGGF 54 (74)
Q Consensus 2 dQ~~Cgscwafa~~~~~e~~~~i~~~~~~~~~lS~q~lidC~~----------------~-----------~~~gC~GG~ 54 (74)
||..-|-||.||++-.+-..+.-+-+ .+.+.||..++.-=+. . -.--=+||-
T Consensus 62 NQk~SGRCWmFAAlNtfRhk~~~el~-le~fElSQaytfFwDKlEKaN~FleqIi~tadq~ldsRlv~~LL~~PqqDGGQ 140 (444)
T COG3579 62 NQKQSGRCWMFAALNTFRHKLISELK-LEDFELSQAYTFFWDKLEKANWFLEQIIETADQELDSRLVSFLLATPQQDGGQ 140 (444)
T ss_pred cccccceehHHHHHHHHHHHHHHhcC-cceeehhhHHHHHHHHHHHhhHHHHHHHhhcccchHHHHHHHHHcCccccCch
Confidence 78888999999999888544433322 2345666544332221 0 011246787
Q ss_pred HHHHHHHHHhcCCCCCCCCC
Q psy8704 55 PGMAWRYWVKNGINTYKPVK 74 (74)
Q Consensus 55 ~~~a~~y~~~~Gi~~e~~Y~ 74 (74)
-++....+++.|+++.+.|+
T Consensus 141 wdM~v~l~eKYGvVpK~~yp 160 (444)
T COG3579 141 WDMFVSLFEKYGVVPKSVYP 160 (444)
T ss_pred HHHHHHHHHHhCCCchhhcc
Confidence 77777777778999988875
No 21
>KOG4128|consensus
Probab=66.25 E-value=6.4 Score=27.69 Aligned_cols=72 Identities=17% Similarity=-0.048 Sum_probs=46.4
Q ss_pred CCCCCchHHHHHHHHHHHHHHHHHcCCCcceecCHHHHhhhc--------------------CC---------CCCCCCC
Q psy8704 2 NRAEMSSDEAFGAVEAMSDRVCIASGGKKHVRLSSDDLVSCC--------------------RL---------CGFGCNG 52 (74)
Q Consensus 2 dQ~~Cgscwafa~~~~~e~~~~i~~~~~~~~~lS~q~lidC~--------------------~~---------~~~gC~G 52 (74)
||..-|-||.|+.+..+--.+..+.+- ..+.||..+|..=+ +. .+-.=+|
T Consensus 67 nqkssGrcWift~ln~lrl~~~~kLnl-~eFElSqayLFFwdKlErcnyFL~~vvd~a~r~ep~DgRlvq~Ll~nP~~DG 145 (457)
T KOG4128|consen 67 NQKSSGRCWIFTGLNLLRLEMDRKLNL-PEFELSQAYLFFWDKLERCNYFLWTVVDLAMRCEPLDGRLVQNLLKNPVPDG 145 (457)
T ss_pred cCcCCCceEEEechhHHHHHHHhcCCc-chhhhhhHHHHHHHHHHHHHHHHHHHHHHHhhcCCcccHHHHHHHhCCCCCC
Confidence 677889999999999885444444331 13567766654322 10 0123467
Q ss_pred CCHHHHHHHHHhcCCCCCCCCC
Q psy8704 53 GFPGMAWRYWVKNGINTYKPVK 74 (74)
Q Consensus 53 G~~~~a~~y~~~~Gi~~e~~Y~ 74 (74)
|.-..-...+++.|+...++|.
T Consensus 146 Gqw~MfvNlVkKYGviPKkcy~ 167 (457)
T KOG4128|consen 146 GQWQMFVNLVKKYGVIPKKCYL 167 (457)
T ss_pred chHHHHHHHHHHhCCCcHHhcc
Confidence 8777777777778988888874
No 22
>KOG2735|consensus
Probab=63.49 E-value=8.7 Score=27.47 Aligned_cols=22 Identities=27% Similarity=0.306 Sum_probs=19.8
Q ss_pred hHHHHHHHHHHHHHHHHHcCCC
Q psy8704 8 SDEAFGAVEAMSDRVCIASGGK 29 (74)
Q Consensus 8 scwafa~~~~~e~~~~i~~~~~ 29 (74)
-||.|.++.++|..++|+.+..
T Consensus 374 qcWv~~aI~~~El~IciKfg~~ 395 (466)
T KOG2735|consen 374 QCWVFLAICALELLICIKFGSH 395 (466)
T ss_pred hHHHHHHHHHHHhhhheeeCCc
Confidence 3999999999999999998853
No 23
>PF12301 CD99L2: CD99 antigen like protein 2; InterPro: IPR022078 This family of proteins is found in eukaryotes. Proteins in this family are typically between 165 and 237 amino acids in length. CD99L2 and CD99 are involved in trans-endothelial migration of neutrophils in vitro and in the recruitment of neutrophils into inflamed peritoneum.
Probab=53.61 E-value=15 Score=23.02 Aligned_cols=29 Identities=10% Similarity=0.074 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHHHHHHHcCCCcceecCHHHHh
Q psy8704 9 DEAFGAVEAMSDRVCIASGGKKHVRLSSDDLV 40 (74)
Q Consensus 9 cwafa~~~~~e~~~~i~~~~~~~~~lS~q~li 40 (74)
-.+++.++++.+.++.+.. .+.||.|+=+
T Consensus 123 av~valvGAvsSyiaYqkK---KlCF~iq~g~ 151 (169)
T PF12301_consen 123 AVVVALVGAVSSYIAYQKK---KLCFKIQQGL 151 (169)
T ss_pred HHHHHHHHHHHHHHHHHhh---ccceeecccc
Confidence 4678999999999998765 3677776543
No 24
>PF04060 FeS: Putative Fe-S cluster; InterPro: IPR007202 These proteins contain a domain with four conserved cysteines that probably form an Fe-S redox cluster.; GO: 0051536 iron-sulfur cluster binding; PDB: 2YCL_A 4DJF_E 4DJD_C 4DJE_C.
Probab=41.23 E-value=22 Score=16.25 Aligned_cols=7 Identities=29% Similarity=0.411 Sum_probs=4.8
Q ss_pred hHHHHHH
Q psy8704 8 SDEAFGA 14 (74)
Q Consensus 8 scwafa~ 14 (74)
+|-+||.
T Consensus 14 ~C~~fA~ 20 (35)
T PF04060_consen 14 TCRAFAE 20 (35)
T ss_dssp SHHHHHH
T ss_pred cHHHHHH
Confidence 4788864
No 25
>PF12368 DUF3650: Protein of unknown function (DUF3650) ; InterPro: IPR022111 This domain family is found in bacteria, and is approximately 30 amino acids in length. The family is found in association with PF00581 from PFAM. There is a single completely conserved residue N that may be functionally important.
Probab=38.85 E-value=8.3 Score=17.14 Aligned_cols=11 Identities=27% Similarity=0.549 Sum_probs=7.8
Q ss_pred HHHHhcCCCCC
Q psy8704 60 RYWVKNGINTY 70 (74)
Q Consensus 60 ~y~~~~Gi~~e 70 (74)
.|+++|||..|
T Consensus 9 rYV~eh~ls~e 19 (28)
T PF12368_consen 9 RYVKEHGLSEE 19 (28)
T ss_pred hhHHhcCCCHH
Confidence 57888887654
No 26
>PRK15364 pathogenicity island 2 effector protein SseB; Provisional
Probab=37.90 E-value=23 Score=22.70 Aligned_cols=19 Identities=26% Similarity=0.356 Sum_probs=15.5
Q ss_pred CCCCHHHHHHHHHhcCCCC
Q psy8704 51 NGGFPGMAWRYWVKNGINT 69 (74)
Q Consensus 51 ~GG~~~~a~~y~~~~Gi~~ 69 (74)
.+-.|.++++||++|||.-
T Consensus 96 k~~LPddVI~YmrdNgI~V 114 (196)
T PRK15364 96 KEEVPEDVIKYMRDNGILI 114 (196)
T ss_pred cccCCHHHHHHHHHcCcee
Confidence 3457999999999999753
No 27
>PF00648 Peptidase_C2: Calpain family cysteine protease This is family C2 in the peptidase classification. ; InterPro: IPR001300 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. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C2 (calpain family, clan CA). A type example is calpain, which is an intracellular protease involved in many important cellular functions that are regulated by calcium []. The protein is a complex of 2 polypeptide chains (light and heavy), with three known forms in mammals [, ]: a highly calcium-sensitive (i.e., micro-molar range) form known as mu-calpain, mu-CANP or calpain I; a form sensitive to calcium in the milli-molar range, known as m-calpain, m-CANP or calpain II; and a third form, known as p94, which is found in skeletal muscle only []. All forms have identical light but different heavy chains. Both mu- and m-calpain are heterodimers containing an identical 28kDa subunit and an 80kDa subunit that shares 55-65% sequence homology between the two proteases [, ]. The crystallographic structure of m-calpain reveals six "domains" in the 80kDa subunit: A 19-amino acid NH2-terminal sequence; Active site domain IIa; Active site domain IIb. Domain 2 shows low levels of sequence similarity to papain; although the catalytic His has not been located by biochemical means, it is likely that calpain and papain are related []. Domain III; An 18-amino acid extended sequence linking domain III to domain IV; Domain IV, which resembles the penta EF-hand family of polypeptides, binds calcium and regulates activity []. />]. Ca2+-binding causes a rearrangement of the protein backbone, the net effect of which is that a Trp side chain, which acts as a wedge between catalytic domains IIa and IIb in the apo state, moves away from the active site cleft allowing for the proper formation of the catalytic triad []. Calpain-like mRNAs have been identified in other organisms including bacteria, but the molecules encoded by these mRNAs have not been isolated, so little is known about their properties. How calpain activity is regulated in these organisms cells is still unclear In metazoans, the activity of calpain is controlled by a single proteinase inhibitor, calpastatin (IPR001259 from INTERPRO). The calpastatin gene can produce eight or more calpastatin polypeptides ranging from 17 to 85 kDa by use of different promoters and alternative splicing events. The physiological significance of these different calpastatins is unclear, although all bind to three different places on the calpain molecule; binding to at least two of the sites is Ca2+ dependent. The calpains ostensibly participate in a variety of cellular processes including remodelling of cytoskeletal/membrane attachments, different signal transduction pathways, and apoptosis. Deregulated calpain activity following loss of Ca2+ homeostasis results in tissue damage in response to events such as myocardial infarcts, stroke, and brain trauma []. Calpains are a family of cytosolic cysteine proteinases (see PDOC00126 from PROSITEDOC). Members of the calpain family are believed to function in various biological processes, including integrin-mediated cell migration, cytoskeletal remodeling, cell differentiation and apoptosis [, ]. The calpain family includes numerous members from C. elegans to mammals and with homologues in yeast and bacteria. The best characterised members are the m- and mu-calpains, both proteins are heterodimer composed of a large catalytic subunit and a small regulatory subunit. The large subunit comprises four domains (dI-dIV) while the small subunit has two domains (dV-dVI). Domain dI is a short region cleaved by autolysis, dII is the catalytic core, dIII is a C2-like domain, dIV consists of five calcium binding EF-hand motifs []. The crystal structure of calpain has been solved [, ]. The catalytic region consists of two distinct structural domains (dIIa and dIIb). dIIa contains a central helix flanked on three faces by a cluster of alpha-helices and is entirely unrelated to the corresponding domain in the typical thiol proteinases. The fold of dIIb is similar to the corresponding domain in other cysteine proteinases and contains two three-stranded anti-parallel beta-sheets. The catalytic triad residues (C,H,N) are located in dIIa and dIIb. The activation of the domain is dependent on the binding of two calcium atoms in two non EF-hand calcium binding sites located in the catalytic core, one close to the Cys active site in dIIa and one at the end of dIIb. Calcium-binding induced conformational changes in the catalytic domain which align the active site [][]. The profile covers the whole catalytic domain.; GO: 0004198 calcium-dependent cysteine-type endopeptidase activity, 0006508 proteolysis, 0005622 intracellular; PDB: 2NQA_A 1KFU_L 1KFX_L 1QXP_B 2R9C_A 1TL9_A 2G8E_A 1KXR_B 2G8J_A 2NQG_A ....
Probab=33.26 E-value=32 Score=22.67 Aligned_cols=19 Identities=11% Similarity=0.233 Sum_probs=15.1
Q ss_pred CCCCCchHHHHHHHHHHHH
Q psy8704 2 NRAEMSSDEAFGAVEAMSD 20 (74)
Q Consensus 2 dQ~~Cgscwafa~~~~~e~ 20 (74)
.||.=|.||..|+++++..
T Consensus 49 ~QG~lgDc~llaaL~~la~ 67 (298)
T PF00648_consen 49 RQGSLGDCWLLAALAALAE 67 (298)
T ss_dssp BE-SSSSHHHHHHHHHHTT
T ss_pred cccccCChhHHHHHHHHHh
Confidence 3788899999999998873
No 28
>PF08723 Gag_p15: Gag protein p15; InterPro: IPR014834 Gag p15 is a viral membrane-binding matrix protein which is alpha helical in structure. ; PDB: 1HEK_B.
Probab=33.11 E-value=24 Score=20.89 Aligned_cols=15 Identities=20% Similarity=0.144 Sum_probs=11.8
Q ss_pred chH-HHHHHHHHHHHH
Q psy8704 7 SSD-EAFGAVEAMSDR 21 (74)
Q Consensus 7 gsc-wafa~~~~~e~~ 21 (74)
|.| ||.+++.++++.
T Consensus 27 GNC~Walslvdl~hDt 42 (123)
T PF08723_consen 27 GNCNWALSLVDLYHDT 42 (123)
T ss_dssp HHHHHHHHHHHHHTT-
T ss_pred cchHHHHHHHHHHhhc
Confidence 567 999999988876
No 29
>PF12854 PPR_1: PPR repeat
Probab=32.23 E-value=34 Score=15.09 Aligned_cols=15 Identities=20% Similarity=0.463 Sum_probs=12.0
Q ss_pred CCCCCHHHHHHHHHh
Q psy8704 50 CNGGFPGMAWRYWVK 64 (74)
Q Consensus 50 C~GG~~~~a~~y~~~ 64 (74)
|.-|..++|++.+.+
T Consensus 18 Ck~G~~~~A~~l~~~ 32 (34)
T PF12854_consen 18 CKAGRVDEAFELFDE 32 (34)
T ss_pred HHCCCHHHHHHHHHh
Confidence 778889999887754
No 30
>COG4871 Uncharacterized protein conserved in archaea [Function unknown]
Probab=30.68 E-value=35 Score=21.59 Aligned_cols=10 Identities=20% Similarity=0.248 Sum_probs=6.3
Q ss_pred CCCc--hHHHHH
Q psy8704 4 AEMS--SDEAFG 13 (74)
Q Consensus 4 ~~Cg--scwafa 13 (74)
|.|| +|+|||
T Consensus 140 g~CGEqtCmaFA 151 (193)
T COG4871 140 GKCGEQTCMAFA 151 (193)
T ss_pred ccchhHHHHHHH
Confidence 3444 588885
No 31
>cd00044 CysPc Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction.
Probab=28.67 E-value=51 Score=22.07 Aligned_cols=20 Identities=15% Similarity=0.199 Sum_probs=16.7
Q ss_pred CCCCCchHHHHHHHHHHHHH
Q psy8704 2 NRAEMSSDEAFGAVEAMSDR 21 (74)
Q Consensus 2 dQ~~Cgscwafa~~~~~e~~ 21 (74)
.||.=|.||..+++++|..+
T Consensus 70 ~QG~lgDC~~lsaL~~la~~ 89 (315)
T cd00044 70 CQGILGDCWFLAALAALAER 89 (315)
T ss_pred ccCcccchHHHHHHHHHHcC
Confidence 38888999999999988754
No 32
>PF07249 Cerato-platanin: Cerato-platanin; InterPro: IPR010829 Cerato-platanin (CP) is the first member of the cerato-platanin family. It is produced by the Ascomycete Ceratocystis fimbriata f. sp. platani and causes the severe plant disease: canker stain. This protein occurs in the cell wall of the fungus and is involved in the host-plane interaction and induces both cell necrosis and phytoalexin synthesis which is one of the first plant defense-related events. CP, like other fungal surface proteins, is able to self assemble in vitro []. CP is a 120 amino acid protein, containing 40% hydrophobic residues and two S-S bridges. It contains four cysteine residues that form two disulphide bonds []. The N-terminal region of CP is very similar to cerato-ulmin, a phytotoxic protein produced by the Ophiostoma species belonging to the hydrophobin family, which also self-assembles []. This entry also includes other precursor proteins.; PDB: 2KQA_A 3M3G_A.
Probab=27.43 E-value=12 Score=22.13 Aligned_cols=9 Identities=0% Similarity=-0.134 Sum_probs=5.6
Q ss_pred CCCchHHHH
Q psy8704 4 AEMSSDEAF 12 (74)
Q Consensus 4 ~~Cgscwaf 12 (74)
-+||+||-.
T Consensus 57 ~~CGtC~~l 65 (119)
T PF07249_consen 57 PNCGTCWKL 65 (119)
T ss_dssp TTTT-EEEE
T ss_pred CCCCCeEEE
Confidence 468888853
No 33
>smart00230 CysPc Calpain-like thiol protease family. Calpain-like thiol protease family (peptidase family C2). Calcium activated neutral protease (large subunit).
Probab=26.69 E-value=60 Score=21.94 Aligned_cols=20 Identities=10% Similarity=0.104 Sum_probs=16.7
Q ss_pred CCCCCchHHHHHHHHHHHHH
Q psy8704 2 NRAEMSSDEAFGAVEAMSDR 21 (74)
Q Consensus 2 dQ~~Cgscwafa~~~~~e~~ 21 (74)
.||.=|.||..+++++|...
T Consensus 62 ~QG~lgDC~~lsal~~la~~ 81 (318)
T smart00230 62 CQGVLGDCWLLAALASLTLR 81 (318)
T ss_pred cCcccccHHHHHHHHHHHhC
Confidence 48888999999999988753
No 34
>smart00151 SWIB SWI complex, BAF60b domains.
Probab=24.50 E-value=59 Score=17.28 Aligned_cols=15 Identities=13% Similarity=0.461 Sum_probs=11.6
Q ss_pred HHHHHHHhcCCCCCC
Q psy8704 57 MAWRYWVKNGINTYK 71 (74)
Q Consensus 57 ~a~~y~~~~Gi~~e~ 71 (74)
..|+||+.|++....
T Consensus 28 ~lw~YIk~n~L~d~~ 42 (77)
T smart00151 28 RLWEYIKEHNLQDPQ 42 (77)
T ss_pred HHHHHHHHhcccCCc
Confidence 458899999887643
No 35
>PF09641 DUF2026: Protein of unknown function (DUF2026); InterPro: IPR018599 This protein of approx. 100 residues is found in bacteria. It contains up to five alpha helices and up to seven beta strands and is probably monomeric. Its function is unknown. ; PDB: 2HLY_A.
Probab=24.42 E-value=63 Score=20.95 Aligned_cols=18 Identities=22% Similarity=0.211 Sum_probs=11.3
Q ss_pred hHHHHHHHHH--HHHHHHHH
Q psy8704 8 SDEAFGAVEA--MSDRVCIA 25 (74)
Q Consensus 8 scwafa~~~~--~e~~~~i~ 25 (74)
+||.|++.++ |...+.|+
T Consensus 26 Ac~fFs~~Ga~IL~~hYk~~ 45 (204)
T PF09641_consen 26 ACMFFSTFGAFILRDHYKIE 45 (204)
T ss_dssp HHHHHHHHHHHHHHHHH---
T ss_pred HHHHHHHHHHHHHHHHhccc
Confidence 6999999886 44555554
No 36
>KOG0632|consensus
Probab=24.42 E-value=85 Score=21.87 Aligned_cols=32 Identities=16% Similarity=0.469 Sum_probs=20.7
Q ss_pred HHHHHHHHHHHHHcCCCc--ceecCHHHHhhhcC
Q psy8704 13 GAVEAMSDRVCIASGGKK--HVRLSSDDLVSCCR 44 (74)
Q Consensus 13 a~~~~~e~~~~i~~~~~~--~~~lS~q~lidC~~ 44 (74)
++..++=..+.|.-+..+ +.+.-.+.++||+.
T Consensus 58 ~tL~mvLNsL~vDPgr~WKgpWRwydesMLdCC~ 91 (388)
T KOG0632|consen 58 ATLSMVLNSLSVDPGRKWKGPWRWYDESMLDCCE 91 (388)
T ss_pred HHHHHHHHhhccCCcccccCCchhhhhHHHhhcc
Confidence 445555555556555332 47788899999974
No 37
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=23.46 E-value=30 Score=17.64 Aligned_cols=7 Identities=14% Similarity=-0.258 Sum_probs=4.9
Q ss_pred CCchHHH
Q psy8704 5 EMSSDEA 11 (74)
Q Consensus 5 ~Cgscwa 11 (74)
.|.|||-
T Consensus 32 aC~sCW~ 38 (57)
T PF14445_consen 32 ACNSCWQ 38 (57)
T ss_pred hhhhhhh
Confidence 3778885
No 38
>COG4422 Bacteriophage protein gp37 [Function unknown]
Probab=23.18 E-value=81 Score=20.55 Aligned_cols=19 Identities=5% Similarity=-0.076 Sum_probs=16.0
Q ss_pred CCchHHHHHHHHHHHHHHH
Q psy8704 5 EMSSDEAFGAVEAMSDRVC 23 (74)
Q Consensus 5 ~Cgscwafa~~~~~e~~~~ 23 (74)
.|-.|||...+.-||..-.
T Consensus 26 GCtnCYAM~mA~RLeAMg~ 44 (250)
T COG4422 26 GCTNCYAMRMAKRLEAMGV 44 (250)
T ss_pred CcchHHHHHHHHHHHhhCc
Confidence 5889999999999997643
No 39
>PF05543 Peptidase_C47: Staphopain peptidase C47; InterPro: IPR008750 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. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the peptidase family C47 (staphopain family, clan CA). The type example are the staphopains, which are one of four major families of proteinases secreted by the Gram-positive Staphylococcus aureus. These staphylococcal cysteine proteases are secreted as preproenzymes that are proteolytically cleaved to generate the mature enzyme [, , ].; GO: 0008234 cysteine-type peptidase activity, 0006508 proteolysis; PDB: 1X9Y_D 1Y4H_B 1PXV_B 1CV8_A.
Probab=23.10 E-value=1.6e+02 Score=18.69 Aligned_cols=56 Identities=9% Similarity=0.020 Sum_probs=31.1
Q ss_pred CCCCchHHHHHHHHHHHHHHHHHc-C-----CCcceecCHHHHhhhcCCCCCCCCCCCHHHHHHHHHhcCC
Q psy8704 3 RAEMSSDEAFGAVEAMSDRVCIAS-G-----GKKHVRLSSDDLVSCCRLCGFGCNGGFPGMAWRYWVKNGI 67 (74)
Q Consensus 3 Q~~Cgscwafa~~~~~e~~~~i~~-~-----~~~~~~lS~q~lidC~~~~~~gC~GG~~~~a~~y~~~~Gi 67 (74)
|+.=+=|=+|+.+++|...--... . ....+.+|+++|.++.. .+...++|.+..|.
T Consensus 19 Qg~~pWCa~Ya~aailN~~~~~~~~~A~~iMr~~yPn~s~~~l~~~~~---------~~~~~i~y~ks~g~ 80 (175)
T PF05543_consen 19 QGYNPWCAGYAMAAILNATTNTKIYNAKDIMRYLYPNVSEEQLKFTSL---------TPNQMIKYAKSQGR 80 (175)
T ss_dssp -SSSS-HHHHHHHHHHHHHCT-S---HHHHHHHHSTTS-CCCHHH--B----------HHHHHHHHHHTTE
T ss_pred cCcCcHHHHHHHHHHHHhhhCcCcCCHHHHHHHHCCCCCHHHHhhcCC---------CHHHHHHHHHHcCc
Confidence 566566888988888864421100 0 00125788888877753 36788888887764
No 40
>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]
Probab=22.44 E-value=63 Score=22.17 Aligned_cols=29 Identities=17% Similarity=0.211 Sum_probs=20.3
Q ss_pred HhhhcCCCCCCCCCCCHHHHHHHHHhcCCCC
Q psy8704 39 LVSCCRLCGFGCNGGFPGMAWRYWVKNGINT 69 (74)
Q Consensus 39 lidC~~~~~~gC~GG~~~~a~~y~~~~Gi~~ 69 (74)
|+||-.- -.- ..|+.+.|.+|++++|+..
T Consensus 20 MmdCKkA-L~E-~~Gd~EkAie~LR~kG~ak 48 (296)
T COG0264 20 MMDCKKA-LEE-ANGDIEKAIEWLREKGIAK 48 (296)
T ss_pred HHHHHHH-HHH-cCCCHHHHHHHHHHhchHh
Confidence 6777431 011 2678999999999999764
No 41
>CHL00098 tsf elongation factor Ts
Probab=22.33 E-value=68 Score=20.57 Aligned_cols=29 Identities=14% Similarity=0.228 Sum_probs=19.4
Q ss_pred HhhhcCCCCCCCCCCCHHHHHHHHHhcCCCC
Q psy8704 39 LVSCCRLCGFGCNGGFPGMAWRYWVKNGINT 69 (74)
Q Consensus 39 lidC~~~~~~gC~GG~~~~a~~y~~~~Gi~~ 69 (74)
++||-.- .--.+|..+.|.+||+++|+..
T Consensus 16 ~~dck~A--L~e~~gd~~~A~~~Lr~~g~~~ 44 (200)
T CHL00098 16 MMDCKKA--LQEANGDFEKALESLRQKGLAS 44 (200)
T ss_pred HHHHHHH--HHHcCCCHHHHHHHHHHhhhhH
Confidence 5666421 1123468999999999988643
No 42
>PF14502 HTH_41: Helix-turn-helix domain
Probab=21.67 E-value=71 Score=15.91 Aligned_cols=19 Identities=26% Similarity=0.401 Sum_probs=15.8
Q ss_pred CCCCCCHHHHHHHHHhcCC
Q psy8704 49 GCNGGFPGMAWRYWVKNGI 67 (74)
Q Consensus 49 gC~GG~~~~a~~y~~~~Gi 67 (74)
++.-|..-.|++++++.|.
T Consensus 17 ~vs~GtiQ~Alk~Le~~ga 35 (48)
T PF14502_consen 17 GVSRGTIQNALKFLEENGA 35 (48)
T ss_pred CcchhHHHHHHHHHHHCCc
Confidence 5667889999999999864
No 43
>TIGR00116 tsf translation elongation factor Ts. This protein is found in Bacteria, mitochondria, and chloroplasts.
Probab=21.46 E-value=78 Score=21.52 Aligned_cols=18 Identities=22% Similarity=0.154 Sum_probs=15.1
Q ss_pred CCCHHHHHHHHHhcCCCC
Q psy8704 52 GGFPGMAWRYWVKNGINT 69 (74)
Q Consensus 52 GG~~~~a~~y~~~~Gi~~ 69 (74)
+|+.+.|.+||+++|+..
T Consensus 30 ~gDiekAi~~LRkkG~ak 47 (290)
T TIGR00116 30 NGDFEKAIKNLRESGIAK 47 (290)
T ss_pred CCCHHHHHHHHHHhchhH
Confidence 368999999999999653
No 44
>PF02201 SWIB: SWIB/MDM2 domain; InterPro: IPR003121 The SWI/SNF family of complexes, which are conserved from yeast to humans, are ATP-dependent chromatin-remodelling proteins that facilitate transcription activation []. The mammalian complexes are made up of 9-12 proteins called BAFs (BRG1-associated factors). The BAF60 family have at least three members: BAF60a, which is ubiquitous, BAF60b and BAF60c, which are expressed in muscle and pancreatic tissues, respectively. BAF60b is present in alternative forms of the SWI/SNF complex, including complex B (SWIB), which lacks BAF60a. The SWIB domain is a conserved region found within the BAF60b proteins [], and can be found fused to the C terminus of DNA topoisomerase in Chlamydia. MDM2 is an oncoprotein that acts as a cellular inhibitor of the p53 tumour suppressor by binding to the transactivation domain of p53 and suppressing its ability to activate transcription []. p53 acts in response to DNA damage, inducing cell cycle arrest and apoptosis. Inactivation of p53 is a common occurrence in neoplastic transformations. The core of MDM2 folds into an open bundle of four helices, which is capped by two small 3-stranded beta-sheets. It consists of a duplication of two structural repeats. MDM2 has a deep hydrophobic cleft on which the p53 alpha-helix binds; p53 residues involved in transactivation are buried deep within the cleft of MDM2, thereby concealing the p53 transactivation domain. The SWIB and MDM2 domains are homologous and share a common fold.; GO: 0005515 protein binding; PDB: 1V31_A 3FE7_A 3JZQ_B 3EQY_B 2VYR_A 3JZO_A 3DAB_E 3LBJ_E 3FEA_A 3FDO_A ....
Probab=21.21 E-value=85 Score=16.59 Aligned_cols=15 Identities=27% Similarity=0.581 Sum_probs=11.7
Q ss_pred HHHHHHHhcCCCCCC
Q psy8704 57 MAWRYWVKNGINTYK 71 (74)
Q Consensus 57 ~a~~y~~~~Gi~~e~ 71 (74)
.-|+||+++++....
T Consensus 28 ~lw~YIk~~~L~dp~ 42 (76)
T PF02201_consen 28 RLWQYIKENNLQDPK 42 (76)
T ss_dssp HHHHHHHHTTSBESS
T ss_pred HHHHHHHHhcCCCcc
Confidence 468899999887654
No 45
>cd04407 RhoGAP_myosin_IXB RhoGAP_myosin_IXB: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in myosins IXB. Class IX myosins contain a characteristic head domain, a neck domain and a tail domain which contains a C6H2-zinc binding motif and a Rho-GAP domain. Class IX myosins are single-headed, processive myosins that are partly cytoplasmic, and partly associated with membranes and the actin cytoskeleton. Class IX myosins are implicated in the regulation of neuronal morphogenesis and function of sensory systems, like the inner ear. There are two major isoforms, myosin IXA and IXB with several splice variants, which are both expressed in developing neurons Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell prolifer
Probab=21.19 E-value=92 Score=19.34 Aligned_cols=20 Identities=10% Similarity=-0.117 Sum_probs=15.0
Q ss_pred HHHHHHHHHhcCCCCCCCCC
Q psy8704 55 PGMAWRYWVKNGINTYKPVK 74 (74)
Q Consensus 55 ~~~a~~y~~~~Gi~~e~~Y~ 74 (74)
....++|+.++|+.+|+=|+
T Consensus 19 l~~~i~~l~~~gl~~EGIfR 38 (186)
T cd04407 19 LEKLLEHVEMHGLYTEGIYR 38 (186)
T ss_pred HHHHHHHHHHcCCCCCceee
Confidence 45677888888888887664
No 46
>PF03380 DUF282: Caenorhabditis protein of unknown function, DUF282; InterPro: IPR005044 This family consists of proteins of unknown function found in Caenorhabditis species.
Probab=21.10 E-value=28 Score=16.61 Aligned_cols=19 Identities=16% Similarity=0.202 Sum_probs=11.4
Q ss_pred hcCCCCCCCCCCCHHHHHH
Q psy8704 42 CCRLCGFGCNGGFPGMAWR 60 (74)
Q Consensus 42 C~~~~~~gC~GG~~~~a~~ 60 (74)
|.+.++.+|.|-..-.+..
T Consensus 5 C~~iYdt~CqG~g~Ps~~~ 23 (39)
T PF03380_consen 5 CSKIYDTTCQGFGIPSLSD 23 (39)
T ss_pred cccccCCCCccCCCCCccc
Confidence 5556778999844333333
No 47
>PRK09377 tsf elongation factor Ts; Provisional
Probab=21.03 E-value=82 Score=21.41 Aligned_cols=29 Identities=17% Similarity=0.297 Sum_probs=19.7
Q ss_pred HhhhcCCCCCCCCCCCHHHHHHHHHhcCCCC
Q psy8704 39 LVSCCRLCGFGCNGGFPGMAWRYWVKNGINT 69 (74)
Q Consensus 39 lidC~~~~~~gC~GG~~~~a~~y~~~~Gi~~ 69 (74)
++||-.- ---.+|..+.|.+||+++|+..
T Consensus 20 m~dCKkA--L~e~~gD~ekAi~~Lrk~G~ak 48 (290)
T PRK09377 20 MMDCKKA--LTEADGDIEKAIEWLRKKGLAK 48 (290)
T ss_pred HHHHHHH--HHHcCCCHHHHHHHHHHhchhh
Confidence 5677421 1113478999999999999754
No 48
>PRK11713 16S ribosomal RNA methyltransferase RsmE; Provisional
Probab=20.67 E-value=1e+02 Score=19.80 Aligned_cols=19 Identities=26% Similarity=0.454 Sum_probs=16.6
Q ss_pred CCCCCCHHHHHHHHHhcCC
Q psy8704 49 GCNGGFPGMAWRYWVKNGI 67 (74)
Q Consensus 49 gC~GG~~~~a~~y~~~~Gi 67 (74)
|+.||+.+.=.+++++.|+
T Consensus 185 GPEGGfs~~Ei~~l~~~g~ 203 (234)
T PRK11713 185 GPEGGFSPEEIELLREAGF 203 (234)
T ss_pred CCCCCCCHHHHHHHHHCCC
Confidence 9999999988899988774
No 49
>PF11058 Ral: Antirestriction protein Ral ; InterPro: IPR022759 Ral alleviates restriction and enhances modification by the E.coli restriction and modification system [].
Probab=20.60 E-value=1.4e+02 Score=15.30 Aligned_cols=19 Identities=5% Similarity=0.020 Sum_probs=14.2
Q ss_pred HHHHHHHHHHHHHHHHHcC
Q psy8704 9 DEAFGAVEAMSDRVCIASG 27 (74)
Q Consensus 9 cwafa~~~~~e~~~~i~~~ 27 (74)
=||+-++++|...+-.+.+
T Consensus 45 kwairttamiarelgkq~n 63 (66)
T PF11058_consen 45 KWAIRTTAMIARELGKQNN 63 (66)
T ss_pred hHHHHHHHHHHHHHHhhhc
Confidence 4999999998766665544
No 50
>PF00317 Ribonuc_red_lgN: Ribonucleotide reductase, all-alpha domain; InterPro: IPR013509 Ribonucleotide reductase (1.17.4.1 from EC) [, ] catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs divide into three classes on the basis of their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, bacteriophage and viruses, use a diiron-tyrosyl radical, Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in anaerobic bacteria and bacteriophage, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. Ribonucleotide reductase is an oligomeric enzyme composed of a large subunit (700 to 1000 residues) and a small subunit (300 to 400 residues) - class II RNRs are less complex, using the small molecule B12 in place of the small chain []. The reduction of ribonucleotides to deoxyribonucleotides involves the transfer of free radicals, the function of each metallocofactor is to generate an active site thiyl radical. This thiyl radical then initiates the nucleotide reduction process by hydrogen atom abstraction from the ribonucleotide []. The radical-based reaction involves five cysteines: two of these are located at adjacent anti-parallel strands in a new type of ten-stranded alpha/beta-barrel; two others reside at the carboxyl end in a flexible arm; and the fifth, in a loop in the centre of the barrel, is positioned to initiate the radical reaction []. There are several regions of similarity in the sequence of the large chain of prokaryotes, eukaryotes and viruses spread across 3 domains: an N-terminal domain common to the mammalian and bacterial enzymes; a C-terminal domain common to the mammalian and viral ribonucleotide reductases; and a central domain common to all three [].; GO: 0004748 ribonucleoside-diphosphate reductase activity, 0005524 ATP binding, 0006260 DNA replication, 0055114 oxidation-reduction process; PDB: 1PEM_A 2BQ1_E 1PEU_A 1PEQ_A 1PEO_A 1XJN_A 1XJK_A 3O0O_B 1XJF_A 3O0Q_A ....
Probab=20.46 E-value=1e+02 Score=16.46 Aligned_cols=31 Identities=16% Similarity=0.263 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHHHcCCCcceecCHHHHhhhc
Q psy8704 12 FGAVEAMSDRVCIASGGKKHVRLSSDDLVSCC 43 (74)
Q Consensus 12 fa~~~~~e~~~~i~~~~~~~~~lS~q~lidC~ 43 (74)
+.++..+++++.++....+ +.=|+|++..-.
T Consensus 5 ~~a~~~l~~rYl~k~~~g~-~~Etpq~~~~RV 35 (83)
T PF00317_consen 5 YNAAKVLYDRYLLKDEDGK-VIETPQEMFMRV 35 (83)
T ss_dssp HHHHHHHHHHTS-BETTSC-B--SHHHHHHHH
T ss_pred HHHHHHHHHhhCccCCCcC-EeeCHHHHHHHH
Confidence 4567788999998765322 444889887764
No 51
>COG1854 LuxS LuxS protein involved in autoinducer AI2 synthesis [Signal transduction mechanisms]
Probab=20.04 E-value=37 Score=21.18 Aligned_cols=35 Identities=11% Similarity=0.315 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHH--HcCCCcceecCHHHHhhhcCCCCCCCCCCCH
Q psy8704 13 GAVEAMSDRVCI--ASGGKKHVRLSSDDLVSCCRLCGFGCNGGFP 55 (74)
Q Consensus 13 a~~~~~e~~~~i--~~~~~~~~~lS~q~lidC~~~~~~gC~GG~~ 55 (74)
+.+..||..++- ...... . -++||+++ -||+.|+.
T Consensus 51 ~~iHTlEHL~A~~iRnh~~g----~-~~iID~SP---MGCrTGFY 87 (161)
T COG1854 51 AGIHTLEHLLAGFIRNHLNG----N-VEIIDISP---MGCRTGFY 87 (161)
T ss_pred cchhhHHHHHHHHHHhcccC----c-eeEEEecC---cccccceE
Confidence 345677776663 222111 1 45777765 59998864
Done!