Query psy3039
Match_columns 118
No_of_seqs 114 out of 264
Neff 4.6
Searched_HMMs 46136
Date Fri Aug 16 23:55:41 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3039.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3039hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01401 Peptidase_M2: Angiote 100.0 8.1E-55 1.8E-59 381.1 8.1 109 1-109 287-397 (595)
2 KOG3690|consensus 100.0 1.7E-49 3.7E-54 347.2 8.5 109 1-109 309-419 (646)
3 cd06461 M2_ACE Peptidase famil 100.0 3.4E-44 7.3E-49 307.5 9.2 105 1-105 186-291 (477)
4 cd06258 Peptidase_M3_like The 98.7 2.7E-08 5.9E-13 80.9 6.3 68 35-102 113-196 (365)
5 cd06459 M3B_Oligoendopeptidase 98.3 1.7E-06 3.8E-11 70.9 7.0 95 3-101 161-261 (427)
6 cd06460 M32_Taq Peptidase fami 96.6 0.0048 1E-07 52.9 6.1 63 34-99 130-198 (396)
7 TIGR02289 M3_not_pepF oligoend 96.3 0.011 2.4E-07 51.6 6.5 43 48-90 323-366 (549)
8 TIGR00181 pepF oligoendopeptid 94.0 0.14 3E-06 44.8 5.9 50 48-98 364-414 (591)
9 PF01432 Peptidase_M3: Peptida 93.5 0.13 2.7E-06 43.5 4.7 50 48-97 219-278 (458)
10 TIGR02290 M3_fam_3 oligoendope 92.7 0.35 7.6E-06 42.5 6.4 48 49-97 362-409 (587)
11 COG1164 Oligoendopeptidase F [ 92.0 0.29 6.3E-06 43.9 5.1 48 43-90 361-409 (598)
12 cd06456 M3A_DCP_Oligopeptidase 84.6 1.6 3.4E-05 37.4 4.4 32 59-92 205-237 (422)
13 PF02074 Peptidase_M32: Carbox 79.2 4.1 8.8E-05 36.2 5.1 49 47-97 242-296 (494)
14 PF13485 Peptidase_MA_2: Pepti 78.9 2.3 5E-05 28.1 2.8 32 48-79 9-42 (128)
15 cd06455 M3A_TOP Peptidase M3 T 77.9 4 8.6E-05 35.2 4.6 37 60-97 261-299 (472)
16 PF10263 SprT-like: SprT-like 77.7 3.7 8.1E-05 29.5 3.8 51 49-103 42-97 (157)
17 PF14891 Peptidase_M91: Effect 73.3 2.8 6.1E-05 31.5 2.2 22 60-81 101-122 (174)
18 PF06114 DUF955: Domain of unk 68.7 4.9 0.00011 26.3 2.4 23 57-79 37-59 (122)
19 cd06457 M3A_MIP Peptidase M3 m 67.1 4.4 9.5E-05 34.9 2.3 23 58-80 244-266 (458)
20 KOG3820|consensus 64.5 3.4 7.3E-05 36.5 1.1 60 33-107 249-318 (461)
21 PF00413 Peptidase_M10: Matrix 62.6 5.6 0.00012 28.0 1.8 12 62-73 105-116 (154)
22 cd04279 ZnMc_MMP_like_1 Zinc-d 59.3 11 0.00023 27.3 2.8 29 48-76 89-118 (156)
23 COG2856 Predicted Zn peptidase 57.5 11 0.00024 29.9 2.9 33 47-82 58-90 (213)
24 PRK10280 dipeptidyl carboxypep 56.7 8.4 0.00018 35.3 2.3 21 59-79 461-481 (681)
25 PF13582 Reprolysin_3: Metallo 53.8 8.4 0.00018 26.3 1.5 11 63-73 108-118 (124)
26 PF13398 Peptidase_M50B: Pepti 53.4 9.2 0.0002 29.5 1.8 27 60-86 20-46 (200)
27 KOG2090|consensus 52.7 9.9 0.00021 35.3 2.1 22 57-78 474-495 (704)
28 cd04268 ZnMc_MMP_like Zinc-dep 52.3 9.9 0.00021 27.1 1.7 13 61-73 93-105 (165)
29 smart00235 ZnMc Zinc-dependent 50.8 13 0.00029 26.1 2.1 35 36-74 63-98 (140)
30 PRK10911 oligopeptidase A; Pro 50.6 15 0.00032 33.6 2.9 21 59-79 460-480 (680)
31 smart00731 SprT SprT homologue 50.1 12 0.00025 27.3 1.8 44 49-98 41-89 (146)
32 COG0339 Dcp Zn-dependent oligo 49.2 9.9 0.00022 35.4 1.6 21 59-79 464-484 (683)
33 cd04271 ZnMc_ADAM_fungal Zinc- 47.5 6.2 0.00013 31.1 -0.0 12 63-74 146-157 (228)
34 PF13688 Reprolysin_5: Metallo 47.4 15 0.00032 27.2 2.0 15 59-73 139-153 (196)
35 cd04277 ZnMc_serralysin_like Z 47.1 13 0.00028 27.6 1.6 18 59-76 110-127 (186)
36 cd04278 ZnMc_MMP Zinc-dependen 45.8 10 0.00022 27.5 0.9 14 61-74 106-119 (157)
37 cd04270 ZnMc_TACE_like Zinc-de 45.0 13 0.00029 29.4 1.5 10 64-73 169-178 (244)
38 PF13574 Reprolysin_2: Metallo 44.4 17 0.00036 27.2 1.9 12 62-73 111-122 (173)
39 PF05548 Peptidase_M11: Gameto 42.5 13 0.00029 30.9 1.2 67 4-76 96-164 (314)
40 COG4324 Predicted aminopeptida 42.2 18 0.0004 30.9 2.0 31 63-102 198-230 (376)
41 PF13113 DUF3970: Protein of u 42.0 7.1 0.00015 25.8 -0.4 56 50-111 4-59 (60)
42 COG2317 Zn-dependent carboxype 41.7 39 0.00085 30.5 4.0 59 34-97 230-296 (497)
43 KOG2509|consensus 41.6 14 0.00031 32.8 1.3 15 1-15 317-331 (455)
44 COG0501 HtpX Zn-dependent prot 40.5 16 0.00035 28.5 1.4 18 59-76 153-171 (302)
45 PRK03968 DNA primase large sub 40.3 33 0.00071 30.1 3.3 42 47-92 287-328 (399)
46 PF02031 Peptidase_M7: Strepto 40.2 22 0.00047 26.8 1.9 14 61-74 76-89 (132)
47 PHA02456 zinc metallopeptidase 39.6 19 0.00042 27.0 1.5 44 35-86 59-104 (141)
48 cd04267 ZnMc_ADAM_like Zinc-de 38.9 16 0.00034 27.1 1.0 14 60-73 131-144 (192)
49 PRK05457 heat shock protein Ht 38.2 49 0.0011 26.9 3.9 60 3-74 81-146 (284)
50 PLN02853 Probable phenylalanyl 37.9 21 0.00045 32.0 1.8 44 2-53 227-276 (492)
51 PRK04897 heat shock protein Ht 37.4 42 0.00091 27.4 3.4 60 3-74 84-149 (298)
52 PF01435 Peptidase_M48: Peptid 37.2 23 0.00049 26.2 1.7 36 39-74 61-101 (226)
53 cd06163 S2P-M50_PDZ_RseP-like 37.0 29 0.00063 26.6 2.3 17 63-79 10-26 (182)
54 cd00203 ZnMc Zinc-dependent me 36.4 21 0.00045 25.4 1.3 14 60-73 94-107 (167)
55 COG4307 Uncharacterized protei 35.5 24 0.00052 30.1 1.7 41 66-108 175-238 (349)
56 cd05709 S2P-M50 Site-2 proteas 35.1 32 0.0007 25.3 2.2 19 63-81 9-27 (180)
57 cd04327 ZnMc_MMP_like_3 Zinc-d 35.0 27 0.00059 26.4 1.8 16 61-76 91-106 (198)
58 PF10005 DUF2248: Uncharacteri 34.0 48 0.001 28.5 3.3 43 64-108 181-245 (343)
59 PF04450 BSP: Peptidase of pla 33.6 56 0.0012 25.7 3.4 51 46-104 70-131 (205)
60 cd07235 MRD Mitomycin C resist 33.2 26 0.00057 23.0 1.3 16 2-17 11-26 (122)
61 cd04269 ZnMc_adamalysin_II_lik 32.6 27 0.00059 25.9 1.5 14 61-74 130-143 (194)
62 cd04272 ZnMc_salivary_gland_MP 30.5 32 0.0007 26.3 1.6 13 61-73 144-156 (220)
63 PF14247 DUF4344: Domain of un 29.7 54 0.0012 26.2 2.8 63 24-89 30-117 (220)
64 cd08356 Glo_EDI_BRP_like_17 Th 29.6 28 0.0006 23.3 1.0 19 2-20 12-30 (113)
65 PRK03001 M48 family peptidase; 29.5 33 0.00072 27.6 1.5 17 59-75 121-137 (283)
66 cd09012 Glo_EDI_BRP_like_24 Th 29.4 36 0.00077 22.7 1.5 17 2-18 11-27 (124)
67 PRK03072 heat shock protein Ht 29.1 34 0.00074 27.8 1.5 60 3-74 74-139 (288)
68 PF08325 WLM: WLM domain; Int 28.9 29 0.00063 26.9 1.1 13 62-74 82-94 (186)
69 PF13583 Reprolysin_4: Metallo 28.5 31 0.00067 26.6 1.1 13 61-73 136-148 (206)
70 PRK03982 heat shock protein Ht 27.8 35 0.00077 27.5 1.4 15 60-74 123-137 (288)
71 PRK01345 heat shock protein Ht 27.3 38 0.00083 28.0 1.6 60 3-74 71-136 (317)
72 TIGR00054 RIP metalloprotease 27.0 47 0.001 28.3 2.1 15 63-79 15-29 (420)
73 PF13699 DUF4157: Domain of un 26.6 39 0.00085 22.6 1.3 16 59-74 58-73 (79)
74 PF05572 Peptidase_M43: Pregna 26.6 41 0.00088 25.0 1.5 15 58-72 65-79 (154)
75 PF02163 Peptidase_M50: Peptid 24.8 65 0.0014 23.7 2.3 24 63-86 8-31 (192)
76 PF09471 Peptidase_M64: IgA Pe 24.1 43 0.00094 27.3 1.3 14 61-74 215-228 (264)
77 PF12388 Peptidase_M57: Dual-a 23.6 42 0.00092 26.9 1.2 16 63-78 134-149 (211)
78 cd07267 THT_Oxygenase_N N-term 23.4 53 0.0012 21.6 1.5 16 2-17 14-29 (113)
79 PTZ00326 phenylalanyl-tRNA syn 23.2 46 0.001 29.8 1.4 30 3-32 236-271 (494)
80 cd08350 BLMT_like BLMT, a bleo 23.0 55 0.0012 21.7 1.5 16 2-17 13-28 (120)
81 PF01421 Reprolysin: Reprolysi 22.5 58 0.0013 24.3 1.7 10 64-73 133-142 (199)
82 PF13402 M60-like: Peptidase M 22.3 53 0.0011 26.0 1.5 33 66-108 223-256 (307)
83 smart00733 Mterf Mitochondrial 21.9 56 0.0012 16.1 1.1 11 5-15 21-31 (31)
84 PF12725 DUF3810: Protein of u 21.8 53 0.0011 27.3 1.4 12 62-73 196-207 (318)
85 cd04280 ZnMc_astacin_like Zinc 21.2 52 0.0011 24.8 1.2 12 63-74 75-86 (180)
86 PRK09400 secE preprotein trans 21.0 33 0.0007 22.3 0.0 17 52-68 21-37 (61)
87 COG2514 Predicted ring-cleavag 20.8 58 0.0013 27.1 1.4 28 3-32 180-208 (265)
88 PRK10779 zinc metallopeptidase 20.1 79 0.0017 27.1 2.2 10 63-72 16-25 (449)
89 PF01400 Astacin: Astacin (Pep 20.1 64 0.0014 24.5 1.5 13 62-74 79-91 (191)
90 PRK02391 heat shock protein Ht 20.1 64 0.0014 26.5 1.6 60 3-74 80-145 (296)
91 PRK01265 heat shock protein Ht 20.1 64 0.0014 27.2 1.6 15 60-74 138-152 (324)
92 PRK02870 heat shock protein Ht 20.1 60 0.0013 27.4 1.4 61 3-74 119-185 (336)
No 1
>PF01401 Peptidase_M2: Angiotensin-converting enzyme This Prosite motif covers only the active site.; InterPro: IPR001548 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M2 (clan MA(E)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA. The catalytic residues and zinc ligands have been identified, the zinc ion being ligated to two His residues within the motif HEXXH, showing that the enzyme belongs to the E sub-group of metalloproteases []. Pepetidyl-dipeptidase A (angiotensin-converting enzyme) is a mammalian enzyme responsible for cleavage of dipeptides from the C-termini of proteins, notably converting angiotensin I to angiotensin II []. The enzyme exists in two differentially transcribed forms, the most common of which is from lung endothelium; this contains two homologous domains that have arisen by gene duplication []. The testis-specific form contains only the C-terminal domain, arising from a duplicated promoter region present in intron 12 of the gene []. Both enzymatic forms are membrane proteins that are anchored by means of a C-terminal transmembrane domain. Both domains of the endothelial enzyme are active, but have differing kinetic constants []. ]. A number of insect enzymes have been shown to be similar to peptidyl-dipeptidase A, these containing a single catalytic domain.; GO: 0008237 metallopeptidase activity, 0008241 peptidyl-dipeptidase activity, 0006508 proteolysis, 0016020 membrane; PDB: 2YDM_A 3BKL_A 2C6N_B 1UZE_A 3BKK_A 2C6F_B 2IUX_A 2IUL_A 2XYD_B 3NXQ_B ....
Probab=100.00 E-value=8.1e-55 Score=381.08 Aligned_cols=109 Identities=63% Similarity=1.153 Sum_probs=88.4
Q ss_pred ChHHHHHHHHhcCCCCCChHHHhhcccccCCC-CcccccccccccCCCCceeEEecCCCChhhHHHHHHHHHHHHHHHHh
Q psy3039 1 MFRTAEEFFTSINMSAMPPEFWERSMLEKPQG-REVVCHASAWDFHDGKDFRIKMCTRVNEEDLFTIHHEMGHVEYFIQY 79 (118)
Q Consensus 1 mf~~ae~Ff~SLGl~~lp~sFW~~S~~~kp~d-r~~~ChasAwdf~~~~D~RIkmCt~v~~edf~t~hhemGHi~Y~~~Y 79 (118)
||++||+||+||||++||++||++||++||.| |+++|||||||||+++||||||||+|+++||+||||||||||||++|
T Consensus 287 mf~~ae~ff~SlGl~~mp~~FW~~S~~~kp~d~r~~~Chasawdf~~~~d~Rik~Ct~v~~~df~t~hhemghi~Y~~~y 366 (595)
T PF01401_consen 287 MFKTAEEFFTSLGLPPMPPTFWEKSMFEKPTDGRDVVCHASAWDFYNGDDFRIKMCTEVTMEDFLTAHHEMGHIQYYMQY 366 (595)
T ss_dssp HHHHHHHHHHHTTS----HHHHHHSB-S--SSSS----S-EEEEESSSSEEEEE----SSHHHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHhCCCCcCCHHHHHHHHhcCCCCCCCCCcCcchhhccCCCccceeecccCCHHHHHHHHHHHHHHHHHHHH
Confidence 79999999999999999999999999999998 99999999999999999999999999999999999999999999999
Q ss_pred ccCCCcccCCCCchhhhH-HHHHHHhhcCCC
Q psy3039 80 KDQPMAFREGANPGKNTR-GWVAELNSIHKK 109 (118)
Q Consensus 80 ~~qP~~fR~gANpgFhEA-~~~~~l~s~~~~ 109 (118)
++||++||+||||||||| ||+|+|++..++
T Consensus 367 ~~qp~~fr~gan~gfhEAigd~ials~~tp~ 397 (595)
T PF01401_consen 367 KDQPVLFREGANPGFHEAIGDTIALSVSTPK 397 (595)
T ss_dssp TTS-GGGSS-SSHHHHHHHHHHHHHHHTSHH
T ss_pred hhCChhhhcCCCchHHHHHHHHHHHHcCCHH
Confidence 999999999999999999 999999987654
No 2
>KOG3690|consensus
Probab=100.00 E-value=1.7e-49 Score=347.22 Aligned_cols=109 Identities=55% Similarity=1.053 Sum_probs=106.4
Q ss_pred ChHHHHHHHHhcCCCCCChHHHhhcccccCCCCc-ccccccccccCCCCceeEEecCCCChhhHHHHHHHHHHHHHHHHh
Q psy3039 1 MFRTAEEFFTSINMSAMPPEFWERSMLEKPQGRE-VVCHASAWDFHDGKDFRIKMCTRVNEEDLFTIHHEMGHVEYFIQY 79 (118)
Q Consensus 1 mf~~ae~Ff~SLGl~~lp~sFW~~S~~~kp~dr~-~~ChasAwdf~~~~D~RIkmCt~v~~edf~t~hhemGHi~Y~~~Y 79 (118)
||++|++||+||||++||++||++||+++|+|++ ++|||||||||+++||||||||+++++||++|||||||||||+||
T Consensus 309 mF~~a~efF~SlGl~~lp~sfw~~s~~~~p~d~~~v~C~~sAwdf~~~~Dfrik~Ct~vd~~~f~~~Hhem~hiQY~l~y 388 (646)
T KOG3690|consen 309 MFKLAAEFFTSLGLPALPPSFWTNSILTRPDDRDMVVCHASAWDFYAGPDFRIKYCTKVDEEDFEQAHHEMGHIQYYLQY 388 (646)
T ss_pred HHHHHHHHHHHcCCCcCChHHHhHHHhcCCCCCCceeechhhhccccCCCceeeecCcCCHHHHHHHHHHHHHHHHHHHH
Confidence 7999999999999999999999999999999966 899999999999999999999999999999999999999999999
Q ss_pred ccCCCcccCCCCchhhhH-HHHHHHhhcCCC
Q psy3039 80 KDQPMAFREGANPGKNTR-GWVAELNSIHKK 109 (118)
Q Consensus 80 ~~qP~~fR~gANpgFhEA-~~~~~l~s~~~~ 109 (118)
++||++||+||||||||| ||+++|+|.++|
T Consensus 389 ~~qP~llre~anPgFheAIgd~~als~stPr 419 (646)
T KOG3690|consen 389 KQQPFLLREGANPGFHEAIGDAFALSVSTPR 419 (646)
T ss_pred HhccHHhhCCCCCcHHHHHHHHHHHhcCCHH
Confidence 999999999999999999 999999998876
No 3
>cd06461 M2_ACE Peptidase family M2 Angiotensin converting enzyme (ACE, EC 3.4.15.1) is a membrane-bound, zinc dependent dipeptidase that catalyzes the conversion of the decapeptide angiotensin I to the potent vasopressor ocatapeptide angiotensin II, by removing two C-terminal amino acids. There are two forms of the enzyme in humans, the ubiquitous somatic ACE and the sperm-specific germinal ACE, both encoded by the same gene through transcription from alternative promoters. Somatic ACE has two tandem active sites with distinct catalytic properties, whereas germinal ACE, the function of which is largely unknown, has just a single active site. Recently, an ACE homolog, ACE2, has been identified in humans that differs from ACE; it preferentially removes carboxy-terminal hydrophobic or basic amino acids and appears to be important in cardiac function. ACE homologs (also known as members of the M2 gluzincin family) have been found in a wide variety of species, including those that neither h
Probab=100.00 E-value=3.4e-44 Score=307.53 Aligned_cols=105 Identities=67% Similarity=1.220 Sum_probs=102.2
Q ss_pred ChHHHHHHHHhcCCCCCChHHHhhcccccCCCCcccccccccccCCCCceeEEecCCCChhhHHHHHHHHHHHHHHHHhc
Q psy3039 1 MFRTAEEFFTSINMSAMPPEFWERSMLEKPQGREVVCHASAWDFHDGKDFRIKMCTRVNEEDLFTIHHEMGHVEYFIQYK 80 (118)
Q Consensus 1 mf~~ae~Ff~SLGl~~lp~sFW~~S~~~kp~dr~~~ChasAwdf~~~~D~RIkmCt~v~~edf~t~hhemGHi~Y~~~Y~ 80 (118)
||+++++||+||||.+||++||++||++||.++++.||+|||||++.+|+|||||+++|++||.|+|||||||+||++|+
T Consensus 186 mf~~~~~ff~smgL~dl~~~fw~~s~~~rp~k~~~~C~~sawd~~~~~d~rI~~c~~~t~~D~~t~~HE~GH~~yy~~y~ 265 (477)
T cd06461 186 MFKEAEEFFTSLGLPPMPPSFWTKSMLEKPTDREVVCHASAWDFYNGKDFRIKMCTKVNMEDFVTVHHEMGHIQYYLQYK 265 (477)
T ss_pred HHHHHHHHHHHCCCCcCChHHHhhccccCCCCCCCccCcccccCCCCCCcceeeCCCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCcccCCCCchhhhH-HHHHHHhh
Q psy3039 81 DQPMAFREGANPGKNTR-GWVAELNS 105 (118)
Q Consensus 81 ~qP~~fR~gANpgFhEA-~~~~~l~s 105 (118)
+||++||.||||||||| +|+++++.
T Consensus 266 ~~p~~~r~~anp~fheav~e~~smS~ 291 (477)
T cd06461 266 DQPVLFREGANPGFHEAVGDAIALSV 291 (477)
T ss_pred cCCHHHhCCCCCChHHHHHHHHHHhc
Confidence 99999999999999999 88888665
No 4
>cd06258 Peptidase_M3_like The peptidase M3-like family, also called neurolysin-like family, is part of the "zincins" metallopeptidases, and includes M3, M2 and M32 families of metallopeptidases. The M3 family is subdivided into two subfamilies: the widespread M3A, which comprises a number of high-molecular mass endo- and exopeptidases from bacteria, archaea, protozoa, fungi, plants and animals, and the small M3B, whose members are enzymes primarily from bacteria. Well-known mammalian/eukaryotic M3A endopeptidases are the thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (alias endopeptidase 3.4.24.16), and the mitochondrial intermediate peptidase. The first two are intracellular oligopeptidases, which act only on relatively short substrates of less than 20 amino acid residues, while the latter cleaves N-terminal octapeptides from proteins during their import into the mitochondria. The M3A subfamily also contains several bacterial endopeptidases, collectively called olig
Probab=98.71 E-value=2.7e-08 Score=80.89 Aligned_cols=68 Identities=21% Similarity=0.207 Sum_probs=58.8
Q ss_pred ccccccccccC-----CCCceeEEecCCC---------ChhhHHHHHHHHHHHHHHHHhccCCCc-ccCCCCchhhhH-H
Q psy3039 35 VVCHASAWDFH-----DGKDFRIKMCTRV---------NEEDLFTIHHEMGHVEYFIQYKDQPMA-FREGANPGKNTR-G 98 (118)
Q Consensus 35 ~~ChasAwdf~-----~~~D~RIkmCt~v---------~~edf~t~hhemGHi~Y~~~Y~~qP~~-fR~gANpgFhEA-~ 98 (118)
..|||..|.+. ..+|+||.+|... +.+|+.|++||+||..|.+..+.++.. .+.+.+.+|+|+ .
T Consensus 113 K~~~a~~~~~~~~~~~~~~~~~i~~n~~~~~~~~~~ll~~~~v~tl~HE~GHa~h~~l~~~~~~~~~g~~~~~~~~E~~S 192 (365)
T cd06258 113 KYPHGFCTGLDPGFNRQDKDVRILANFTSPAAPDPVLLGHDDINTLFHEFGHAVHFLLIQQRYPFQERTPTSTDFAEAQS 192 (365)
T ss_pred CCCCCeeccccCCCCCCCCeEEEEccCCCCCCCCCCcCCHHHHHHHHHHHhHHHHHHHhcCCCCcCCCCCCCccHHhccH
Confidence 67899888887 3689999999877 999999999999999999999887654 788899999999 4
Q ss_pred HHHH
Q psy3039 99 WVAE 102 (118)
Q Consensus 99 ~~~~ 102 (118)
-+..
T Consensus 193 ~~~E 196 (365)
T cd06258 193 MFLE 196 (365)
T ss_pred HHHH
Confidence 4444
No 5
>cd06459 M3B_Oligoendopeptidase_F Peptidase family M3B Oligopeptidase F (PepF; Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and includes oligoendopeptidase F from Lactococcus lactis. This enzyme hydrolyzes peptides containing between 7 and 17 amino acids with fairly broad specificity. The PepF gene is duplicated in L. lactis on the plasmid that bears it, while a shortened second copy is found in Bacillus subtilis. Most bacterial PepFs are cytoplasmic endopeptidases; however, the PepF Bacillus amyloliquefaciens oligopeptidase is a secreted protein and may facilitate the process of sporulation. Specifically, the yjbG gene encoding the homolog of the PepF1 and PepF2 oligoendopeptidases of Lactococcus lactis has been identified in Bacillus subtilis as an inhibitor of sporulation initiation when over expressed from a multicopy plasmid.
Probab=98.32 E-value=1.7e-06 Score=70.87 Aligned_cols=95 Identities=18% Similarity=0.200 Sum_probs=60.7
Q ss_pred HHHHHHHHhcC--CCCCChHHHhhc---ccccCCCCcccccccccccCCCCceeEEecCCCChhhHHHHHHHHHH-HHHH
Q psy3039 3 RTAEEFFTSIN--MSAMPPEFWERS---MLEKPQGREVVCHASAWDFHDGKDFRIKMCTRVNEEDLFTIHHEMGH-VEYF 76 (118)
Q Consensus 3 ~~ae~Ff~SLG--l~~lp~sFW~~S---~~~kp~dr~~~ChasAwdf~~~~D~RIkmCt~v~~edf~t~hhemGH-i~Y~ 76 (118)
+.+.+.|.++| +..+-..+|++. +..+|..+.. |-.+.+....+.||.|+-..+.+|+.|++||+|| +|++
T Consensus 161 ~~v~~~~~~l~~~~~~~~~~~~~~~~iD~~~r~gK~~g---af~~~~~~~~~p~i~~n~~~~~~~v~tl~HE~GHa~h~~ 237 (427)
T cd06459 161 ELVLEALSPLGPEYAEFAKRAFEERWIDVEPRKGKRSG---AYCTGLPPGKHPFILMNFNGTLDDVFTLAHELGHAFHSY 237 (427)
T ss_pred HHHHHHHHccCHHHHHHHHHHhhCCCeeccCCCCCCCC---eecCCCCCCCCCeEEecCCCChhhHHHHHHHhhHHHHHH
Confidence 34555666665 222222333433 3445544432 3334455457899999999999999999999999 5666
Q ss_pred HHhccCCCcccCCCCchhhhHHHHH
Q psy3039 77 IQYKDQPMAFREGANPGKNTRGWVA 101 (118)
Q Consensus 77 ~~Y~~qP~~fR~gANpgFhEA~~~~ 101 (118)
+.-..||++.+ +..-.|+|+..+.
T Consensus 238 ~~~~~~~~~~~-~~~~~~~E~~S~~ 261 (427)
T cd06459 238 LSRDNQPYLYS-DYPIFLAEIASTF 261 (427)
T ss_pred HHccCCCcccC-CCCchhhHHHHHH
Confidence 66667776666 4566799984443
No 6
>cd06460 M32_Taq Peptidase family M32 is a subclass of metallocarboxypeptidases which are distributed mainly in bacteria and archaea, and contain a HEXXH motif that coordinates a divalent cation such as Zn2+ or Co2+, so far only observed in the active site of neutral metallopeptidases but not in carboxypeptidases. M32 includes the thermostable carboxypeptidases (E.C. 3.4.17.19) from Thermus aquaticus (TaqCP) and Pyrococcus furiosus (PfuCP), which have broad specificities toward a wide range of C-terminal substrates that include basic, aromatic, neutral and polar amino acids. These enzymes have a similar fold to the M3 peptidases such as neurolysin and the M2 angiotensin converting enzyme (ACE). Novel peptidases from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, are the first eukaryotic M32 enzymes identified so far, thus making these enzymes an attractive potential target for drug development against these o
Probab=96.64 E-value=0.0048 Score=52.93 Aligned_cols=63 Identities=27% Similarity=0.348 Sum_probs=47.5
Q ss_pred cccccccccccCCCCceeEEecCCCC--hhhHHHHHHHHHHHHHHHHh----ccCCCcccCCCCchhhhHHH
Q psy3039 34 EVVCHASAWDFHDGKDFRIKMCTRVN--EEDLFTIHHEMGHVEYFIQY----KDQPMAFREGANPGKNTRGW 99 (118)
Q Consensus 34 ~~~ChasAwdf~~~~D~RIkmCt~v~--~edf~t~hhemGHi~Y~~~Y----~~qP~~fR~gANpgFhEA~~ 99 (118)
++..||-...+. +.|+||.+=-.-+ ..+++++-||+||..|.+.+ +.||+. .++.-|+||+-+
T Consensus 130 D~s~hpF~~~~~-~~dvRItt~y~~~d~~~~l~t~iHE~GHalye~~l~~~~~~~pl~--~~~sm~ihESqS 198 (396)
T cd06460 130 DVSAHPFTGGLG-PGDVRITTRYDENDFRSALFSTIHETGHALYEQGLPPELRGTPLG--GGASMGIHESQS 198 (396)
T ss_pred ecCCCCCCCCCC-CCCceEEeeeCCcchHHHHHHHHHHhhHHHHHhcCCHhHccCCcc--cCCCchhHHHHH
Confidence 455577545555 5699997766555 77889999999999999965 677774 667889999933
No 7
>TIGR02289 M3_not_pepF oligoendopeptidase, M3 family. This family consists of probable oligoendopeptidases in the M3 family, related to lactococcal PepF and group B streptococcal PepB (TIGR00181) but in a distinct clade with considerable sequence differences. The likely substrate is small peptides and not whole proteins, as with PepF, but members are not characterized and the activity profile may differ. Several bacteria have both a member of this family and a member of the PepF family.
Probab=96.31 E-value=0.011 Score=51.56 Aligned_cols=43 Identities=23% Similarity=0.135 Sum_probs=32.3
Q ss_pred CceeEEecCCCChhhHHHHHHHHHHHH-HHHHhccCCCcccCCC
Q psy3039 48 KDFRIKMCTRVNEEDLFTIHHEMGHVE-YFIQYKDQPMAFREGA 90 (118)
Q Consensus 48 ~D~RIkmCt~v~~edf~t~hhemGHi~-Y~~~Y~~qP~~fR~gA 90 (118)
..-+|-|--..+.+|..|+.||+||.. +|+....+|..+|..+
T Consensus 323 ~~P~I~~Nf~~t~~dv~TL~HElGHa~H~~~s~~~~~~~~~~~~ 366 (549)
T TIGR02289 323 KAPFIFSNFNGTSGDIDVLTHEAGHAFHVYESRKDLLPEYRWPT 366 (549)
T ss_pred CCcEEEEeCCCChhHHHHHHHHhhHHHHHHHhcCCcccccccCc
Confidence 345887776889999999999999985 4455555677777543
No 8
>TIGR00181 pepF oligoendopeptidase F. This family represents the oligoendopeptidase F clade of the family of larger M3 or thimet (for thiol-dependent metallopeptidase) oligopeptidase family. Lactococcus lactis PepF hydrolyzed peptides of 7 and 17 amino acids with fairly broad specificity. The homolog of lactococcal PepF in group B Streptococcus was named PepB (PubMed:8757883), with the name difference reflecting a difference in species of origin rather activity; substrate profiles were quite similar. Differences in substrate specificity should be expected in other species. The gene is duplicated in Lactococcus lactis on the plasmid that bears it. A shortened second copy is found in Bacillus subtilis.
Probab=93.98 E-value=0.14 Score=44.80 Aligned_cols=50 Identities=22% Similarity=0.129 Sum_probs=35.9
Q ss_pred CceeEEecCCCChhhHHHHHHHHHHHHHH-HHhccCCCcccCCCCchhhhHH
Q psy3039 48 KDFRIKMCTRVNEEDLFTIHHEMGHVEYF-IQYKDQPMAFREGANPGKNTRG 98 (118)
Q Consensus 48 ~D~RIkmCt~v~~edf~t~hhemGHi~Y~-~~Y~~qP~~fR~gANpgFhEA~ 98 (118)
..-+|-|-=..+.+|..|+.|||||.... +..++||.+..+ .---|.|+.
T Consensus 364 ~~p~il~N~~~~~~dv~TLaHElGHa~H~~~~~~~~~~~~~~-~~~~~aE~a 414 (591)
T TIGR00181 364 VKPYILMNWDGTLNSVFTLAHELGHSMHSYFSSKHQPYPNSD-YSIFYAEIA 414 (591)
T ss_pred CCCeEEEecCCCcchHHHHHHHhhhHHHHHHHccCCCCccCC-CCchhhhHh
Confidence 45678776677999999999999997644 455789977652 333466663
No 9
>PF01432 Peptidase_M3: Peptidase family M3 This Prosite motif covers only the active site. This family belongs to family M3 of the peptidase classification.; InterPro: IPR001567 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M3 (clan MA(E)), subfamilies M3A and M3B. The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA. The Thimet oligopeptidase family, is a large family of archaeal, bacterial and eukaryotic oligopeptidases that cleave medium sized peptides. The group contains: mitochondrial intermediate peptidase (3.4.24.59 from EC) Neurolysin, mitochondrial precursor, (3.4.24.16 from EC) Thimet oligopeptidase (3.4.24.15 from EC) Dipeptidyl carboxypeptidase (3.4.15.5 from EC) Oligopeptidase A (3.4.24.70 from EC) Oligoendopeptidase F ; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 2QR4_B 3CE2_A 1Y79_1 2H1J_A 2H1N_A 2O36_A 1S4B_P 2O3E_A 1I1I_P.
Probab=93.50 E-value=0.13 Score=43.46 Aligned_cols=50 Identities=14% Similarity=-0.012 Sum_probs=33.1
Q ss_pred CceeEEecCCC---------ChhhHHHHHHHHHHHHHHHHhccC-CCcccCCCCchhhhH
Q psy3039 48 KDFRIKMCTRV---------NEEDLFTIHHEMGHVEYFIQYKDQ-PMAFREGANPGKNTR 97 (118)
Q Consensus 48 ~D~RIkmCt~v---------~~edf~t~hhemGHi~Y~~~Y~~q-P~~fR~gANpgFhEA 97 (118)
+..+|-+.-.. +.+|+.|+.||+||....+.-+.. |.+-..+.---|-|.
T Consensus 219 ~~~~i~~n~~~~~~~~~~ll~~~~v~tLfHE~GHa~H~~ls~~~~~~~sg~~~~~d~aE~ 278 (458)
T PF01432_consen 219 PVPYIFCNFTGPSAGKPSLLSHDDVETLFHEFGHAMHSLLSRTKYQHLSGTRVPMDFAEF 278 (458)
T ss_dssp EEEEEEEEE-S-BTTC--B-SHHHHHHHHHHHHHHHHHHHCCCSSGGGSTTSS-CHHCHH
T ss_pred CceEEEecCCCCCCCCCCccChhhHHHHHHHHhHHHHHHHhccccccccCCchhHHHHhc
Confidence 56788888777 999999999999997666655543 333333333345554
No 10
>TIGR02290 M3_fam_3 oligoendopeptidase, pepF/M3 family. The M3 family of metallopeptidases contains several distinct clades. Oligoendopeptidase F as characterized in Lactococcus, the functionally equivalent oligoendopeptidase B of group B Streptococcus, and closely related sequences are described by TIGR00181. The present family is quite similar but forms a distinct clade, and a number of species have one member of each. A greater sequence difference separates members of TIGR02289, probable oligoendopeptidases of the M3 family that probably should not be designated PepF.
Probab=92.74 E-value=0.35 Score=42.51 Aligned_cols=48 Identities=25% Similarity=0.207 Sum_probs=35.2
Q ss_pred ceeEEecCCCChhhHHHHHHHHHHHHHHHHhccCCCcccCCCCchhhhH
Q psy3039 49 DFRIKMCTRVNEEDLFTIHHEMGHVEYFIQYKDQPMAFREGANPGKNTR 97 (118)
Q Consensus 49 D~RIkmCt~v~~edf~t~hhemGHi~Y~~~Y~~qP~~fR~gANpgFhEA 97 (118)
.-+|-|=-..+..|..|+.||+||..++..-++||.+... .--.|.|.
T Consensus 362 ~p~i~~N~~~~~~~v~TL~HE~GHa~H~~ls~~~~~~~~~-~~~~~aE~ 409 (587)
T TIGR02290 362 EPRVLMNYDGSRRDVSTLAHELGHAYHSELAKDQPLLNAR-YPMTLAET 409 (587)
T ss_pred CCEEEEecCCCchhHHHHHHHhhHHHHHHHHccCCcccCC-CCchhhhH
Confidence 3566554466899999999999998877655789876653 44557776
No 11
>COG1164 Oligoendopeptidase F [Amino acid transport and metabolism]
Probab=92.02 E-value=0.29 Score=43.90 Aligned_cols=48 Identities=29% Similarity=0.378 Sum_probs=40.3
Q ss_pred ccCCCCceeEEecCCCChhhHHHHHHHHHHHHHH-HHhccCCCcccCCC
Q psy3039 43 DFHDGKDFRIKMCTRVNEEDLFTIHHEMGHVEYF-IQYKDQPMAFREGA 90 (118)
Q Consensus 43 df~~~~D~RIkmCt~v~~edf~t~hhemGHi~Y~-~~Y~~qP~~fR~gA 90 (118)
.++.+..-+|-|==.-++.|..|+-||+||.... ...+.||+++++.+
T Consensus 361 ~~~~~~~p~IlmN~~gt~~dV~TLaHElGHs~Hs~~s~~~qp~~~~~~~ 409 (598)
T COG1164 361 GFYKGDHPFILMNYDGTLRDVFTLAHELGHSVHSYFSRKHQPYLYADYS 409 (598)
T ss_pred CCCCCCCCeEEEeCCCchhHHHHHHHHccHHHHHHHHhccCCccccCCc
Confidence 3555578899999999999999999999997665 77788998887765
No 12
>cd06456 M3A_DCP_Oligopeptidase_A Peptidase family M3 dipeptidyl carboxypeptidase (DCP; Dcp II; peptidyl dipeptidase; EC 3.4.15.5). This metal-binding M3A family also includes oligopeptidase A (OpdA; EC 3.4.24.70) enzyme. DCP cleaves dipeptides off the C-termini of various peptides and proteins, the smallest substrate being N-blocked tripeptides and unblocked tetrapeptides. DCP from E. coli is inhibited by the anti-hypertensive drug captopril, an inhibitor of the mammalian angiotensin converting enzyme (ACE, also called peptidyl dipeptidase A). Oligopeptidase A (OpdA) may play a specific role in the degradation of signal peptides after they are released from precursor forms of secreted proteins. It can also cleave N-acetyl-L-Ala.
Probab=84.60 E-value=1.6 Score=37.40 Aligned_cols=32 Identities=25% Similarity=0.445 Sum_probs=22.6
Q ss_pred ChhhHHHHHHHHHHHHHHH-HhccCCCcccCCCCc
Q psy3039 59 NEEDLFTIHHEMGHVEYFI-QYKDQPMAFREGANP 92 (118)
Q Consensus 59 ~~edf~t~hhemGHi~Y~~-~Y~~qP~~fR~gANp 92 (118)
+.+|+.|+.||+||..-.+ .-.++|.+ .|.+.
T Consensus 205 ~~~~v~tLfHEfGHalH~~ls~~~~~~l--~~~~~ 237 (422)
T cd06456 205 THDEVTTLFHEFGHALHHLLTDVEYPSL--GGTNV 237 (422)
T ss_pred CHHHHHHHHHHHHHHHHHHHhcCCcccc--CCCcC
Confidence 8999999999999976544 43455544 44443
No 13
>PF02074 Peptidase_M32: Carboxypeptidase Taq (M32) metallopeptidase; InterPro: IPR001333 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M32 (carboxypeptidase Taq family, clan MA(E)). The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH. Carboxypeptidase Taq is a zinc-containing thermostable metallopeptidase. It was originally discovered and purified from Thermus aquaticus; optimal enzymatic activity occurs at 80 celcius. Although very little is known about this enzyme, it is thought either to be associated with a membrane or to be particle bound.; GO: 0004181 metallocarboxypeptidase activity, 0006508 proteolysis; PDB: 1K9X_A 1KA4_A 1KA2_A 3DWC_A 1WGZ_A 3HQ2_A 3HOA_B.
Probab=79.18 E-value=4.1 Score=36.18 Aligned_cols=49 Identities=31% Similarity=0.438 Sum_probs=33.8
Q ss_pred CCceeEEecCCCC--hhhHHHHHHHHHHHHHHHH----hccCCCcccCCCCchhhhH
Q psy3039 47 GKDFRIKMCTRVN--EEDLFTIHHEMGHVEYFIQ----YKDQPMAFREGANPGKNTR 97 (118)
Q Consensus 47 ~~D~RIkmCt~v~--~edf~t~hhemGHi~Y~~~----Y~~qP~~fR~gANpgFhEA 97 (118)
.+|+||..=-.-+ ..-++.+-||.||.-|-+. |..+|+ -.|+.-|+||+
T Consensus 242 ~~DvRiTTry~e~d~~~~l~s~iHE~GHalYEq~~~~~~~~tpl--~~~~smgiHES 296 (494)
T PF02074_consen 242 PNDVRITTRYDEDDFLSALFSTIHETGHALYEQGLPPEYYGTPL--GEGVSMGIHES 296 (494)
T ss_dssp TTEEEEEE--BTTBTHHHHHHHHHHHHHHHHHHTS-GGGTTSTT--SS-S-HHHHHH
T ss_pred CCceeeecccccccHHHHHHHHHHHHHHHHHHcCCChhHccCcc--ccccccchHHH
Confidence 5899997543222 4456788899999999875 445654 58888899998
No 14
>PF13485 Peptidase_MA_2: Peptidase MA superfamily
Probab=78.87 E-value=2.3 Score=28.13 Aligned_cols=32 Identities=19% Similarity=0.076 Sum_probs=19.3
Q ss_pred CceeEEecCCC-Chhh-HHHHHHHHHHHHHHHHh
Q psy3039 48 KDFRIKMCTRV-NEED-LFTIHHEMGHVEYFIQY 79 (118)
Q Consensus 48 ~D~RIkmCt~v-~~ed-f~t~hhemGHi~Y~~~Y 79 (118)
..-+|...... +.+. ..++-||++|..-....
T Consensus 9 ~~~~i~~~~~~~~~~~~~~~l~HE~~H~~~~~~~ 42 (128)
T PF13485_consen 9 GFNRIVVYFQGSDEDWLDRVLAHELAHQWFGNYF 42 (128)
T ss_pred CCCEEEEecCCCCHHHHHHHHHHHHHHHHHHHHc
Confidence 33455555443 3443 38899999998544443
No 15
>cd06455 M3A_TOP Peptidase M3 Thimet oligopeptidase (TOP; PZ-peptidase; endo-oligopeptidase A; endopeptidase 24.15; soluble metallo-endopeptidase; EC 3.4.24.15) family also includes neurolysin (endopeptidase 24.16, microsomal endopeptidase, mitochondrial oligopeptidase M, neurotensin endopeptidase, soluble angiotensin II-binding protein, thimet oligopeptidase II) which hydrolyzes oligopeptides such as neurotensin, bradykinin and dynorphin A. TOP and neurolysin are neuropeptidases expressed abundantly in the testis, but also found in the liver, lung and kidney. They are involved in the metabolism of neuropeptides under 20 amino acid residues long and cleave most bioactive peptides at the same sites, but recognize different positions on some naturally occurring and synthetic peptides; they cleave at distinct sites on the 13-residue bioactive peptide neurotensin, which modulates central dopaminergic and cholinergic circuits. TOP has been shown to degrade peptides released by the proteasom
Probab=77.94 E-value=4 Score=35.18 Aligned_cols=37 Identities=22% Similarity=0.204 Sum_probs=23.9
Q ss_pred hhhHHHHHHHHHHHHHHHHhccCCCcccCCCCch--hhhH
Q psy3039 60 EEDLFTIHHEMGHVEYFIQYKDQPMAFREGANPG--KNTR 97 (118)
Q Consensus 60 ~edf~t~hhemGHi~Y~~~Y~~qP~~fR~gANpg--FhEA 97 (118)
.+|..|+.||+||..-.+.-+... .-..|.+.. |.|.
T Consensus 261 ~~~V~TLfHEfGHalH~~ls~~~~-~~~sg~~~~~d~aE~ 299 (472)
T cd06455 261 HDEVETFFHEFGHVIHHLLGRTKY-ARFSGTRVERDFVEA 299 (472)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCc-cccCCCcCChhhhhc
Confidence 699999999999987655433332 223455544 6665
No 16
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=77.68 E-value=3.7 Score=29.48 Aligned_cols=51 Identities=20% Similarity=0.214 Sum_probs=35.2
Q ss_pred ceeEEecCCC-----ChhhHHHHHHHHHHHHHHHHhccCCCcccCCCCchhhhHHHHHHH
Q psy3039 49 DFRIKMCTRV-----NEEDLFTIHHEMGHVEYFIQYKDQPMAFREGANPGKNTRGWVAEL 103 (118)
Q Consensus 49 D~RIkmCt~v-----~~edf~t~hhemGHi~Y~~~Y~~qP~~fR~gANpgFhEA~~~~~l 103 (118)
...|..-..+ .++-..|+-|||.|..-|+.+ .--+.+-++.|.+...-+..
T Consensus 42 ~~~I~ls~~~~~~~~~~~~~~tL~HEm~H~~~~~~~----~~~~~~Hg~~fk~~~~~ig~ 97 (157)
T PF10263_consen 42 PCEIRLSPKLLDRNPEEELIDTLLHEMAHAAAYVFG----GGRRRGHGKEFKQWARRIGA 97 (157)
T ss_pred ceEEEECHHHHHhhHHHHHHHHHHHHHHHHHhhhcc----CCCCCCCCHHHHHHHHHHCC
Confidence 4456555433 245567999999998888887 33567788899998444444
No 17
>PF14891 Peptidase_M91: Effector protein
Probab=73.30 E-value=2.8 Score=31.52 Aligned_cols=22 Identities=14% Similarity=0.181 Sum_probs=17.9
Q ss_pred hhhHHHHHHHHHHHHHHHHhcc
Q psy3039 60 EEDLFTIHHEMGHVEYFIQYKD 81 (118)
Q Consensus 60 ~edf~t~hhemGHi~Y~~~Y~~ 81 (118)
.+-+..+.|||+|.+.+++=.-
T Consensus 101 ~~p~v~L~HEL~HA~~~~~Gt~ 122 (174)
T PF14891_consen 101 RPPFVVLYHELIHAYDYMNGTM 122 (174)
T ss_pred HHHHHHHHHHHHHHHHHHCCCC
Confidence 4558999999999999986443
No 18
>PF06114 DUF955: Domain of unknown function (DUF955); InterPro: IPR010359 This is a family of bacterial and viral proteins with undetermined function. A conserved H-E-X-X-H motif is suggestive of a catalytic active site and shows similarity to IPR001915 from INTERPRO.; PDB: 3DTE_A 3DTK_A 3DTI_A.
Probab=68.67 E-value=4.9 Score=26.29 Aligned_cols=23 Identities=30% Similarity=0.426 Sum_probs=16.3
Q ss_pred CCChhhHHHHHHHHHHHHHHHHh
Q psy3039 57 RVNEEDLFTIHHEMGHVEYFIQY 79 (118)
Q Consensus 57 ~v~~edf~t~hhemGHi~Y~~~Y 79 (118)
....+.-+++-||+||+.+-...
T Consensus 37 ~~~~~~~f~laHELgH~~~~~~~ 59 (122)
T PF06114_consen 37 LSPERQRFTLAHELGHILLHHGD 59 (122)
T ss_dssp S-HHHHHHHHHHHHHHHHHHH-H
T ss_pred CCHHHHHHHHHHHHHHHHhhhcc
Confidence 44577788999999997655443
No 19
>cd06457 M3A_MIP Peptidase M3 mitochondrial intermediate peptidase (MIP; EC 3.4.24.59) belongs to the widespread subfamily M3A, that show similarity to the Thimet oligopeptidase (TOP). It is one of three peptidases responsible for the proteolytic processing of both, nuclear and mitochondrial encoded precursor polypeptides targeted to the various subcompartments of the mitochondria. It cleaves intermediate-size proteins initially processed by mitochondrial processing peptidase (MPP) to yield a processing intermediate with a typical N-terminal octapeptide that is sequentially cleaved by MIP to mature-size protein. MIP cleaves precursor proteins of respiratory components, including subunits of the electron transport chain and tri-carboxylic acid cycle enzymes, and components of the mitochondrial genetic machinery, including ribosomal proteins, translation factors, and proteins required for mitochondrial DNA metabolism. It has been suggested that the human MIP (HMIP polypeptide; gene symbo
Probab=67.05 E-value=4.4 Score=34.88 Aligned_cols=23 Identities=26% Similarity=0.401 Sum_probs=19.2
Q ss_pred CChhhHHHHHHHHHHHHHHHHhc
Q psy3039 58 VNEEDLFTIHHEMGHVEYFIQYK 80 (118)
Q Consensus 58 v~~edf~t~hhemGHi~Y~~~Y~ 80 (118)
.+-+|..|+.||+||.--.+.-+
T Consensus 244 L~~~~v~TLfHEfGHalH~~ls~ 266 (458)
T cd06457 244 LSPHEVETLFHEMGHAMHSMLGR 266 (458)
T ss_pred cCHHHHHHHHHHHhHHHHHHHcC
Confidence 46789999999999988766654
No 20
>KOG3820|consensus
Probab=64.51 E-value=3.4 Score=36.54 Aligned_cols=60 Identities=37% Similarity=0.474 Sum_probs=46.6
Q ss_pred CcccccccccccCCCCceeEEecCCC----------ChhhHHHHHHHHHHHHHHHHhccCCCcccCCCCchhhhHHHHHH
Q psy3039 33 REVVCHASAWDFHDGKDFRIKMCTRV----------NEEDLFTIHHEMGHVEYFIQYKDQPMAFREGANPGKNTRGWVAE 102 (118)
Q Consensus 33 r~~~ChasAwdf~~~~D~RIkmCt~v----------~~edf~t~hhemGHi~Y~~~Y~~qP~~fR~gANpgFhEA~~~~~ 102 (118)
|.+-=-=||=||-.+--||+-.||+- .+.| ++|..||| -|++ |+|.|..=..-|+
T Consensus 249 RPvAGlLSaRDFLagLAFRVFhcTQYiRH~s~P~yTPEPD--~cHELLGH---------vPLf----ADp~FAQFSQEIG 313 (461)
T KOG3820|consen 249 RPVAGLLSARDFLAGLAFRVFHCTQYIRHHSSPFYTPEPD--TCHELLGH---------VPLF----ADPSFAQFSQEIG 313 (461)
T ss_pred ecccccCcHHHHHhhhhhhheeeeeeeecCCCCCCCCCCc--hHHHHhcc---------chhc----cChhHHHHhHHhh
Confidence 44544558999999999999999963 2444 68999999 4654 8899987777889
Q ss_pred HhhcC
Q psy3039 103 LNSIH 107 (118)
Q Consensus 103 l~s~~ 107 (118)
|+|+-
T Consensus 314 LASLG 318 (461)
T KOG3820|consen 314 LASLG 318 (461)
T ss_pred hhhcC
Confidence 99873
No 21
>PF00413 Peptidase_M10: Matrixin This Prosite motif covers only the active site.; InterPro: IPR001818 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M10 (clan MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA. Sequences having this domain are extracellular metalloproteases, such as collagenase and stromelysin, which degrade the extracellular matrix, are known as matrixins. They are zinc-dependent, calcium-activated proteases synthesised as inactive precursors (zymogens), which are proteolytically cleaved to yield the active enzyme [, ]. All matrixins and related proteins possess 2 domains: an N-terminal domain, and a zinc-binding active site domain. The N-terminal domain peptide, cleaved during the activation step, includes a conserved PRCGVPDV octapeptide, known as the cysteine switch, whose Cys residue chelates the active site zinc atom, rendering the enzyme inactive [, ]. The active enzyme degrades components of the extracellular matrix, playing a role in the initial steps of tissue remodelling during morphogenesis, wound healing, angiogenesis and tumour invasion [, ].; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis, 0031012 extracellular matrix; PDB: 1Q3A_C 3V96_B 1HV5_D 1CXV_A 1SRP_A 1FBL_A 1ZVX_A 1JH1_A 1I76_A 2OY4_A ....
Probab=62.64 E-value=5.6 Score=28.03 Aligned_cols=12 Identities=33% Similarity=0.374 Sum_probs=10.1
Q ss_pred hHHHHHHHHHHH
Q psy3039 62 DLFTIHHEMGHV 73 (118)
Q Consensus 62 df~t~hhemGHi 73 (118)
-..++-||+||+
T Consensus 105 ~~~v~~HEiGHa 116 (154)
T PF00413_consen 105 LQSVAIHEIGHA 116 (154)
T ss_dssp HHHHHHHHHHHH
T ss_pred hhhhhhhccccc
Confidence 347899999996
No 22
>cd04279 ZnMc_MMP_like_1 Zinc-dependent metalloprotease; MMP_like sub-family 1. A group of bacterial, archaeal, and fungal metalloproteinase domains similar to matrix metalloproteinases and astacin.
Probab=59.32 E-value=11 Score=27.27 Aligned_cols=29 Identities=21% Similarity=0.161 Sum_probs=16.9
Q ss_pred CceeEEecCCC-ChhhHHHHHHHHHHHHHH
Q psy3039 48 KDFRIKMCTRV-NEEDLFTIHHEMGHVEYF 76 (118)
Q Consensus 48 ~D~RIkmCt~v-~~edf~t~hhemGHi~Y~ 76 (118)
.++..-.|..- ..+-+.++-||+||+-=.
T Consensus 89 ~~~~~~~~~~~~~~~~~~~~~HEiGHaLGL 118 (156)
T cd04279 89 TDINLGPGQPRGAENLQAIALHELGHALGL 118 (156)
T ss_pred ceEeecCCcCccchHHHHHHHHHhhhhhcC
Confidence 34444445432 233457789999997433
No 23
>COG2856 Predicted Zn peptidase [Amino acid transport and metabolism]
Probab=57.46 E-value=11 Score=29.94 Aligned_cols=33 Identities=24% Similarity=0.318 Sum_probs=25.4
Q ss_pred CCceeEEecCCCChhhHHHHHHHHHHHHHHHHhccC
Q psy3039 47 GKDFRIKMCTRVNEEDLFTIHHEMGHVEYFIQYKDQ 82 (118)
Q Consensus 47 ~~D~RIkmCt~v~~edf~t~hhemGHi~Y~~~Y~~q 82 (118)
.+++-|-.|. ....+.+|+-||+|| +.+.=..+
T Consensus 58 ~~~I~iN~n~-~~~r~rFtlAHELGH--~llH~~~~ 90 (213)
T COG2856 58 KPVIYINANN-SLERKRFTLAHELGH--ALLHTDLN 90 (213)
T ss_pred CceEEEeCCC-CHHHHHHHHHHHHhH--HHhccccc
Confidence 3577788887 778899999999999 55554443
No 24
>PRK10280 dipeptidyl carboxypeptidase II; Provisional
Probab=56.72 E-value=8.4 Score=35.30 Aligned_cols=21 Identities=29% Similarity=0.314 Sum_probs=17.4
Q ss_pred ChhhHHHHHHHHHHHHHHHHh
Q psy3039 59 NEEDLFTIHHEMGHVEYFIQY 79 (118)
Q Consensus 59 ~~edf~t~hhemGHi~Y~~~Y 79 (118)
+-++..|++||+||.---|--
T Consensus 461 ~~~eV~TlFHEfGHalH~lls 481 (681)
T PRK10280 461 LWDDVITLFHEFGHTLHGLFA 481 (681)
T ss_pred CHHHHHHHHHHHHHHHHHHHh
Confidence 678999999999998775544
No 25
>PF13582 Reprolysin_3: Metallo-peptidase family M12B Reprolysin-like; PDB: 3P24_C.
Probab=53.85 E-value=8.4 Score=26.31 Aligned_cols=11 Identities=45% Similarity=0.682 Sum_probs=9.6
Q ss_pred HHHHHHHHHHH
Q psy3039 63 LFTIHHEMGHV 73 (118)
Q Consensus 63 f~t~hhemGHi 73 (118)
-.++-||+||.
T Consensus 108 ~~~~~HEiGH~ 118 (124)
T PF13582_consen 108 VDTFAHEIGHN 118 (124)
T ss_dssp TTHHHHHHHHH
T ss_pred ceEeeehhhHh
Confidence 38999999996
No 26
>PF13398 Peptidase_M50B: Peptidase M50B-like
Probab=53.42 E-value=9.2 Score=29.45 Aligned_cols=27 Identities=22% Similarity=0.175 Sum_probs=19.2
Q ss_pred hhhHHHHHHHHHHHHHHHHhccCCCcc
Q psy3039 60 EEDLFTIHHEMGHVEYFIQYKDQPMAF 86 (118)
Q Consensus 60 ~edf~t~hhemGHi~Y~~~Y~~qP~~f 86 (118)
..-+.|+.||+||.---+..-.+..-+
T Consensus 20 ~~~l~t~~HE~gHal~a~l~G~~v~~i 46 (200)
T PF13398_consen 20 FRLLVTFVHELGHALAALLTGGRVKGI 46 (200)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCcceE
Confidence 345779999999987776665554433
No 27
>KOG2090|consensus
Probab=52.65 E-value=9.9 Score=35.32 Aligned_cols=22 Identities=27% Similarity=0.353 Sum_probs=17.6
Q ss_pred CCChhhHHHHHHHHHHHHHHHH
Q psy3039 57 RVNEEDLFTIHHEMGHVEYFIQ 78 (118)
Q Consensus 57 ~v~~edf~t~hhemGHi~Y~~~ 78 (118)
.++.-+.-|++|||||..-=|+
T Consensus 474 ~L~~~~vetLFHEmGHAMHSmL 495 (704)
T KOG2090|consen 474 FLSLSEVETLFHEMGHAMHSML 495 (704)
T ss_pred ccCHHHHHHHHHHHHHHHHHHh
Confidence 4577889999999999866554
No 28
>cd04268 ZnMc_MMP_like Zinc-dependent metalloprotease, MMP_like subfamily. This group contains matrix metalloproteinases (MMPs), serralysins, and the astacin_like family of proteases.
Probab=52.32 E-value=9.9 Score=27.13 Aligned_cols=13 Identities=38% Similarity=0.470 Sum_probs=11.4
Q ss_pred hhHHHHHHHHHHH
Q psy3039 61 EDLFTIHHEMGHV 73 (118)
Q Consensus 61 edf~t~hhemGHi 73 (118)
.-+.|+-||+||.
T Consensus 93 ~~~~~~~HEiGHa 105 (165)
T cd04268 93 RLRNTAEHELGHA 105 (165)
T ss_pred HHHHHHHHHHHHH
Confidence 5689999999996
No 29
>smart00235 ZnMc Zinc-dependent metalloprotease. Neutral zinc metallopeptidases. This alignment represents a subset of known subfamilies. Highest similarity occurs in the HExxH zinc-binding site/ active site.
Probab=50.82 E-value=13 Score=26.07 Aligned_cols=35 Identities=23% Similarity=0.212 Sum_probs=20.0
Q ss_pred ccc-ccccccCCCCceeEEecCCCChhhHHHHHHHHHHHH
Q psy3039 36 VCH-ASAWDFHDGKDFRIKMCTRVNEEDLFTIHHEMGHVE 74 (118)
Q Consensus 36 ~Ch-asAwdf~~~~D~RIkmCt~v~~edf~t~hhemGHi~ 74 (118)
-|. +.++-. +.+.+|... .....+.++-||+||+-
T Consensus 63 g~~~a~~g~~--~g~~~~~~~--~~~~~~~~~~HEigHaL 98 (140)
T smart00235 63 GCTLSHAGRP--GGDQHFSLG--NGCINTGVAAHELGHAL 98 (140)
T ss_pred CcceeeeecC--CCceEEEcc--CCcCCcccHHHHHHHHh
Confidence 453 444332 455666552 22234569999999973
No 30
>PRK10911 oligopeptidase A; Provisional
Probab=50.57 E-value=15 Score=33.60 Aligned_cols=21 Identities=24% Similarity=0.457 Sum_probs=16.9
Q ss_pred ChhhHHHHHHHHHHHHHHHHh
Q psy3039 59 NEEDLFTIHHEMGHVEYFIQY 79 (118)
Q Consensus 59 ~~edf~t~hhemGHi~Y~~~Y 79 (118)
+-+|..|++||+||.-.-+.-
T Consensus 460 ~~~~v~tlfHEfGHalH~~ls 480 (680)
T PRK10911 460 THDEVITLFHEFGHGLHHMLT 480 (680)
T ss_pred CHHHHHHHHHHHhHHHHHHHh
Confidence 459999999999998765533
No 31
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=50.14 E-value=12 Score=27.33 Aligned_cols=44 Identities=16% Similarity=0.335 Sum_probs=28.5
Q ss_pred ceeEEecCCC----ChhhHH-HHHHHHHHHHHHHHhccCCCcccCCCCchhhhHH
Q psy3039 49 DFRIKMCTRV----NEEDLF-TIHHEMGHVEYFIQYKDQPMAFREGANPGKNTRG 98 (118)
Q Consensus 49 D~RIkmCt~v----~~edf~-t~hhemGHi~Y~~~Y~~qP~~fR~gANpgFhEA~ 98 (118)
+-.|..-+.+ ..+++. |+-|||.|...++. +. .. +=.|.|.+..
T Consensus 41 ~~~I~ln~~l~~~~~~~~l~~~l~HEm~H~~~~~~--g~--~~--~Hg~~f~~~~ 89 (146)
T smart00731 41 SAEIRLNPKLLTENGRDRLRETLLHELCHAALYLF--GR--GY--GHGDEWKRWM 89 (146)
T ss_pred CCEEEeCHHHHhhccHHHHHhhHHHHHHHHHHHHh--CC--CC--CcCHHHHHHH
Confidence 4455555544 335555 99999999988874 32 11 5558898883
No 32
>COG0339 Dcp Zn-dependent oligopeptidases [Amino acid transport and metabolism]
Probab=49.25 E-value=9.9 Score=35.35 Aligned_cols=21 Identities=24% Similarity=0.417 Sum_probs=17.1
Q ss_pred ChhhHHHHHHHHHHHHHHHHh
Q psy3039 59 NEEDLFTIHHEMGHVEYFIQY 79 (118)
Q Consensus 59 ~~edf~t~hhemGHi~Y~~~Y 79 (118)
+.+|..|++|||||.--=|.-
T Consensus 464 s~dEV~TLFHEfGHgLH~mlt 484 (683)
T COG0339 464 SHDEVTTLFHEFGHGLHHLLT 484 (683)
T ss_pred eHHHHHHHHHHhhhHHHHHhh
Confidence 688999999999997665543
No 33
>cd04271 ZnMc_ADAM_fungal Zinc-dependent metalloprotease, ADAM_fungal subgroup. The adamalysin_like or ADAM (A Disintegrin And Metalloprotease) family of metalloproteases are integral membrane proteases acting on a variety of extracellular targets. They are involved in shedding soluble peptides or proteins from the cell surface. This subfamily contains fungal ADAMs, whose precise function has yet to be determined.
Probab=47.53 E-value=6.2 Score=31.13 Aligned_cols=12 Identities=33% Similarity=0.493 Sum_probs=9.7
Q ss_pred HHHHHHHHHHHH
Q psy3039 63 LFTIHHEMGHVE 74 (118)
Q Consensus 63 f~t~hhemGHi~ 74 (118)
..|+-|||||+-
T Consensus 146 ~~t~AHElGHnL 157 (228)
T cd04271 146 WQVFAHEIGHTF 157 (228)
T ss_pred ceehhhhhhhhc
Confidence 358999999963
No 34
>PF13688 Reprolysin_5: Metallo-peptidase family M12; PDB: 2FV5_B 3EWJ_A 3KME_A 3L0T_B 1BKC_E 3G42_D 2I47_D 2FV9_B 3LEA_A 1ZXC_B ....
Probab=47.41 E-value=15 Score=27.22 Aligned_cols=15 Identities=33% Similarity=0.530 Sum_probs=13.1
Q ss_pred ChhhHHHHHHHHHHH
Q psy3039 59 NEEDLFTIHHEMGHV 73 (118)
Q Consensus 59 ~~edf~t~hhemGHi 73 (118)
+.....++-||+||.
T Consensus 139 ~~~~~~~~AHEiGH~ 153 (196)
T PF13688_consen 139 TYNGAITFAHEIGHN 153 (196)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred CCceehhhHHhHHHh
Confidence 577889999999995
No 35
>cd04277 ZnMc_serralysin_like Zinc-dependent metalloprotease, serralysin_like subfamily. Serralysins and related proteases are important virulence factors in pathogenic bacteria. They may be secreted into the medium via a mechanism found in gram-negative bacteria, that does not require n-terminal signal sequences which are cleaved after the transmembrane translocation. A calcium-binding domain c-terminal to the metalloprotease domain, which contains multiple tandem repeats of a nine-residue motif including the pattern GGxGxD, and which forms a parallel beta roll may be involved in the translocation mechanism and/or substrate binding. Serralysin family members may have a broad spectrum of substrates each, including host immunoglobulins, complement proteins, cell matrix and cytoskeletal proteins, as well as antimicrobial peptides.
Probab=47.11 E-value=13 Score=27.63 Aligned_cols=18 Identities=33% Similarity=0.366 Sum_probs=14.4
Q ss_pred ChhhHHHHHHHHHHHHHH
Q psy3039 59 NEEDLFTIHHEMGHVEYF 76 (118)
Q Consensus 59 ~~edf~t~hhemGHi~Y~ 76 (118)
....+.|+-||+||.--.
T Consensus 110 g~~~~~t~~HEiGHaLGL 127 (186)
T cd04277 110 GSYGYQTIIHEIGHALGL 127 (186)
T ss_pred ChhhHHHHHHHHHHHhcC
Confidence 356789999999998654
No 36
>cd04278 ZnMc_MMP Zinc-dependent metalloprotease, matrix metalloproteinase (MMP) sub-family. MMPs are responsible for a great deal of pericellular proteolysis of extracellular matrix and cell surface molecules, playing crucial roles in morphogenesis, cell fate specification, cell migration, tissue repair, tumorigenesis, gain or loss of tissue-specific functions, and apoptosis. In many instances, they are anchored to cell membranes via trans-membrane domains, and their activity is controlled via TIMPs (tissue inhibitors of metalloproteinases).
Probab=45.85 E-value=10 Score=27.47 Aligned_cols=14 Identities=29% Similarity=0.437 Sum_probs=11.3
Q ss_pred hhHHHHHHHHHHHH
Q psy3039 61 EDLFTIHHEMGHVE 74 (118)
Q Consensus 61 edf~t~hhemGHi~ 74 (118)
.-+.++-||+||.-
T Consensus 106 ~~~~~~~HEiGHaL 119 (157)
T cd04278 106 DLFSVAAHEIGHAL 119 (157)
T ss_pred hHHHHHHHHhcccc
Confidence 45779999999973
No 37
>cd04270 ZnMc_TACE_like Zinc-dependent metalloprotease; TACE_like subfamily. TACE, the tumor-necrosis factor-alpha converting enzyme, releases soluble TNF-alpha from transmembrane pro-TNF-alpha.
Probab=44.98 E-value=13 Score=29.39 Aligned_cols=10 Identities=40% Similarity=0.780 Sum_probs=9.1
Q ss_pred HHHHHHHHHH
Q psy3039 64 FTIHHEMGHV 73 (118)
Q Consensus 64 ~t~hhemGHi 73 (118)
.|+-|||||.
T Consensus 169 ~t~AHElGHn 178 (244)
T cd04270 169 LVTAHELGHN 178 (244)
T ss_pred HHHHHHHHHh
Confidence 7899999995
No 38
>PF13574 Reprolysin_2: Metallo-peptidase family M12B Reprolysin-like; PDB: 1KAP_P 1JIW_P 1AKL_A 1OM7_A 1OM8_A 1O0T_A 1OM6_A 1H71_P 1O0Q_A 1OMJ_A ....
Probab=44.37 E-value=17 Score=27.22 Aligned_cols=12 Identities=42% Similarity=0.684 Sum_probs=10.3
Q ss_pred hHHHHHHHHHHH
Q psy3039 62 DLFTIHHEMGHV 73 (118)
Q Consensus 62 df~t~hhemGHi 73 (118)
+..++-|||||.
T Consensus 111 ~~~~~aHElGH~ 122 (173)
T PF13574_consen 111 GIDTFAHELGHQ 122 (173)
T ss_dssp HHHHHHHHHHHH
T ss_pred eeeeehhhhHhh
Confidence 567899999994
No 39
>PF05548 Peptidase_M11: Gametolysin peptidase M11; InterPro: IPR008752 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M11 (gametolysin family, clan MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA and the predicted active site residues for members of this family and thermolysin occur in the motif HEXXH []. The type example is gametolysin from the unicellular biflagellated alga, Chlamydomonas reinhardtii Gametolysin is a zinc-containing metallo-protease, which is responsible for the degradation of the cell wall. Homologues of gametolysin have also been reported in the simple multicellular organism, Volvox [, ].
Probab=42.50 E-value=13 Score=30.91 Aligned_cols=67 Identities=19% Similarity=0.254 Sum_probs=33.3
Q ss_pred HHHHHHHhc-CCCCCChHHHhhcccccCCCCccccccc-ccccCCCCceeEEecCCCChhhHHHHHHHHHHHHHH
Q psy3039 4 TAEEFFTSI-NMSAMPPEFWERSMLEKPQGREVVCHAS-AWDFHDGKDFRIKMCTRVNEEDLFTIHHEMGHVEYF 76 (118)
Q Consensus 4 ~ae~Ff~SL-Gl~~lp~sFW~~S~~~kp~dr~~~Chas-Awdf~~~~D~RIkmCt~v~~edf~t~hhemGHi~Y~ 76 (118)
.|+..=+.+ |...+ +..++-++.-|.+ ..|-=. --.+. +...++ .+......++.++.|||||.+.-
T Consensus 96 ~Ad~~a~~~lG~~~~--s~y~h~vyvlP~~--~~C~w~Gla~v~-G~~~~~-~~~~~~~~~~~~~~HElgHN~GL 164 (314)
T PF05548_consen 96 AADAAARAQLGVNAF--SSYTHRVYVLPPG--FACGWAGLATVP-GSQSWL-WISGYGVQDWATIMHELGHNLGL 164 (314)
T ss_pred HHHHHHHhhcCcccc--cccceEEEEcCCC--CCCCceEEeecC-Ccceee-eecCcccccHHHHHHHhhhhccc
Confidence 455555555 66544 2234445545543 226211 11222 222222 23333456788999999998763
No 40
>COG4324 Predicted aminopeptidase [General function prediction only]
Probab=42.16 E-value=18 Score=30.89 Aligned_cols=31 Identities=23% Similarity=0.149 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHHHHhccCCCcccCC--CCchhhhHHHHHH
Q psy3039 63 LFTIHHEMGHVEYFIQYKDQPMAFREG--ANPGKNTRGWVAE 102 (118)
Q Consensus 63 f~t~hhemGHi~Y~~~Y~~qP~~fR~g--ANpgFhEA~~~~~ 102 (118)
-..|+|||+| |-+..++. =|..|..|+++++
T Consensus 198 A~LIFHELAH---------Qk~Y~~~DtAFNEsFAtaVEt~G 230 (376)
T COG4324 198 ASLIFHELAH---------QKIYVNNDTAFNESFATAVETSG 230 (376)
T ss_pred HHHHHHHHhh---------heEeecCcchHhHHHHHHHHHHh
Confidence 3568999999 66655543 2666666666665
No 41
>PF13113 DUF3970: Protein of unknown function (DUF3970)
Probab=42.04 E-value=7.1 Score=25.80 Aligned_cols=56 Identities=16% Similarity=0.172 Sum_probs=43.1
Q ss_pred eeEEecCCCChhhHHHHHHHHHHHHHHHHhccCCCcccCCCCchhhhHHHHHHHhhcCCCCC
Q psy3039 50 FRIKMCTRVNEEDLFTIHHEMGHVEYFIQYKDQPMAFREGANPGKNTRGWVAELNSIHKKPN 111 (118)
Q Consensus 50 ~RIkmCt~v~~edf~t~hhemGHi~Y~~~Y~~qP~~fR~gANpgFhEA~~~~~l~s~~~~~~ 111 (118)
+||.--.+ .+++|+...-++-| |-..|-.+|. .+.||-..-+-||.+..++..|+|
T Consensus 4 VRl~G~~e-Ei~~fi~~~~~~~~--~ei~h~sk~~---~~nNPKY~~sKdv~~Yl~~K~k~~ 59 (60)
T PF13113_consen 4 VRLSGTKE-EIEEFIKSFEKLKG--FEITHTSKPY---KKNNPKYKYSKDVRVYLSLKLKEA 59 (60)
T ss_pred EEecCCHH-HHHHHHHhhhhcCC--ceEEEecccc---cCCCcccccchhhHHHHHhhhhcc
Confidence 45554434 67777777777766 6677777775 899999999999999999988765
No 42
>COG2317 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]
Probab=41.66 E-value=39 Score=30.47 Aligned_cols=59 Identities=34% Similarity=0.476 Sum_probs=39.8
Q ss_pred cccccccccccCCCCceeEEecCCCChhhH----HHHHHHHHHHHHHHHh----ccCCCcccCCCCchhhhH
Q psy3039 34 EVVCHASAWDFHDGKDFRIKMCTRVNEEDL----FTIHHEMGHVEYFIQY----KDQPMAFREGANPGKNTR 97 (118)
Q Consensus 34 ~~~ChasAwdf~~~~D~RIkmCt~v~~edf----~t~hhemGHi~Y~~~Y----~~qP~~fR~gANpgFhEA 97 (118)
++.=||=+=.+- .+|+||+ |+.+..|| +.+-||-||.-|=++- ..+|+ =+|+.=|+||.
T Consensus 230 D~S~HPF~~g~~-~~DVRIT--TRy~~~df~~aL~g~iHE~GHAlYEqn~~~~l~gtPl--g~g~smgiHES 296 (497)
T COG2317 230 DVSVHPFTTGLP-INDVRIT--TRYNEQDFRSALFGTIHETGHALYEQNLDEALLGTPL--GEGRSMGIHES 296 (497)
T ss_pred cCCCCCccCCCC-CCceeEE--eecCCccHHHHHHHHHHhhhhHHHHcCCCHHHcCCcc--cCCcccccccH
Confidence 444566433342 5899998 45566665 5678999999998754 56665 46666667765
No 43
>KOG2509|consensus
Probab=41.55 E-value=14 Score=32.82 Aligned_cols=15 Identities=33% Similarity=0.751 Sum_probs=13.5
Q ss_pred ChHHHHHHHHhcCCC
Q psy3039 1 MFRTAEEFFTSINMS 15 (118)
Q Consensus 1 mf~~ae~Ff~SLGl~ 15 (118)
|.+.+++||+|||++
T Consensus 317 mi~~~eef~qsLgip 331 (455)
T KOG2509|consen 317 MINNQEEFYQSLGLP 331 (455)
T ss_pred HHHHHHHHHHHhCCc
Confidence 567899999999998
No 44
>COG0501 HtpX Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]
Probab=40.48 E-value=16 Score=28.48 Aligned_cols=18 Identities=33% Similarity=0.746 Sum_probs=12.8
Q ss_pred ChhhH-HHHHHHHHHHHHH
Q psy3039 59 NEEDL-FTIHHEMGHVEYF 76 (118)
Q Consensus 59 ~~edf-~t~hhemGHi~Y~ 76 (118)
|.|.+ -.+-||+||+.+.
T Consensus 153 ~~dEl~aVlaHElgHi~~r 171 (302)
T COG0501 153 NDDELEAVLAHELGHIKNR 171 (302)
T ss_pred CHHHHHHHHHHHHHHHhcc
Confidence 55444 4678999998754
No 45
>PRK03968 DNA primase large subunit; Validated
Probab=40.26 E-value=33 Score=30.13 Aligned_cols=42 Identities=19% Similarity=0.288 Sum_probs=38.0
Q ss_pred CCceeEEecCCCChhhHHHHHHHHHHHHHHHHhccCCCcccCCCCc
Q psy3039 47 GKDFRIKMCTRVNEEDLFTIHHEMGHVEYFIQYKDQPMAFREGANP 92 (118)
Q Consensus 47 ~~D~RIkmCt~v~~edf~t~hhemGHi~Y~~~Y~~qP~~fR~gANp 92 (118)
+.|+||+.|. .|+..++.|+--+-|--+=+--|+||.+.+|.
T Consensus 287 ~~~vkv~D~~----~~l~~~~~ei~p~i~ea~~~c~pplf~DqP~E 328 (399)
T PRK03968 287 RRDVKVSDCD----PDLRIIEEEILPLIIEAANRCSPPLFEDQPQE 328 (399)
T ss_pred ccCcchhhcc----chhHHHHHHHHHHHHHHhhcCCCCccccCchH
Confidence 5689999997 68999999999999999999999999999874
No 46
>PF02031 Peptidase_M7: Streptomyces extracellular neutral proteinase (M7) family; InterPro: IPR000013 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M7 (snapalysin family, clan MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA. With a molecular weight of around 16kDa, Streptomyces extracellular neutral protease is one of the smallest known proteases []; it is capable of hydrolysing milk proteins []. The enzyme is synthesised as a proenzyme with a signal peptide, a propeptide and an active domain that contains the conserved HEXXH motif characteristic of metalloproteases. Although family M7 shows active site sequence similarity to other members, it differs in one major respect: the third zinc ligand appears to be an aspartate residue rather than the usual histidine.; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis, 0005576 extracellular region; PDB: 1C7K_A 1KUH_A.
Probab=40.15 E-value=22 Score=26.84 Aligned_cols=14 Identities=29% Similarity=0.477 Sum_probs=10.7
Q ss_pred hhHHHHHHHHHHHH
Q psy3039 61 EDLFTIHHEMGHVE 74 (118)
Q Consensus 61 edf~t~hhemGHi~ 74 (118)
+....+-||+|||-
T Consensus 76 ~~~RIaaHE~GHiL 89 (132)
T PF02031_consen 76 NSTRIAAHELGHIL 89 (132)
T ss_dssp -HHHHHHHHHHHHH
T ss_pred ccceeeeehhcccc
Confidence 44667899999985
No 47
>PHA02456 zinc metallopeptidase motif-containing protein
Probab=39.55 E-value=19 Score=27.02 Aligned_cols=44 Identities=30% Similarity=0.526 Sum_probs=31.0
Q ss_pred ccccc-cccccCCCCceeEEecCCCChhhHHHHHHHHHHHHHHHHhc-cCCCcc
Q psy3039 35 VVCHA-SAWDFHDGKDFRIKMCTRVNEEDLFTIHHEMGHVEYFIQYK-DQPMAF 86 (118)
Q Consensus 35 ~~Cha-sAwdf~~~~D~RIkmCt~v~~edf~t~hhemGHi~Y~~~Y~-~qP~~f 86 (118)
..|-. -+|--- ++|+.=|-|. -|.-||+.|+-=|+.|. -||+.|
T Consensus 59 ~LCG~~~~~i~I-DP~~~~KGC~-------~TL~HEL~H~WQ~RsYG~i~PITY 104 (141)
T PHA02456 59 DLCGQFVGWIEI-DPDYANKGCR-------DTLAHELNHAWQFRTYGLVQPITY 104 (141)
T ss_pred chhhcceeEEEE-CCcccccchH-------HHHHHHHHHHHhhhccceeeeeeh
Confidence 44553 255333 4667777775 37899999999999997 688876
No 48
>cd04267 ZnMc_ADAM_like Zinc-dependent metalloprotease, ADAM_like or reprolysin_like subgroup. The adamalysin_like or ADAM family of metalloproteases contains proteolytic domains from snake venoms, proteases from the mammalian reproductive tract, and the tumor necrosis factor alpha convertase, TACE. ADAMs (A Disintegrin And Metalloprotease) are glycoproteins, which play roles in cell signaling, cell fusion, and cell-cell interactions.
Probab=38.94 E-value=16 Score=27.09 Aligned_cols=14 Identities=36% Similarity=0.529 Sum_probs=11.6
Q ss_pred hhhHHHHHHHHHHH
Q psy3039 60 EEDLFTIHHEMGHV 73 (118)
Q Consensus 60 ~edf~t~hhemGHi 73 (118)
...-.++-|||||.
T Consensus 131 ~~~~~~~aHElGH~ 144 (192)
T cd04267 131 LLTALTMAHELGHN 144 (192)
T ss_pred eeehhhhhhhHHhh
Confidence 56667999999995
No 49
>PRK05457 heat shock protein HtpX; Provisional
Probab=38.20 E-value=49 Score=26.93 Aligned_cols=60 Identities=15% Similarity=0.228 Sum_probs=31.9
Q ss_pred HHHHHHHHhcCCCCCChHHHhhcccccCCCCcccccccccccCCCC-ceeEEecC----CCChhh-HHHHHHHHHHHH
Q psy3039 3 RTAEEFFTSINMSAMPPEFWERSMLEKPQGREVVCHASAWDFHDGK-DFRIKMCT----RVNEED-LFTIHHEMGHVE 74 (118)
Q Consensus 3 ~~ae~Ff~SLGl~~lp~sFW~~S~~~kp~dr~~~ChasAwdf~~~~-D~RIkmCt----~v~~ed-f~t~hhemGHi~ 74 (118)
+..++--...|++ +|+=+.-. . . ++.|+-..... .-+|-..+ ..+.|. --.+-||+||+.
T Consensus 81 ~~v~~la~~~g~p-~p~v~v~~------~-~----~~NAfa~G~~~~~~~V~vt~gLl~~L~~~El~aVlAHElgHi~ 146 (284)
T PRK05457 81 ETVARQARQAGIG-MPEVAIYH------S-P----EINAFATGASKNNSLVAVSTGLLQNMSRDEVEAVLAHEISHIA 146 (284)
T ss_pred HHHHHHHHhCCCC-CCCEEEEe------C-C----CceEEEecCCCCCeEEEeehHHhhhCCHHHHHHHHHHHHHHHH
Confidence 4456666777776 66543221 1 1 35566544222 33343333 234444 456899999974
No 50
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=37.91 E-value=21 Score=32.03 Aligned_cols=44 Identities=32% Similarity=0.581 Sum_probs=30.8
Q ss_pred hHHHHHHHHhcCCCCCC------hHHHhhcccccCCCCcccccccccccCCCCceeEE
Q psy3039 2 FRTAEEFFTSINMSAMP------PEFWERSMLEKPQGREVVCHASAWDFHDGKDFRIK 53 (118)
Q Consensus 2 f~~ae~Ff~SLGl~~lp------~sFW~~S~~~kp~dr~~~ChasAwdf~~~~D~RIk 53 (118)
.+...++|.+|||..|+ .+||+.-.+--|.| || |=|+. +.|-|+
T Consensus 227 ~~ei~~if~~mGF~e~~~g~~ves~f~NFDaL~~Pqd-----HP-ARd~q--DTFyl~ 276 (492)
T PLN02853 227 RQQFRKIFLQMGFEEMPTNNFVESSFWNFDALFQPQQ-----HP-ARDSH--DTFFLK 276 (492)
T ss_pred HHHHHHHHHhCCCEEecCCCCeechhhhhhhhcCCCC-----CC-CCCcc--ceEEEc
Confidence 35678999999998885 58999987766765 44 33442 345664
No 51
>PRK04897 heat shock protein HtpX; Provisional
Probab=37.43 E-value=42 Score=27.40 Aligned_cols=60 Identities=22% Similarity=0.225 Sum_probs=32.1
Q ss_pred HHHHHHHHhcCCCCCChHHHhhcccccCCCCcccccccccccCCCCceeEEecC-----CCC-hhhHHHHHHHHHHHH
Q psy3039 3 RTAEEFFTSINMSAMPPEFWERSMLEKPQGREVVCHASAWDFHDGKDFRIKMCT-----RVN-EEDLFTIHHEMGHVE 74 (118)
Q Consensus 3 ~~ae~Ff~SLGl~~lp~sFW~~S~~~kp~dr~~~ChasAwdf~~~~D~RIkmCt-----~v~-~edf~t~hhemGHi~ 74 (118)
+..++--...|++ +|+=+.-.+ . .+.|+-......=|+--.+ ..+ .|=--.+-|||||+.
T Consensus 84 ~~v~~la~~~gip-~p~v~v~~~-------~----~~NAfa~G~~~~~~~v~vt~gLl~~l~~~El~aVlAHElgHi~ 149 (298)
T PRK04897 84 HIVEDMAMVAQIP-MPRVFIIDD-------P----SPNAFATGSSPKNAAVAVTTGLLAIMNREELEGVIGHEISHIR 149 (298)
T ss_pred HHHHHHHHHcCCC-CCcEEEecC-------C----CCceEEeccCCCCcEEEeehHHHhhCCHHHHHHHHHHHHHHHh
Confidence 4566777788886 665543321 1 3555544322222222111 224 444556899999986
No 52
>PF01435 Peptidase_M48: Peptidase family M48 This is family M48 in the peptidase classification. ; InterPro: IPR001915 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M48 (Ste24 endopeptidase family, clan M-); members of both subfamily are represented. The members of this set of proteins are mostly described as probable protease htpX homologue (3.4.24 from EC) or CAAX prenyl protease 1, which proteolytically removes the C-terminal three residues of farnesylated proteins. They are integral membrane proteins associated with the endoplasmic reticulum and Golgi, binding one zinc ion per subunit. In Saccharomyces cerevisiae (Baker's yeast) Ste24p is required for the first NH2-terminal proteolytic processing event within the a-factor precursor, which takes place after COOH-terminal CAAX modification is complete. The Ste24p contains multiple predicted membrane spans, a zinc metalloprotease motif (HEXXH), and a COOH-terminal ER retrieval signal (KKXX). The HEXXH protease motif is critical for Ste24p activity, since Ste24p fails to function when conserved residues within this motif are mutated. The Ste24p homologues occur in a diverse group of organisms, including Escherichia coli, Schizosaccharomyces pombe (Fission yeast), Haemophilus influenzae, and Homo sapiens (Human), which indicates that the gene is highly conserved throughout evolution. Ste24p and the proteins related to it define a subfamily of proteins that are likely to function as intracellular, membrane-associated zinc metalloproteases []. HtpX is a zinc-dependent endoprotease member of the membrane-localized proteolytic system in E. coli, which participates in the proteolytic quality control of membrane proteins in conjunction with FtsH, a membrane-bound and ATP-dependent protease. Biochemical characterisation revealed that HtpX undergoes self-degradation upon cell disruption or membrane solubilization. It can also degraded casein and cleaves solubilized membrane proteins, for example, SecY []. Expression of HtpX in the plasma membrane is under the control of CpxR, with the metalloproteinase active site of HtpX located on the cytosolic side of the membrane. This suggests a potential role for HtpX in the response to mis-folded proteins [].; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis, 0016020 membrane; PDB: 3CQB_A 3C37_B.
Probab=37.22 E-value=23 Score=26.23 Aligned_cols=36 Identities=28% Similarity=0.555 Sum_probs=19.5
Q ss_pred ccccccCCCCceeEEecC----CCChhhH-HHHHHHHHHHH
Q psy3039 39 ASAWDFHDGKDFRIKMCT----RVNEEDL-FTIHHEMGHVE 74 (118)
Q Consensus 39 asAwdf~~~~D~RIkmCt----~v~~edf-~t~hhemGHi~ 74 (118)
+.||-...+..-+|-... ..+.+.+ ..+-|||||+.
T Consensus 61 ~NA~~~g~~~~~~I~v~~~ll~~~~~~el~aVlaHElgH~~ 101 (226)
T PF01435_consen 61 PNAFATGGGPRKRIVVTSGLLESLSEDELAAVLAHELGHIK 101 (226)
T ss_dssp EEEEEETTTC--EEEEEHHHHHHSSHHHHHHHHHHHHHHHH
T ss_pred CcEEEEccCCCcEEEEeChhhhcccHHHHHHHHHHHHHHHH
Confidence 445544444333444333 2355444 48899999976
No 53
>cd06163 S2P-M50_PDZ_RseP-like RseP-like Site-2 proteases (S2P), zinc metalloproteases (MEROPS family M50A), cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. In Escherichia coli, the S2P homolog RseP is involved in the sigmaE pathway of extracytoplasmic stress responses. Also included in this group are such homologs as Bacillus subtilis YluC, Mycobacterium tuberculosis Rv2869c S2P, and Bordetella bronchiseptica HurP. Rv2869c S2P appears to have a role in the regulation of prokaryotic lipid biosynthesis and membrane composition and YluC of Bacillus has a role in transducing membrane stress. This group includes bacterial and eukaryotic S2P/M50s homologs with either one or two PDZ domains present. PDZ domains are believed to have a regulatory role. The RseP PDZ domain is required for the inhibitory reaction that prevents cleavage of its substrate, RseA.
Probab=37.01 E-value=29 Score=26.62 Aligned_cols=17 Identities=24% Similarity=0.462 Sum_probs=11.3
Q ss_pred HHHHHHHHHHHHHHHHh
Q psy3039 63 LFTIHHEMGHVEYFIQY 79 (118)
Q Consensus 63 f~t~hhemGHi~Y~~~Y 79 (118)
+..+-||+||..=-+.+
T Consensus 10 ~~v~iHElGH~~~Ar~~ 26 (182)
T cd06163 10 ILIFVHELGHFLVAKLF 26 (182)
T ss_pred HHHHHHHHHHHHHHHHc
Confidence 45788999994444433
No 54
>cd00203 ZnMc Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease.
Probab=36.43 E-value=21 Score=25.36 Aligned_cols=14 Identities=50% Similarity=0.760 Sum_probs=11.7
Q ss_pred hhhHHHHHHHHHHH
Q psy3039 60 EEDLFTIHHEMGHV 73 (118)
Q Consensus 60 ~edf~t~hhemGHi 73 (118)
..-..++-|||||.
T Consensus 94 ~~~~~~~~HElGH~ 107 (167)
T cd00203 94 KEGAQTIAHELGHA 107 (167)
T ss_pred ccchhhHHHHHHHH
Confidence 36678999999995
No 55
>COG4307 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.52 E-value=24 Score=30.09 Aligned_cols=41 Identities=22% Similarity=0.370 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHhcc----------------------CCCcccCCCCchhhhHHHHH-HHhhcCC
Q psy3039 66 IHHEMGHVEYFIQYKD----------------------QPMAFREGANPGKNTRGWVA-ELNSIHK 108 (118)
Q Consensus 66 ~hhemGHi~Y~~~Y~~----------------------qP~~fR~gANpgFhEA~~~~-~l~s~~~ 108 (118)
--||+||.++++.-++ +--.||.|+-|+..+- .| +.+++|+
T Consensus 175 FRHE~GHy~~drLI~d~a~~L~afralFGDeraDYaqAL~~~Y~~Gp~pdWqqn--~ISsYAt~Hp 238 (349)
T COG4307 175 FRHEIGHYYFDRLIADSADRLSAFRALFGDERADYAQALDRYYRGGPPPDWQQN--FISSYATMHP 238 (349)
T ss_pred hhhhhhhHHHHHHHhhHHHHHHHHHHHhCCchhHHHHHHHHHhcCCCCCcchhh--HHHHhhhcCc
Confidence 3599999888776554 2345788888888777 33 2566654
No 56
>cd05709 S2P-M50 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. The domain core structure appears to contain at least three transmembrane helices with a catalytic zinc atom coordinated by three conserved residues contained within the consensus sequence HExxH, together with a conserved aspartate residue. The S2P/M50 family of RIP proteases is widely distributed; in eukaryotic cells, they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum (ER) stress responses. In sterol-depleted mammalian cells, a two-step proteolytic process releases the N-terminal domains of sterol regulatory element-bindin
Probab=35.08 E-value=32 Score=25.25 Aligned_cols=19 Identities=21% Similarity=0.202 Sum_probs=13.1
Q ss_pred HHHHHHHHHHHHHHHHhcc
Q psy3039 63 LFTIHHEMGHVEYFIQYKD 81 (118)
Q Consensus 63 f~t~hhemGHi~Y~~~Y~~ 81 (118)
+..+-||+||..=-..|..
T Consensus 9 i~i~iHE~gH~~~A~~~G~ 27 (180)
T cd05709 9 ISVTVHELGHALVARRLGV 27 (180)
T ss_pred HHHHHHHHHHHHHHHHcCC
Confidence 4567899999555555554
No 57
>cd04327 ZnMc_MMP_like_3 Zinc-dependent metalloprotease; MMP_like sub-family 3. A group of bacterial and fungal metalloproteinase domains similar to matrix metalloproteinases and astacin.
Probab=34.96 E-value=27 Score=26.45 Aligned_cols=16 Identities=38% Similarity=0.399 Sum_probs=11.9
Q ss_pred hhHHHHHHHHHHHHHH
Q psy3039 61 EDLFTIHHEMGHVEYF 76 (118)
Q Consensus 61 edf~t~hhemGHi~Y~ 76 (118)
+.+.+|-||+||.-=+
T Consensus 91 ~~~~~i~HElgHaLG~ 106 (198)
T cd04327 91 EFSRVVLHEFGHALGF 106 (198)
T ss_pred hHHHHHHHHHHHHhcC
Confidence 3457999999996433
No 58
>PF10005 DUF2248: Uncharacterized protein conserved in bacteria (DUF2248); InterPro: IPR011201 This is a family of uncharacterised bacterial proteins.
Probab=34.02 E-value=48 Score=28.51 Aligned_cols=43 Identities=19% Similarity=0.273 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHHHhccCCC---------------------cccCCCCchhhhH-HHHHHHhhcCC
Q psy3039 64 FTIHHEMGHVEYFIQYKDQPM---------------------AFREGANPGKNTR-GWVAELNSIHK 108 (118)
Q Consensus 64 ~t~hhemGHi~Y~~~Y~~qP~---------------------~fR~gANpgFhEA-~~~~~l~s~~~ 108 (118)
--..||.||.+..+.-++.+. -|++||-++-.|- |+ +.+++|+
T Consensus 181 GHfRHE~GHYywd~Lv~~~~~l~~fR~lFGDer~DY~~AL~~hY~~Gpp~~W~~~~IS--aYAt~HP 245 (343)
T PF10005_consen 181 GHFRHEIGHYYWDRLVRDPPWLEAFRALFGDERADYGAALQRHYANGPPADWQENFIS--AYATMHP 245 (343)
T ss_pred HHhcchhHHHHHHHHhcCchHHHHHHHHhCCChhhHHHHHHHhhccCCchhhhhhhhH--HHhhcCc
Confidence 346799999776665554433 4566777777776 33 3666664
No 59
>PF04450 BSP: Peptidase of plants and bacteria; InterPro: IPR007541 These basic secretory proteins (BSPs) are believed to be part of the plants defence mechanism against pathogens [].
Probab=33.56 E-value=56 Score=25.68 Aligned_cols=51 Identities=25% Similarity=0.231 Sum_probs=32.6
Q ss_pred CCCceeEEecC----------CCChhhHHHHHHHHHHHHHHHHhccCCCcccCCCCchhhhH-HHHHHHh
Q psy3039 46 DGKDFRIKMCT----------RVNEEDLFTIHHEMGHVEYFIQYKDQPMAFREGANPGKNTR-GWVAELN 104 (118)
Q Consensus 46 ~~~D~RIkmCt----------~v~~edf~t~hhemGHi~Y~~~Y~~qP~~fR~gANpgFhEA-~~~~~l~ 104 (118)
+.++..|..-+ .+..|..-.+-|||.|+. |+ -| +..|-+++-|. .|.+-|.
T Consensus 70 d~~~~~I~~S~~~i~~~~~~~~~~~Ei~Gvl~HE~~H~~---Q~--~~---~~~~P~~liEGIADyVRl~ 131 (205)
T PF04450_consen 70 DDDHKEIHFSARYIAKYPADGDVRDEIIGVLYHEMVHCW---QW--DG---RGTAPGGLIEGIADYVRLK 131 (205)
T ss_pred CCCccEEEEeHHHHhhcccccchHHHHHHHHHHHHHHHh---hc--CC---CCCCChhheecHHHHHHHH
Confidence 45556666533 223567899999999982 22 22 55566779998 6666554
No 60
>cd07235 MRD Mitomycin C resistance protein (MRD). Mitomycin C (MC) is a naturally occurring antibiotic, and antitumor agent used in the treatment of cancer. Its antitumor activity is exerted primarily through monofunctional and bifunctional alkylation of DNA. MRD binds to MC and functions as a component of the MC exporting system. MC is bound to MRD by a stacking interaction between a His and a Trp. MRD adopts a structural fold similar to bleomycin resistance protein, glyoxalase I, and extradiol dioxygenases; and it has binding sites at an identical location to binding sites in these evolutionarily related enzymes.
Probab=33.23 E-value=26 Score=23.02 Aligned_cols=16 Identities=6% Similarity=0.301 Sum_probs=13.1
Q ss_pred hHHHHHHHHhcCCCCC
Q psy3039 2 FRTAEEFFTSINMSAM 17 (118)
Q Consensus 2 f~~ae~Ff~SLGl~~l 17 (118)
++.|.+||+.|||...
T Consensus 11 ~~~a~~FY~~LGf~~~ 26 (122)
T cd07235 11 MAKSLDFYRRLGFDFP 26 (122)
T ss_pred HHHHHHHHHHhCceec
Confidence 4678999999999754
No 61
>cd04269 ZnMc_adamalysin_II_like Zinc-dependent metalloprotease; adamalysin_II_like subfamily. Adamalysin II is a snake venom zinc endopeptidase. This subfamily contains other snake venom metalloproteinases, as well as membrane-anchored metalloproteases belonging to the ADAM family. ADAMs (A Disintegrin And Metalloprotease) are glycoproteins, which play roles in cell signaling, cell fusion, and cell-cell interactions.
Probab=32.56 E-value=27 Score=25.89 Aligned_cols=14 Identities=36% Similarity=0.377 Sum_probs=11.0
Q ss_pred hhHHHHHHHHHHHH
Q psy3039 61 EDLFTIHHEMGHVE 74 (118)
Q Consensus 61 edf~t~hhemGHi~ 74 (118)
..-.++-|||||.-
T Consensus 130 ~~a~~~AHElGH~l 143 (194)
T cd04269 130 LFAVTMAHELGHNL 143 (194)
T ss_pred HHHHHHHHHHHhhc
Confidence 44588999999963
No 62
>cd04272 ZnMc_salivary_gland_MPs Zinc-dependent metalloprotease, salivary_gland_MPs. Metalloproteases secreted by the salivary glands of arthropods.
Probab=30.54 E-value=32 Score=26.31 Aligned_cols=13 Identities=31% Similarity=0.761 Sum_probs=10.9
Q ss_pred hhHHHHHHHHHHH
Q psy3039 61 EDLFTIHHEMGHV 73 (118)
Q Consensus 61 edf~t~hhemGHi 73 (118)
..-.++-|||||.
T Consensus 144 ~~~~~~AHElGH~ 156 (220)
T cd04272 144 YGVYTMTHELAHL 156 (220)
T ss_pred ccHHHHHHHHHHH
Confidence 4479999999995
No 63
>PF14247 DUF4344: Domain of unknown function (DUF4344)
Probab=29.66 E-value=54 Score=26.22 Aligned_cols=63 Identities=30% Similarity=0.504 Sum_probs=41.0
Q ss_pred hcccccCCC---CcccccccccccCCCCceeEEecCCC-------------Ch---------hhHHHHHHHHHHHHHHHH
Q psy3039 24 RSMLEKPQG---REVVCHASAWDFHDGKDFRIKMCTRV-------------NE---------EDLFTIHHEMGHVEYFIQ 78 (118)
Q Consensus 24 ~S~~~kp~d---r~~~ChasAwdf~~~~D~RIkmCt~v-------------~~---------edf~t~hhemGHi~Y~~~ 78 (118)
+..|.=|.+ +-..| +.+=-||++.+-.|.||-+- +. .-+.|..||+||. ++.
T Consensus 30 n~~f~LP~~l~i~~~~C-Ge~nA~ydPe~~~I~iCYEf~~~~~~~f~~~~~~~~~~~~~~~~~~~~~l~HE~GHA--lI~ 106 (220)
T PF14247_consen 30 NDYFPLPRDLTIRFAEC-GEDNAFYDPENRSITICYEFVDEILDRFAKANDPDEEYGQAAIGNVLFTLYHELGHA--LID 106 (220)
T ss_pred hhcCCCCCCeEEEEeec-CCCCCccCCCCCEEEECHHHHHHHHHHHHhCCcCcchHHHHHHHHHHHHHHHHHHHH--HHH
Confidence 444555555 22237 54445788899999999642 11 1256889999995 445
Q ss_pred hccCCCcccCC
Q psy3039 79 YKDQPMAFREG 89 (118)
Q Consensus 79 Y~~qP~~fR~g 89 (118)
--++|++=|++
T Consensus 107 ~~~lPv~GrEE 117 (220)
T PF14247_consen 107 DLDLPVLGREE 117 (220)
T ss_pred HhcCCcccchh
Confidence 56899887763
No 64
>cd08356 Glo_EDI_BRP_like_17 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.
Probab=29.60 E-value=28 Score=23.30 Aligned_cols=19 Identities=11% Similarity=0.364 Sum_probs=15.2
Q ss_pred hHHHHHHHHhcCCCCCChH
Q psy3039 2 FRTAEEFFTSINMSAMPPE 20 (118)
Q Consensus 2 f~~ae~Ff~SLGl~~lp~s 20 (118)
++.+.+||+.|||......
T Consensus 12 l~~s~~FY~~LGf~~~~~~ 30 (113)
T cd08356 12 FAESKQFYQALGFELEWEN 30 (113)
T ss_pred HHHHHHHHHHhCCeeEecC
Confidence 3678899999999877654
No 65
>PRK03001 M48 family peptidase; Provisional
Probab=29.47 E-value=33 Score=27.56 Aligned_cols=17 Identities=29% Similarity=0.329 Sum_probs=12.1
Q ss_pred ChhhHHHHHHHHHHHHH
Q psy3039 59 NEEDLFTIHHEMGHVEY 75 (118)
Q Consensus 59 ~~edf~t~hhemGHi~Y 75 (118)
+.|=--.+-|||||+.-
T Consensus 121 ~~El~aVlAHElgHi~~ 137 (283)
T PRK03001 121 EREIRGVMAHELAHVKH 137 (283)
T ss_pred HHHHHHHHHHHHHHHhC
Confidence 34445578999999863
No 66
>cd09012 Glo_EDI_BRP_like_24 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.
Probab=29.43 E-value=36 Score=22.67 Aligned_cols=17 Identities=18% Similarity=0.536 Sum_probs=13.7
Q ss_pred hHHHHHHHHhcCCCCCC
Q psy3039 2 FRTAEEFFTSINMSAMP 18 (118)
Q Consensus 2 f~~ae~Ff~SLGl~~lp 18 (118)
++.+.+||+.|||...+
T Consensus 11 l~~s~~FY~~lGf~~~~ 27 (124)
T cd09012 11 LEKSTAFYTALGFEFNP 27 (124)
T ss_pred HHHHHHHHHHCCCEEcc
Confidence 36788999999998653
No 67
>PRK03072 heat shock protein HtpX; Provisional
Probab=29.06 E-value=34 Score=27.83 Aligned_cols=60 Identities=25% Similarity=0.316 Sum_probs=31.8
Q ss_pred HHHHHHHHhcCCCCCChHHHhhcccccCCCCcccccccccccCCCCceeEEecCC-----CC-hhhHHHHHHHHHHHH
Q psy3039 3 RTAEEFFTSINMSAMPPEFWERSMLEKPQGREVVCHASAWDFHDGKDFRIKMCTR-----VN-EEDLFTIHHEMGHVE 74 (118)
Q Consensus 3 ~~ae~Ff~SLGl~~lp~sFW~~S~~~kp~dr~~~ChasAwdf~~~~D~RIkmCt~-----v~-~edf~t~hhemGHi~ 74 (118)
+..++.-...|++ +|+-|- -+. . .+.|+-......-.+-.+++ .+ .|=--.+-||||||.
T Consensus 74 ~~v~~la~~~g~p-~p~vyv------~~~-~----~~NAFa~G~~~~~~~v~vt~gLl~~l~~~El~aVlAHElgHi~ 139 (288)
T PRK03072 74 RIVRELSTAARQP-MPRLYI------SPT-A----APNAFATGRNPRNAAVCCTEGILQILNERELRGVLGHELSHVY 139 (288)
T ss_pred HHHHHHHHHcCCC-CCCEEE------ecC-C----CCceEEecCCCCCcEEEecHHHHHhCCHHHHHHHHHHHHHHHh
Confidence 4567777888886 665322 211 1 35566543222211122221 23 444557899999985
No 68
>PF08325 WLM: WLM domain; InterPro: IPR013536 The WLM (WSS1-like metalloprotease) domain is a globular domain related to the zincin-like superfamily of Zn-dependent peptidase. Since the WLM domain contains all known active site residues of zincins, it is predicted to be a catalytically active peptidase domain. The WLM domain is a eukaryotic domain represented in plants, fungi, Plasmodium, and kinetoplastids. By contrast, it is absent in animals, Cryptosporidium, and Microsporidia, suggesting that it has been lost on multiple occasions during the evolution of eukaryotes. The WLM domain is found either in stand-alone form or in association with other domains such as the RanBP2 zinc finger , the ubiquitin domain, or the PUB/PUG domain. This domain could function as a specific de-SUMOylating domain of distinct protein complexes in the nucleus and the cytoplasm []. It has been suggested to form a segregated alpha/beta structure with eight helices and five strands. Proteins containign this domain include yeast WSS1 (a weak suppressor of the Ub-related protein SMT3), and various putative metalloproteases from plant and fungal species.
Probab=28.88 E-value=29 Score=26.87 Aligned_cols=13 Identities=38% Similarity=0.332 Sum_probs=10.7
Q ss_pred hHHHHHHHHHHHH
Q psy3039 62 DLFTIHHEMGHVE 74 (118)
Q Consensus 62 df~t~hhemGHi~ 74 (118)
=+.|+-|||+|+.
T Consensus 82 i~~t~lHELaH~~ 94 (186)
T PF08325_consen 82 ILGTMLHELAHNV 94 (186)
T ss_pred HHHHHHHHHHhcc
Confidence 3568999999986
No 69
>PF13583 Reprolysin_4: Metallo-peptidase family M12B Reprolysin-like
Probab=28.46 E-value=31 Score=26.61 Aligned_cols=13 Identities=38% Similarity=0.606 Sum_probs=10.8
Q ss_pred hhHHHHHHHHHHH
Q psy3039 61 EDLFTIHHEMGHV 73 (118)
Q Consensus 61 edf~t~hhemGHi 73 (118)
..+.++-||+||.
T Consensus 136 ~~~~~~aHEiGH~ 148 (206)
T PF13583_consen 136 NGYQTFAHEIGHN 148 (206)
T ss_pred ccchHHHHHHHHH
Confidence 4668899999996
No 70
>PRK03982 heat shock protein HtpX; Provisional
Probab=27.85 E-value=35 Score=27.48 Aligned_cols=15 Identities=33% Similarity=0.426 Sum_probs=11.4
Q ss_pred hhhHHHHHHHHHHHH
Q psy3039 60 EEDLFTIHHEMGHVE 74 (118)
Q Consensus 60 ~edf~t~hhemGHi~ 74 (118)
.|=--.+-||+||+.
T Consensus 123 ~El~AVlAHElgHi~ 137 (288)
T PRK03982 123 DELEGVIAHELTHIK 137 (288)
T ss_pred HHHHHHHHHHHHHHH
Confidence 444557899999986
No 71
>PRK01345 heat shock protein HtpX; Provisional
Probab=27.25 E-value=38 Score=28.05 Aligned_cols=60 Identities=20% Similarity=0.288 Sum_probs=30.3
Q ss_pred HHHHHHHHhcCCCCCChHHHhhcccccCCCCcccccccccccCCCCceeEEecC-----CCC-hhhHHHHHHHHHHHH
Q psy3039 3 RTAEEFFTSINMSAMPPEFWERSMLEKPQGREVVCHASAWDFHDGKDFRIKMCT-----RVN-EEDLFTIHHEMGHVE 74 (118)
Q Consensus 3 ~~ae~Ff~SLGl~~lp~sFW~~S~~~kp~dr~~~ChasAwdf~~~~D~RIkmCt-----~v~-~edf~t~hhemGHi~ 74 (118)
+..++.-...|++ +|+=|.- + +. ++.|+-......-++...+ ..+ .|=--.+-||||||.
T Consensus 71 ~~v~~La~~agi~-~p~v~vi------d-~~----~~NAFa~G~~~~~~~V~vt~gLL~~L~~dEL~aVlAHElgHi~ 136 (317)
T PRK01345 71 RMVRDLARRAGLP-MPKVYII------D-NP----QPNAFATGRNPENAAVAATTGLLQRLSPEEVAGVMAHELAHVK 136 (317)
T ss_pred HHHHHHHHHcCCC-CCcEEEE------c-CC----CcceEEecCCCCCeEEEechHHHhhCCHHHHHHHHHHHHHHHH
Confidence 4456666778887 4543221 1 11 3556554322222222222 224 444456899999985
No 72
>TIGR00054 RIP metalloprotease RseP. A model that detects fragments as well matches a number of members of the PEPTIDASE FAMILY S2C. The region of match appears not to overlap the active site domain.
Probab=27.02 E-value=47 Score=28.33 Aligned_cols=15 Identities=27% Similarity=0.700 Sum_probs=10.6
Q ss_pred HHHHHHHHHHHHHHHHh
Q psy3039 63 LFTIHHEMGHVEYFIQY 79 (118)
Q Consensus 63 f~t~hhemGHi~Y~~~Y 79 (118)
+..+-||+|| |..+-
T Consensus 15 ~~v~~HE~gH--~~~a~ 29 (420)
T TIGR00054 15 VLIFVHELGH--FLAAR 29 (420)
T ss_pred HHHHHHhHHH--HHHHH
Confidence 4678899999 44443
No 73
>PF13699 DUF4157: Domain of unknown function (DUF4157)
Probab=26.57 E-value=39 Score=22.59 Aligned_cols=16 Identities=31% Similarity=0.432 Sum_probs=13.1
Q ss_pred ChhhHHHHHHHHHHHH
Q psy3039 59 NEEDLFTIHHEMGHVE 74 (118)
Q Consensus 59 ~~edf~t~hhemGHi~ 74 (118)
+.++...+-||++||.
T Consensus 58 s~~~~~llaHEl~Hv~ 73 (79)
T PF13699_consen 58 SPEGRALLAHELAHVV 73 (79)
T ss_pred CCCcchhHhHHHHHHH
Confidence 4567788999999974
No 74
>PF05572 Peptidase_M43: Pregnancy-associated plasma protein-A; InterPro: IPR008754 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase M43 (cytophagalysin family, clan MA(M)), subfamily M43. The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH. The type example of this family is the pregnancy-associated plasma protein A (PAPP-A), which cleaves insulin-like growth factor (IGF) binding protein-4 (IGFBP-4), causing a dramatic reduction in its affinity for IGF-I and -II. Through this mechanism, PAPP-A is a regulator of IGF bioactivity in several systems, including the Homo sapiens ovary and the cardiovascular system [, , , ].; PDB: 3LUN_A 3LUM_B 2J83_A 2CKI_A.
Probab=26.56 E-value=41 Score=25.04 Aligned_cols=15 Identities=33% Similarity=0.324 Sum_probs=11.1
Q ss_pred CChhhHHHHHHHHHH
Q psy3039 58 VNEEDLFTIHHEMGH 72 (118)
Q Consensus 58 v~~edf~t~hhemGH 72 (118)
.....-.|+-||+||
T Consensus 65 ~~~~~g~TltHEvGH 79 (154)
T PF05572_consen 65 SQYNFGKTLTHEVGH 79 (154)
T ss_dssp TTS-SSHHHHHHHHH
T ss_pred Cccccccchhhhhhh
Confidence 344556899999999
No 75
>PF02163 Peptidase_M50: Peptidase family M50; InterPro: IPR008915 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This entry contains metallopeptidases belonging to MEROPS peptidase family M50 (S2P protease family, clan MM). Members of the M50 metallopeptidase family include: mammalian sterol-regulatory element binding protein (SREBP) site 2 protease, Escherichia coli protease EcfE, stage IV sporulation protein FB and various hypothetical bacterial and eukaryotic homologues. A number of proteins are classified as non-peptidase homologues as they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity.; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 3B4R_A 3ID4_A 3ID2_A 2ZPL_B 3ID1_A 2ZPM_A 3ID3_B 2HGA_A.
Probab=24.75 E-value=65 Score=23.69 Aligned_cols=24 Identities=29% Similarity=0.411 Sum_probs=14.8
Q ss_pred HHHHHHHHHHHHHHHHhccCCCcc
Q psy3039 63 LFTIHHEMGHVEYFIQYKDQPMAF 86 (118)
Q Consensus 63 f~t~hhemGHi~Y~~~Y~~qP~~f 86 (118)
+..+-||+||..=...|......+
T Consensus 8 i~i~~HE~gH~~~a~~~G~~~~~~ 31 (192)
T PF02163_consen 8 ISIVLHELGHALAARLYGDKVPRF 31 (192)
T ss_dssp HHHHHHHHHHHHHHHTTT--B--E
T ss_pred cccccccccccccccccccccccc
Confidence 356789999977776666655555
No 76
>PF09471 Peptidase_M64: IgA Peptidase M64; InterPro: IPR019026 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This is a family of highly selective metallo-endopeptidases belonging to the MEROPS peptidase family M64 (IgA peptidase, clan MA). The primary structure of the Clostridium ramosum IgA peptidase shows no significant overall similarity to any other known metallo-endopeptidase []. ; PDB: 3P1V_A 4DF9_D.
Probab=24.09 E-value=43 Score=27.32 Aligned_cols=14 Identities=29% Similarity=0.264 Sum_probs=10.7
Q ss_pred hhHHHHHHHHHHHH
Q psy3039 61 EDLFTIHHEMGHVE 74 (118)
Q Consensus 61 edf~t~hhemGHi~ 74 (118)
.--.++.||+||-.
T Consensus 215 ~~~~v~vHE~GHsf 228 (264)
T PF09471_consen 215 SFKQVVVHEFGHSF 228 (264)
T ss_dssp THHHHHHHHHHHHT
T ss_pred cccceeeeeccccc
Confidence 44578899999953
No 77
>PF12388 Peptidase_M57: Dual-action HEIGH metallo-peptidase; InterPro: IPR024653 This entry represents the metallopeptidases M10, M27 and M57. The catalytic triad for proteases in this entry is HE-H-H, which in many members is in the sequence motif HEIGH [].
Probab=23.65 E-value=42 Score=26.89 Aligned_cols=16 Identities=38% Similarity=0.513 Sum_probs=12.2
Q ss_pred HHHHHHHHHHHHHHHH
Q psy3039 63 LFTIHHEMGHVEYFIQ 78 (118)
Q Consensus 63 f~t~hhemGHi~Y~~~ 78 (118)
--+|-|||||.-=|++
T Consensus 134 ~hvi~HEiGH~IGfRH 149 (211)
T PF12388_consen 134 EHVITHEIGHCIGFRH 149 (211)
T ss_pred HHHHHHHhhhhccccc
Confidence 3478999999866654
No 78
>cd07267 THT_Oxygenase_N N-terminal domain of 2,4,5-trihydroxytoluene (THT) oxygenase. This subfamily contains the N-terminal, non-catalytic, domain of THT oxygenase. THT oxygenase is an extradiol dioxygenase in the 2,4-dinitrotoluene (DNT) degradation pathway. It catalyzes the conversion of 2,4,5-trihydroxytoluene to an unstable ring fission product, 2,4-dihydroxy-5-methyl-6-oxo-2,4-hexadienoic acid. The native protein was determined to be a dimer by gel filtration. The enzyme belongs to the type I family of extradiol dioxygenases which contains two structurally homologous barrel-shaped domains at the N- and C-terminus of each monomer. The active-site metal is located in the C-terminal barrel. Fe(II) is required for its catalytic activity.
Probab=23.38 E-value=53 Score=21.62 Aligned_cols=16 Identities=25% Similarity=0.501 Sum_probs=12.9
Q ss_pred hHHHHHHHHhcCCCCC
Q psy3039 2 FRTAEEFFTSINMSAM 17 (118)
Q Consensus 2 f~~ae~Ff~SLGl~~l 17 (118)
.+.+.+||+.|||...
T Consensus 14 l~~s~~FY~~lGl~~~ 29 (113)
T cd07267 14 LDKAERFLTDFGLEVA 29 (113)
T ss_pred HHHHHHHHHHcCCEEE
Confidence 3578899999999754
No 79
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=23.19 E-value=46 Score=29.82 Aligned_cols=30 Identities=30% Similarity=0.612 Sum_probs=23.9
Q ss_pred HHHHHHHHhcCCCCCC------hHHHhhcccccCCC
Q psy3039 3 RTAEEFFTSINMSAMP------PEFWERSMLEKPQG 32 (118)
Q Consensus 3 ~~ae~Ff~SLGl~~lp------~sFW~~S~~~kp~d 32 (118)
+...++|.+|||..|+ .+||+.-.+--|.|
T Consensus 236 ~~i~~if~~mGF~e~~~~~~ves~f~NFDaL~~Pqd 271 (494)
T PTZ00326 236 REFREILLEMGFEEMPTNRYVESSFWNFDALFQPQQ 271 (494)
T ss_pred HHHHHHHHhCCCEEecCCCCccccchhhhhhcCCCC
Confidence 5678999999998774 47999987767765
No 80
>cd08350 BLMT_like BLMT, a bleomycin resistance protein encoded on the transposon Tn5, and similar proteins. BLMT is a bleomycin (Bm) resistance protein, encoded by the ble gene on the transposon Tn5. This protein confers a survival advantage to Escherichia coli host cells. Bm is a glycopeptide antibiotic produced naturally by actinomycetes. It is a potent anti-cancer drug, which acts as a strong DNA-cutting agent, thereby causing cell death. BLMT has strong binding affinity to Bm and it protects against this lethal compound through drug sequestering. BLMT has two identically-folded subdomains, with the same alpha/beta fold; these two halves have no sequence similarity. BLMT is a dimer with two Bm-binding pockets formed at the dimer interface.
Probab=23.00 E-value=55 Score=21.67 Aligned_cols=16 Identities=19% Similarity=0.472 Sum_probs=12.9
Q ss_pred hHHHHHHHHhcCCCCC
Q psy3039 2 FRTAEEFFTSINMSAM 17 (118)
Q Consensus 2 f~~ae~Ff~SLGl~~l 17 (118)
++.+.+||+.|||...
T Consensus 13 l~~s~~FY~~lG~~~~ 28 (120)
T cd08350 13 LDATEAFYARLGFSVG 28 (120)
T ss_pred HHHHHHHHHHcCCEEE
Confidence 3678899999999754
No 81
>PF01421 Reprolysin: Reprolysin (M12B) family zinc metalloprotease This Prosite motif covers only the active site.; InterPro: IPR001590 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M12, subfamily M12B (adamalysin family, clan (MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA and the predicted active site residues for members of this family and thermolysin occur in the motif HEXXH []. The adamalysins are zinc dependent endopeptidases found in snake venom. There are some mammalian proteins such as P78325 from SWISSPROT, and fertilin Q28472 from SWISSPROT. Fertilin and closely related proteins appear to not have some active site residues and may not be active enzymes. CD156 (also called ADAM8 (3.4.24 from EC) or MS2 human) has been implicated in extravasation of leukocytes. CD molecules are leucocyte antigens on cell surfaces. CD antigens nomenclature is updated at Protein Reviews On The Web (http://prow.nci.nih.gov/). ; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 2E3X_A 2W15_A 2W14_A 2W13_A 2W12_A 1ND1_A 3K7L_A 2DW2_A 2DW0_B 2DW1_A ....
Probab=22.46 E-value=58 Score=24.27 Aligned_cols=10 Identities=50% Similarity=0.850 Sum_probs=8.5
Q ss_pred HHHHHHHHHH
Q psy3039 64 FTIHHEMGHV 73 (118)
Q Consensus 64 ~t~hhemGHi 73 (118)
.++-|||||.
T Consensus 133 ~~~AHelGH~ 142 (199)
T PF01421_consen 133 VIIAHELGHN 142 (199)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHHHHHh
Confidence 5679999996
No 82
>PF13402 M60-like: Peptidase M60-like family; PDB: 4FCA_A.
Probab=22.33 E-value=53 Score=25.97 Aligned_cols=33 Identities=24% Similarity=0.370 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHHHhccCCCcccCCCCchhhhH-HHHHHHhhcCC
Q psy3039 66 IHHEMGHVEYFIQYKDQPMAFREGANPGKNTR-GWVAELNSIHK 108 (118)
Q Consensus 66 ~hhemGHi~Y~~~Y~~qP~~fR~gANpgFhEA-~~~~~l~s~~~ 108 (118)
..||+||.+ ...|.-++ |.-|. ..+.+|.+...
T Consensus 223 ~~HE~GH~~-----Q~~~~~~~-----g~~EvTnNi~sl~~~~~ 256 (307)
T PF13402_consen 223 PWHELGHNH-----QQGPWTWS-----GMGEVTNNIYSLYVQEK 256 (307)
T ss_dssp HHHHHHHHH------BGGG--T-----T-TTTTHHHHHHHHHHH
T ss_pred ehhhhhhhc-----CccccccC-----CCCchhhHHHHHHHHHH
Confidence 579999953 22234333 46677 77766655443
No 83
>smart00733 Mterf Mitochondrial termination factor repeats. Human mitochondrial termination factor is a DNA-binding protein that acts as a transcription termination factor. Six repeats occur in human mTERF, that also are present in numerous plant proteins.
Probab=21.92 E-value=56 Score=16.13 Aligned_cols=11 Identities=27% Similarity=0.534 Sum_probs=8.3
Q ss_pred HHHHHHhcCCC
Q psy3039 5 AEEFFTSINMS 15 (118)
Q Consensus 5 ae~Ff~SLGl~ 15 (118)
-=+|++++|++
T Consensus 21 ~~~~l~~~g~~ 31 (31)
T smart00733 21 KVEFLKELGFS 31 (31)
T ss_pred HHHHHHHcCCC
Confidence 34788999974
No 84
>PF12725 DUF3810: Protein of unknown function (DUF3810); InterPro: IPR024294 This family of bacterial proteins is functionally uncharacterised. Proteins in this family are typically between 333 and 377 amino acids in length and contain a conserved HEXXH sequence motif that is characteristic of metallopeptidases. This family may therefore belong to an as yet uncharacterised family of peptidase enzymes.
Probab=21.80 E-value=53 Score=27.34 Aligned_cols=12 Identities=50% Similarity=0.648 Sum_probs=9.7
Q ss_pred hHHHHHHHHHHH
Q psy3039 62 DLFTIHHEMGHV 73 (118)
Q Consensus 62 df~t~hhemGHi 73 (118)
-=.|+-|||+|-
T Consensus 196 ~P~T~~HElAHq 207 (318)
T PF12725_consen 196 LPFTICHELAHQ 207 (318)
T ss_pred ccHHHHHHHHHH
Confidence 347899999993
No 85
>cd04280 ZnMc_astacin_like Zinc-dependent metalloprotease, astacin_like subfamily or peptidase family M12A, a group of zinc-dependent proteolytic enzymes with a HExxH zinc-binding site/active site. Members of this family may have an amino terminal propeptide, which is cleaved to yield the active protease domain, which is consequently always found at the N-terminus in multi-domain architectures. This family includes: astacin, a digestive enzyme from Crayfish; meprin, a multiple domain membrane component that is constructed from a homologous alpha and beta chain, proteins involved in (bone) morphogenesis, tolloid from drosophila, and the sea urchin SPAN protein, which may also play a role in development.
Probab=21.24 E-value=52 Score=24.77 Aligned_cols=12 Identities=50% Similarity=0.432 Sum_probs=10.4
Q ss_pred HHHHHHHHHHHH
Q psy3039 63 LFTIHHEMGHVE 74 (118)
Q Consensus 63 f~t~hhemGHi~ 74 (118)
+.++-|||||.-
T Consensus 75 ~g~v~HE~~Hal 86 (180)
T cd04280 75 LGTIVHELMHAL 86 (180)
T ss_pred CchhHHHHHHHh
Confidence 689999999973
No 86
>PRK09400 secE preprotein translocase subunit SecE; Reviewed
Probab=21.04 E-value=33 Score=22.35 Aligned_cols=17 Identities=12% Similarity=0.425 Sum_probs=14.6
Q ss_pred EEecCCCChhhHHHHHH
Q psy3039 52 IKMCTRVNEEDLFTIHH 68 (118)
Q Consensus 52 IkmCt~v~~edf~t~hh 68 (118)
++.|+++|.++|.++--
T Consensus 21 l~~~~KPd~~Ef~~ia~ 37 (61)
T PRK09400 21 LKVARKPTREEFLLVAK 37 (61)
T ss_pred HHHhcCCCHHHHHHHHH
Confidence 68999999999988754
No 87
>COG2514 Predicted ring-cleavage extradiol dioxygenase [General function prediction only]
Probab=20.77 E-value=58 Score=27.10 Aligned_cols=28 Identities=11% Similarity=0.277 Sum_probs=22.8
Q ss_pred HHHHHHHHh-cCCCCCChHHHhhcccccCCC
Q psy3039 3 RTAEEFFTS-INMSAMPPEFWERSMLEKPQG 32 (118)
Q Consensus 3 ~~ae~Ff~S-LGl~~lp~sFW~~S~~~kp~d 32 (118)
.+|+.||++ |||+.... |..+.|-.-.|
T Consensus 180 ~eA~~fY~~~LG~~~~~~--~~~A~F~a~G~ 208 (265)
T COG2514 180 EEAEQFYEDVLGLEVTAR--GPSALFLASGD 208 (265)
T ss_pred HHHHHHHHHhcCCeeeec--CCcceEEecCC
Confidence 689999999 99997766 77778776555
No 88
>PRK10779 zinc metallopeptidase RseP; Provisional
Probab=20.15 E-value=79 Score=27.12 Aligned_cols=10 Identities=40% Similarity=0.813 Sum_probs=7.7
Q ss_pred HHHHHHHHHH
Q psy3039 63 LFTIHHEMGH 72 (118)
Q Consensus 63 f~t~hhemGH 72 (118)
+...-||+||
T Consensus 16 ~li~vHElGH 25 (449)
T PRK10779 16 VLITVHEFGH 25 (449)
T ss_pred HHHHHHHHHH
Confidence 3556899999
No 89
>PF01400 Astacin: Astacin (Peptidase family M12A) This Prosite motif covers only the active site.; InterPro: IPR001506 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M12, subfamily M12A (astacin family, clan MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA and the predicted active site residues for members of this family and thermolysin occur in the motif HEXXH []. The astacin () family of metalloendopeptidases encompasses a range of proteins found in hydra to humans, in mature and developmental systems []. Their functions include activation of growth factors, degradation of polypeptides, and processing of extracellular proteins []. The proteins are synthesised with N-terminal signal and pro-enzyme sequences, and many contain multiple domains C-terminal to the protease domain. They are either secreted from cells, or are associated with the plasma membrane. The astacin molecule adopts a kidney shape, with a deep active-site cleft between its N- and C-terminal domains []. The zinc ion, which lies at the bottom of the cleft, exhibits a unique penta-coordinated mode of binding, involving 3 histidine residues, a tyrosine and a water molecule (which is also bound to the carboxylate side chain of Glu93) []. The N-terminal domain comprises 2 alpha-helices and a 5-stranded beta-sheet. The overall topology of this domain is shared by the archetypal zinc-endopeptidase thermolysin. Astacin protease domains also share common features with serralysins, matrix metalloendopeptidases, and snake venom proteases; they cleave peptide bonds in polypeptides such as insulin B chain and bradykinin, and in proteins such as casein and gelatin; and they have arylamidase activity [].; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 3LQB_A 3EDH_A 3EDG_A 3EDI_A 1IAE_A 1IAB_A 1IAA_A 1AST_A 1IAC_A 1QJJ_A ....
Probab=20.14 E-value=64 Score=24.49 Aligned_cols=13 Identities=46% Similarity=0.616 Sum_probs=11.0
Q ss_pred hHHHHHHHHHHHH
Q psy3039 62 DLFTIHHEMGHVE 74 (118)
Q Consensus 62 df~t~hhemGHi~ 74 (118)
..-+|-||+||.-
T Consensus 79 ~~~~i~HEl~HaL 91 (191)
T PF01400_consen 79 SVGTILHELGHAL 91 (191)
T ss_dssp SHHHHHHHHHHHH
T ss_pred CccchHHHHHHHH
Confidence 5679999999974
No 90
>PRK02391 heat shock protein HtpX; Provisional
Probab=20.13 E-value=64 Score=26.46 Aligned_cols=60 Identities=17% Similarity=0.210 Sum_probs=32.3
Q ss_pred HHHHHHHHhcCCCCCChHHHhhcccccCCCCcccccccccccCCCCceeEEecC-----CCC-hhhHHHHHHHHHHHH
Q psy3039 3 RTAEEFFTSINMSAMPPEFWERSMLEKPQGREVVCHASAWDFHDGKDFRIKMCT-----RVN-EEDLFTIHHEMGHVE 74 (118)
Q Consensus 3 ~~ae~Ff~SLGl~~lp~sFW~~S~~~kp~dr~~~ChasAwdf~~~~D~RIkmCt-----~v~-~edf~t~hhemGHi~ 74 (118)
+..++--...|++ +|+-|.-. +. ++.|+-......-|+--.+ ..+ .|=--.+-||+||+.
T Consensus 80 ~~v~~la~~~~~~-~p~v~v~~-------~~----~~NAfa~G~~~~~~~V~vt~gLl~~L~~~El~aVlaHElgHi~ 145 (296)
T PRK02391 80 AMVERLCALADLP-KPRVAVAD-------SD----VPNAFATGRSPKNAVVCVTTGLMRRLDPDELEAVLAHELSHVK 145 (296)
T ss_pred HHHHHHHHHcCCC-CCcEEEEe-------CC----CCceEEecCCCCCcEEEecHHHHhhCCHHHHHHHHHHHHHHHH
Confidence 4456666778886 56443321 11 4566655433222333332 224 444557899999975
No 91
>PRK01265 heat shock protein HtpX; Provisional
Probab=20.12 E-value=64 Score=27.15 Aligned_cols=15 Identities=33% Similarity=0.532 Sum_probs=10.8
Q ss_pred hhhHHHHHHHHHHHH
Q psy3039 60 EEDLFTIHHEMGHVE 74 (118)
Q Consensus 60 ~edf~t~hhemGHi~ 74 (118)
.|=--.+-|||||+.
T Consensus 138 ~El~aVlAHElgHik 152 (324)
T PRK01265 138 DEIKAVAGHELGHLK 152 (324)
T ss_pred HHHHHHHHHHHHHHH
Confidence 344456899999974
No 92
>PRK02870 heat shock protein HtpX; Provisional
Probab=20.10 E-value=60 Score=27.39 Aligned_cols=61 Identities=16% Similarity=0.364 Sum_probs=30.6
Q ss_pred HHHHHHHHhcCCCCCChHHHhhcccccCCCCcccccccccccCCC-CceeEEecC----CCChhh-HHHHHHHHHHHH
Q psy3039 3 RTAEEFFTSINMSAMPPEFWERSMLEKPQGREVVCHASAWDFHDG-KDFRIKMCT----RVNEED-LFTIHHEMGHVE 74 (118)
Q Consensus 3 ~~ae~Ff~SLGl~~lp~sFW~~S~~~kp~dr~~~ChasAwdf~~~-~D~RIkmCt----~v~~ed-f~t~hhemGHi~ 74 (118)
+..++--...|++.+|+=|. +. . . ++.|+-+... ++-+|-.=+ ..+.+. --.+-|||||+.
T Consensus 119 ~~ve~La~~ag~p~~p~V~v----i~--~-~----~~NAFA~G~~~~~~~Ivvt~GLL~~L~~dEL~aVlAHELgHik 185 (336)
T PRK02870 119 NVVEELLVAAGLRFMPKVYI----ID--A-P----YMNAFASGYSEKSAMVAITTGLLEKLDRDELQAVMAHELSHIR 185 (336)
T ss_pred HHHHHHHHHcCCCCCCeEEE----Ec--C-C----CCceEEecCCCCCcEEEEehHHhhhCCHHHHHHHHHHHHHHHH
Confidence 34566666777765664322 11 1 1 3556655322 233332111 124444 456889999983
Done!