Query 015798
Match_columns 400
No_of_seqs 288 out of 1274
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 09:40:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015798.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015798hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd06160 S2P-M50_like_2 Unchara 99.7 1.7E-17 3.6E-22 153.1 9.6 111 254-367 3-113 (183)
2 cd06164 S2P-M50_SpoIVFB_CBS Sp 99.7 5.9E-16 1.3E-20 146.7 12.8 89 278-372 36-124 (227)
3 cd06161 S2P-M50_SpoIVFB SpoIVF 99.5 7.2E-14 1.6E-18 130.3 12.2 83 282-370 25-107 (208)
4 PRK10779 zinc metallopeptidase 99.4 3.8E-13 8.3E-18 138.0 9.3 84 287-370 7-120 (449)
5 cd06163 S2P-M50_PDZ_RseP-like 99.4 4.1E-13 8.8E-18 124.0 8.3 79 289-367 3-111 (182)
6 cd06159 S2P-M50_PDZ_Arch Uncha 99.3 7.1E-12 1.5E-16 121.8 11.2 83 283-367 106-191 (263)
7 TIGR00054 RIP metalloprotease 99.3 5.5E-12 1.2E-16 128.8 8.7 83 288-370 7-120 (420)
8 cd05709 S2P-M50 Site-2 proteas 99.3 3.5E-12 7.6E-17 114.8 4.7 83 290-372 3-101 (180)
9 cd06162 S2P-M50_PDZ_SREBP Ster 99.1 2.3E-10 5.1E-15 112.3 9.3 72 289-366 129-207 (277)
10 PF02163 Peptidase_M50: Peptid 99.0 3.6E-10 7.8E-15 102.2 3.3 83 290-372 2-113 (192)
11 cd06158 S2P-M50_like_1 Unchara 98.7 3.1E-08 6.6E-13 91.3 6.2 81 290-370 4-105 (181)
12 PF13398 Peptidase_M50B: Pepti 97.8 3E-05 6.5E-10 72.5 6.0 65 296-368 23-88 (200)
13 COG0750 Predicted membrane-ass 97.7 0.00016 3.6E-09 71.5 8.5 82 288-369 6-120 (375)
14 KOG2921 Intramembrane metallop 97.0 0.00056 1.2E-08 70.9 4.2 80 287-369 122-206 (484)
15 COG1994 SpoIVFB Zn-dependent p 96.4 0.0023 5.1E-08 60.9 3.2 75 284-364 41-123 (230)
16 PF11667 DUF3267: Protein of u 87.4 0.27 5.9E-06 41.6 1.2 71 295-372 4-74 (111)
17 PF00413 Peptidase_M10: Matrix 76.5 1.5 3.3E-05 37.9 1.7 14 296-309 106-119 (154)
18 cd04279 ZnMc_MMP_like_1 Zinc-d 72.3 2.3 4.9E-05 37.6 1.8 22 295-316 104-125 (156)
19 PF13485 Peptidase_MA_2: Pepti 66.1 4.9 0.00011 32.6 2.4 17 297-313 27-43 (128)
20 PF05572 Peptidase_M43: Pregna 64.7 3.3 7.1E-05 37.7 1.2 13 296-308 70-82 (154)
21 cd04268 ZnMc_MMP_like Zinc-dep 63.4 4.8 0.0001 35.3 1.9 21 294-314 93-113 (165)
22 cd04278 ZnMc_MMP Zinc-dependen 63.1 3.3 7.2E-05 36.7 0.9 17 295-311 107-123 (157)
23 PF12315 DUF3633: Protein of u 63.0 5.4 0.00012 38.8 2.3 28 285-315 85-112 (212)
24 PF06114 DUF955: Domain of unk 61.9 5.1 0.00011 32.2 1.7 17 297-313 44-60 (122)
25 PF01435 Peptidase_M48: Peptid 58.6 7 0.00015 35.6 2.2 12 296-307 90-101 (226)
26 PF13688 Reprolysin_5: Metallo 58.5 5.5 0.00012 36.1 1.5 21 294-314 141-161 (196)
27 cd00203 ZnMc Zinc-dependent me 55.5 6.1 0.00013 34.5 1.2 20 294-313 95-114 (167)
28 cd04277 ZnMc_serralysin_like Z 55.4 6.6 0.00014 35.7 1.5 20 296-315 114-133 (186)
29 smart00235 ZnMc Zinc-dependent 54.8 6.5 0.00014 33.9 1.3 14 298-311 89-102 (140)
30 PF13582 Reprolysin_3: Metallo 54.6 6.4 0.00014 33.0 1.2 13 297-309 109-121 (124)
31 PF07423 DUF1510: Protein of u 52.3 7.9 0.00017 37.6 1.5 54 173-230 159-213 (217)
32 PF14891 Peptidase_M91: Effect 51.9 9.7 0.00021 34.9 2.0 17 296-312 104-120 (174)
33 PF14247 DUF4344: Domain of un 51.7 15 0.00033 35.6 3.4 25 291-316 88-112 (220)
34 cd04269 ZnMc_adamalysin_II_lik 50.6 11 0.00023 34.4 2.1 20 294-313 130-149 (194)
35 PF01434 Peptidase_M41: Peptid 49.5 14 0.0003 34.9 2.7 60 296-358 29-97 (213)
36 cd04270 ZnMc_TACE_like Zinc-de 49.2 11 0.00023 36.5 1.9 18 294-311 166-183 (244)
37 PF13574 Reprolysin_2: Metallo 49.1 11 0.00024 34.5 1.9 20 295-314 111-130 (173)
38 COG2856 Predicted Zn peptidase 48.7 10 0.00022 36.7 1.6 17 297-313 74-90 (213)
39 PF02031 Peptidase_M7: Strepto 47.4 12 0.00025 34.1 1.7 10 298-307 80-89 (132)
40 cd04327 ZnMc_MMP_like_3 Zinc-d 46.9 11 0.00024 35.0 1.5 14 297-310 94-107 (198)
41 cd04267 ZnMc_ADAM_like Zinc-de 46.8 8.9 0.00019 34.8 0.9 21 294-314 132-152 (192)
42 KOG1832 HIV-1 Vpr-binding prot 46.2 32 0.00068 40.4 5.1 20 4-23 1353-1372(1516)
43 PTZ00429 beta-adaptin; Provisi 44.7 20 0.00044 40.6 3.4 32 75-106 608-639 (746)
44 TIGR01241 FtsH_fam ATP-depende 44.2 12 0.00026 39.5 1.5 58 297-360 313-382 (495)
45 PHA02456 zinc metallopeptidase 42.8 15 0.00032 33.1 1.6 19 298-316 82-100 (141)
46 PRK03001 M48 family peptidase; 42.7 16 0.00034 36.0 2.0 12 296-307 125-136 (283)
47 PF13583 Reprolysin_4: Metallo 41.9 14 0.00029 34.9 1.3 18 297-314 139-156 (206)
48 PF01421 Reprolysin: Reprolysi 41.7 19 0.00041 33.0 2.2 22 293-314 129-150 (199)
49 PRK03982 heat shock protein Ht 41.3 17 0.00037 35.8 2.0 12 296-307 126-137 (288)
50 PF10263 SprT-like: SprT-like 41.2 20 0.00043 31.5 2.2 18 294-311 59-76 (157)
51 PF13699 DUF4157: Domain of un 40.5 17 0.00036 29.8 1.5 12 297-308 63-74 (79)
52 PF12388 Peptidase_M57: Dual-a 39.1 18 0.00039 35.1 1.7 24 291-314 129-152 (211)
53 COG5309 Exo-beta-1,3-glucanase 38.7 48 0.001 33.8 4.6 61 158-222 218-281 (305)
54 smart00731 SprT SprT homologue 38.1 20 0.00043 31.9 1.7 16 296-311 60-75 (146)
55 COG0501 HtpX Zn-dependent prot 37.8 21 0.00046 34.2 2.0 11 297-307 159-169 (302)
56 PRK04897 heat shock protein Ht 37.0 22 0.00047 35.5 2.0 12 296-307 138-149 (298)
57 PRK01345 heat shock protein Ht 35.6 23 0.00051 35.8 2.0 12 296-307 125-136 (317)
58 cd04272 ZnMc_salivary_gland_MP 35.0 24 0.00051 33.2 1.8 19 296-314 146-164 (220)
59 PF01432 Peptidase_M3: Peptida 34.8 25 0.00053 36.4 2.0 21 296-316 243-263 (458)
60 PF01447 Peptidase_M4: Thermol 34.8 25 0.00055 32.1 1.9 12 297-308 137-148 (150)
61 COG3824 Predicted Zn-dependent 34.6 18 0.00038 32.9 0.8 15 293-307 107-121 (136)
62 cd06459 M3B_Oligoendopeptidase 34.4 23 0.0005 35.7 1.7 13 296-308 223-235 (427)
63 PRK03072 heat shock protein Ht 34.2 26 0.00056 34.9 2.0 12 296-307 128-139 (288)
64 PF09471 Peptidase_M64: IgA Pe 33.3 22 0.00048 35.3 1.3 15 295-309 216-230 (264)
65 PRK02391 heat shock protein Ht 33.2 27 0.00059 35.0 2.0 10 297-306 135-144 (296)
66 PRK05457 heat shock protein Ht 32.4 29 0.00062 34.6 2.0 11 296-306 135-145 (284)
67 PRK12462 phosphoserine aminotr 31.4 86 0.0019 32.6 5.3 67 149-223 8-76 (364)
68 TIGR02289 M3_not_pepF oligoend 30.9 29 0.00062 37.3 1.8 12 296-307 338-349 (549)
69 PRK02870 heat shock protein Ht 30.3 32 0.0007 35.3 2.0 11 296-306 174-184 (336)
70 PRK01265 heat shock protein Ht 30.3 32 0.0007 35.2 2.0 10 297-306 142-151 (324)
71 KOG2719 Metalloprotease [Gener 29.0 32 0.00069 36.8 1.7 19 295-313 280-298 (428)
72 PLN02452 phosphoserine transam 28.9 1E+02 0.0023 31.6 5.4 67 149-223 11-79 (365)
73 cd04280 ZnMc_astacin_like Zinc 28.4 30 0.00066 31.9 1.3 14 297-310 76-89 (180)
74 PRK04860 hypothetical protein; 28.2 56 0.0012 30.3 3.0 21 293-313 61-81 (160)
75 TIGR00181 pepF oligoendopeptid 27.8 32 0.0007 37.0 1.6 12 296-307 379-390 (591)
76 cd06258 Peptidase_M3_like The 27.4 37 0.0008 33.9 1.8 14 297-310 156-169 (365)
77 KOG3320 40S ribosomal protein 27.2 90 0.0019 30.1 4.2 29 195-223 72-100 (192)
78 PF06167 Peptidase_M90: Glucos 26.7 38 0.00082 33.5 1.7 14 297-310 156-169 (253)
79 cd06455 M3A_TOP Peptidase M3 T 26.2 41 0.00088 35.5 1.9 23 195-217 157-179 (472)
80 TIGR02290 M3_fam_3 oligoendope 26.2 38 0.00082 36.6 1.7 11 297-307 377-387 (587)
81 cd04283 ZnMc_hatching_enzyme Z 26.1 38 0.00082 31.9 1.5 14 298-311 80-93 (182)
82 COG4783 Putative Zn-dependent 25.6 42 0.00091 36.4 1.9 12 295-306 130-141 (484)
83 KOG0391 SNF2 family DNA-depend 25.5 77 0.0017 38.6 4.0 36 159-194 583-618 (1958)
84 PF01431 Peptidase_M13: Peptid 25.2 39 0.00085 31.0 1.4 18 292-309 33-50 (206)
85 PF04298 Zn_peptidase_2: Putat 24.9 52 0.0011 32.3 2.2 15 296-310 90-104 (222)
86 PF04228 Zn_peptidase: Putativ 24.6 64 0.0014 32.7 2.9 16 296-311 171-186 (292)
87 PF06262 DUF1025: Possibl zinc 24.0 52 0.0011 28.2 1.9 14 294-307 72-85 (97)
88 PRK10733 hflB ATP-dependent me 24.0 62 0.0013 35.8 2.9 38 296-336 409-448 (644)
89 PF01400 Astacin: Astacin (Pep 23.9 47 0.001 30.9 1.7 13 298-310 82-94 (191)
90 PRK11037 hypothetical protein; 23.9 1.9E+02 0.0042 24.5 5.1 65 152-217 4-81 (83)
91 cd04281 ZnMc_BMP1_TLD Zinc-dep 23.9 43 0.00093 32.0 1.5 12 298-309 90-101 (200)
92 cd04275 ZnMc_pappalysin_like Z 22.9 12 0.00027 36.1 -2.4 12 297-308 139-150 (225)
93 cd04276 ZnMc_MMP_like_2 Zinc-d 22.8 58 0.0013 31.0 2.1 18 294-311 115-132 (197)
94 PF01863 DUF45: Protein of unk 22.2 44 0.00096 30.4 1.2 14 294-307 163-176 (205)
95 cd04927 ACT_ACR-like_2 Second 22.1 1.2E+02 0.0026 24.0 3.5 35 169-214 40-74 (76)
96 TIGR00341 conserved hypothetic 22.1 9E+02 0.02 25.1 11.0 64 155-224 9-79 (325)
97 cd06456 M3A_DCP_Oligopeptidase 21.9 56 0.0012 34.3 2.0 20 196-215 106-125 (422)
98 COG5495 Uncharacterized conser 21.5 55 0.0012 33.0 1.7 37 157-215 129-165 (289)
99 TIGR01364 serC_1 phosphoserine 21.5 1.6E+02 0.0035 29.8 5.0 60 155-222 2-63 (349)
100 TIGR03296 M6dom_TIGR03296 M6 f 21.5 22 0.00048 35.2 -1.0 12 296-307 166-177 (286)
101 cd04271 ZnMc_ADAM_fungal Zinc- 21.2 33 0.00072 33.0 0.1 15 297-311 147-161 (228)
102 cd06457 M3A_MIP Peptidase M3 m 20.7 60 0.0013 34.2 1.9 16 297-312 250-265 (458)
103 KOG2661 Peptidase family M48 [ 20.6 70 0.0015 33.7 2.3 38 159-196 144-185 (424)
104 PF04155 Ground-like: Ground-l 20.3 75 0.0016 25.4 2.0 28 191-218 18-46 (76)
No 1
>cd06160 S2P-M50_like_2 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the S2P/M50 family of RIP proteases use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. In eukaryotic cells they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum stress responses. In prokaryotes they regulate such processes as sporulation, cell division, stress response, and cell differentiation. This group includes bacterial, eukaryotic, and Archaeal S2P/M50s homologs with additional putative N- and C-terminal transmembrane spanning regions, relative to the core protein, and no PDZ domains.
Probab=99.72 E-value=1.7e-17 Score=153.09 Aligned_cols=111 Identities=39% Similarity=0.644 Sum_probs=92.8
Q ss_pred HHHHHHHHHHhhccccccccccccccchHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHcCCeecCcccccceeeeeeeEE
Q 015798 254 FGLVTVFTLLLRNVPALQSNLLSTFDNLNLLTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAI 333 (400)
Q Consensus 254 l~L~Tl~Tl~~~g~p~L~p~~~~~~~~~~~l~~glp~aL~l~~iLliHElGH~laARr~GVkvs~P~FIP~i~Lg~fGg~ 333 (400)
++++|+.+....+.-.... +..+++..+..++++++++++++++||+||+++||++|+|+..+.++|.+.+|++|++
T Consensus 3 ~~~~s~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~l~l~~~l~iHElgH~~~A~~~G~~~~~~~l~P~~~~G~~G~~ 79 (183)
T cd06160 3 LLVLTLLTTLLVGAWLSGN---DVPGNPLLLLQGLPFALALLAILGIHEMGHYLAARRHGVKASLPYFIPFPFIGTFGAF 79 (183)
T ss_pred HHHHHHHHHHHHHHHHhcc---cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCccceeeeehHhcCcEEEE
Confidence 4566666665544322111 2235677888899999999999999999999999999999999999998889999999
Q ss_pred EEeccCCCCccceeEEEEhhHHHHHHHHHHHHHH
Q 015798 334 TRIRNIVSKREDLLKVAAAGPLAGFSLGFVLFLV 367 (400)
Q Consensus 334 t~i~s~~~~r~alfdIAiAGPlaglllAlill~i 367 (400)
+++++..++++++++|++|||++|++++++++++
T Consensus 80 ~~~~~~~~~~~~~~~IalAGPl~nl~lali~~~~ 113 (183)
T cd06160 80 IRMRSPIPNRKALFDIALAGPLAGLLLALPVLII 113 (183)
T ss_pred EEecCCCCChhHhehhhhhHHHHHHHHHHHHHHH
Confidence 9999988899999999999999999999887664
No 2
>cd06164 S2P-M50_SpoIVFB_CBS SpoIVFB Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50B), regulates intramembrane proteolysis (RIP), and is involved in the pro-sigmaK pathway of bacterial spore formation. In this subgroup, SpoIVFB (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain. SpoIVFB is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA (bypass-of-forespore A), and SpoIVB (sporulation protein, stage IV cell wall formation, B locus). SpoIVFB is negatively regulated by SpoIVFA and BofA and activated by SpoIVB. It is thought that SpoIVFB, SpoIVFA, and BofA are located in the mother-cell membrane that surrounds the forespore and that SpoIVB is secreted from the forespore into the space between the two where it activates SpoIVFB. It has been proposed tha
Probab=99.67 E-value=5.9e-16 Score=146.68 Aligned_cols=89 Identities=27% Similarity=0.416 Sum_probs=80.6
Q ss_pred ccchHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHcCCeecCcccccceeeeeeeEEEEeccCCCCccceeEEEEhhHHHH
Q 015798 278 FDNLNLLTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAITRIRNIVSKREDLLKVAAAGPLAG 357 (400)
Q Consensus 278 ~~~~~~l~~glp~aL~l~~iLliHElGH~laARr~GVkvs~P~FIP~i~Lg~fGg~t~i~s~~~~r~alfdIAiAGPlag 357 (400)
..+..+|..++.+++++++++++||+||+++||++|+++. ++++.+|||++++++..+++++++.|++|||++|
T Consensus 36 ~~~~~~~~~g~~~~~~l~~~v~iHElgH~~~A~~~G~~v~------~i~l~p~Gg~~~~~~~~~~~~~~~~IalAGPl~N 109 (227)
T cd06164 36 ALGAVAWLLGLAAALLLFASVLLHELGHSLVARRYGIPVR------SITLFLFGGVARLEREPETPGQEFVIAIAGPLVS 109 (227)
T ss_pred ccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCeEC------eEEEEeeeEEEEecCCCCCHHHHhhhhhhHHHHH
Confidence 3456678889999999999999999999999999999996 8899999999999998889999999999999999
Q ss_pred HHHHHHHHHHHHhcC
Q 015798 358 FSLGFVLFLVGFIFP 372 (400)
Q Consensus 358 lllAlill~iGl~ls 372 (400)
++++++++++....+
T Consensus 110 llla~i~~~l~~~~~ 124 (227)
T cd06164 110 LVLALLFLLLSLALP 124 (227)
T ss_pred HHHHHHHHHHHHHhc
Confidence 999998887766544
No 3
>cd06161 S2P-M50_SpoIVFB SpoIVFB Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50B), regulates intramembrane proteolysis (RIP), and is involved in the pro-sigmaK pathway of bacterial spore formation. SpoIVFB (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA (bypass-of-forespore A), and SpoIVB (sporulation protein, stage IV cell wall formation, B locus). SpoIVFB is negatively regulated by SpoIVFA and BofA and activated by SpoIVB. It is thought that SpoIVFB, SpoIVFA, and BofA are located in the mother-cell membrane that surrounds the forespore and that SpoIVB is secreted from the forespore into the space between the two where it activates SpoIVFB.
Probab=99.53 E-value=7.2e-14 Score=130.31 Aligned_cols=83 Identities=28% Similarity=0.437 Sum_probs=75.1
Q ss_pred HHHHhhHHHHHHHHHHHHHHHHHHHHHHHHcCCeecCcccccceeeeeeeEEEEeccCCCCccceeEEEEhhHHHHHHHH
Q 015798 282 NLLTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAITRIRNIVSKREDLLKVAAAGPLAGFSLG 361 (400)
Q Consensus 282 ~~l~~glp~aL~l~~iLliHElGH~laARr~GVkvs~P~FIP~i~Lg~fGg~t~i~s~~~~r~alfdIAiAGPlaglllA 361 (400)
..|..++.++++++.++++||+||+++||++|+++. .+.+.+|||++++++...++++++.|++|||++|++++
T Consensus 25 ~~~~~~~~~~l~l~~~v~iHElgH~~~A~~~G~~v~------~i~l~p~Gg~~~~~~~~~~~~~~~lIalAGPl~n~~la 98 (208)
T cd06161 25 VAWLLGLLEALLLFLSVLLHELGHALVARRYGIRVR------SITLLPFGGVAELEEEPETPKEEFVIALAGPLVSLLLA 98 (208)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcc------ceEEEeeeeeeeeccCCCChhHheeeeeehHHHHHHHH
Confidence 457788999999999999999999999999999985 89999999999998877789999999999999999999
Q ss_pred HHHHHHHHh
Q 015798 362 FVLFLVGFI 370 (400)
Q Consensus 362 lill~iGl~ 370 (400)
++++++...
T Consensus 99 ~~~~~l~~~ 107 (208)
T cd06161 99 GLFYLLYLL 107 (208)
T ss_pred HHHHHHHHH
Confidence 988765543
No 4
>PRK10779 zinc metallopeptidase RseP; Provisional
Probab=99.42 E-value=3.8e-13 Score=137.96 Aligned_cols=84 Identities=21% Similarity=0.316 Sum_probs=66.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHcCCeec-----Ccccccc----------eeeeeeeEEEEeccCC-----------
Q 015798 287 GLPGALVTALVIGVHELGHILAAKSTGVELG-----VPYFVPS----------WQIGSFGAITRIRNIV----------- 340 (400)
Q Consensus 287 glp~aL~l~~iLliHElGH~laARr~GVkvs-----~P~FIP~----------i~Lg~fGg~t~i~s~~----------- 340 (400)
.+.+.+++.+++++||+|||++||++||++. ++.-|.+ +.+.|+|||++|.++.
T Consensus 7 i~~fil~l~~li~vHElGHfl~Ar~~gv~V~~FsiGfGp~l~~~~~~~~Tey~i~~iPlGGyVk~~~e~~~~~~~~~~~~ 86 (449)
T PRK10779 7 LAAFIVALGVLITVHEFGHFWVARRCGVRVERFSIGFGKALWRRTDRQGTEYVIALIPLGGYVKMLDERVEPVAPELRHH 86 (449)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHcCCeeeEEEeecChhHeeEecCCCcEEEEEEEcCCCeeecCCCCCCcCChhhhhh
Confidence 4456677778999999999999999999993 2222222 3467899999997652
Q ss_pred ----CCccceeEEEEhhHHHHHHHHHHHHHHHHh
Q 015798 341 ----SKREDLLKVAAAGPLAGFSLGFVLFLVGFI 370 (400)
Q Consensus 341 ----~~r~alfdIAiAGPlaglllAlill~iGl~ 370 (400)
++.|+++.|++|||++|+++|++++++-+.
T Consensus 87 ~f~~k~~~~R~~i~~AGp~~N~ila~~~~~~~~~ 120 (449)
T PRK10779 87 AFNNKTVGQRAAIIAAGPIANFIFAIFAYWLVFI 120 (449)
T ss_pred hhccCCHHHhhhhhhhhHHHHHHHHHHHHHHHHh
Confidence 357889999999999999999998876553
No 5
>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=99.42 E-value=4.1e-13 Score=123.99 Aligned_cols=79 Identities=34% Similarity=0.375 Sum_probs=62.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCeec-----Cccccc---------ceeeeeeeEEEEeccCCC-------------
Q 015798 289 PGALVTALVIGVHELGHILAAKSTGVELG-----VPYFVP---------SWQIGSFGAITRIRNIVS------------- 341 (400)
Q Consensus 289 p~aL~l~~iLliHElGH~laARr~GVkvs-----~P~FIP---------~i~Lg~fGg~t~i~s~~~------------- 341 (400)
.+.+++.+++++||+||+++||++|+++. ++..+- .+.+.++||+++++++.+
T Consensus 3 ~~~i~l~~~v~iHElGH~~~Ar~~Gv~v~~f~iGfGp~l~~~~~~~t~~~i~~iPlGGyv~~~~~~~~~~~~~~~~~~~f 82 (182)
T cd06163 3 AFILVLGILIFVHELGHFLVAKLFGVKVEEFSIGFGPKLFSFKKGETEYSISAIPLGGYVKMLGEDPEEEADPEDDPRSF 82 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCeeeEeeeecCceeeeeecCCeEEEEEEEEeccEEEecCCCcccccccccchHHH
Confidence 45667888999999999999999999984 111111 145788999999986432
Q ss_pred ---CccceeEEEEhhHHHHHHHHHHHHHH
Q 015798 342 ---KREDLLKVAAAGPLAGFSLGFVLFLV 367 (400)
Q Consensus 342 ---~r~alfdIAiAGPlaglllAlill~i 367 (400)
++++++.|++|||++|+++|++++++
T Consensus 83 ~~~~~~~ri~V~lAGP~~NlilA~i~~~~ 111 (182)
T cd06163 83 NSKPVWQRILIVFAGPLANFLLAIVLFAV 111 (182)
T ss_pred ccCCcchhhhhhhhHHHHHHHHHHHHHHH
Confidence 57889999999999999999987653
No 6
>cd06159 S2P-M50_PDZ_Arch Uncharacterized Archaeal homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the S2P/M50 family of RIP proteases use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. In eukaryotic cells they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum stress responses. In prokaryotes they regulate such processes as sporulation, cell division, stress response, and cell differentiation. This group appears to be limited to Archaeal S2P/M50s homologs with additional putative N-terminal transmembrane spanning regions, relative to the core protein, and either one or two PDZ domains present.
Probab=99.33 E-value=7.1e-12 Score=121.83 Aligned_cols=83 Identities=23% Similarity=0.264 Sum_probs=65.6
Q ss_pred HHHhhHHHHHHHHHHHHHHHHHHHHHHHHcCCeecCcccccceeeeeeeEEEEeccCC---CCccceeEEEEhhHHHHHH
Q 015798 283 LLTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAITRIRNIV---SKREDLLKVAAAGPLAGFS 359 (400)
Q Consensus 283 ~l~~glp~aL~l~~iLliHElGH~laARr~GVkvs~P~FIP~i~Lg~fGg~t~i~s~~---~~r~alfdIAiAGPlagll 359 (400)
++...+.+++++++++.+||+||+++||++|+++..--+ .+.+.++||++++.+.. .++++++.|++|||++|++
T Consensus 106 ~~i~~~~~~iaL~isv~iHElgHa~~Ar~~G~~V~~iGl--~l~~ip~Gg~v~~~~~~~~~~~~~~~~~Ia~AGP~~Nlv 183 (263)
T cd06159 106 IFIPLPYGIIALVVGVVVHELSHGILARVEGIKVKSGGL--LLLIIPPGAFVEPDEEELNKADRRIRLRIFAAGVTANFV 183 (263)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCEECchhH--HHHhhhcEEEEEecchhhccCChhheeeeeeehHHHHHH
Confidence 445666777888899999999999999999999962100 01123589999997755 4688999999999999999
Q ss_pred HHHHHHHH
Q 015798 360 LGFVLFLV 367 (400)
Q Consensus 360 lAlill~i 367 (400)
+|++++++
T Consensus 184 la~i~~~l 191 (263)
T cd06159 184 VALIAFAL 191 (263)
T ss_pred HHHHHHHH
Confidence 99988764
No 7
>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=99.30 E-value=5.5e-12 Score=128.75 Aligned_cols=83 Identities=25% Similarity=0.390 Sum_probs=64.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHcCCeec-----Ccccccc---------eeeeeeeEEEEeccCC-------------
Q 015798 288 LPGALVTALVIGVHELGHILAAKSTGVELG-----VPYFVPS---------WQIGSFGAITRIRNIV------------- 340 (400)
Q Consensus 288 lp~aL~l~~iLliHElGH~laARr~GVkvs-----~P~FIP~---------i~Lg~fGg~t~i~s~~------------- 340 (400)
+.+.+++.+++++||+|||++||++|+++. ++.-|.+ +.+.++|||+++.++.
T Consensus 7 i~~~~~~~~~v~~HE~gH~~~a~~~g~~v~~FsiGfGp~l~~~~~~~tey~i~~~plGg~v~~~g~~~~~~~~~~~~~~~ 86 (420)
T TIGR00054 7 LASILALAVLIFVHELGHFLAARLCGIKVERFSIGFGPKILKFKKNGTEYAISLIPLGGYVKMKGLDKEMEVKPPETDGD 86 (420)
T ss_pred HHHHHHHHHHHHHHhHHHHHHHHHcCCEEEEEEEccCchheEEecCCeEEEEEEecCcceEeeccCCcccccCCcchhhh
Confidence 334667778999999999999999999983 3222222 4578899999995221
Q ss_pred ----CCccceeEEEEhhHHHHHHHHHHHHHHHHh
Q 015798 341 ----SKREDLLKVAAAGPLAGFSLGFVLFLVGFI 370 (400)
Q Consensus 341 ----~~r~alfdIAiAGPlaglllAlill~iGl~ 370 (400)
.++++++.|++|||++|+++|++++++.+.
T Consensus 87 ~f~~~~~~~r~~i~~aGp~~N~~~a~~~~~~~~~ 120 (420)
T TIGR00054 87 LFNNKSVFQKAIIIFAGPLANFIFAIFVYIFISL 120 (420)
T ss_pred hhccCCHHHHHHhhhcccHHHHHHHHHHHHHHHh
Confidence 367789999999999999999999886543
No 8
>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=99.27 E-value=3.5e-12 Score=114.80 Aligned_cols=83 Identities=30% Similarity=0.398 Sum_probs=65.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCeec----Cccccc-------ceeeeeeeEEEEeccCCCC-----ccceeEEEEhh
Q 015798 290 GALVTALVIGVHELGHILAAKSTGVELG----VPYFVP-------SWQIGSFGAITRIRNIVSK-----REDLLKVAAAG 353 (400)
Q Consensus 290 ~aL~l~~iLliHElGH~laARr~GVkvs----~P~FIP-------~i~Lg~fGg~t~i~s~~~~-----r~alfdIAiAG 353 (400)
+.+++++++.+||+||+++||++|+++. ...+.| .+.+.++||++++.+...+ +++++.|++||
T Consensus 3 ~~~~~~i~i~iHE~gH~~~A~~~G~~~~~~~~~~~~~~~~~~~~~~~~~ip~gG~~~~~~~~~~~~~~~~~~~~~i~laG 82 (180)
T cd05709 3 FILALLISVTVHELGHALVARRLGVKVARFSGGFTLNPLKHGDPYGIILIPLGGYAKPVGENPRAFKKPRWQRLLVALAG 82 (180)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCCchheeeeEEECCcCCCCEehHHHHhccCeeccCCCChhhhccchhhhhhhhhhh
Confidence 5667788999999999999999999872 001111 2234568999999887654 88999999999
Q ss_pred HHHHHHHHHHHHHHHHhcC
Q 015798 354 PLAGFSLGFVLFLVGFIFP 372 (400)
Q Consensus 354 PlaglllAlill~iGl~ls 372 (400)
|++|+++|++++++....+
T Consensus 83 Pl~nllla~i~~~~~~~~~ 101 (180)
T cd05709 83 PLANLLLALLLLLLLLLLG 101 (180)
T ss_pred HHHHHHHHHHHHHHHHHHc
Confidence 9999999999988766543
No 9
>cd06162 S2P-M50_PDZ_SREBP Sterol regulatory element-binding protein (SREBP) Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50A), regulates intramembrane proteolysis (RIP) of SREBP and is part of a signal transduction mechanism involved in sterol and lipid metabolism. In sterol-depleted mammalian cells, a two-step proteolytic process releases the N-terminal domains of SREBPs from membranes of the endoplasmic reticulum (ER). These domains translocate into the nucleus, where they activate genes of cholesterol and fatty acid biosynthesis. The first cleavage occurs at Site-1 within the ER lumen to generate an intermediate that is subsequently released from the membrane by cleavage at Site-2, which lies within the first transmembrane domain. It is the second proteolytic step that is carried out by the SREBP Site-2 protease (S2P) which is present in this CD family. This group appears to be limited to eumetazoan proteins and contains one PDZ domain.
Probab=99.11 E-value=2.3e-10 Score=112.31 Aligned_cols=72 Identities=28% Similarity=0.289 Sum_probs=60.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCeecCcccccceeeeee----eEEEEeccC---CCCccceeEEEEhhHHHHHHHH
Q 015798 289 PGALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSF----GAITRIRNI---VSKREDLLKVAAAGPLAGFSLG 361 (400)
Q Consensus 289 p~aL~l~~iLliHElGH~laARr~GVkvs~P~FIP~i~Lg~f----Gg~t~i~s~---~~~r~alfdIAiAGPlaglllA 361 (400)
.+.+++++++.+||+||+++||++|+++. ++.+..| ||+++..+. ..++++++.|++|||++|+++|
T Consensus 129 ~~l~al~isvvvHElgHal~A~~~gi~V~------~iGl~l~~~~pGa~ve~~~e~~~~~~~~~~l~Ia~AGp~~NlvLa 202 (277)
T cd06162 129 YYFTALLISGVVHEMGHGVAAVREQVRVN------GFGIFFFIIYPGAYVDLFTDHLNLISPVQQLRIFCAGVWHNFVLG 202 (277)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCeec------eEEEeeeeccCeeEEeecccccccCChhhhhheehhhHHHHHHHH
Confidence 34566788999999999999999999997 6666566 999998543 2467789999999999999999
Q ss_pred HHHHH
Q 015798 362 FVLFL 366 (400)
Q Consensus 362 lill~ 366 (400)
+++++
T Consensus 203 ~i~~~ 207 (277)
T cd06162 203 LVGYL 207 (277)
T ss_pred HHHHH
Confidence 98765
No 10
>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=98.96 E-value=3.6e-10 Score=102.19 Aligned_cols=83 Identities=27% Similarity=0.297 Sum_probs=47.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCeecCc-----cccc---------ceeeeeeeEEEEeccC---------------C
Q 015798 290 GALVTALVIGVHELGHILAAKSTGVELGVP-----YFVP---------SWQIGSFGAITRIRNI---------------V 340 (400)
Q Consensus 290 ~aL~l~~iLliHElGH~laARr~GVkvs~P-----~FIP---------~i~Lg~fGg~t~i~s~---------------~ 340 (400)
+.+++.+++.+||+||+++||++|+|+... ..+. .+.+.++||+..+.+. .
T Consensus 2 ~~~~~~i~i~~HE~gH~~~a~~~G~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~g~~~~~G~~~~~~~~~~~~~~~~~ 81 (192)
T PF02163_consen 2 FILALLISIVLHELGHALAARLYGDKVPRFEGGFGLNIFSHRDGFTIWSIRLIPLGGYVGGFGWSNVNPFPAPISESFRK 81 (192)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHTTT--B--EEE------------------------------------------------
T ss_pred CcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccCC
Confidence 456777899999999999999999998422 1111 1123456776544332 2
Q ss_pred CCccceeEEEEhhHHHHHHHHHHHHHHHHhcC
Q 015798 341 SKREDLLKVAAAGPLAGFSLGFVLFLVGFIFP 372 (400)
Q Consensus 341 ~~r~alfdIAiAGPlaglllAlill~iGl~ls 372 (400)
.++++++.|++|||++|++++++++++....+
T Consensus 82 ~~~~~~~~i~laGp~~nllla~i~~~l~~~~~ 113 (192)
T PF02163_consen 82 RSRWKRILIALAGPLANLLLAIIALLLLYLLS 113 (192)
T ss_dssp --TTCHHHHHHHHHHHHHHHHHHHHHHTTS--
T ss_pred CCccceEEEEEEcHHHHHHHHHHHHHHHHHHh
Confidence 46788999999999999999999887765443
No 11
>cd06158 S2P-M50_like_1 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the S2P/M50 family of RIP proteases use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. In eukaryotic cells they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum stress responses. In prokaryotes they regulate such processes as sporulation, cell division, stress response, and cell differentiation. This group includes bacterial, eukaryotic, and Archaeal S2P/M50s homologs with a minimal core protein and no PDZ domains.
Probab=98.68 E-value=3.1e-08 Score=91.28 Aligned_cols=81 Identities=21% Similarity=0.232 Sum_probs=53.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCeecC----cccccc--------ee--e--eeeeEEEEecc-----CCCCccceeE
Q 015798 290 GALVTALVIGVHELGHILAAKSTGVELGV----PYFVPS--------WQ--I--GSFGAITRIRN-----IVSKREDLLK 348 (400)
Q Consensus 290 ~aL~l~~iLliHElGH~laARr~GVkvs~----P~FIP~--------i~--L--g~fGg~t~i~s-----~~~~r~alfd 348 (400)
..++++.++..||+||+++|+++|.+... -.+-|- +. + ...+|..+-.. ..++|++++.
T Consensus 4 ~~~~~~~~i~~HE~aHa~~A~~~Gd~t~~~~Grltlnp~~hid~~g~l~~~~~~~~~~G~a~p~~~~~~~~~~~r~~~~~ 83 (181)
T cd06158 4 VIIAVLLAITLHEFAHAYVAYRLGDPTARRAGRLTLNPLAHIDPIGTIILPLLLPFLFGWAKPVPVNPRNFKNPRRGMLL 83 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCcHHHHcCceecCcHHhcCcchHHHHHHHHHhCeEEecccccChHhhcccHhhHhh
Confidence 44567779999999999999999998731 111110 00 0 01244443221 1235678999
Q ss_pred EEEhhHHHHHHHHHHHHHHHHh
Q 015798 349 VAAAGPLAGFSLGFVLFLVGFI 370 (400)
Q Consensus 349 IAiAGPlaglllAlill~iGl~ 370 (400)
|++|||++|++++++++++...
T Consensus 84 valAGP~~n~~la~i~~~~~~~ 105 (181)
T cd06158 84 VSLAGPLSNLLLALLFALLLRL 105 (181)
T ss_pred hhhhhHHHHHHHHHHHHHHHHH
Confidence 9999999999999887765443
No 12
>PF13398 Peptidase_M50B: Peptidase M50B-like
Probab=97.83 E-value=3e-05 Score=72.46 Aligned_cols=65 Identities=31% Similarity=0.274 Sum_probs=55.6
Q ss_pred HHHHHHHHHHHHHHHHcCCeecCcccccceeeee-eeEEEEeccCCCCccceeEEEEhhHHHHHHHHHHHHHHH
Q 015798 296 LVIGVHELGHILAAKSTGVELGVPYFVPSWQIGS-FGAITRIRNIVSKREDLLKVAAAGPLAGFSLGFVLFLVG 368 (400)
Q Consensus 296 ~iLliHElGH~laARr~GVkvs~P~FIP~i~Lg~-fGg~t~i~s~~~~r~alfdIAiAGPlaglllAlill~iG 368 (400)
...++||+||.++|...|-++. .+.+.+ -+|.+..+. +++...+.+++|||++..+++..++..+
T Consensus 23 l~t~~HE~gHal~a~l~G~~v~------~i~l~~~~~G~~~~~~--~~~~~~~~i~~aGyl~~~l~g~~~~~~~ 88 (200)
T PF13398_consen 23 LVTFVHELGHALAALLTGGRVK------GIVLFPDGSGVTVSSG--PSGIGRFLIALAGYLGPALFGLLLLWLL 88 (200)
T ss_pred HHHHHHHHHHHHHHHHhCCCcc------eEEEEeCCCceEEEec--CCCcchhHHhcccchHHHHHHHHHHHHH
Confidence 3588999999999999999997 777766 588888877 6777889999999999999998777665
No 13
>COG0750 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]
Probab=97.66 E-value=0.00016 Score=71.55 Aligned_cols=82 Identities=26% Similarity=0.373 Sum_probs=59.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHcCCeec-----Ccc-c--cc-c------eeeeeeeEEEEeccCCC-----------
Q 015798 288 LPGALVTALVIGVHELGHILAAKSTGVELG-----VPY-F--VP-S------WQIGSFGAITRIRNIVS----------- 341 (400)
Q Consensus 288 lp~aL~l~~iLliHElGH~laARr~GVkvs-----~P~-F--IP-~------i~Lg~fGg~t~i~s~~~----------- 341 (400)
+.+.+.+..++..||+||+|.||++|+++. +.. + +. . +...++||++++..+..
T Consensus 6 i~~i~~~~~lv~~he~gh~~~a~~~~~~v~~f~ig~g~~l~~~~~~~~~~~~i~~~plggyv~~~~~~~~~~~~~~~~~~ 85 (375)
T COG0750 6 IAFIIALGVLVFVHELGHFWVARRCGVKVERFSIGFGPKLFSRKDKGGTEYVLSAIPLGGYVKMLGEDAEEVVLKGPEPR 85 (375)
T ss_pred HHHHHHHHHHHHHHHHhhHHHHHhcCceeEEEEeccCcceEEEEcCCceEEEEeecCccceEEEecCccccccccccCcc
Confidence 445566777899999999999999999994 111 0 00 1 23456899988776432
Q ss_pred -------CccceeEEEEhhHHHHHHHHHHHHHHHH
Q 015798 342 -------KREDLLKVAAAGPLAGFSLGFVLFLVGF 369 (400)
Q Consensus 342 -------~r~alfdIAiAGPlaglllAlill~iGl 369 (400)
+-+.++.+.++||++|+++++..++...
T Consensus 86 ~~~f~~~~~~~~~~~~~~Gp~~n~i~~~~~~~~~~ 120 (375)
T COG0750 86 PRAFNAKSVWQRIAIVFAGPLFNFILAIVLFVVLF 120 (375)
T ss_pred hhhhhcccccchhheeechHHHHHHHHHHHHHhhh
Confidence 2233789999999999998888777654
No 14
>KOG2921 consensus Intramembrane metalloprotease (sterol-regulatory element-binding protein (SREBP) protease) [Posttranslational modification, protein turnover, chaperones]
Probab=97.04 E-value=0.00056 Score=70.89 Aligned_cols=80 Identities=29% Similarity=0.361 Sum_probs=57.0
Q ss_pred hHHH-HHHHHHHHHHHHHHHHHHHHHcCCeec-CcccccceeeeeeeEEEEeccCCC---CccceeEEEEhhHHHHHHHH
Q 015798 287 GLPG-ALVTALVIGVHELGHILAAKSTGVELG-VPYFVPSWQIGSFGAITRIRNIVS---KREDLLKVAAAGPLAGFSLG 361 (400)
Q Consensus 287 glp~-aL~l~~iLliHElGH~laARr~GVkvs-~P~FIP~i~Lg~fGg~t~i~s~~~---~r~alfdIAiAGPlaglllA 361 (400)
.++| ...+.+.+.+||+||+|+|.+.||++. +..|| ..-.-||++.+....- ++-..+.|.-||-.=||++|
T Consensus 122 ~I~yf~t~lvi~~vvHElGHalAA~segV~vngfgIfi---~aiyPgafvdl~~dhLqsl~~fr~LrIfcAGIWHNfvfa 198 (484)
T KOG2921|consen 122 GIAYFLTSLVITVVVHELGHALAAASEGVQVNGFGIFI---AAIYPGAFVDLDNDHLQSLPSFRALRIFCAGIWHNFVFA 198 (484)
T ss_pred cchhhhhhHHHHHHHHHhhHHHHHHhcCceeeeeEEEE---EEEcCchhhhhhhhHHhhcchHHHHHHHhhhHHHHHHHH
Confidence 4443 344566888999999999999999995 22222 2223688888765321 34457889999999999999
Q ss_pred HHHHHHHH
Q 015798 362 FVLFLVGF 369 (400)
Q Consensus 362 lill~iGl 369 (400)
+++.+.-.
T Consensus 199 llc~lal~ 206 (484)
T KOG2921|consen 199 LLCVLALF 206 (484)
T ss_pred HHHHHHHH
Confidence 98776544
No 15
>COG1994 SpoIVFB Zn-dependent proteases [General function prediction only]
Probab=96.42 E-value=0.0023 Score=60.93 Aligned_cols=75 Identities=24% Similarity=0.259 Sum_probs=55.1
Q ss_pred HHhhHHHHHHHHHHHHHHHHHHHHHHHHcCCeecCcccccceeeeeeeEEEEeccCCCCcc-------ceeEEEEh-hHH
Q 015798 284 LTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAITRIRNIVSKRE-------DLLKVAAA-GPL 355 (400)
Q Consensus 284 l~~glp~aL~l~~iLliHElGH~laARr~GVkvs~P~FIP~i~Lg~fGg~t~i~s~~~~r~-------alfdIAiA-GPl 355 (400)
+..+....++++..+..||+||+..++++|+++. .+.++.+||+..++..+.+.+ +...++.| ||+
T Consensus 41 ~~~~~~~~~~l~~rl~l~~~gh~~~~~~~~~~l~------~~~i~~~~g~~~~~~~~v~~~~~~~~~~~g~lvs~algpl 114 (230)
T COG1994 41 LGDGTAAFVGLAHRLVLHPLGHSDEAGRLGLKLL------LALLFGFGGFGFLKPVPVNPRGEFLIRLAGPLVSLALGPL 114 (230)
T ss_pred HhhhHHHHHHHhHHHhhhHhhHHHHHHHHHHHHH------HHHHHhccceeeecCcCcCHHHHhhhhccchhHHHHHHHH
Confidence 4445555555778999999999999999999985 444445888888887665543 45556667 888
Q ss_pred HHHHHHHHH
Q 015798 356 AGFSLGFVL 364 (400)
Q Consensus 356 aglllAlil 364 (400)
.|++++++.
T Consensus 115 ~ni~la~~~ 123 (230)
T COG1994 115 TNIALAVLG 123 (230)
T ss_pred HHHHHHHHH
Confidence 888877664
No 16
>PF11667 DUF3267: Protein of unknown function (DUF3267); InterPro: IPR021683 This family of proteins has no known function.
Probab=87.39 E-value=0.27 Score=41.64 Aligned_cols=71 Identities=23% Similarity=0.271 Sum_probs=39.6
Q ss_pred HHHHHHHHHHHHHHHHHcCCeecCcccccceeeeeeeEEEEeccCCCCccceeEEEEhhHHHHHHHHHHHHHHHHhcC
Q 015798 295 ALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAITRIRNIVSKREDLLKVAAAGPLAGFSLGFVLFLVGFIFP 372 (400)
Q Consensus 295 ~~iLliHElGH~laARr~GVkvs~P~FIP~i~Lg~fGg~t~i~s~~~~r~alfdIAiAGPlaglllAlill~iGl~ls 372 (400)
+..+.+||+-|.+..+.+|-+....+ .+....+-.++. .+. +=.+.++.+...-|. ++++++.+++++.+|
T Consensus 4 ~~~~~~HEliH~l~~~~~~~~~~~~~---g~~~~~~~~~~~-~~~-~~sk~~~~i~~l~P~--ivl~~~~~~~~~~~p 74 (111)
T PF11667_consen 4 IVLIPLHELIHGLFFKLFGKKPKVKF---GFKWKLGPFYAT-CNE-PISKWRFIIILLAPF--IVLTILPLILGFFFP 74 (111)
T ss_pred EeeHHHHHHHHHHHHHHhCCCCceEE---EEEeeeEEEEEe-cCc-EEeHHHHHHHHHHHH--HHHHHHHHHHHHHHH
Confidence 34678999999999999998532000 111111222322 333 334455666666675 556666666555544
No 17
>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=76.47 E-value=1.5 Score=37.87 Aligned_cols=14 Identities=36% Similarity=0.752 Sum_probs=11.1
Q ss_pred HHHHHHHHHHHHHH
Q 015798 296 LVIGVHELGHILAA 309 (400)
Q Consensus 296 ~iLliHElGH~laA 309 (400)
..+++||+||++=-
T Consensus 106 ~~v~~HEiGHaLGL 119 (154)
T PF00413_consen 106 QSVAIHEIGHALGL 119 (154)
T ss_dssp HHHHHHHHHHHTTB
T ss_pred hhhhhhccccccCc
Confidence 46789999998743
No 18
>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=72.33 E-value=2.3 Score=37.63 Aligned_cols=22 Identities=32% Similarity=0.364 Sum_probs=17.1
Q ss_pred HHHHHHHHHHHHHHHHHcCCee
Q 015798 295 ALVIGVHELGHILAAKSTGVEL 316 (400)
Q Consensus 295 ~~iLliHElGH~laARr~GVkv 316 (400)
+..+++||+||.+=.+...-+-
T Consensus 104 ~~~~~~HEiGHaLGL~H~~~~~ 125 (156)
T cd04279 104 LQAIALHELGHALGLWHHSDRP 125 (156)
T ss_pred HHHHHHHHhhhhhcCCCCCCCc
Confidence 4578899999999777666653
No 19
>PF13485 Peptidase_MA_2: Peptidase MA superfamily
Probab=66.14 E-value=4.9 Score=32.57 Aligned_cols=17 Identities=29% Similarity=0.311 Sum_probs=15.4
Q ss_pred HHHHHHHHHHHHHHHcC
Q 015798 297 VIGVHELGHILAAKSTG 313 (400)
Q Consensus 297 iLliHElGH~laARr~G 313 (400)
-+++||++|.|.....+
T Consensus 27 ~~l~HE~~H~~~~~~~~ 43 (128)
T PF13485_consen 27 RVLAHELAHQWFGNYFG 43 (128)
T ss_pred HHHHHHHHHHHHHHHcC
Confidence 67899999999999976
No 20
>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=64.70 E-value=3.3 Score=37.68 Aligned_cols=13 Identities=38% Similarity=0.401 Sum_probs=10.7
Q ss_pred HHHHHHHHHHHHH
Q 015798 296 LVIGVHELGHILA 308 (400)
Q Consensus 296 ~iLliHElGH~la 308 (400)
.-.++||+||++=
T Consensus 70 g~TltHEvGH~LG 82 (154)
T PF05572_consen 70 GKTLTHEVGHWLG 82 (154)
T ss_dssp SHHHHHHHHHHTT
T ss_pred ccchhhhhhhhhc
Confidence 4778999999863
No 21
>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=63.36 E-value=4.8 Score=35.28 Aligned_cols=21 Identities=29% Similarity=0.300 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHHHHHcCC
Q 015798 294 TALVIGVHELGHILAAKSTGV 314 (400)
Q Consensus 294 l~~iLliHElGH~laARr~GV 314 (400)
-...+++||+||.+=-+.-.-
T Consensus 93 ~~~~~~~HEiGHaLGL~H~~~ 113 (165)
T cd04268 93 RLRNTAEHELGHALGLRHNFA 113 (165)
T ss_pred HHHHHHHHHHHHHhcccccCc
Confidence 345788999999986555443
No 22
>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=63.08 E-value=3.3 Score=36.73 Aligned_cols=17 Identities=29% Similarity=0.583 Sum_probs=13.0
Q ss_pred HHHHHHHHHHHHHHHHH
Q 015798 295 ALVIGVHELGHILAAKS 311 (400)
Q Consensus 295 ~~iLliHElGH~laARr 311 (400)
+..++.||+||++=-..
T Consensus 107 ~~~~~~HEiGHaLGL~H 123 (157)
T cd04278 107 LFSVAAHEIGHALGLGH 123 (157)
T ss_pred HHHHHHHHhccccccCC
Confidence 45788999999975543
No 23
>PF12315 DUF3633: Protein of unknown function (DUF3633); InterPro: IPR022087 This domain family is found in bacteria and eukaryotes, and is approximately 210 amino acids in length. The family is found in association with PF00412 from PFAM.
Probab=62.97 E-value=5.4 Score=38.80 Aligned_cols=28 Identities=32% Similarity=0.330 Sum_probs=20.4
Q ss_pred HhhHHHHHHHHHHHHHHHHHHHHHHHHcCCe
Q 015798 285 TNGLPGALVTALVIGVHELGHILAAKSTGVE 315 (400)
Q Consensus 285 ~~glp~aL~l~~iLliHElGH~laARr~GVk 315 (400)
+.++|-. ++.++++||++|+|. |..|.+
T Consensus 85 l~GLPrl--l~gsiLAHE~mHa~L-rl~g~~ 112 (212)
T PF12315_consen 85 LYGLPRL--LTGSILAHELMHAWL-RLNGFP 112 (212)
T ss_pred ECCCCHH--HHhhHHHHHHHHHHh-cccCCC
Confidence 4456644 456999999999998 556654
No 24
>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=61.86 E-value=5.1 Score=32.22 Aligned_cols=17 Identities=41% Similarity=0.542 Sum_probs=12.8
Q ss_pred HHHHHHHHHHHHHHHcC
Q 015798 297 VIGVHELGHILAAKSTG 313 (400)
Q Consensus 297 iLliHElGH~laARr~G 313 (400)
..++||+||++.-+...
T Consensus 44 f~laHELgH~~~~~~~~ 60 (122)
T PF06114_consen 44 FTLAHELGHILLHHGDE 60 (122)
T ss_dssp HHHHHHHHHHHHHH-HH
T ss_pred HHHHHHHHHHHhhhccc
Confidence 46789999999876654
No 25
>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=58.63 E-value=7 Score=35.60 Aligned_cols=12 Identities=50% Similarity=0.717 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHH
Q 015798 296 LVIGVHELGHIL 307 (400)
Q Consensus 296 ~iLliHElGH~l 307 (400)
..+++||+||+.
T Consensus 90 ~aVlaHElgH~~ 101 (226)
T PF01435_consen 90 AAVLAHELGHIK 101 (226)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 467899999987
No 26
>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=58.47 E-value=5.5 Score=36.12 Aligned_cols=21 Identities=33% Similarity=0.464 Sum_probs=13.2
Q ss_pred HHHHHHHHHHHHHHHHHHcCC
Q 015798 294 TALVIGVHELGHILAAKSTGV 314 (400)
Q Consensus 294 l~~iLliHElGH~laARr~GV 314 (400)
...++++||+||-|=|..=+-
T Consensus 141 ~~~~~~AHEiGH~lGa~HD~~ 161 (196)
T PF13688_consen 141 NGAITFAHEIGHNLGAPHDGD 161 (196)
T ss_dssp HHHHHHHHHHHHHTT-----S
T ss_pred ceehhhHHhHHHhcCCCCCCC
Confidence 445889999999998886444
No 27
>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=55.53 E-value=6.1 Score=34.50 Aligned_cols=20 Identities=30% Similarity=0.278 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHHHHHcC
Q 015798 294 TALVIGVHELGHILAAKSTG 313 (400)
Q Consensus 294 l~~iLliHElGH~laARr~G 313 (400)
....+++||+||.+=.+.-.
T Consensus 95 ~~~~~~~HElGH~LGl~H~~ 114 (167)
T cd00203 95 EGAQTIAHELGHALGFYHDH 114 (167)
T ss_pred cchhhHHHHHHHHhCCCccC
Confidence 44678899999998665443
No 28
>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=55.44 E-value=6.6 Score=35.71 Aligned_cols=20 Identities=30% Similarity=0.436 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHHHHHHcCCe
Q 015798 296 LVIGVHELGHILAAKSTGVE 315 (400)
Q Consensus 296 ~iLliHElGH~laARr~GVk 315 (400)
.-+++||+||.+=-+.-+-.
T Consensus 114 ~~t~~HEiGHaLGL~H~~~~ 133 (186)
T cd04277 114 YQTIIHEIGHALGLEHPGDY 133 (186)
T ss_pred HHHHHHHHHHHhcCCCCCcC
Confidence 46789999999866544433
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=54.76 E-value=6.5 Score=33.89 Aligned_cols=14 Identities=43% Similarity=0.717 Sum_probs=11.2
Q ss_pred HHHHHHHHHHHHHH
Q 015798 298 IGVHELGHILAAKS 311 (400)
Q Consensus 298 LliHElGH~laARr 311 (400)
+++||+||++-.+.
T Consensus 89 ~~~HEigHaLGl~H 102 (140)
T smart00235 89 VAAHELGHALGLYH 102 (140)
T ss_pred cHHHHHHHHhcCCc
Confidence 78999999984443
No 30
>PF13582 Reprolysin_3: Metallo-peptidase family M12B Reprolysin-like; PDB: 3P24_C.
Probab=54.57 E-value=6.4 Score=32.98 Aligned_cols=13 Identities=38% Similarity=0.434 Sum_probs=10.3
Q ss_pred HHHHHHHHHHHHH
Q 015798 297 VIGVHELGHILAA 309 (400)
Q Consensus 297 iLliHElGH~laA 309 (400)
..++||+||.+=+
T Consensus 109 ~~~~HEiGH~lGl 121 (124)
T PF13582_consen 109 DTFAHEIGHNLGL 121 (124)
T ss_dssp THHHHHHHHHTT-
T ss_pred eEeeehhhHhcCC
Confidence 7789999998644
No 31
>PF07423 DUF1510: Protein of unknown function (DUF1510); InterPro: IPR009988 This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.
Probab=52.31 E-value=7.9 Score=37.65 Aligned_cols=54 Identities=26% Similarity=0.338 Sum_probs=37.8
Q ss_pred eeeeccccccCceEEEEeecCCchHHHHHHHHHHHHhhhCCceEEEEEec-CCCCCcEE
Q 015798 173 TFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFGDQYKLFLLVN-PEDDKPVA 230 (400)
Q Consensus 173 TFf~T~~e~~~~GvifrGNLRg~~eevy~kL~~~Le~~fGdrY~lfl~ee-~ed~KPV~ 230 (400)
..|+|++..-.=-+.|.||= |.|.++|..|+.+=. +++|+|++-=- .++=||+-
T Consensus 159 is~atgi~~~~mi~w~ign~-G~~~~a~gtVs~k~~---~~~YrV~i~WVd~eGWkP~k 213 (217)
T PF07423_consen 159 ISYATGISEDNMIVWFIGNN-GSPQKAIGTVSDKDT---GKKYRVYIEWVDNEGWKPVK 213 (217)
T ss_pred HHHhhCCChhheEEEhhhcC-CcccceeEEeccCCC---CceEEEEEEEecCCCcccee
Confidence 46889888777788999996 777999999876533 56899964211 12227764
No 32
>PF14891 Peptidase_M91: Effector protein
Probab=51.87 E-value=9.7 Score=34.92 Aligned_cols=17 Identities=29% Similarity=0.260 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHHHHHHc
Q 015798 296 LVIGVHELGHILAAKST 312 (400)
Q Consensus 296 ~iLliHElGH~laARr~ 312 (400)
++++.|||+|++=...=
T Consensus 104 ~v~L~HEL~HA~~~~~G 120 (174)
T PF14891_consen 104 FVVLYHELIHAYDYMNG 120 (174)
T ss_pred HHHHHHHHHHHHHHHCC
Confidence 57889999999977643
No 33
>PF14247 DUF4344: Domain of unknown function (DUF4344)
Probab=51.66 E-value=15 Score=35.64 Aligned_cols=25 Identities=32% Similarity=0.417 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHcCCee
Q 015798 291 ALVTALVIGVHELGHILAAKSTGVEL 316 (400)
Q Consensus 291 aL~l~~iLliHElGH~laARr~GVkv 316 (400)
++..+..++.||+||++... +++++
T Consensus 88 ~~~~~~~~l~HE~GHAlI~~-~~lPv 112 (220)
T PF14247_consen 88 AIGNVLFTLYHELGHALIDD-LDLPV 112 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHH-hcCCc
Confidence 55566678899999999975 45665
No 34
>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=50.65 E-value=11 Score=34.43 Aligned_cols=20 Identities=35% Similarity=0.383 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHHHHHcC
Q 015798 294 TALVIGVHELGHILAAKSTG 313 (400)
Q Consensus 294 l~~iLliHElGH~laARr~G 313 (400)
..+.+++||+||-+=+..-+
T Consensus 130 ~~a~~~AHElGH~lG~~HD~ 149 (194)
T cd04269 130 LFAVTMAHELGHNLGMEHDD 149 (194)
T ss_pred HHHHHHHHHHHhhcCCCcCC
Confidence 34678899999998766543
No 35
>PF01434 Peptidase_M41: Peptidase family M41 This is family M41 in the peptidase classification. ; InterPro: IPR000642 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 M41 (FtsH endopeptidase 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. The peptidase M41 family belong to a larger family of zinc metalloproteases. This family includes the cell division protein FtsH, and the yeast mitochondrial respiratory chain complexes assembly protein, which is a putative ATP-dependent protease required for assembly of the mitochondrial respiratory chain and ATPase complexes. FtsH is an integral membrane protein, which seems to act as an ATP-dependent zinc metallopeptidase that binds one zinc ion.; GO: 0004222 metalloendopeptidase activity, 0005524 ATP binding, 0006508 proteolysis; PDB: 4EIW_C 2DHR_E 1IY1_A 1IY2_A 1IY0_A 1IXZ_A 2CE7_F 2CEA_F 3KDS_E 2QZ4_A ....
Probab=49.48 E-value=14 Score=34.93 Aligned_cols=60 Identities=28% Similarity=0.211 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHHHHHHcCC--eecCcccccceeeeeeeEEEEeccCC----CCcc---ceeEEEEhhHHHHH
Q 015798 296 LVIGVHELGHILAAKSTGV--ELGVPYFVPSWQIGSFGAITRIRNIV----SKRE---DLLKVAAAGPLAGF 358 (400)
Q Consensus 296 ~iLliHElGH~laARr~GV--kvs~P~FIP~i~Lg~fGg~t~i~s~~----~~r~---alfdIAiAGPlagl 358 (400)
-.+.+||.||+++|-.++- ++..--.+|. +.-+|++.+.... .++. +.+.+.+||-++-=
T Consensus 29 ~~~A~HEAGhAvva~~l~~~~~v~~vsi~pr---g~~~G~~~~~~~~~~~~~t~~~l~~~i~v~LaGraAEe 97 (213)
T PF01434_consen 29 RRIAYHEAGHAVVAYLLPPADPVSKVSIVPR---GSALGFTQFTPDEDRYIRTRSYLEDRICVLLAGRAAEE 97 (213)
T ss_dssp HHHHHHHHHHHHHHHHSSS---EEEEESSTT---CCCCHCCEECHHTT-SS-BHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhcccccEEEEEEecC---CCcceeEEeccchhcccccHHHHHhhHHHHHHHHHHHH
Confidence 3677899999999998873 3321112332 2244555553211 1222 35567777777633
No 36
>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=49.24 E-value=11 Score=36.52 Aligned_cols=18 Identities=28% Similarity=0.503 Sum_probs=14.5
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 015798 294 TALVIGVHELGHILAAKS 311 (400)
Q Consensus 294 l~~iLliHElGH~laARr 311 (400)
.++++++||+||-|=+..
T Consensus 166 ~~a~t~AHElGHnlGm~H 183 (244)
T cd04270 166 ESDLVTAHELGHNFGSPH 183 (244)
T ss_pred HHHHHHHHHHHHhcCCCC
Confidence 456889999999987754
No 37
>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=49.10 E-value=11 Score=34.49 Aligned_cols=20 Identities=35% Similarity=0.285 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHHHHHHHcCC
Q 015798 295 ALVIGVHELGHILAAKSTGV 314 (400)
Q Consensus 295 ~~iLliHElGH~laARr~GV 314 (400)
...+++||+||.|=|..=+-
T Consensus 111 ~~~~~aHElGH~lGa~Hd~~ 130 (173)
T PF13574_consen 111 GIDTFAHELGHQLGAPHDFD 130 (173)
T ss_dssp HHHHHHHHHHHHHT---SSS
T ss_pred eeeeehhhhHhhcCCCCCCC
Confidence 45669999999999887654
No 38
>COG2856 Predicted Zn peptidase [Amino acid transport and metabolism]
Probab=48.71 E-value=10 Score=36.71 Aligned_cols=17 Identities=35% Similarity=0.438 Sum_probs=12.9
Q ss_pred HHHHHHHHHHHHHHHcC
Q 015798 297 VIGVHELGHILAAKSTG 313 (400)
Q Consensus 297 iLliHElGH~laARr~G 313 (400)
-.++||+||+|.=+...
T Consensus 74 FtlAHELGH~llH~~~~ 90 (213)
T COG2856 74 FTLAHELGHALLHTDLN 90 (213)
T ss_pred HHHHHHHhHHHhccccc
Confidence 35689999999766543
No 39
>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=47.38 E-value=12 Score=34.13 Aligned_cols=10 Identities=80% Similarity=1.291 Sum_probs=8.8
Q ss_pred HHHHHHHHHH
Q 015798 298 IGVHELGHIL 307 (400)
Q Consensus 298 LliHElGH~l 307 (400)
+.+||+||.+
T Consensus 80 IaaHE~GHiL 89 (132)
T PF02031_consen 80 IAAHELGHIL 89 (132)
T ss_dssp HHHHHHHHHH
T ss_pred eeeehhcccc
Confidence 6799999986
No 40
>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=46.85 E-value=11 Score=35.02 Aligned_cols=14 Identities=36% Similarity=0.551 Sum_probs=10.9
Q ss_pred HHHHHHHHHHHHHH
Q 015798 297 VIGVHELGHILAAK 310 (400)
Q Consensus 297 iLliHElGH~laAR 310 (400)
-+++|||||++=-.
T Consensus 94 ~~i~HElgHaLG~~ 107 (198)
T cd04327 94 RVVLHEFGHALGFI 107 (198)
T ss_pred HHHHHHHHHHhcCc
Confidence 46789999998543
No 41
>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=46.84 E-value=8.9 Score=34.83 Aligned_cols=21 Identities=38% Similarity=0.485 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHHHHHHHHcCC
Q 015798 294 TALVIGVHELGHILAAKSTGV 314 (400)
Q Consensus 294 l~~iLliHElGH~laARr~GV 314 (400)
..+.+++||+||.+=+..-+-
T Consensus 132 ~~~~~~aHElGH~lG~~HD~~ 152 (192)
T cd04267 132 LTALTMAHELGHNLGAEHDGG 152 (192)
T ss_pred eehhhhhhhHHhhcCCcCCCC
Confidence 345789999999987766553
No 42
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=46.16 E-value=32 Score=40.37 Aligned_cols=20 Identities=25% Similarity=0.290 Sum_probs=11.5
Q ss_pred ccccccccccCCCCcccccc
Q 015798 4 TTTFRGNLSLLPHCSSCCDI 23 (400)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~ 23 (400)
.+||-|.-..+--|++-.+.
T Consensus 1353 iaTi~v~R~~~Dlct~~~D~ 1372 (1516)
T KOG1832|consen 1353 IATIPVDRCLLDLCTEPTDS 1372 (1516)
T ss_pred ceeeecccchhhhhcCCccc
Confidence 45555555556667665443
No 43
>PTZ00429 beta-adaptin; Provisional
Probab=44.68 E-value=20 Score=40.56 Aligned_cols=32 Identities=28% Similarity=0.251 Sum_probs=15.7
Q ss_pred ChhhhhccCCCCCCCCCCCcccCCCCCCCccC
Q 015798 75 NDKEKEVHDGQENQPATASDQEDDKSQPDSQL 106 (400)
Q Consensus 75 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 106 (400)
.|||++|+++.++.+++.++...+++..++++
T Consensus 608 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 639 (746)
T PTZ00429 608 LDEEDTEDDDAVELPSTPSMGTQDGSPAPSAA 639 (746)
T ss_pred cccccccchhhccCCCCCCCCCCCCCCCcccc
Confidence 33444444444555555555545554444444
No 44
>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH. HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.
Probab=44.16 E-value=12 Score=39.50 Aligned_cols=58 Identities=19% Similarity=0.143 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHHHHcC--CeecCcccccceee---eeeeEEEEeccCC----CCcc---ceeEEEEhhHHHHHHH
Q 015798 297 VIGVHELGHILAAKSTG--VELGVPYFVPSWQI---GSFGAITRIRNIV----SKRE---DLLKVAAAGPLAGFSL 360 (400)
Q Consensus 297 iLliHElGH~laARr~G--Vkvs~P~FIP~i~L---g~fGg~t~i~s~~----~~r~---alfdIAiAGPlaglll 360 (400)
.+..||.||+++|..++ .++. .+.+ +.-+|++.+.... .++. ..+.+.+||-+|=-++
T Consensus 313 ~~A~hEaGhAlv~~~l~~~~~v~------~vsi~prg~~~G~~~~~~~~~~~~~t~~~l~~~i~v~LaGraAE~~~ 382 (495)
T TIGR01241 313 LVAYHEAGHALVGLLLKDADPVH------KVTIIPRGQALGYTQFLPEEDKYLYTKSQLLAQIAVLLGGRAAEEII 382 (495)
T ss_pred HHHHHHHhHHHHHHhcCCCCceE------EEEEeecCCccceEEecCccccccCCHHHHHHHHHHHhhHHHHHHHH
Confidence 57889999999998874 3332 3333 3345677654321 1222 3556667776665543
No 45
>PHA02456 zinc metallopeptidase motif-containing protein
Probab=42.85 E-value=15 Score=33.09 Aligned_cols=19 Identities=26% Similarity=0.323 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHHHcCCee
Q 015798 298 IGVHELGHILAAKSTGVEL 316 (400)
Q Consensus 298 LliHElGH~laARr~GVkv 316 (400)
-+.||+.|.|.-|.||.-.
T Consensus 82 TL~HEL~H~WQ~RsYG~i~ 100 (141)
T PHA02456 82 TLAHELNHAWQFRTYGLVQ 100 (141)
T ss_pred HHHHHHHHHHhhhccceee
Confidence 3589999999999999754
No 46
>PRK03001 M48 family peptidase; Provisional
Probab=42.72 E-value=16 Score=36.01 Aligned_cols=12 Identities=33% Similarity=0.426 Sum_probs=9.9
Q ss_pred HHHHHHHHHHHH
Q 015798 296 LVIGVHELGHIL 307 (400)
Q Consensus 296 ~iLliHElGH~l 307 (400)
..+++||+||+-
T Consensus 125 ~aVlAHElgHi~ 136 (283)
T PRK03001 125 RGVMAHELAHVK 136 (283)
T ss_pred HHHHHHHHHHHh
Confidence 467899999974
No 47
>PF13583 Reprolysin_4: Metallo-peptidase family M12B Reprolysin-like
Probab=41.86 E-value=14 Score=34.93 Aligned_cols=18 Identities=28% Similarity=0.237 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHHcCC
Q 015798 297 VIGVHELGHILAAKSTGV 314 (400)
Q Consensus 297 iLliHElGH~laARr~GV 314 (400)
-+++||+||.+=|+.-+-
T Consensus 139 ~~~aHEiGH~lGl~H~~~ 156 (206)
T PF13583_consen 139 QTFAHEIGHNLGLRHDFD 156 (206)
T ss_pred hHHHHHHHHHhcCCCCcc
Confidence 448899999998887665
No 48
>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=41.66 E-value=19 Score=33.04 Aligned_cols=22 Identities=41% Similarity=0.499 Sum_probs=14.4
Q ss_pred HHHHHHHHHHHHHHHHHHHcCC
Q 015798 293 VTALVIGVHELGHILAAKSTGV 314 (400)
Q Consensus 293 ~l~~iLliHElGH~laARr~GV 314 (400)
..++.+++||+||.+=+..=+-
T Consensus 129 ~~~a~~~AHelGH~lGm~HD~~ 150 (199)
T PF01421_consen 129 LSFAVIIAHELGHNLGMPHDGD 150 (199)
T ss_dssp HHHHHHHHHHHHHHTT---TTT
T ss_pred HHHHHHHHHHHHHhcCCCCCCC
Confidence 4556788999999876665544
No 49
>PRK03982 heat shock protein HtpX; Provisional
Probab=41.27 E-value=17 Score=35.84 Aligned_cols=12 Identities=42% Similarity=0.362 Sum_probs=9.8
Q ss_pred HHHHHHHHHHHH
Q 015798 296 LVIGVHELGHIL 307 (400)
Q Consensus 296 ~iLliHElGH~l 307 (400)
..+++||+||+-
T Consensus 126 ~AVlAHElgHi~ 137 (288)
T PRK03982 126 EGVIAHELTHIK 137 (288)
T ss_pred HHHHHHHHHHHH
Confidence 367899999975
No 50
>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=41.19 E-value=20 Score=31.49 Aligned_cols=18 Identities=22% Similarity=0.150 Sum_probs=14.4
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 015798 294 TALVIGVHELGHILAAKS 311 (400)
Q Consensus 294 l~~iLliHElGH~laARr 311 (400)
.+.-.++|||.|+++-..
T Consensus 59 ~~~~tL~HEm~H~~~~~~ 76 (157)
T PF10263_consen 59 ELIDTLLHEMAHAAAYVF 76 (157)
T ss_pred HHHHHHHHHHHHHHhhhc
Confidence 445788999999999655
No 51
>PF13699 DUF4157: Domain of unknown function (DUF4157)
Probab=40.50 E-value=17 Score=29.79 Aligned_cols=12 Identities=33% Similarity=0.650 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHH
Q 015798 297 VIGVHELGHILA 308 (400)
Q Consensus 297 iLliHElGH~la 308 (400)
-+++||++|.+-
T Consensus 63 ~llaHEl~Hv~Q 74 (79)
T PF13699_consen 63 ALLAHELAHVVQ 74 (79)
T ss_pred hhHhHHHHHHHh
Confidence 578999999875
No 52
>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=39.11 E-value=18 Score=35.14 Aligned_cols=24 Identities=21% Similarity=0.315 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHcCC
Q 015798 291 ALVTALVIGVHELGHILAAKSTGV 314 (400)
Q Consensus 291 aL~l~~iLliHElGH~laARr~GV 314 (400)
..-...-+++||+||.+=-|.-..
T Consensus 129 ~~~~~~hvi~HEiGH~IGfRHTD~ 152 (211)
T PF12388_consen 129 SVNVIEHVITHEIGHCIGFRHTDY 152 (211)
T ss_pred chhHHHHHHHHHhhhhccccccCc
Confidence 334456789999999987776443
No 53
>COG5309 Exo-beta-1,3-glucanase [Carbohydrate transport and metabolism]
Probab=38.66 E-value=48 Score=33.84 Aligned_cols=61 Identities=16% Similarity=0.312 Sum_probs=44.1
Q ss_pred HhHHHHHhcccccc-eeeeeccccccCceEEEEeecC--CchHHHHHHHHHHHHhhhCCceEEEEEec
Q 015798 158 KETIDILKDQVFGF-DTFFVTNQEPYEGGVLFKGNLR--GQAAKTYEKISTRMKNKFGDQYKLFLLVN 222 (400)
Q Consensus 158 ~edl~~ik~~~Fg~-dTFf~T~~e~~~~GvifrGNLR--g~~eevy~kL~~~Le~~fGdrY~lfl~ee 222 (400)
.|.+++||. .||= .+||+||+-.--.|--+-++.- .+..+.++.+...|+.. | |.+|+++-
T Consensus 218 ~~q~e~vqs-a~g~~k~~~v~EtGWPS~G~~~G~a~pS~anq~~~~~~i~~~~~~~-G--~d~fvfeA 281 (305)
T COG5309 218 LEQLERVQS-ACGTKKTVWVTETGWPSDGRTYGSAVPSVANQKIAVQEILNALRSC-G--YDVFVFEA 281 (305)
T ss_pred HHHHHHHHH-hcCCCccEEEeeccCCCCCCccCCcCCChhHHHHHHHHHHhhhhcc-C--ccEEEeee
Confidence 688999998 6776 9999999865555555555543 34567788888888884 7 66666653
No 54
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=38.12 E-value=20 Score=31.90 Aligned_cols=16 Identities=25% Similarity=0.003 Sum_probs=13.4
Q ss_pred HHHHHHHHHHHHHHHH
Q 015798 296 LVIGVHELGHILAAKS 311 (400)
Q Consensus 296 ~iLliHElGH~laARr 311 (400)
.-++.|||.|+++-..
T Consensus 60 ~~~l~HEm~H~~~~~~ 75 (146)
T smart00731 60 RETLLHELCHAALYLF 75 (146)
T ss_pred HhhHHHHHHHHHHHHh
Confidence 4588999999999864
No 55
>COG0501 HtpX Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]
Probab=37.81 E-value=21 Score=34.22 Aligned_cols=11 Identities=55% Similarity=0.818 Sum_probs=9.1
Q ss_pred HHHHHHHHHHH
Q 015798 297 VIGVHELGHIL 307 (400)
Q Consensus 297 iLliHElGH~l 307 (400)
.+++||+||..
T Consensus 159 aVlaHElgHi~ 169 (302)
T COG0501 159 AVLAHELGHIK 169 (302)
T ss_pred HHHHHHHHHHh
Confidence 57899999974
No 56
>PRK04897 heat shock protein HtpX; Provisional
Probab=36.98 E-value=22 Score=35.50 Aligned_cols=12 Identities=33% Similarity=0.274 Sum_probs=9.7
Q ss_pred HHHHHHHHHHHH
Q 015798 296 LVIGVHELGHIL 307 (400)
Q Consensus 296 ~iLliHElGH~l 307 (400)
..+++||+||+-
T Consensus 138 ~aVlAHElgHi~ 149 (298)
T PRK04897 138 EGVIGHEISHIR 149 (298)
T ss_pred HHHHHHHHHHHh
Confidence 367899999974
No 57
>PRK01345 heat shock protein HtpX; Provisional
Probab=35.59 E-value=23 Score=35.75 Aligned_cols=12 Identities=33% Similarity=0.454 Sum_probs=10.0
Q ss_pred HHHHHHHHHHHH
Q 015798 296 LVIGVHELGHIL 307 (400)
Q Consensus 296 ~iLliHElGH~l 307 (400)
..+++||+||.-
T Consensus 125 ~aVlAHElgHi~ 136 (317)
T PRK01345 125 AGVMAHELAHVK 136 (317)
T ss_pred HHHHHHHHHHHH
Confidence 467899999985
No 58
>cd04272 ZnMc_salivary_gland_MPs Zinc-dependent metalloprotease, salivary_gland_MPs. Metalloproteases secreted by the salivary glands of arthropods.
Probab=35.00 E-value=24 Score=33.17 Aligned_cols=19 Identities=37% Similarity=0.548 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHHHcCC
Q 015798 296 LVIGVHELGHILAAKSTGV 314 (400)
Q Consensus 296 ~iLliHElGH~laARr~GV 314 (400)
+.+++||+||-+=+..=+-
T Consensus 146 ~~~~AHElGH~lG~~HD~~ 164 (220)
T cd04272 146 VYTMTHELAHLLGAPHDGS 164 (220)
T ss_pred HHHHHHHHHHHhCCCCCCC
Confidence 4888999999997776543
No 59
>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=34.81 E-value=25 Score=36.44 Aligned_cols=21 Identities=19% Similarity=0.303 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHHHHHHcCCee
Q 015798 296 LVIGVHELGHILAAKSTGVEL 316 (400)
Q Consensus 296 ~iLliHElGH~laARr~GVkv 316 (400)
+..++||+||++-.-.-.-+.
T Consensus 243 v~tLfHE~GHa~H~~ls~~~~ 263 (458)
T PF01432_consen 243 VETLFHEFGHAMHSLLSRTKY 263 (458)
T ss_dssp HHHHHHHHHHHHHHHHCCCSS
T ss_pred HHHHHHHHhHHHHHHHhcccc
Confidence 367899999998877665543
No 60
>PF01447 Peptidase_M4: Thermolysin metallopeptidase, catalytic domain This Prosite motif covers only the active site. This is family M4 in the peptidase classification. ; InterPro: IPR013856 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 that belong to the MEROPS peptidase family M4 (thermolysin family, clan MA(E)). The protein fold of the peptidase domain of thermolysin, is the type example for members of the clan MA. The thermolysin family is composed only of secreted eubacterial endopeptidases. The zinc-binding residues are H-142, H-146 and E-166, with E-143 acting as the catalytic residue. Thermolysin also contains 4 calcium-binding sites, which contribute to its unusual thermostability. The family also includes enzymes from a number of pathogens, including Legionella and Listeria, and the protein pseudolysin, all with a substrate specificity for an aromatic residue in the P1' position. Three-dimensional structure analysis has shown that the enzymes undergo a hinge-bend motion during catalysis. Pseudolysin has a broader specificity, acting on large molecules such as elastin and collagen, possibly due to its wider active site cleft []. This entry represents a domain found in peptidase M4 family members.; GO: 0004222 metalloendopeptidase activity; PDB: 3NQX_A 3NQZ_B 3NQY_B 1BQB_A 1U4G_A 1EZM_A 3DBK_A 1ESP_A 1NPC_A 1LND_E ....
Probab=34.76 E-value=25 Score=32.05 Aligned_cols=12 Identities=33% Similarity=0.373 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHH
Q 015798 297 VIGVHELGHILA 308 (400)
Q Consensus 297 iLliHElGH~la 308 (400)
=+++|||+|.++
T Consensus 137 DVvaHEltHGVt 148 (150)
T PF01447_consen 137 DVVAHELTHGVT 148 (150)
T ss_dssp HHHHHHHHHHHH
T ss_pred ceeeeccccccc
Confidence 467999999886
No 61
>COG3824 Predicted Zn-dependent protease [General function prediction only]
Probab=34.59 E-value=18 Score=32.88 Aligned_cols=15 Identities=27% Similarity=0.457 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHHHHH
Q 015798 293 VTALVIGVHELGHIL 307 (400)
Q Consensus 293 ~l~~iLliHElGH~l 307 (400)
=++..+++||+||.+
T Consensus 107 d~vthvliHEIgHhF 121 (136)
T COG3824 107 DQVTHVLIHEIGHHF 121 (136)
T ss_pred hHhhhhhhhhhhhhc
Confidence 356789999999975
No 62
>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=34.38 E-value=23 Score=35.73 Aligned_cols=13 Identities=38% Similarity=0.606 Sum_probs=9.9
Q ss_pred HHHHHHHHHHHHH
Q 015798 296 LVIGVHELGHILA 308 (400)
Q Consensus 296 ~iLliHElGH~la 308 (400)
+..++||+||++=
T Consensus 223 v~tl~HE~GHa~h 235 (427)
T cd06459 223 VFTLAHELGHAFH 235 (427)
T ss_pred HHHHHHHhhHHHH
Confidence 3567999999753
No 63
>PRK03072 heat shock protein HtpX; Provisional
Probab=34.16 E-value=26 Score=34.87 Aligned_cols=12 Identities=33% Similarity=0.362 Sum_probs=9.5
Q ss_pred HHHHHHHHHHHH
Q 015798 296 LVIGVHELGHIL 307 (400)
Q Consensus 296 ~iLliHElGH~l 307 (400)
..+++||+||.-
T Consensus 128 ~aVlAHElgHi~ 139 (288)
T PRK03072 128 RGVLGHELSHVY 139 (288)
T ss_pred HHHHHHHHHHHh
Confidence 367899999963
No 64
>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=33.27 E-value=22 Score=35.32 Aligned_cols=15 Identities=33% Similarity=0.505 Sum_probs=11.3
Q ss_pred HHHHHHHHHHHHHHH
Q 015798 295 ALVIGVHELGHILAA 309 (400)
Q Consensus 295 ~~iLliHElGH~laA 309 (400)
+.-+++||+||.+.-
T Consensus 216 ~~~v~vHE~GHsf~~ 230 (264)
T PF09471_consen 216 FKQVVVHEFGHSFGG 230 (264)
T ss_dssp HHHHHHHHHHHHTT-
T ss_pred ccceeeeeccccccc
Confidence 456789999998753
No 65
>PRK02391 heat shock protein HtpX; Provisional
Probab=33.19 E-value=27 Score=34.96 Aligned_cols=10 Identities=40% Similarity=0.733 Sum_probs=8.7
Q ss_pred HHHHHHHHHH
Q 015798 297 VIGVHELGHI 306 (400)
Q Consensus 297 iLliHElGH~ 306 (400)
.+++||+||+
T Consensus 135 aVlaHElgHi 144 (296)
T PRK02391 135 AVLAHELSHV 144 (296)
T ss_pred HHHHHHHHHH
Confidence 6789999996
No 66
>PRK05457 heat shock protein HtpX; Provisional
Probab=32.37 E-value=29 Score=34.55 Aligned_cols=11 Identities=36% Similarity=0.573 Sum_probs=9.1
Q ss_pred HHHHHHHHHHH
Q 015798 296 LVIGVHELGHI 306 (400)
Q Consensus 296 ~iLliHElGH~ 306 (400)
..+++||+||.
T Consensus 135 ~aVlAHElgHi 145 (284)
T PRK05457 135 EAVLAHEISHI 145 (284)
T ss_pred HHHHHHHHHHH
Confidence 35789999997
No 67
>PRK12462 phosphoserine aminotransferase; Provisional
Probab=31.40 E-value=86 Score=32.57 Aligned_cols=67 Identities=12% Similarity=0.162 Sum_probs=46.3
Q ss_pred cccccCCCCHhHHHHHhcccccceeeeeccccccCceEEEEeecCCchHHHHHHHHHHHHhhhC--CceEEEEEecC
Q 015798 149 QLDEYIRIPKETIDILKDQVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFG--DQYKLFLLVNP 223 (400)
Q Consensus 149 ~~~~~~~i~~edl~~ik~~~Fg~dTFf~T~~e~~~~GvifrGNLRg~~eevy~kL~~~Le~~fG--drY~lfl~ee~ 223 (400)
....+..+|+|.++++++++.-|.. -+-+++=.+---.+=.++|+.+.++|++.|+ +.|.+++++-.
T Consensus 8 F~aGPa~lp~~Vl~~~~~~~~~~~~--------~g~si~eisHRs~~F~~i~~~~~~~Lr~Ll~~P~~y~Vlfl~Gg 76 (364)
T PRK12462 8 FSGGPGALPDTVLEQVRQAVVELPE--------TGLSVLGMSHRSSWFSSLLAQAEADLRDLLGIPDEYGVVFLQGG 76 (364)
T ss_pred ecCCCcCCCHHHHHHHHHHHhcccc--------cCccccccccccHHHHHHHHHHHHHHHHHhCCCCCCeEEEEecc
Confidence 4567889999999999975544321 1113333333234678899999999999998 68988777654
No 68
>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=30.87 E-value=29 Score=37.32 Aligned_cols=12 Identities=33% Similarity=0.578 Sum_probs=10.1
Q ss_pred HHHHHHHHHHHH
Q 015798 296 LVIGVHELGHIL 307 (400)
Q Consensus 296 ~iLliHElGH~l 307 (400)
+..++||+||++
T Consensus 338 v~TL~HElGHa~ 349 (549)
T TIGR02289 338 IDVLTHEAGHAF 349 (549)
T ss_pred HHHHHHHhhHHH
Confidence 466899999997
No 69
>PRK02870 heat shock protein HtpX; Provisional
Probab=30.33 E-value=32 Score=35.34 Aligned_cols=11 Identities=45% Similarity=0.673 Sum_probs=9.4
Q ss_pred HHHHHHHHHHH
Q 015798 296 LVIGVHELGHI 306 (400)
Q Consensus 296 ~iLliHElGH~ 306 (400)
..+++||+||+
T Consensus 174 ~aVlAHELgHi 184 (336)
T PRK02870 174 QAVMAHELSHI 184 (336)
T ss_pred HHHHHHHHHHH
Confidence 36789999998
No 70
>PRK01265 heat shock protein HtpX; Provisional
Probab=30.28 E-value=32 Score=35.18 Aligned_cols=10 Identities=50% Similarity=0.979 Sum_probs=8.7
Q ss_pred HHHHHHHHHH
Q 015798 297 VIGVHELGHI 306 (400)
Q Consensus 297 iLliHElGH~ 306 (400)
.+++||+||+
T Consensus 142 aVlAHElgHi 151 (324)
T PRK01265 142 AVAGHELGHL 151 (324)
T ss_pred HHHHHHHHHH
Confidence 5789999996
No 71
>KOG2719 consensus Metalloprotease [General function prediction only]
Probab=28.96 E-value=32 Score=36.79 Aligned_cols=19 Identities=26% Similarity=0.309 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHHHHHHHcC
Q 015798 295 ALVIGVHELGHILAAKSTG 313 (400)
Q Consensus 295 ~~iLliHElGH~laARr~G 313 (400)
...+++||+||+---.-++
T Consensus 280 l~AVl~HELGHW~~~H~~K 298 (428)
T KOG2719|consen 280 LVAVLAHELGHWKLNHVLK 298 (428)
T ss_pred HHHHHHHHhhHHHHhhHHH
Confidence 3578899999986544433
No 72
>PLN02452 phosphoserine transaminase
Probab=28.89 E-value=1e+02 Score=31.61 Aligned_cols=67 Identities=9% Similarity=0.186 Sum_probs=47.9
Q ss_pred cccccCCCCHhHHHHHhcccccceeeeeccccccCceEEEEeecCCchHHHHHHHHHHHHhhhC--CceEEEEEecC
Q 015798 149 QLDEYIRIPKETIDILKDQVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFG--DQYKLFLLVNP 223 (400)
Q Consensus 149 ~~~~~~~i~~edl~~ik~~~Fg~dTFf~T~~e~~~~GvifrGNLRg~~eevy~kL~~~Le~~fG--drY~lfl~ee~ 223 (400)
....|..+|++.+++++.+++.|. .-+-+++-.+---.+=.++++.++++|++.++ +.|.+++++-.
T Consensus 11 f~pGP~~lp~~Vl~~~~~~~~~~~--------~~g~s~~~~sHRs~~f~~i~~~~~~~L~~l~~~p~~y~v~~l~Gs 79 (365)
T PLN02452 11 FSAGPATLPANVLAKAQAELYNWE--------GSGMSVMEMSHRGKEFLSIIQKAEADLRELLDIPDNYEVLFLQGG 79 (365)
T ss_pred eeCCCCCCCHHHHHHHHHHHhccc--------ccCccccccCCCchHHHHHHHHHHHHHHHHhCCCCCceEEEEeCc
Confidence 445788999999999987555443 12334444444444567999999999999997 68988777544
No 73
>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=28.37 E-value=30 Score=31.85 Aligned_cols=14 Identities=43% Similarity=0.249 Sum_probs=10.8
Q ss_pred HHHHHHHHHHHHHH
Q 015798 297 VIGVHELGHILAAK 310 (400)
Q Consensus 297 iLliHElGH~laAR 310 (400)
-.++||+||++-..
T Consensus 76 g~v~HE~~HalG~~ 89 (180)
T cd04280 76 GTIVHELMHALGFY 89 (180)
T ss_pred chhHHHHHHHhcCc
Confidence 46789999997554
No 74
>PRK04860 hypothetical protein; Provisional
Probab=28.20 E-value=56 Score=30.30 Aligned_cols=21 Identities=29% Similarity=0.284 Sum_probs=17.5
Q ss_pred HHHHHHHHHHHHHHHHHHHcC
Q 015798 293 VTALVIGVHELGHILAAKSTG 313 (400)
Q Consensus 293 ~l~~iLliHElGH~laARr~G 313 (400)
..+.-++.||++|+++=..+|
T Consensus 61 ~~l~~~v~HEl~H~~~~~~~g 81 (160)
T PRK04860 61 AFIDEVVPHELAHLLVYQLFG 81 (160)
T ss_pred HHHHhHHHHHHHHHHHHHHcC
Confidence 344577899999999999888
No 75
>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=27.82 E-value=32 Score=36.97 Aligned_cols=12 Identities=42% Similarity=0.672 Sum_probs=9.9
Q ss_pred HHHHHHHHHHHH
Q 015798 296 LVIGVHELGHIL 307 (400)
Q Consensus 296 ~iLliHElGH~l 307 (400)
+..++||+||.+
T Consensus 379 v~TLaHElGHa~ 390 (591)
T TIGR00181 379 VFTLAHELGHSM 390 (591)
T ss_pred HHHHHHHhhhHH
Confidence 356799999987
No 76
>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=27.36 E-value=37 Score=33.92 Aligned_cols=14 Identities=29% Similarity=0.309 Sum_probs=10.7
Q ss_pred HHHHHHHHHHHHHH
Q 015798 297 VIGVHELGHILAAK 310 (400)
Q Consensus 297 iLliHElGH~laAR 310 (400)
..++||+||++=-.
T Consensus 156 ~tl~HE~GHa~h~~ 169 (365)
T cd06258 156 NTLFHEFGHAVHFL 169 (365)
T ss_pred HHHHHHHhHHHHHH
Confidence 55789999998443
No 77
>KOG3320 consensus 40S ribosomal protein S7 [Translation, ribosomal structure and biogenesis]
Probab=27.21 E-value=90 Score=30.06 Aligned_cols=29 Identities=14% Similarity=0.271 Sum_probs=22.0
Q ss_pred chHHHHHHHHHHHHhhhCCceEEEEEecC
Q 015798 195 QAAKTYEKISTRMKNKFGDQYKLFLLVNP 223 (400)
Q Consensus 195 ~~eevy~kL~~~Le~~fGdrY~lfl~ee~ 223 (400)
-=.++|.+|...|+++|+|+|.+|+.+..
T Consensus 72 ~fqki~~~LvreleKKF~gk~Vifia~Rr 100 (192)
T KOG3320|consen 72 AFQKIQVRLVRELEKKFSGKHVIFIAQRR 100 (192)
T ss_pred HHHHHHHHHHHHHHHhcCCceEEEEEeee
Confidence 34556666667999999999999876554
No 78
>PF06167 Peptidase_M90: Glucose-regulated metallo-peptidase M90; InterPro: IPR010384 MtfA (earlier known as YeeI) is a transcription factor that binds Mlc (make large colonies), itself a repressor of glucose and hence a protein important in regulation of the phosphoenolpyruvate:glucose-phosphotransferase (PtsG) system, the major glucose transporter in Escherichia coli. Mlc is a repressor of ptsG, and MtfA is found to bind and inactivate Mlc with high affinity []. The membrane-bound protein EIICBGlc encoded by the ptsG gene is the major glucose transporter in E. coli. ; PDB: 3DL1_A 3KHI_A.
Probab=26.65 E-value=38 Score=33.49 Aligned_cols=14 Identities=29% Similarity=0.498 Sum_probs=11.1
Q ss_pred HHHHHHHHHHHHHH
Q 015798 297 VIGVHELGHILAAK 310 (400)
Q Consensus 297 iLliHElGH~laAR 310 (400)
=+++||++|.+-..
T Consensus 156 NVviHEfAH~LD~~ 169 (253)
T PF06167_consen 156 NVVIHEFAHKLDME 169 (253)
T ss_dssp -HHHHHHHHHHHCT
T ss_pred chHHHHHHHHHHhh
Confidence 47899999999664
No 79
>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=26.25 E-value=41 Score=35.53 Aligned_cols=23 Identities=13% Similarity=0.158 Sum_probs=17.3
Q ss_pred chHHHHHHHHHHHHhhhCCceEE
Q 015798 195 QAAKTYEKISTRMKNKFGDQYKL 217 (400)
Q Consensus 195 ~~eevy~kL~~~Le~~fGdrY~l 217 (400)
+-+++.+.|.+-++..||.+|.-
T Consensus 157 ~~~~~~~~i~~~~~~lfg~~~~~ 179 (472)
T cd06455 157 PLEVVIEGMLDIYQRLFGLRFEE 179 (472)
T ss_pred cHHHHHHHHHHHHHHHhCeEEEe
Confidence 34577777888888789988855
No 80
>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=26.18 E-value=38 Score=36.60 Aligned_cols=11 Identities=45% Similarity=0.591 Sum_probs=9.6
Q ss_pred HHHHHHHHHHH
Q 015798 297 VIGVHELGHIL 307 (400)
Q Consensus 297 iLliHElGH~l 307 (400)
..++||+||.+
T Consensus 377 ~TL~HE~GHa~ 387 (587)
T TIGR02290 377 STLAHELGHAY 387 (587)
T ss_pred HHHHHHhhHHH
Confidence 56799999998
No 81
>cd04283 ZnMc_hatching_enzyme Zinc-dependent metalloprotease, hatching enzyme-like subfamily. Hatching enzymes are secreted by teleost embryos to digest the egg envelope or chorion. In some teleosts, the hatching enzyme may be a system consisting of two evolutionary related metalloproteases, high choriolytic enzyme and low choriolytic enzyme (HCE and LCE), which may have different substrate specificities and cooperatively digest the chorion.
Probab=26.06 E-value=38 Score=31.91 Aligned_cols=14 Identities=43% Similarity=0.294 Sum_probs=11.1
Q ss_pred HHHHHHHHHHHHHH
Q 015798 298 IGVHELGHILAAKS 311 (400)
Q Consensus 298 LliHElGH~laARr 311 (400)
.++||+||++-...
T Consensus 80 ~i~HEl~HaLG~~H 93 (182)
T cd04283 80 IIQHELLHALGFYH 93 (182)
T ss_pred hHHHHHHHHhCCcc
Confidence 67899999986543
No 82
>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]
Probab=25.60 E-value=42 Score=36.39 Aligned_cols=12 Identities=33% Similarity=0.587 Sum_probs=9.9
Q ss_pred HHHHHHHHHHHH
Q 015798 295 ALVIGVHELGHI 306 (400)
Q Consensus 295 ~~iLliHElGH~ 306 (400)
++.|++||+||.
T Consensus 130 lagViAHEigHv 141 (484)
T COG4783 130 LAGVIAHEIGHV 141 (484)
T ss_pred HHHHHHHHHHHH
Confidence 357889999995
No 83
>KOG0391 consensus SNF2 family DNA-dependent ATPase [General function prediction only]
Probab=25.51 E-value=77 Score=38.55 Aligned_cols=36 Identities=22% Similarity=0.211 Sum_probs=23.8
Q ss_pred hHHHHHhcccccceeeeeccccccCceEEEEeecCC
Q 015798 159 ETIDILKDQVFGFDTFFVTNQEPYEGGVLFKGNLRG 194 (400)
Q Consensus 159 edl~~ik~~~Fg~dTFf~T~~e~~~~GvifrGNLRg 194 (400)
+|+...-.++-+..-=-+|..-..+---+.|||||.
T Consensus 583 adIaavae~~qpKgytl~tTqVktpvPsLLrGqLRe 618 (1958)
T KOG0391|consen 583 ADIAAVAEAIQPKGYTLVTTQVKTPVPSLLRGQLRE 618 (1958)
T ss_pred hhHHHHHHhhCccceeeeeeeeccCchHHHHHHHHH
Confidence 455544444445444456666777778899999995
No 84
>PF01431 Peptidase_M13: Peptidase family M13 This is family M13 in the peptidase classification. ; InterPro: IPR018497 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 M13 (neprilysin family, 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 and the predicted active site residues for members of this family and thermolysin occur in the motif HEXXH []. M13 peptidases are well-studied proteases found in a wide range of organisms including mammals and bacteria. In mammals they participate in processes such as cardiovascular development, blood-pressure regulation, nervous control of respiration, and regulation of the function of neuropeptides in the central nervous system. In bacteria they may be used for digestion of milk [, ]. The family includes eukaryotic and prokaryotic oligopeptidases, as well as some of the proteins responsible for the molecular basis of the blood group antigens e.g. Kell []. Neprilysin (3.4.24.11 from EC), is another member of this group, it is variously known as common acute lymphoblastic leukemia antigen (CALLA), enkephalinase (gp100) and neutral endopeptidase metalloendopeptidase (NEP). It is a plasma membrane-bound mammalian enzyme that is able to digest biologically-active peptides, including enkephalins []. The zinc ligands of neprilysin are known and are analogous to those in thermolysin, a related peptidase [, ]. Neprilysins, like thermolysin, are inhibited by phosphoramidon, which appears to selectively inhibit this family in mammals. The enzymes are all oligopeptidases, digesting oligo- and polypeptides, but not proteins []. Neprilysin consists of a short cytoplasmic domain, a membrane-spanning region and a large extracellular domain. The cytoplasmic domain contains a conformationally-restrained octapeptide, which is thought to act as a stop transfer sequence that prevents proteolysis and secretion [, ].; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 2QPJ_A 1R1I_A 1R1J_A 1Y8J_A 1R1H_A 1DMT_A 2YB9_A 3DWB_A 3ZUK_A.
Probab=25.20 E-value=39 Score=31.00 Aligned_cols=18 Identities=28% Similarity=0.134 Sum_probs=13.9
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 015798 292 LVTALVIGVHELGHILAA 309 (400)
Q Consensus 292 L~l~~iLliHElGH~laA 309 (400)
.+.++.+++||++|.+--
T Consensus 33 yg~lG~ilahel~hafd~ 50 (206)
T PF01431_consen 33 YGGLGFILAHELMHAFDP 50 (206)
T ss_dssp HHTHHHHHHHHHHHCTST
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 456678899999998743
No 85
>PF04298 Zn_peptidase_2: Putative neutral zinc metallopeptidase; InterPro: IPR007395 Members of this family of bacterial proteins are described as hypothetical proteins or zinc-dependent proteases. The majority have a HExxH zinc-binding motif characteristic of neutral zinc metallopeptidases, however there is no evidence to support their function as metallopeptidases.
Probab=24.94 E-value=52 Score=32.33 Aligned_cols=15 Identities=27% Similarity=0.671 Sum_probs=11.6
Q ss_pred HHHHHHHHHHHHHHH
Q 015798 296 LVIGVHELGHILAAK 310 (400)
Q Consensus 296 ~iLliHElGH~laAR 310 (400)
+.+.+||.||++.=.
T Consensus 90 vaVAAHEvGHAiQ~a 104 (222)
T PF04298_consen 90 VAVAAHEVGHAIQHA 104 (222)
T ss_pred HHHHHHHHhHHHhcc
Confidence 357899999998643
No 86
>PF04228 Zn_peptidase: Putative neutral zinc metallopeptidase; InterPro: IPR007343 Members of this family of bacterial proteins are described as hypothetical proteins or zinc metallopeptidases. The majority have a HExxH zinc-binding motif characteristic of neutral zinc metallopeptidases, however there is no evidence to support their function as metallopeptidases.
Probab=24.65 E-value=64 Score=32.67 Aligned_cols=16 Identities=25% Similarity=0.285 Sum_probs=12.6
Q ss_pred HHHHHHHHHHHHHHHH
Q 015798 296 LVIGVHELGHILAAKS 311 (400)
Q Consensus 296 ~iLliHElGH~laARr 311 (400)
+.+++||+||-+-...
T Consensus 171 ayVlAHEyGHHVQ~l~ 186 (292)
T PF04228_consen 171 AYVLAHEYGHHVQNLL 186 (292)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 3578999999987654
No 87
>PF06262 DUF1025: Possibl zinc metallo-peptidase; InterPro: IPR010428 This is a family of bacterial protein with undetermined function.; PDB: 3E11_A.
Probab=24.01 E-value=52 Score=28.16 Aligned_cols=14 Identities=29% Similarity=0.237 Sum_probs=11.6
Q ss_pred HHHHHHHHHHHHHH
Q 015798 294 TALVIGVHELGHIL 307 (400)
Q Consensus 294 l~~iLliHElGH~l 307 (400)
++-..++||+||++
T Consensus 72 ~I~~tlvhEiah~f 85 (97)
T PF06262_consen 72 LIRDTLVHEIAHHF 85 (97)
T ss_dssp HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHc
Confidence 55688999999985
No 88
>PRK10733 hflB ATP-dependent metalloprotease; Reviewed
Probab=23.98 E-value=62 Score=35.77 Aligned_cols=38 Identities=18% Similarity=0.207 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHHHHHHcC--CeecCcccccceeeeeeeEEEEe
Q 015798 296 LVIGVHELGHILAAKSTG--VELGVPYFVPSWQIGSFGAITRI 336 (400)
Q Consensus 296 ~iLliHElGH~laARr~G--Vkvs~P~FIP~i~Lg~fGg~t~i 336 (400)
-.+..||.||+++|..+. .++.-...+|. |.-+|++.+
T Consensus 409 ~~~a~he~gha~~~~~~~~~~~~~~v~i~pr---g~~~g~~~~ 448 (644)
T PRK10733 409 ESTAYHEAGHAIIGRLVPEHDPVHKVTIIPR---GRALGVTFF 448 (644)
T ss_pred HHHHHHHHHHHHHHHHccCCCceeEEEEecc---CCCcceeEE
Confidence 467899999999998875 33332223342 334566654
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=23.89 E-value=47 Score=30.91 Aligned_cols=13 Identities=46% Similarity=0.534 Sum_probs=9.9
Q ss_pred HHHHHHHHHHHHH
Q 015798 298 IGVHELGHILAAK 310 (400)
Q Consensus 298 LliHElGH~laAR 310 (400)
.++||++|++=-.
T Consensus 82 ~i~HEl~HaLG~~ 94 (191)
T PF01400_consen 82 TILHELGHALGFW 94 (191)
T ss_dssp HHHHHHHHHHTB-
T ss_pred chHHHHHHHHhhh
Confidence 5699999998544
No 90
>PRK11037 hypothetical protein; Provisional
Probab=23.88 E-value=1.9e+02 Score=24.48 Aligned_cols=65 Identities=22% Similarity=0.441 Sum_probs=41.9
Q ss_pred ccCCCCHhHH-----HHHhcccccceeeeeccccccCceEEEEee--cC--C----chHHHHHHHHHHHHhhhCCceEE
Q 015798 152 EYIRIPKETI-----DILKDQVFGFDTFFVTNQEPYEGGVLFKGN--LR--G----QAAKTYEKISTRMKNKFGDQYKL 217 (400)
Q Consensus 152 ~~~~i~~edl-----~~ik~~~Fg~dTFf~T~~e~~~~GvifrGN--LR--g----~~eevy~kL~~~Le~~fGdrY~l 217 (400)
+..+|++++| +.||+.===+.--.+|++|-..+..+|||. |. | +...||. +-+-|.-.+..+|.|
T Consensus 4 ~~~~I~~~~LL~~AN~iI~~Hedyi~GM~a~~Veqk~~VLVFkGeyFLD~~GlPT~KtTAvFN-MFK~LAh~LS~~y~L 81 (83)
T PRK11037 4 ETQPIDRETLLLEANKIIREHEDYLAGMRATDVEQKNGVLVFRGEYFLDEQGLPTAKTTAVFN-MFKHLAHVLSEKYHL 81 (83)
T ss_pred CCcccCHHHHHHHHHHHHHhhHHHhcccccceeeeeCCEEEEecceeecCCCCCCccchHHHH-HHHHHHHHhCcceec
Confidence 4557888888 456553222344678999999999999999 33 2 2334544 334455556667876
No 91
>cd04281 ZnMc_BMP1_TLD Zinc-dependent metalloprotease; BMP1/TLD-like subfamily. BMP1 (Bone morphogenetic protein 1) and TLD (tolloid)-like metalloproteases play vital roles in extracellular matrix formation, by cleaving precursor proteins such as enzymes, structural proteins, and proteins involved in the mineralization of the extracellular matrix. The drosophila protein tolloid and its Xenopus homologue xolloid cleave and inactivate Sog and chordin, respectively, which are inhibitors of Dpp (the Drosophila decapentaplegic gene product) and its homologue BMP4, involved in dorso-ventral patterning.
Probab=23.87 E-value=43 Score=31.95 Aligned_cols=12 Identities=58% Similarity=0.955 Sum_probs=10.0
Q ss_pred HHHHHHHHHHHH
Q 015798 298 IGVHELGHILAA 309 (400)
Q Consensus 298 LliHElGH~laA 309 (400)
.++||++|++=-
T Consensus 90 ti~HEl~HaLGf 101 (200)
T cd04281 90 IVVHELGHVIGF 101 (200)
T ss_pred hHHHHHHHHhcC
Confidence 678999999854
No 92
>cd04275 ZnMc_pappalysin_like Zinc-dependent metalloprotease, pappalysin_like subfamily. The pregnancy-associated plasma protein A (PAPP-A or pappalysin-1) cleaves insulin-like growth factor-binding proteins 4 and 5, thereby promoting cell growth by releasing bound growth factor. This model includes pappalysins and related metalloprotease domains from all three kingdoms of life. The three-dimensional structure of an archaeal representative, ulilysin, has been solved.
Probab=22.86 E-value=12 Score=36.12 Aligned_cols=12 Identities=42% Similarity=0.659 Sum_probs=9.9
Q ss_pred HHHHHHHHHHHH
Q 015798 297 VIGVHELGHILA 308 (400)
Q Consensus 297 iLliHElGH~la 308 (400)
..++||+||++-
T Consensus 139 ~t~~HEvGH~lG 150 (225)
T cd04275 139 DTATHEVGHWLG 150 (225)
T ss_pred ceeEEeccceee
Confidence 578999999863
No 93
>cd04276 ZnMc_MMP_like_2 Zinc-dependent metalloprotease; MMP_like sub-family 2. A group of bacterial metalloproteinase domains similar to matrix metalloproteinases and astacin.
Probab=22.85 E-value=58 Score=31.00 Aligned_cols=18 Identities=28% Similarity=0.458 Sum_probs=13.3
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 015798 294 TALVIGVHELGHILAAKS 311 (400)
Q Consensus 294 l~~iLliHElGH~laARr 311 (400)
.+..+++||+||.+=-+.
T Consensus 115 ~~~~~~~he~gh~lGl~h 132 (197)
T cd04276 115 SLRYLLAHEVGHTLGLRH 132 (197)
T ss_pred HHHHHHHHHHHHHhcCcc
Confidence 445688999999975443
No 94
>PF01863 DUF45: Protein of unknown function DUF45; InterPro: IPR002725 Members of this family are found in some archaebacteria, as well as Helicobacter pylori. The proteins are 190-240 amino acids long, with the C terminus being the most conserved region, containing three conserved histidines.
Probab=22.19 E-value=44 Score=30.41 Aligned_cols=14 Identities=36% Similarity=0.370 Sum_probs=11.4
Q ss_pred HHHHHHHHHHHHHH
Q 015798 294 TALVIGVHELGHIL 307 (400)
Q Consensus 294 l~~iLliHElGH~l 307 (400)
++=-+++||++|..
T Consensus 163 ~idYVvvHEL~Hl~ 176 (205)
T PF01863_consen 163 VIDYVVVHELCHLR 176 (205)
T ss_pred HHHHHHHHHHHHhc
Confidence 44578899999985
No 95
>cd04927 ACT_ACR-like_2 Second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=22.14 E-value=1.2e+02 Score=24.03 Aligned_cols=35 Identities=23% Similarity=0.314 Sum_probs=24.6
Q ss_pred ccceeeeeccccccCceEEEEeecCCchHHHHHHHHHHHHhhhCCc
Q 015798 169 FGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFGDQ 214 (400)
Q Consensus 169 Fg~dTFf~T~~e~~~~GvifrGNLRg~~eevy~kL~~~Le~~fGdr 214 (400)
.-+||||+++.. |. ...++..++|++.|++.+|+-
T Consensus 40 ~v~D~F~V~d~~---------~~--~~~~~~~~~l~~~L~~~L~~~ 74 (76)
T cd04927 40 RVLDLFFITDAR---------EL--LHTKKRREETYDYLRAVLGDS 74 (76)
T ss_pred EEEEEEEEeCCC---------CC--CCCHHHHHHHHHHHHHHHchh
Confidence 457999997531 11 244567788999999999863
No 96
>TIGR00341 conserved hypothetical protein TIGR00341. This conserved hypothetical protein is found so far only in three archaeal genomes and in Streptomyces coelicolor. It shares a hydrophobic uncharacterized domain (see model TIGR00271) of about 180 residues with several eubacterial proteins, including the much longer protein sll1151 of Synechocystis PCC6803.
Probab=22.07 E-value=9e+02 Score=25.12 Aligned_cols=64 Identities=13% Similarity=0.176 Sum_probs=37.9
Q ss_pred CCCHhHHHHHhcccc------cceeeeeccccccCceEEEEeecCCchHHHHHHHHHH-HHhhhCCceEEEEEecCC
Q 015798 155 RIPKETIDILKDQVF------GFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTR-MKNKFGDQYKLFLLVNPE 224 (400)
Q Consensus 155 ~i~~edl~~ik~~~F------g~dTFf~T~~e~~~~GvifrGNLRg~~eevy~kL~~~-Le~~fGdrY~lfl~ee~e 224 (400)
-|||++.+.+++ +. ++| ||+++...-.+.++--=.-|++.|++-++|++. +.+ +.|++ ++++++
T Consensus 9 ~iP~~~~~~v~~-~l~~~~~~~i~-~~~~~~~~~~~~~i~~~v~~~~~e~vld~L~~lgl~~---~~~~~-vv~~~e 79 (325)
T TIGR00341 9 LIPKEGVVMRKE-IVRGEDLEEIA-IELGDKTFIYDDRIELYVQDSDTEKIVSRLKDKLLGY---KESII-VVYKPE 79 (325)
T ss_pred EeccchHHHHHH-HHhccCcccce-EEeccCCCCcceEEEEEcChhhHHHHHHHHHHcCCCC---CCcEE-EEeccc
Confidence 578888887764 33 244 777764444445555556666777776666554 333 34766 344443
No 97
>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=21.90 E-value=56 Score=34.28 Aligned_cols=20 Identities=10% Similarity=0.219 Sum_probs=13.6
Q ss_pred hHHHHHHHHHHHHhhhCCce
Q 015798 196 AAKTYEKISTRMKNKFGDQY 215 (400)
Q Consensus 196 ~eevy~kL~~~Le~~fGdrY 215 (400)
-+.+.+-|-+-.++.||-++
T Consensus 106 l~~v~~gl~~~~~~lfgi~~ 125 (422)
T cd06456 106 LEKVLDGLFELAERLYGITF 125 (422)
T ss_pred HHHHHHHHHHHHHHHcCeeE
Confidence 34566667777788888654
No 98
>COG5495 Uncharacterized conserved protein [Function unknown]
Probab=21.51 E-value=55 Score=33.01 Aligned_cols=37 Identities=24% Similarity=0.379 Sum_probs=25.7
Q ss_pred CHhHHHHHhcccccceeeeeccccccCceEEEEeecCCchHHHHHHHHHHHHhhhCCce
Q 015798 157 PKETIDILKDQVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFGDQY 215 (400)
Q Consensus 157 ~~edl~~ik~~~Fg~dTFf~T~~e~~~~GvifrGNLRg~~eevy~kL~~~Le~~fGdrY 215 (400)
.+||+++||+.||++ |+.+ ++.-.|-++|..+.|.+|
T Consensus 129 l~edl~rl~d~~~~i-----~eaD-----------------~~g~ai~q~la~emgg~~ 165 (289)
T COG5495 129 LDEDLSRLKDTIFGI-----TEAD-----------------DVGYAIVQSLALEMGGEP 165 (289)
T ss_pred CHHHHHhCcccEEEe-----eccc-----------------ccccHHHHHHHHHhCCCc
Confidence 579999999977765 3333 333346677777788777
No 99
>TIGR01364 serC_1 phosphoserine aminotransferase. This model represents the common form of the phosphoserine aminotransferase SerC. The phosphoserine aminotransferase of the archaeon Methanosarcina barkeri and putative phosphoserine aminotransferase of Mycobacterium tuberculosis are represented by separate models. All are members of the class V aminotransferases (pfam00266).
Probab=21.47 E-value=1.6e+02 Score=29.76 Aligned_cols=60 Identities=10% Similarity=0.208 Sum_probs=42.3
Q ss_pred CCCHhHHHHHhcccccceeeeeccccccCceEEEEeecCCchHHHHHHHHHHHHhhhC--CceEEEEEec
Q 015798 155 RIPKETIDILKDQVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFG--DQYKLFLLVN 222 (400)
Q Consensus 155 ~i~~edl~~ik~~~Fg~dTFf~T~~e~~~~GvifrGNLRg~~eevy~kL~~~Le~~fG--drY~lfl~ee 222 (400)
..|.+.++++++ ||.+.- .-.-|..-.+.--.+-.+.|+.++++|++.|+ +.|.++++..
T Consensus 2 ~~p~~v~~~~~~-------~~~~~~-~~~~~~~~~~hr~~~f~~~~~~~~~~l~~l~~~~~~~~v~~~~g 63 (349)
T TIGR01364 2 ALPEEVLEQAQK-------ELLNFN-GTGMSVMEISHRSKEFEAVANEAESDLRELLNIPDNYEVLFLQG 63 (349)
T ss_pred CCCHHHHHHHHH-------HHhCcc-CCCccccccCCCchHHHHHHHHHHHHHHHHhCCCCCceEEEEcC
Confidence 368889999998 444333 33345555555444556999999999999998 5788876755
No 100
>TIGR03296 M6dom_TIGR03296 M6 family metalloprotease domain. This model describes a metalloproteinase domain, with a characteristic HExxH motif. Examples of this domain are found in proteins in the family of immune inhibitor A, which cleaves antibacterial peptides, and in other, only distantly related proteases. This model is built to be broader and more inclusive than Pfam model pfam05547.
Probab=21.46 E-value=22 Score=35.16 Aligned_cols=12 Identities=50% Similarity=0.656 Sum_probs=9.7
Q ss_pred HHHHHHHHHHHH
Q 015798 296 LVIGVHELGHIL 307 (400)
Q Consensus 296 ~iLliHElGH~l 307 (400)
+-+++||+||.+
T Consensus 166 igv~~HE~gH~l 177 (286)
T TIGR03296 166 VGVIAHELGHDL 177 (286)
T ss_pred eeeeehhhhccc
Confidence 467899999954
No 101
>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=21.17 E-value=33 Score=32.99 Aligned_cols=15 Identities=33% Similarity=0.532 Sum_probs=12.4
Q ss_pred HHHHHHHHHHHHHHH
Q 015798 297 VIGVHELGHILAAKS 311 (400)
Q Consensus 297 iLliHElGH~laARr 311 (400)
..++||+||-+=+..
T Consensus 147 ~t~AHElGHnLGm~H 161 (228)
T cd04271 147 QVFAHEIGHTFGAVH 161 (228)
T ss_pred eehhhhhhhhcCCCC
Confidence 588999999987654
No 102
>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=20.72 E-value=60 Score=34.22 Aligned_cols=16 Identities=25% Similarity=0.333 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHHHHHc
Q 015798 297 VIGVHELGHILAAKST 312 (400)
Q Consensus 297 iLliHElGH~laARr~ 312 (400)
.-++||+||.+=--.-
T Consensus 250 ~TLfHEfGHalH~~ls 265 (458)
T cd06457 250 ETLFHEMGHAMHSMLG 265 (458)
T ss_pred HHHHHHHhHHHHHHHc
Confidence 5679999998764443
No 103
>KOG2661 consensus Peptidase family M48 [Posttranslational modification, protein turnover, chaperones]
Probab=20.62 E-value=70 Score=33.75 Aligned_cols=38 Identities=21% Similarity=0.026 Sum_probs=24.3
Q ss_pred hHHHHHhcccc----cceeeeeccccccCceEEEEeecCCch
Q 015798 159 ETIDILKDQVF----GFDTFFVTNQEPYEGGVLFKGNLRGQA 196 (400)
Q Consensus 159 edl~~ik~~~F----g~dTFf~T~~e~~~~GvifrGNLRg~~ 196 (400)
|.+++++..+| +..+||.|..|..|=.-.-|=+|-+.|
T Consensus 144 ~n~rk~f~~lf~G~~~~~vfyfthlE~~Pit~Rsrfillskp 185 (424)
T KOG2661|consen 144 ENIRKNFWKLFLGLLLFVVFYFTHLEVSPITGRSRFILLSKP 185 (424)
T ss_pred hhHHHHHHHHHhhccceEEEEEeeeeeeccCCcceeeeccCH
Confidence 44455554444 389999999988875544455555544
No 104
>PF04155 Ground-like: Ground-like domain; InterPro: IPR007284 This group of proteins contain one or more copies of the ground-like domain, which are specific to Caenorhabditis elegans and Caenorhabditis briggsae. It has been proposed that the ground-like domain containing proteins may bind and modulate the activity of Patched-like membrane molecules, reminiscent of the modulating activities of neuropeptides [].
Probab=20.31 E-value=75 Score=25.38 Aligned_cols=28 Identities=14% Similarity=0.428 Sum_probs=24.6
Q ss_pred ecC-CchHHHHHHHHHHHHhhhCCceEEE
Q 015798 191 NLR-GQAAKTYEKISTRMKNKFGDQYKLF 218 (400)
Q Consensus 191 NLR-g~~eevy~kL~~~Le~~fGdrY~lf 218 (400)
|++ .++..+-+.|++.++++||.+|.+.
T Consensus 18 ~~~~~~~~~s~~~Iq~~~e~~f~~~f~vI 46 (76)
T PF04155_consen 18 NMKECNLSISKRAIQKAAEKRFGGSFEVI 46 (76)
T ss_pred HhccCCHHHHHHHHHHHHHHHhCCCEEEE
Confidence 445 7889999999999999999999984
Done!