Query 020494
Match_columns 325
No_of_seqs 236 out of 1530
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 02:50:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020494.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020494hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2661 Peptidase family M48 [ 100.0 1.4E-55 3E-60 423.2 8.2 245 1-319 44-294 (424)
2 COG4783 Putative Zn-dependent 99.8 3.4E-19 7.3E-24 178.9 13.0 118 121-320 32-150 (484)
3 COG4784 Putative Zn-dependent 99.8 2E-18 4.4E-23 168.1 10.1 123 118-321 21-145 (479)
4 COG0501 HtpX Zn-dependent prot 99.5 3.6E-14 7.8E-19 132.3 7.0 57 261-318 115-175 (302)
5 PF01435 Peptidase_M48: Peptid 99.4 1.3E-13 2.7E-18 122.9 6.3 77 236-319 29-108 (226)
6 PRK03982 heat shock protein Ht 99.4 1.1E-12 2.3E-17 124.8 8.8 75 237-320 67-145 (288)
7 PRK02870 heat shock protein Ht 99.4 2.9E-12 6.3E-17 125.3 10.8 56 263-319 133-192 (336)
8 PRK01345 heat shock protein Ht 99.4 1.4E-12 3.1E-17 126.2 8.6 76 237-321 66-145 (317)
9 PRK03072 heat shock protein Ht 99.3 6.5E-12 1.4E-16 120.0 8.3 77 236-321 68-148 (288)
10 PRK04897 heat shock protein Ht 99.3 7.4E-12 1.6E-16 120.0 8.5 77 236-321 78-158 (298)
11 PRK03001 M48 family peptidase; 99.3 8.4E-12 1.8E-16 118.4 8.6 56 264-320 85-144 (283)
12 PRK05457 heat shock protein Ht 99.2 1.8E-11 3.9E-16 116.9 8.5 64 254-320 87-154 (284)
13 PRK02391 heat shock protein Ht 99.2 2.1E-11 4.5E-16 117.1 8.1 77 236-321 74-154 (296)
14 PRK01265 heat shock protein Ht 99.2 3.7E-11 8.1E-16 117.1 8.6 75 237-320 82-160 (324)
15 KOG2719 Metalloprotease [Gener 97.4 0.00027 5.9E-09 71.6 6.3 57 265-321 236-301 (428)
16 PF13203 DUF2201_N: Putative m 96.9 0.0016 3.5E-08 61.8 5.9 55 265-320 26-80 (292)
17 PF05569 Peptidase_M56: BlaR1 96.2 0.0064 1.4E-07 57.8 5.1 52 266-318 160-214 (299)
18 PF06114 DUF955: Domain of unk 95.1 0.041 8.9E-07 43.5 5.0 50 264-318 6-60 (122)
19 PF04228 Zn_peptidase: Putativ 94.1 0.045 9.6E-07 53.4 3.4 44 273-316 136-186 (292)
20 smart00731 SprT SprT homologue 93.0 0.14 3E-06 44.4 4.3 39 281-320 41-86 (146)
21 PF13699 DUF4157: Domain of un 92.7 0.068 1.5E-06 42.4 1.7 39 273-314 37-75 (79)
22 PF10263 SprT-like: SprT-like 91.7 0.27 5.9E-06 42.2 4.5 32 283-315 44-75 (157)
23 PRK04351 hypothetical protein; 90.6 0.38 8.3E-06 42.6 4.5 33 279-312 41-73 (149)
24 PF01863 DUF45: Protein of unk 90.0 0.37 8.1E-06 42.8 4.0 54 264-319 130-184 (205)
25 PF12388 Peptidase_M57: Dual-a 88.8 0.29 6.2E-06 45.9 2.3 38 280-320 116-154 (211)
26 PF04450 BSP: Peptidase of pla 87.6 1.5 3.2E-05 40.7 6.2 34 282-315 74-111 (205)
27 COG4219 MecR1 Antirepressor re 87.5 1.1 2.3E-05 44.7 5.5 43 274-317 165-207 (337)
28 PF13485 Peptidase_MA_2: Pepti 87.5 0.47 1E-05 37.7 2.6 23 295-317 20-42 (128)
29 PF10026 DUF2268: Predicted Zn 87.2 1.1 2.3E-05 40.7 5.0 32 282-315 49-80 (195)
30 COG1451 Predicted metal-depend 85.9 1.5 3.2E-05 41.2 5.3 49 266-316 143-191 (223)
31 COG2856 Predicted Zn peptidase 83.7 1 2.3E-05 42.1 3.2 30 282-316 59-88 (213)
32 COG2321 Predicted metalloprote 82.4 1.2 2.6E-05 43.5 3.2 39 276-314 136-181 (295)
33 PF00413 Peptidase_M10: Matrix 81.3 1 2.2E-05 38.0 2.0 21 296-316 101-122 (154)
34 PRK04860 hypothetical protein; 81.1 1.7 3.8E-05 38.9 3.5 34 281-315 45-78 (160)
35 PF10463 Peptidase_U49: Peptid 77.9 1.4 3.1E-05 41.1 2.0 20 299-318 100-119 (206)
36 cd04279 ZnMc_MMP_like_1 Zinc-d 77.9 1.4 3.1E-05 37.8 1.9 20 297-316 101-121 (156)
37 PF02031 Peptidase_M7: Strepto 76.6 5.9 0.00013 34.8 5.3 47 262-312 40-89 (132)
38 COG3590 PepO Predicted metallo 76.5 0.52 1.1E-05 50.0 -1.4 86 232-320 409-507 (654)
39 cd04268 ZnMc_MMP_like Zinc-dep 76.1 1.9 4.2E-05 36.8 2.2 19 296-314 90-108 (165)
40 cd04270 ZnMc_TACE_like Zinc-de 75.4 1.9 4E-05 40.6 2.1 30 284-313 146-180 (244)
41 cd04276 ZnMc_MMP_like_2 Zinc-d 74.8 2.3 4.9E-05 39.2 2.4 32 282-313 92-129 (197)
42 cd04269 ZnMc_adamalysin_II_lik 72.4 2.7 5.8E-05 37.3 2.3 16 297-312 128-143 (194)
43 PF01421 Reprolysin: Reprolysi 72.0 3.3 7.1E-05 37.0 2.7 17 296-312 127-143 (199)
44 PF13688 Reprolysin_5: Metallo 70.9 3.4 7.3E-05 36.5 2.6 18 296-313 138-155 (196)
45 PF06262 DUF1025: Possibl zinc 69.3 11 0.00024 31.2 5.1 40 282-321 50-94 (97)
46 PF13582 Reprolysin_3: Metallo 68.7 2.9 6.2E-05 34.1 1.5 11 302-312 109-119 (124)
47 PF14891 Peptidase_M91: Effect 68.4 3.1 6.7E-05 37.1 1.8 16 297-312 100-115 (174)
48 cd00203 ZnMc Zinc-dependent me 68.1 2.5 5.3E-05 36.0 1.0 15 298-312 94-108 (167)
49 cd04272 ZnMc_salivary_gland_MP 66.2 3.6 7.8E-05 37.6 1.8 14 299-312 144-157 (220)
50 cd04267 ZnMc_ADAM_like Zinc-de 65.2 2.6 5.6E-05 37.3 0.6 16 297-312 130-145 (192)
51 PF01447 Peptidase_M4: Thermol 64.4 5.1 0.00011 35.4 2.3 43 272-315 108-150 (150)
52 COG3091 SprT Zn-dependent meta 64.3 7.4 0.00016 35.1 3.3 31 282-313 44-74 (156)
53 cd04278 ZnMc_MMP Zinc-dependen 64.1 3.4 7.3E-05 35.7 1.1 20 297-316 104-124 (157)
54 KOG3624 M13 family peptidase [ 63.6 4.8 0.0001 43.0 2.4 47 273-319 481-537 (687)
55 TIGR02411 leuko_A4_hydro leuko 63.2 6 0.00013 42.1 3.0 30 282-314 264-293 (601)
56 PF01433 Peptidase_M1: Peptida 62.2 9.6 0.00021 36.8 4.0 54 263-316 253-311 (390)
57 PF13574 Reprolysin_2: Metallo 61.9 4.5 9.7E-05 36.0 1.5 14 300-313 111-124 (173)
58 PF01431 Peptidase_M13: Peptid 60.4 5.9 0.00013 35.4 2.0 25 296-320 32-56 (206)
59 PRK09672 phage exclusion prote 59.7 6.1 0.00013 39.1 2.1 19 299-317 164-182 (305)
60 PF01457 Peptidase_M8: Leishma 58.8 9.5 0.00021 39.8 3.5 56 258-314 156-224 (521)
61 TIGR02412 pepN_strep_liv amino 58.1 9.4 0.0002 42.1 3.4 45 272-316 254-303 (831)
62 cd04277 ZnMc_serralysin_like Z 57.9 7.3 0.00016 34.5 2.1 35 282-316 94-130 (186)
63 smart00235 ZnMc Zinc-dependent 57.8 5.3 0.00011 33.5 1.2 45 263-313 51-99 (140)
64 KOG1047 Bifunctional leukotrie 57.1 5.3 0.00011 42.6 1.2 29 283-314 274-302 (613)
65 PF14521 Aspzincin_M35: Lysine 57.1 14 0.00031 32.2 3.8 40 272-311 64-107 (148)
66 PF13583 Reprolysin_4: Metallo 56.5 5.8 0.00012 36.4 1.3 15 302-316 139-154 (206)
67 PF14247 DUF4344: Domain of un 54.8 26 0.00055 33.1 5.3 51 263-313 38-105 (220)
68 cd04271 ZnMc_ADAM_fungal Zinc- 54.5 4.6 0.0001 37.7 0.3 12 302-313 147-158 (228)
69 PF08325 WLM: WLM domain; Int 52.7 11 0.00024 34.5 2.5 21 296-316 78-98 (186)
70 PTZ00337 surface protease GP63 52.2 27 0.00059 37.3 5.6 54 257-313 177-242 (567)
71 PF06861 BALF1: BALF1 protein; 52.2 9.5 0.00021 35.1 1.9 26 292-317 124-149 (182)
72 cd06459 M3B_Oligoendopeptidase 51.4 9.6 0.00021 37.5 2.0 44 270-317 193-239 (427)
73 cd04273 ZnMc_ADAMTS_like Zinc- 51.2 2.1 4.6E-05 38.7 -2.4 13 300-312 140-152 (207)
74 PF13402 M60-like: Peptidase M 50.6 20 0.00044 33.9 4.0 51 264-314 178-233 (307)
75 PF04298 Zn_peptidase_2: Putat 50.2 9.5 0.00021 36.2 1.7 16 301-316 90-105 (222)
76 COG2738 Predicted Zn-dependent 48.8 9.5 0.00021 35.9 1.4 17 301-317 93-109 (226)
77 TIGR02414 pepN_proteo aminopep 48.1 9.8 0.00021 42.4 1.6 17 299-315 282-298 (863)
78 KOG1046 Puromycin-sensitive am 48.0 20 0.00044 40.0 4.0 49 267-315 284-339 (882)
79 PF10023 DUF2265: Predicted am 47.8 9.6 0.00021 38.2 1.4 17 296-312 161-177 (337)
80 TIGR00181 pepF oligoendopeptid 47.1 6 0.00013 41.4 -0.2 48 266-317 346-395 (591)
81 COG0308 PepN Aminopeptidase N 46.7 16 0.00035 40.6 3.0 54 262-315 262-322 (859)
82 PF12315 DUF3633: Protein of u 46.4 12 0.00027 35.2 1.8 26 284-314 82-107 (212)
83 cd04327 ZnMc_MMP_like_3 Zinc-d 45.5 15 0.00032 33.2 2.1 19 298-316 90-108 (198)
84 PF05572 Peptidase_M43: Pregna 44.1 13 0.00028 32.8 1.5 22 296-317 65-87 (154)
85 PRK14015 pepN aminopeptidase N 42.6 16 0.00036 40.7 2.3 24 72-95 112-135 (875)
86 COG3824 Predicted Zn-dependent 38.9 23 0.00049 31.1 2.1 23 132-154 11-33 (136)
87 cd06161 S2P-M50_SpoIVFB SpoIVF 37.3 22 0.00048 32.5 2.0 15 299-313 37-51 (208)
88 PF09768 Peptidase_M76: Peptid 36.7 72 0.0016 29.1 5.1 48 262-312 36-83 (173)
89 TIGR02289 M3_not_pepF oligoend 36.7 18 0.0004 37.7 1.5 44 270-317 308-354 (549)
90 PTZ00257 Glycoprotein GP63 (le 35.6 72 0.0016 34.7 5.6 57 257-314 201-270 (622)
91 KOG3658 Tumor necrosis factor- 35.5 9.6 0.00021 41.5 -0.8 50 263-312 341-404 (764)
92 COG3864 Uncharacterized protei 34.8 44 0.00095 33.8 3.7 37 280-317 50-86 (396)
93 PF12725 DUF3810: Protein of u 33.9 23 0.0005 34.9 1.6 16 297-312 193-208 (318)
94 KOG3314 Ku70-binding protein [ 31.9 44 0.00095 30.9 2.9 36 280-318 74-109 (194)
95 KOG3607 Meltrins, fertilins an 31.5 28 0.00061 38.2 1.9 18 296-313 319-336 (716)
96 PF09715 Plasmod_dom_1: Plasmo 29.6 22 0.00048 27.9 0.5 31 2-32 1-31 (67)
97 PF01432 Peptidase_M3: Peptida 29.5 31 0.00066 34.8 1.7 18 296-314 239-256 (458)
98 COG1164 Oligoendopeptidase F [ 29.2 22 0.00048 38.0 0.6 53 265-321 346-401 (598)
99 cd06164 S2P-M50_SpoIVFB_CBS Sp 29.0 37 0.00079 31.8 2.0 15 299-313 52-66 (227)
100 COG4324 Predicted aminopeptida 27.7 42 0.0009 33.3 2.1 46 261-312 162-209 (376)
101 TIGR03296 M6dom_TIGR03296 M6 f 27.5 15 0.00032 35.4 -1.0 12 301-312 166-177 (286)
102 COG4900 Predicted metallopepti 27.3 51 0.0011 28.7 2.4 30 283-313 64-93 (133)
103 cd06455 M3A_TOP Peptidase M3 T 26.6 36 0.00078 34.9 1.6 19 297-316 261-279 (472)
104 TIGR02290 M3_fam_3 oligoendope 26.6 34 0.00073 36.0 1.4 46 266-315 342-390 (587)
105 cd06160 S2P-M50_like_2 Unchara 26.3 45 0.00097 30.3 2.0 16 298-313 39-54 (183)
106 PF01400 Astacin: Astacin (Pep 26.0 41 0.00089 30.4 1.7 17 301-317 80-96 (191)
107 cd04281 ZnMc_BMP1_TLD Zinc-dep 24.7 37 0.00079 31.4 1.1 17 301-317 88-104 (200)
108 TIGR01519 plasmod_dom_1 Plasmo 24.5 33 0.00071 27.2 0.7 31 2-32 1-31 (70)
109 cd04283 ZnMc_hatching_enzyme Z 24.0 39 0.00084 30.8 1.2 16 301-316 78-93 (182)
110 cd06159 S2P-M50_PDZ_Arch Uncha 23.9 51 0.0011 31.8 2.0 33 275-313 97-131 (263)
111 PF07225 NDUF_B4: NADH-ubiquin 23.1 44 0.00095 29.1 1.2 37 72-116 62-99 (125)
112 cd06258 Peptidase_M3_like The 21.8 44 0.00096 32.5 1.1 20 296-316 151-170 (365)
113 cd06162 S2P-M50_PDZ_SREBP Ster 21.6 60 0.0013 31.7 2.0 15 300-314 135-149 (277)
114 KOG1565 Gelatinase A and relat 21.5 37 0.0008 35.5 0.5 15 299-313 210-224 (469)
115 cd04280 ZnMc_astacin_like Zinc 20.6 48 0.001 29.6 1.0 17 301-317 75-91 (180)
No 1
>KOG2661 consensus Peptidase family M48 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.4e-55 Score=423.20 Aligned_cols=245 Identities=28% Similarity=0.420 Sum_probs=224.8
Q ss_pred ChhhhhhHHHHHHHhh-cccCCCCCCCcccccc-ccccCC----CCCccccccccccceehhhccccccCCCCCCCCcce
Q 020494 1 MAYYRRAKAALDAFRN-LSSKAVPKSPVQESCS-RVYSNG----SANSAKFSSGFYSYSCISQRLRNSYCNPNFNTAKRY 74 (325)
Q Consensus 1 ~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~-~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~ 74 (325)
|.|||+.|+.+|.+++ ++++|.|++....+.+ .+.++. .+...+.+.+++++.+.-+.+++.-+|+|.+.+.+|
T Consensus 44 ~~~~~~~~~~~~~l~~~~~~~i~~~t~~~t~~n~~~~~~~~~~~~t~v~S~~v~l~~~~~s~Rn~Ng~~y~rFqsnp~~y 123 (424)
T KOG2661|consen 44 HFYSTFNNKRTGGLSSTKSKEIWRITSKCTVWNDAFSRQLLIKEVTAVPSLSVLLPLSPASIRNINGHTYPRFQSNPVPY 123 (424)
T ss_pred eeeeeecchhcccccccCCccceecccccceehhhhhhccchhhhhcccccccccccchhhhhccCccccchhhcCCccH
Confidence 7899999999999999 9999999999987776 333222 344477789999999999999999999999999999
Q ss_pred EEeecceeeeecCCCCCCcccCCchhHHHHHHHHHHHHHHHhhccCcCCCccchhccCCCHHHHHHHHHHHHHHHHHHhc
Q 020494 75 YYVDRYHVQHFRPRGPRKWLQNPRTVFIVVVIGSGAFITLYLGNLETVPYTKRTHFVLLSKAVERQLGESQFQQMKAAFK 154 (325)
Q Consensus 75 y~~~~~~~~hf~~rg~~~w~~~~r~~~~~v~~g~g~~~~~y~~~letvP~TgR~rfillS~~~E~~Lge~~y~qil~e~~ 154 (325)
|+.+++.|+||+|+++.+|++|+|++++++.+|+.++++|||+|+|++|+|||+||+++|.++|+-||+.+|+++++||+
T Consensus 124 s~~~r~~~~sfkpn~~dk~f~n~rk~f~~lf~G~~~~~vfyfthlE~~Pit~Rsrfillskp~ekllge~~ye~im~eyq 203 (424)
T KOG2661|consen 124 SLMIRKWWQSFKPNKKDKVFENIRKNFWKLFLGLLLFVVFYFTHLEVSPITGRSRFILLSKPQEKLLGELEYEAIMEEYQ 203 (424)
T ss_pred HHHHHHHHHhcCCCCccchhhhHHHHHHHHHhhccceEEEEEeeeeeeccCCcceeeeccCHHHHHhhHHHHHHHHHHhc
Confidence 99999999999999999999999999999999876677899999999999999999999999999999999999999999
Q ss_pred CCCCCCCChhHHHHHHHHHHHHHHHHhcccccccccccCCCCccccccccchhhhhHHhhhhcccccccccCcccccccc
Q 020494 155 GKILPAIHPDSVRVRLIAKDIIEALQRGLKHETVWSDMGYASTETDFVNEGRAARDTLRALSENSERGKTEGKWHQEDEI 234 (325)
Q Consensus 155 ~kiLP~~hp~s~rVr~Ia~rIi~a~~~~l~~~~~~~~~gy~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~l 234 (325)
++|||+.||++.+|++|+.+||+++..
T Consensus 204 ~~mLp~~hp~sl~V~~vlk~iIea~~~----------------------------------------------------- 230 (424)
T KOG2661|consen 204 NDMLPEKHPRSLAVKEVLKHIIEANKD----------------------------------------------------- 230 (424)
T ss_pred CccCCcCCchhhHHHHHHHHHHHHhcc-----------------------------------------------------
Confidence 999999999999999999999998520
Q ss_pred cchHHHHHHhhhcccccccccccCCCCCCeEEEEEeCCCCcEEEeCCCeEEEcHhHHhhcCCHHHHHHHHHHHHHHHhcC
Q 020494 235 LDDKWVQQSRKKGQEKGLQSATSHLDGLNWEVLVVNEPVINAFCLPGGKIVVFTGLLEHFRTDAEIATIIGHEDGNGSRL 314 (325)
Q Consensus 235 l~D~~v~~~~~~g~~~~~~~~~s~l~~~~w~v~Vv~~~~~NAfalpgG~I~V~tGLL~~~~~ddELAaVLaHEiaHv~~r 314 (325)
...+++..|+++||+||.+||||+|||+|||+||+|..|++||+||+|||||+||.++|
T Consensus 231 ---------------------~~slsgIkWeihVVndPipNAFvLPgGKvfVFtgiLn~ck~ddglAtvLgHE~aHaVar 289 (424)
T KOG2661|consen 231 ---------------------VPSLSGIKWEIHVVNDPIPNAFVLPGGKVFVFTGILNSCKDDDGLATVLGHEIAHAVAR 289 (424)
T ss_pred ---------------------CCcccCceeEEEEecCCCCceeeccCCeEEEEechhhcccChHHHHHHHHHHHHHHHHH
Confidence 01256789999999999999999999999999999999999999999999999999999
Q ss_pred cHHhh
Q 020494 315 YRAAF 319 (325)
Q Consensus 315 H~~~~ 319 (325)
|++|.
T Consensus 290 H~AEk 294 (424)
T KOG2661|consen 290 HAAEK 294 (424)
T ss_pred HHHHh
Confidence 99953
No 2
>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]
Probab=99.80 E-value=3.4e-19 Score=178.89 Aligned_cols=118 Identities=29% Similarity=0.370 Sum_probs=98.7
Q ss_pred cCCCccchhccCCCHHHHHHHHHHHHHHHHHHhcCCCCCCCChh-HHHHHHHHHHHHHHHHhcccccccccccCCCCccc
Q 020494 121 TVPYTKRTHFVLLSKAVERQLGESQFQQMKAAFKGKILPAIHPD-SVRVRLIAKDIIEALQRGLKHETVWSDMGYASTET 199 (325)
Q Consensus 121 tvP~TgR~rfillS~~~E~~Lge~~y~qil~e~~~kiLP~~hp~-s~rVr~Ia~rIi~a~~~~l~~~~~~~~~gy~~~~~ 199 (325)
..|.+|....-.+|+++|..+|...+.|+..+ ..++ .||+ ...|+.++++|+++
T Consensus 32 ~lp~ig~~~~s~ls~~qev~~g~~~~~Qlr~~--~~~i--~D~el~~yv~~~g~rL~~~--------------------- 86 (484)
T COG4783 32 LLPDIGVSAGSTLSPAQEVALGDPANAQLRGS--VPLI--RDPELEEYVNSLGQRLAAA--------------------- 86 (484)
T ss_pred hcchhhhhhhhcCCHHHHHHhhHHHHHHhccC--CCCc--CCHHHHHHHHHHHHHHHHh---------------------
Confidence 46788999999999999999999988877654 2333 3444 44666666666654
Q ss_pred cccccchhhhhHHhhhhcccccccccCcccccccccchHHHHHHhhhcccccccccccCCCCCCeEEEEEeCCCCcEEEe
Q 020494 200 DFVNEGRAARDTLRALSENSERGKTEGKWHQEDEILDDKWVQQSRKKGQEKGLQSATSHLDGLNWEVLVVNEPVINAFCL 279 (325)
Q Consensus 200 ~~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~ll~D~~v~~~~~~g~~~~~~~~~s~l~~~~w~v~Vv~~~~~NAfal 279 (325)
+++++.+++|.+|+|+.+||||+
T Consensus 87 ---------------------------------------------------------a~~~~~~f~f~lV~d~~iNAFA~ 109 (484)
T COG4783 87 ---------------------------------------------------------ADLVKTPFTFFLVNDDSINAFAT 109 (484)
T ss_pred ---------------------------------------------------------cCCCCCCeEEEEecCCccchhhc
Confidence 33457789999999999999999
Q ss_pred CCCeEEEcHhHHhhcCCHHHHHHHHHHHHHHHhcCcHHhhh
Q 020494 280 PGGKIVVFTGLLEHFRTDAEIATIIGHEDGNGSRLYRAAFD 320 (325)
Q Consensus 280 pgG~I~V~tGLL~~~~~ddELAaVLaHEiaHv~~rH~~~~~ 320 (325)
|||.|+|+||||-..+||.|||+||||||||+..||.++..
T Consensus 110 ~Gg~v~vntGLll~ae~esElagViAHEigHv~qrH~aR~~ 150 (484)
T COG4783 110 PGGYVVVNTGLLLTAENESELAGVIAHEIGHVAQRHLARSM 150 (484)
T ss_pred CCceEEEehHHHHhcCCHHHHHHHHHHHHHHHhhhhHHHHH
Confidence 99999999999999999999999999999999999998654
No 3
>COG4784 Putative Zn-dependent protease [General function prediction only]
Probab=99.76 E-value=2e-18 Score=168.06 Aligned_cols=123 Identities=23% Similarity=0.330 Sum_probs=101.3
Q ss_pred ccCcCCCccchhccCCCHHHHHH-HHHHHHHHHHHHhcCCCCCCCChhHH-HHHHHHHHHHHHHHhcccccccccccCCC
Q 020494 118 NLETVPYTKRTHFVLLSKAVERQ-LGESQFQQMKAAFKGKILPAIHPDSV-RVRLIAKDIIEALQRGLKHETVWSDMGYA 195 (325)
Q Consensus 118 ~letvP~TgR~rfillS~~~E~~-Lge~~y~qil~e~~~kiLP~~hp~s~-rVr~Ia~rIi~a~~~~l~~~~~~~~~gy~ 195 (325)
.|...|-|+-.-+..+++.++.. ||.++-..|+++|++.. +||-.+ .|.+|+.++..
T Consensus 21 ~~~~~Ps~~p~~v~~v~~n~~laqmgar~hprIla~yggeY---~D~Kler~Vari~g~lt~------------------ 79 (479)
T COG4784 21 ESGVQPSDNPQTVDNVQKNDPLAQMGARQHPRILATYGGEY---RDPKLERMVARIVGALTA------------------ 79 (479)
T ss_pred ccccCCCCCcchHHHhhccChHhHhhhhhChhHHHhcCCcc---CCHHHHHHHHHHHhHhhh------------------
Confidence 56778999999999999998776 99999999999999765 344433 44444443322
Q ss_pred CccccccccchhhhhHHhhhhcccccccccCcccccccccchHHHHHHhhhcccccccccccCCCCCCeEEEEEeCCCCc
Q 020494 196 STETDFVNEGRAARDTLRALSENSERGKTEGKWHQEDEILDDKWVQQSRKKGQEKGLQSATSHLDGLNWEVLVVNEPVIN 275 (325)
Q Consensus 196 ~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~ll~D~~v~~~~~~g~~~~~~~~~s~l~~~~w~v~Vv~~~~~N 275 (325)
.++-++..|.+.|+|+|.+|
T Consensus 80 ------------------------------------------------------------~S~~p~q~YriTilnSP~IN 99 (479)
T COG4784 80 ------------------------------------------------------------VSENPQQTYRITILNSPNIN 99 (479)
T ss_pred ------------------------------------------------------------hccCCCceEEEEEecCCCcc
Confidence 22345778999999999999
Q ss_pred EEEeCCCeEEEcHhHHhhcCCHHHHHHHHHHHHHHHhcCcHHhhhh
Q 020494 276 AFCLPGGKIVVFTGLLEHFRTDAEIATIIGHEDGNGSRLYRAAFDR 321 (325)
Q Consensus 276 AfalpgG~I~V~tGLL~~~~~ddELAaVLaHEiaHv~~rH~~~~~~ 321 (325)
||++|||.++|+.|||.++.+..|+|+||+|||||+.++|..+..+
T Consensus 100 AFALPGGYlYitRGLlAland~sEvAAVl~HEmgHVtAnHgi~rQ~ 145 (479)
T COG4784 100 AFALPGGYLYITRGLLALANDSSEVAAVLAHEMGHVTANHGIQRQQ 145 (479)
T ss_pred ccccCCceEEEehhHHHHcCCHHHHHHHHHhhhhheecchhHHHHH
Confidence 9999999999999999999999999999999999999999985543
No 4
>COG0501 HtpX Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]
Probab=99.49 E-value=3.6e-14 Score=132.31 Aligned_cols=57 Identities=35% Similarity=0.510 Sum_probs=53.9
Q ss_pred CCCeEEEEEeCCCCcEEEeCC----CeEEEcHhHHhhcCCHHHHHHHHHHHHHHHhcCcHHh
Q 020494 261 GLNWEVLVVNEPVINAFCLPG----GKIVVFTGLLEHFRTDAEIATIIGHEDGNGSRLYRAA 318 (325)
Q Consensus 261 ~~~w~v~Vv~~~~~NAfalpg----G~I~V~tGLL~~~~~ddELAaVLaHEiaHv~~rH~~~ 318 (325)
...|+++|+++|.+||||+|+ |.|+|++||++.+ |||||++|||||+||+.++|+..
T Consensus 115 ~~~~~v~i~~~~~~NAFa~g~~~~~~~V~vt~gLl~~l-~~dEl~aVlaHElgHi~~rd~~~ 175 (302)
T COG0501 115 PHMPEVYILETPQPNAFALGGGPKNGRVVVTTGLLDLL-NDDELEAVLAHELGHIKNRHTLV 175 (302)
T ss_pred CCCCeeEEecCCCccceecCCCCCCeeEEecHHHHhhC-CHHHHHHHHHHHHHHHhcccHHH
Confidence 457999999999999999999 7999999999976 99999999999999999999986
No 5
>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=99.44 E-value=1.3e-13 Score=122.89 Aligned_cols=77 Identities=29% Similarity=0.365 Sum_probs=58.9
Q ss_pred chHHHHHHhhhcccccccccccCCCCCCeEEEEEeCCCCcEEEeCCCe---EEEcHhHHhhcCCHHHHHHHHHHHHHHHh
Q 020494 236 DDKWVQQSRKKGQEKGLQSATSHLDGLNWEVLVVNEPVINAFCLPGGK---IVVFTGLLEHFRTDAEIATIIGHEDGNGS 312 (325)
Q Consensus 236 ~D~~v~~~~~~g~~~~~~~~~s~l~~~~w~v~Vv~~~~~NAfalpgG~---I~V~tGLL~~~~~ddELAaVLaHEiaHv~ 312 (325)
+++++++.++. +++..+.....++++|++++.+|||++|+|. |+|++||++.+ ++|||++|||||+||+.
T Consensus 29 ~~~~L~~~v~~------l~~~~~~~~~~~~v~v~~~~~~NA~~~g~~~~~~I~v~~~ll~~~-~~~el~aVlaHElgH~~ 101 (226)
T PF01435_consen 29 EDPELRRIVEE------LARRAGLGIPPPRVYVIDSPSPNAFATGGGPRKRIVVTSGLLESL-SEDELAAVLAHELGHIK 101 (226)
T ss_dssp HHHHHHHHHHH------HHHHHHCTSS--EEEEE--SSEEEEEETTTC--EEEEEHHHHHHS-SHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHH------HHHHhcCCCCCCeEEEEcCCCCcEEEEccCCCcEEEEeChhhhcc-cHHHHHHHHHHHHHHHH
Confidence 45666666653 2222333455689999999999999999999 99999999765 99999999999999999
Q ss_pred cCcHHhh
Q 020494 313 RLYRAAF 319 (325)
Q Consensus 313 ~rH~~~~ 319 (325)
.+|....
T Consensus 102 ~~h~~~~ 108 (226)
T PF01435_consen 102 HRHILKS 108 (226)
T ss_dssp TTHCCCC
T ss_pred cCCcchH
Confidence 9998654
No 6
>PRK03982 heat shock protein HtpX; Provisional
Probab=99.38 E-value=1.1e-12 Score=124.82 Aligned_cols=75 Identities=16% Similarity=0.165 Sum_probs=59.9
Q ss_pred hHHHHHHhhhcccccccccccCCCCCCeEEEEEeCCCCcEEEeC----CCeEEEcHhHHhhcCCHHHHHHHHHHHHHHHh
Q 020494 237 DKWVQQSRKKGQEKGLQSATSHLDGLNWEVLVVNEPVINAFCLP----GGKIVVFTGLLEHFRTDAEIATIIGHEDGNGS 312 (325)
Q Consensus 237 D~~v~~~~~~g~~~~~~~~~s~l~~~~w~v~Vv~~~~~NAfalp----gG~I~V~tGLL~~~~~ddELAaVLaHEiaHv~ 312 (325)
+|++++.+++ +++..+++ ..+++|++++.+|||+++ ++.|+|++||++.+ |+|||++|||||+||+.
T Consensus 67 ~p~L~~~v~~------la~~~g~~--~p~v~v~~~~~~NAfa~G~~~~~~~V~vt~gLl~~l-~~~El~AVlAHElgHi~ 137 (288)
T PRK03982 67 APELYRIVER------LAERANIP--KPKVAIVPTQTPNAFATGRDPKHAVVAVTEGILNLL-NEDELEGVIAHELTHIK 137 (288)
T ss_pred hHHHHHHHHH------HHHHcCCC--CCeEEEEeCCCcceEEeccCCCCeEEEeehHHHhhC-CHHHHHHHHHHHHHHHH
Confidence 4566666543 23334444 358999999999999994 46789999999998 99999999999999999
Q ss_pred cCcHHhhh
Q 020494 313 RLYRAAFD 320 (325)
Q Consensus 313 ~rH~~~~~ 320 (325)
++|.....
T Consensus 138 ~~h~~~~~ 145 (288)
T PRK03982 138 NRDTLIQT 145 (288)
T ss_pred cCCHHHHH
Confidence 99987554
No 7
>PRK02870 heat shock protein HtpX; Provisional
Probab=99.36 E-value=2.9e-12 Score=125.28 Aligned_cols=56 Identities=23% Similarity=0.326 Sum_probs=51.9
Q ss_pred CeEEEEEeCCCCcEEEe----CCCeEEEcHhHHhhcCCHHHHHHHHHHHHHHHhcCcHHhh
Q 020494 263 NWEVLVVNEPVINAFCL----PGGKIVVFTGLLEHFRTDAEIATIIGHEDGNGSRLYRAAF 319 (325)
Q Consensus 263 ~w~v~Vv~~~~~NAfal----pgG~I~V~tGLL~~~~~ddELAaVLaHEiaHv~~rH~~~~ 319 (325)
.++|+|++++.+||||+ +++.|+|++||++.+ ++|||++|||||+||+.++|....
T Consensus 133 ~p~V~vi~~~~~NAFA~G~~~~~~~Ivvt~GLL~~L-~~dEL~aVlAHELgHik~~di~~~ 192 (336)
T PRK02870 133 MPKVYIIDAPYMNAFASGYSEKSAMVAITTGLLEKL-DRDELQAVMAHELSHIRHGDIRLT 192 (336)
T ss_pred CCeEEEEcCCCCceEEecCCCCCcEEEEehHHhhhC-CHHHHHHHHHHHHHHHHcccHHHH
Confidence 47999999999999999 478999999999998 999999999999999999998654
No 8
>PRK01345 heat shock protein HtpX; Provisional
Probab=99.36 E-value=1.4e-12 Score=126.16 Aligned_cols=76 Identities=18% Similarity=0.235 Sum_probs=60.5
Q ss_pred hHHHHHHhhhcccccccccccCCCCCCeEEEEEeCCCCcEEEeCC----CeEEEcHhHHhhcCCHHHHHHHHHHHHHHHh
Q 020494 237 DKWVQQSRKKGQEKGLQSATSHLDGLNWEVLVVNEPVINAFCLPG----GKIVVFTGLLEHFRTDAEIATIIGHEDGNGS 312 (325)
Q Consensus 237 D~~v~~~~~~g~~~~~~~~~s~l~~~~w~v~Vv~~~~~NAfalpg----G~I~V~tGLL~~~~~ddELAaVLaHEiaHv~ 312 (325)
+|++.+.+++ ++...+++ ..+|+|++++.+|||+++. +.|+|++|||+.+ |+|||++||||||||+.
T Consensus 66 ~p~L~~~v~~------La~~agi~--~p~v~vid~~~~NAFa~G~~~~~~~V~vt~gLL~~L-~~dEL~aVlAHElgHi~ 136 (317)
T PRK01345 66 APELYRMVRD------LARRAGLP--MPKVYIIDNPQPNAFATGRNPENAAVAATTGLLQRL-SPEEVAGVMAHELAHVK 136 (317)
T ss_pred CHHHHHHHHH------HHHHcCCC--CCcEEEEcCCCcceEEecCCCCCeEEEechHHHhhC-CHHHHHHHHHHHHHHHH
Confidence 4555555543 23445555 3589999999999999953 4799999999998 89999999999999999
Q ss_pred cCcHHhhhh
Q 020494 313 RLYRAAFDR 321 (325)
Q Consensus 313 ~rH~~~~~~ 321 (325)
++|......
T Consensus 137 ~~d~~~~~l 145 (317)
T PRK01345 137 NRDTLTMTI 145 (317)
T ss_pred cCCHHHHHH
Confidence 999976543
No 9
>PRK03072 heat shock protein HtpX; Provisional
Probab=99.29 E-value=6.5e-12 Score=119.97 Aligned_cols=77 Identities=13% Similarity=0.119 Sum_probs=61.9
Q ss_pred chHHHHHHhhhcccccccccccCCCCCCeEEEEEeCCCCcEEEeCC----CeEEEcHhHHhhcCCHHHHHHHHHHHHHHH
Q 020494 236 DDKWVQQSRKKGQEKGLQSATSHLDGLNWEVLVVNEPVINAFCLPG----GKIVVFTGLLEHFRTDAEIATIIGHEDGNG 311 (325)
Q Consensus 236 ~D~~v~~~~~~g~~~~~~~~~s~l~~~~w~v~Vv~~~~~NAfalpg----G~I~V~tGLL~~~~~ddELAaVLaHEiaHv 311 (325)
+||++.+.+++ ++...+++ ..+++|++++.+|||+.+. ..|+|++||++.+ ++|||++|||||+||+
T Consensus 68 ~~p~L~~~v~~------la~~~g~p--~p~vyv~~~~~~NAFa~G~~~~~~~v~vt~gLl~~l-~~~El~aVlAHElgHi 138 (288)
T PRK03072 68 QAPAMYRIVRE------LSTAARQP--MPRLYISPTAAPNAFATGRNPRNAAVCCTEGILQIL-NERELRGVLGHELSHV 138 (288)
T ss_pred hhHHHHHHHHH------HHHHcCCC--CCCEEEecCCCCceEEecCCCCCcEEEecHHHHHhC-CHHHHHHHHHHHHHHH
Confidence 46667666653 33445554 4689999999999999952 2499999999998 9999999999999999
Q ss_pred hcCcHHhhhh
Q 020494 312 SRLYRAAFDR 321 (325)
Q Consensus 312 ~~rH~~~~~~ 321 (325)
.++|......
T Consensus 139 ~~~d~~~~~~ 148 (288)
T PRK03072 139 YNRDILISSV 148 (288)
T ss_pred hcCCHHHHHH
Confidence 9999887654
No 10
>PRK04897 heat shock protein HtpX; Provisional
Probab=99.29 E-value=7.4e-12 Score=119.98 Aligned_cols=77 Identities=19% Similarity=0.242 Sum_probs=61.9
Q ss_pred chHHHHHHhhhcccccccccccCCCCCCeEEEEEeCCCCcEEEeCC----CeEEEcHhHHhhcCCHHHHHHHHHHHHHHH
Q 020494 236 DDKWVQQSRKKGQEKGLQSATSHLDGLNWEVLVVNEPVINAFCLPG----GKIVVFTGLLEHFRTDAEIATIIGHEDGNG 311 (325)
Q Consensus 236 ~D~~v~~~~~~g~~~~~~~~~s~l~~~~w~v~Vv~~~~~NAfalpg----G~I~V~tGLL~~~~~ddELAaVLaHEiaHv 311 (325)
++|++.+.+++ ++...+++ ..++++++++.+|||+++. +.|+|++||++.+ ++|||++|||||+||+
T Consensus 78 ~~p~L~~~v~~------la~~~gip--~p~v~v~~~~~~NAfa~G~~~~~~~v~vt~gLl~~l-~~~El~aVlAHElgHi 148 (298)
T PRK04897 78 EAPELWHIVED------MAMVAQIP--MPRVFIIDDPSPNAFATGSSPKNAAVAVTTGLLAIM-NREELEGVIGHEISHI 148 (298)
T ss_pred hhHHHHHHHHH------HHHHcCCC--CCcEEEecCCCCceEEeccCCCCcEEEeehHHHhhC-CHHHHHHHHHHHHHHH
Confidence 35666666653 23445554 3589999999999999973 5799999999998 9999999999999999
Q ss_pred hcCcHHhhhh
Q 020494 312 SRLYRAAFDR 321 (325)
Q Consensus 312 ~~rH~~~~~~ 321 (325)
.++|....+.
T Consensus 149 ~~~d~~~~~~ 158 (298)
T PRK04897 149 RNYDIRLSTI 158 (298)
T ss_pred hcCCHHHHHH
Confidence 9999876553
No 11
>PRK03001 M48 family peptidase; Provisional
Probab=99.28 E-value=8.4e-12 Score=118.39 Aligned_cols=56 Identities=23% Similarity=0.255 Sum_probs=51.1
Q ss_pred eEEEEEeCCCCcEEEeCC----CeEEEcHhHHhhcCCHHHHHHHHHHHHHHHhcCcHHhhh
Q 020494 264 WEVLVVNEPVINAFCLPG----GKIVVFTGLLEHFRTDAEIATIIGHEDGNGSRLYRAAFD 320 (325)
Q Consensus 264 w~v~Vv~~~~~NAfalpg----G~I~V~tGLL~~~~~ddELAaVLaHEiaHv~~rH~~~~~ 320 (325)
.+++|++++.+|||+.+. +.|+|++||++.+ ++|||++|||||+||+.++|.....
T Consensus 85 p~v~v~~~~~~NAfa~G~~~~~~~Ivvt~gLl~~l-~~~El~aVlAHElgHi~~~h~~~~~ 144 (283)
T PRK03001 85 PKVYLINEDQPNAFATGRNPEHAAVAATTGILRVL-SEREIRGVMAHELAHVKHRDILIST 144 (283)
T ss_pred CeEEEecCCCcceEEecCCCCCeEEEecHHHHhhC-CHHHHHHHHHHHHHHHhCCChHHHH
Confidence 589999999999999964 3599999999988 9999999999999999999998654
No 12
>PRK05457 heat shock protein HtpX; Provisional
Probab=99.24 E-value=1.8e-11 Score=116.87 Aligned_cols=64 Identities=23% Similarity=0.325 Sum_probs=54.2
Q ss_pred ccccCCCCCCeEEEEEeCCCCcEEEeCC----CeEEEcHhHHhhcCCHHHHHHHHHHHHHHHhcCcHHhhh
Q 020494 254 SATSHLDGLNWEVLVVNEPVINAFCLPG----GKIVVFTGLLEHFRTDAEIATIIGHEDGNGSRLYRAAFD 320 (325)
Q Consensus 254 ~~~s~l~~~~w~v~Vv~~~~~NAfalpg----G~I~V~tGLL~~~~~ddELAaVLaHEiaHv~~rH~~~~~ 320 (325)
++..+++ ..+++|++++.+|||+.+. +.|+|++||++.+ |+|||++|||||+||+.++|....+
T Consensus 87 a~~~g~p--~p~v~v~~~~~~NAfa~G~~~~~~~V~vt~gLl~~L-~~~El~aVlAHElgHi~~~d~~~~~ 154 (284)
T PRK05457 87 ARQAGIG--MPEVAIYHSPEINAFATGASKNNSLVAVSTGLLQNM-SRDEVEAVLAHEISHIANGDMVTMT 154 (284)
T ss_pred HHhCCCC--CCCEEEEeCCCceEEEecCCCCCeEEEeehHHhhhC-CHHHHHHHHHHHHHHHHcCCHHHHH
Confidence 3444554 5689999999999999974 3589999999998 9999999999999999999987643
No 13
>PRK02391 heat shock protein HtpX; Provisional
Probab=99.23 E-value=2.1e-11 Score=117.15 Aligned_cols=77 Identities=21% Similarity=0.220 Sum_probs=60.6
Q ss_pred chHHHHHHhhhcccccccccccCCCCCCeEEEEEeCCCCcEEEeCC----CeEEEcHhHHhhcCCHHHHHHHHHHHHHHH
Q 020494 236 DDKWVQQSRKKGQEKGLQSATSHLDGLNWEVLVVNEPVINAFCLPG----GKIVVFTGLLEHFRTDAEIATIIGHEDGNG 311 (325)
Q Consensus 236 ~D~~v~~~~~~g~~~~~~~~~s~l~~~~w~v~Vv~~~~~NAfalpg----G~I~V~tGLL~~~~~ddELAaVLaHEiaHv 311 (325)
++|++.+.++. ++...+++ ..+++|++++.+|||+.+. +.|+|++||++.+ |+|||++|||||+||+
T Consensus 74 ~~p~L~~~v~~------la~~~~~~--~p~v~v~~~~~~NAfa~G~~~~~~~V~vt~gLl~~L-~~~El~aVlaHElgHi 144 (296)
T PRK02391 74 EYPELHAMVER------LCALADLP--KPRVAVADSDVPNAFATGRSPKNAVVCVTTGLMRRL-DPDELEAVLAHELSHV 144 (296)
T ss_pred hCHHHHHHHHH------HHHHcCCC--CCcEEEEeCCCCceEEecCCCCCcEEEecHHHHhhC-CHHHHHHHHHHHHHHH
Confidence 35566655543 23444554 3589999999999999963 3599999999998 8999999999999999
Q ss_pred hcCcHHhhhh
Q 020494 312 SRLYRAAFDR 321 (325)
Q Consensus 312 ~~rH~~~~~~ 321 (325)
.++|......
T Consensus 145 ~~~di~~~~i 154 (296)
T PRK02391 145 KNRDVAVMTI 154 (296)
T ss_pred HcCCHHHHHH
Confidence 9999876543
No 14
>PRK01265 heat shock protein HtpX; Provisional
Probab=99.20 E-value=3.7e-11 Score=117.07 Aligned_cols=75 Identities=21% Similarity=0.274 Sum_probs=60.1
Q ss_pred hHHHHHHhhhcccccccccccCCCCCCeEEEEEeCCCCcEEEeC----CCeEEEcHhHHhhcCCHHHHHHHHHHHHHHHh
Q 020494 237 DKWVQQSRKKGQEKGLQSATSHLDGLNWEVLVVNEPVINAFCLP----GGKIVVFTGLLEHFRTDAEIATIIGHEDGNGS 312 (325)
Q Consensus 237 D~~v~~~~~~g~~~~~~~~~s~l~~~~w~v~Vv~~~~~NAfalp----gG~I~V~tGLL~~~~~ddELAaVLaHEiaHv~ 312 (325)
++++.+.+++ ++...+++ ..+++|++++.+||||.+ ++.|+|++||++.+ ++|||.+|||||+||+.
T Consensus 82 ~~~L~~~v~~------la~~~g~~--~p~vyv~~~~~~NAfa~G~~~~~~~Ivvt~gLl~~l-~~~El~aVlAHElgHik 152 (324)
T PRK01265 82 YGWLYSIVAE------VAKYNGIR--VPKVYIADVPFPNAFAYGSPIAGKRIAITLPLLKIL-NRDEIKAVAGHELGHLK 152 (324)
T ss_pred cHHHHHHHHH------HHHHcCCC--CCeEEEecCCCCCeEEeccCCCCCEEEEehHHHhhC-CHHHHHHHHHHHHHHHH
Confidence 4555555543 23344554 468999999999999963 46899999999998 99999999999999999
Q ss_pred cCcHHhhh
Q 020494 313 RLYRAAFD 320 (325)
Q Consensus 313 ~rH~~~~~ 320 (325)
++|.....
T Consensus 153 ~~d~~~~~ 160 (324)
T PRK01265 153 HRDVELLM 160 (324)
T ss_pred cccHHHHH
Confidence 99997654
No 15
>KOG2719 consensus Metalloprotease [General function prediction only]
Probab=97.41 E-value=0.00027 Score=71.63 Aligned_cols=57 Identities=21% Similarity=0.217 Sum_probs=45.7
Q ss_pred EEEEEeC--C--CCcEEEeCC---CeEEEcHhHH--hhcCCHHHHHHHHHHHHHHHhcCcHHhhhh
Q 020494 265 EVLVVNE--P--VINAFCLPG---GKIVVFTGLL--EHFRTDAEIATIIGHEDGNGSRLYRAAFDR 321 (325)
Q Consensus 265 ~v~Vv~~--~--~~NAfalpg---G~I~V~tGLL--~~~~~ddELAaVLaHEiaHv~~rH~~~~~~ 321 (325)
+++|++. + ..||+-.+= -.|++|.-|+ +...|+||++||+|||+||-.++|..+...
T Consensus 236 k~~vi~~s~rs~hsNAyfyG~~~~KRIvIyDtLl~~~~~~~~eel~AVl~HELGHW~~~H~~K~~i 301 (428)
T KOG2719|consen 236 KYRVIDGSKRSSHSNAYFYGLCKNKRIVIYDTLLLEEEHLNNEELVAVLAHELGHWKLNHVLKNII 301 (428)
T ss_pred EEEEEecCCCCCCCCeeeeeccccceEEEehhhhhhhhccccHHHHHHHHHHhhHHHHhhHHHHHH
Confidence 5777772 2 489998864 3699999999 332389999999999999999999987653
No 16
>PF13203 DUF2201_N: Putative metallopeptidase domain
Probab=96.91 E-value=0.0016 Score=61.78 Aligned_cols=55 Identities=15% Similarity=0.027 Sum_probs=47.6
Q ss_pred EEEEEeCCCCcEEEeCCCeEEEcHhHHhhcCCHHHHHHHHHHHHHHHhcCcHHhhh
Q 020494 265 EVLVVNEPVINAFCLPGGKIVVFTGLLEHFRTDAEIATIIGHEDGNGSRLYRAAFD 320 (325)
Q Consensus 265 ~v~Vv~~~~~NAfalpgG~I~V~tGLL~~~~~ddELAaVLaHEiaHv~~rH~~~~~ 320 (325)
.+.++.++.+..++..|..|+++-..+..+ +.+|+.+||+||+-|++.+|..+..
T Consensus 26 ~l~~~~~~~~~t~~tDg~~l~~nP~~~~~l-~~~~~~~~l~HevlH~~~~H~~r~~ 80 (292)
T PF13203_consen 26 SLPPVEDDGIPTAATDGRRLYYNPEFLESL-SPEERVGLLLHEVLHCLLRHPWRRG 80 (292)
T ss_pred hCeeeeCCCCceeeEcCcEEEECcHHHhcC-CHHHHHHHHHHHHHHHHccchhhhc
Confidence 344555788889999999999999999887 8999999999999999999987543
No 17
>PF05569 Peptidase_M56: BlaR1 peptidase M56; InterPro: IPR008756 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 M56 (clan M-). The predicted active site residues for members of this family occur in the motif HEXXH. The type example is BlaR1 peptidase from Bacillus licheniformis. Production of beta-Lactamase and penicillin-binding protein 2a (which mediate staphylococcal resistance to beta-lactam antibiotics) is regulated by a signal-transducing integral membrane protein and a transcriptional repressor. The signal transducer is a fusion protein with penicillin-binding and zinc metalloprotease domains. The signal for protein expression is transmitted by site-specific proteolytic cleavage of both the transducer, which auto-activates, and the repressor, which is inactivated, unblocking gene transcription.
Probab=96.25 E-value=0.0064 Score=57.75 Aligned_cols=52 Identities=21% Similarity=0.195 Sum_probs=41.4
Q ss_pred EEEEeCC-CCcEEEeCC--CeEEEcHhHHhhcCCHHHHHHHHHHHHHHHhcCcHHh
Q 020494 266 VLVVNEP-VINAFCLPG--GKIVVFTGLLEHFRTDAEIATIIGHEDGNGSRLYRAA 318 (325)
Q Consensus 266 v~Vv~~~-~~NAfalpg--G~I~V~tGLL~~~~~ddELAaVLaHEiaHv~~rH~~~ 318 (325)
+.++.++ ....|+++- .+|++..++++.+ +++|+..||.||++|+..+|..-
T Consensus 160 ~~i~~s~~i~sP~~~G~~~p~I~lP~~~~~~~-~~~el~~il~HEl~Hikr~D~~~ 214 (299)
T PF05569_consen 160 IRIRVSSGISSPFVFGFLRPVIVLPESLLEDL-SEEELRAILLHELAHIKRRDLLW 214 (299)
T ss_pred eEEEEcCCCCCCeeecCcceEEEecCcccccc-CHHHHHHHHHHHHHHHHCCChHH
Confidence 3344443 346777643 5899999999887 99999999999999999999763
No 18
>PF06114 DUF955: Domain of unknown function (DUF955); InterPro: IPR010359 This is a family of bacterial and viral proteins with undetermined function. A conserved H-E-X-X-H motif is suggestive of a catalytic active site and shows similarity to IPR001915 from INTERPRO.; PDB: 3DTE_A 3DTK_A 3DTI_A.
Probab=95.15 E-value=0.041 Score=43.45 Aligned_cols=50 Identities=14% Similarity=0.143 Sum_probs=32.3
Q ss_pred eEEEEEeCCC--CcEEEeC---CCeEEEcHhHHhhcCCHHHHHHHHHHHHHHHhcCcHHh
Q 020494 264 WEVLVVNEPV--INAFCLP---GGKIVVFTGLLEHFRTDAEIATIIGHEDGNGSRLYRAA 318 (325)
Q Consensus 264 w~v~Vv~~~~--~NAfalp---gG~I~V~tGLL~~~~~ddELAaVLaHEiaHv~~rH~~~ 318 (325)
.+|...+... ...++.+ .+.|+|++. .++.+...+|+||+||+..+|...
T Consensus 6 i~v~~~~~~~~~~~~~~~~~~~~~~I~in~~-----~~~~~~~f~laHELgH~~~~~~~~ 60 (122)
T PF06114_consen 6 IDVVYTDLGPKDLGGFSIPKENNPIIFINSN-----LSPERQRFTLAHELGHILLHHGDE 60 (122)
T ss_dssp -EEEEE--TT--EEEETT----TTEEEEESS-----S-HHHHHHHHHHHHHHHHHHH-HH
T ss_pred EEEEEEcCCCCCcCEEEEecCcCCEEEECCC-----CCHHHHHHHHHHHHHHHHhhhccc
Confidence 4555555443 3344443 568888876 368888999999999999998764
No 19
>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=94.09 E-value=0.045 Score=53.35 Aligned_cols=44 Identities=18% Similarity=0.283 Sum_probs=33.1
Q ss_pred CCcEEEeCC-CeEEEcHhHHhhcC------CHHHHHHHHHHHHHHHhcCcH
Q 020494 273 VINAFCLPG-GKIVVFTGLLEHFR------TDAEIATIIGHEDGNGSRLYR 316 (325)
Q Consensus 273 ~~NAfalpg-G~I~V~tGLL~~~~------~ddELAaVLaHEiaHv~~rH~ 316 (325)
..|||=+|. .+|++-..+++.+. .+-..+.|||||.||.+....
T Consensus 136 ~~gpFYCp~D~tIYlD~~f~~~L~~~~ga~G~~a~ayVlAHEyGHHVQ~l~ 186 (292)
T PF04228_consen 136 ATGPFYCPADQTIYLDLSFFDELQQRFGASGDFAQAYVLAHEYGHHVQNLL 186 (292)
T ss_pred CCCCEeCCCCCEEEechHHHHHHHHHhCCccHHHHHHHHHHHHHHHHHHHh
Confidence 457775565 79999998876553 244567899999999988765
No 20
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=92.97 E-value=0.14 Score=44.36 Aligned_cols=39 Identities=13% Similarity=0.054 Sum_probs=33.0
Q ss_pred CCeEEEcHhHHhhcCCHHHHHHHHHHHHHHHhc-------CcHHhhh
Q 020494 281 GGKIVVFTGLLEHFRTDAEIATIIGHEDGNGSR-------LYRAAFD 320 (325)
Q Consensus 281 gG~I~V~tGLL~~~~~ddELAaVLaHEiaHv~~-------rH~~~~~ 320 (325)
.+.|.++.-|++.. .+++|..||.|||+|+.. .|..++.
T Consensus 41 ~~~I~ln~~l~~~~-~~~~l~~~l~HEm~H~~~~~~g~~~~Hg~~f~ 86 (146)
T smart00731 41 SAEIRLNPKLLTEN-GRDRLRETLLHELCHAALYLFGRGYGHGDEWK 86 (146)
T ss_pred CCEEEeCHHHHhhc-cHHHHHhhHHHHHHHHHHHHhCCCCCcCHHHH
Confidence 68999999999864 789999999999999998 5776543
No 21
>PF13699 DUF4157: Domain of unknown function (DUF4157)
Probab=92.65 E-value=0.068 Score=42.41 Aligned_cols=39 Identities=21% Similarity=0.244 Sum_probs=28.8
Q ss_pred CCcEEEeCCCeEEEcHhHHhhcCCHHHHHHHHHHHHHHHhcC
Q 020494 273 VINAFCLPGGKIVVFTGLLEHFRTDAEIATIIGHEDGNGSRL 314 (325)
Q Consensus 273 ~~NAfalpgG~I~V~tGLL~~~~~ddELAaVLaHEiaHv~~r 314 (325)
...||++ |+.|++-.|-... +..+=..+|+||++|++..
T Consensus 37 ~A~A~T~-G~~I~f~~g~~~~--~s~~~~~llaHEl~Hv~Qq 75 (79)
T PF13699_consen 37 GARAFTV-GNDIYFAPGKYNP--DSPEGRALLAHELAHVVQQ 75 (79)
T ss_pred CCeEEEE-CCEEEEcCCCcCC--CCCCcchhHhHHHHHHHhh
Confidence 4678887 7899998776553 2233457899999999753
No 22
>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=91.73 E-value=0.27 Score=42.16 Aligned_cols=32 Identities=19% Similarity=0.285 Sum_probs=28.9
Q ss_pred eEEEcHhHHhhcCCHHHHHHHHHHHHHHHhcCc
Q 020494 283 KIVVFTGLLEHFRTDAEIATIIGHEDGNGSRLY 315 (325)
Q Consensus 283 ~I~V~tGLL~~~~~ddELAaVLaHEiaHv~~rH 315 (325)
.|.++.-+++. .+++++..+|.|||+|+...+
T Consensus 44 ~I~ls~~~~~~-~~~~~~~~tL~HEm~H~~~~~ 75 (157)
T PF10263_consen 44 EIRLSPKLLDR-NPEEELIDTLLHEMAHAAAYV 75 (157)
T ss_pred EEEECHHHHHh-hHHHHHHHHHHHHHHHHHhhh
Confidence 79999999997 489999999999999998843
No 23
>PRK04351 hypothetical protein; Provisional
Probab=90.65 E-value=0.38 Score=42.57 Aligned_cols=33 Identities=27% Similarity=0.240 Sum_probs=28.7
Q ss_pred eCCCeEEEcHhHHhhcCCHHHHHHHHHHHHHHHh
Q 020494 279 LPGGKIVVFTGLLEHFRTDAEIATIIGHEDGNGS 312 (325)
Q Consensus 279 lpgG~I~V~tGLL~~~~~ddELAaVLaHEiaHv~ 312 (325)
+....|-++.-+++.. .+++|..||.||++|+.
T Consensus 41 l~~~~I~lnp~ll~~~-~~~~l~~vv~HElcH~~ 73 (149)
T PRK04351 41 LKDHHIEFNPKMLEEY-GLEELIGIIKHELCHYH 73 (149)
T ss_pred cCCCeEEeCHHHHhhc-cHHHHHhhHHHHHHHHH
Confidence 4567899999999864 89999999999999984
No 24
>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=90.02 E-value=0.37 Score=42.84 Aligned_cols=54 Identities=15% Similarity=0.053 Sum_probs=41.6
Q ss_pred eEEEEEeCCCCcEEEeCCCeEEEcHhHHhhcCCHHHHHHHHHHHHHHHh-cCcHHhh
Q 020494 264 WEVLVVNEPVINAFCLPGGKIVVFTGLLEHFRTDAEIATIIGHEDGNGS-RLYRAAF 319 (325)
Q Consensus 264 w~v~Vv~~~~~NAfalpgG~I~V~tGLL~~~~~ddELAaVLaHEiaHv~-~rH~~~~ 319 (325)
-++.|-+...--.-|...|.|-++.-|+. ..++-+..|+.||++|.. .+|..++
T Consensus 130 ~~i~ir~~ksrWGsc~~~~~I~ln~~L~~--~P~~~idYVvvHEL~Hl~~~nHs~~F 184 (205)
T PF01863_consen 130 PKIKIRDMKSRWGSCSSKGNITLNWRLVM--APPEVIDYVVVHELCHLRHPNHSKRF 184 (205)
T ss_pred ceEEEeehhhccccCCCCCcEEeeccccc--CCccHHHHHHHHHHHHhccCCCCHHH
Confidence 35666666666666855799999999988 388899999999999995 4555554
No 25
>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=88.79 E-value=0.29 Score=45.90 Aligned_cols=38 Identities=26% Similarity=0.224 Sum_probs=27.9
Q ss_pred CCCeEEEcHhHHhhcCCHHHHHHHHHHHHHHHh-cCcHHhhh
Q 020494 280 PGGKIVVFTGLLEHFRTDAEIATIIGHEDGNGS-RLYRAAFD 320 (325)
Q Consensus 280 pgG~I~V~tGLL~~~~~ddELAaVLaHEiaHv~-~rH~~~~~ 320 (325)
|++.|.| .|+-. .+-+.++.||.|||||.+ .||+-.++
T Consensus 116 P~~~I~I-~~~~~--~~~~~~~hvi~HEiGH~IGfRHTD~~~ 154 (211)
T PF12388_consen 116 PYKFIQI-YGLSN--YSVNVIEHVITHEIGHCIGFRHTDYFN 154 (211)
T ss_pred CCceEEE-EecCC--CchhHHHHHHHHHhhhhccccccCcCC
Confidence 4567888 45533 267889999999999987 68875444
No 26
>PF04450 BSP: Peptidase of plants and bacteria; InterPro: IPR007541 These basic secretory proteins (BSPs) are believed to be part of the plants defence mechanism against pathogens [].
Probab=87.58 E-value=1.5 Score=40.75 Aligned_cols=34 Identities=15% Similarity=0.114 Sum_probs=29.1
Q ss_pred CeEEEcHhHHhhcCC----HHHHHHHHHHHHHHHhcCc
Q 020494 282 GKIVVFTGLLEHFRT----DAEIATIIGHEDGNGSRLY 315 (325)
Q Consensus 282 G~I~V~tGLL~~~~~----ddELAaVLaHEiaHv~~rH 315 (325)
..|.+++..|....+ .+|+.+||-|||.|+...-
T Consensus 74 ~~I~~S~~~i~~~~~~~~~~~Ei~Gvl~HE~~H~~Q~~ 111 (205)
T PF04450_consen 74 KEIHFSARYIAKYPADGDVRDEIIGVLYHEMVHCWQWD 111 (205)
T ss_pred cEEEEeHHHHhhcccccchHHHHHHHHHHHHHHHhhcC
Confidence 689999999997753 3699999999999998754
No 27
>COG4219 MecR1 Antirepressor regulating drug resistance, predicted signal transduction N-terminal membrane component [Transcription / Signal transduction mechanisms]
Probab=87.54 E-value=1.1 Score=44.73 Aligned_cols=43 Identities=30% Similarity=0.211 Sum_probs=36.7
Q ss_pred CcEEEeCCCeEEEcHhHHhhcCCHHHHHHHHHHHHHHHhcCcHH
Q 020494 274 INAFCLPGGKIVVFTGLLEHFRTDAEIATIIGHEDGNGSRLYRA 317 (325)
Q Consensus 274 ~NAfalpgG~I~V~tGLL~~~~~ddELAaVLaHEiaHv~~rH~~ 317 (325)
+=.|-++-..|++-+.+.+.+ +++|+.-|++||.+|+..++..
T Consensus 165 P~v~gl~kp~IvlP~d~~~r~-~~ee~~yIilHEl~Hlk~gD~i 207 (337)
T COG4219 165 PMVFGLVKPCIVLPADFVERL-TDEELKYIILHELSHLKRGDAI 207 (337)
T ss_pred ceeeccCcceEEccHHHHhhc-CHHhhhhhHhHHHhhhhcccHH
Confidence 444555557899999999998 9999999999999999988864
No 28
>PF13485 Peptidase_MA_2: Peptidase MA superfamily
Probab=87.54 E-value=0.47 Score=37.67 Aligned_cols=23 Identities=9% Similarity=-0.048 Sum_probs=19.4
Q ss_pred CCHHHHHHHHHHHHHHHhcCcHH
Q 020494 295 RTDAEIATIIGHEDGNGSRLYRA 317 (325)
Q Consensus 295 ~~ddELAaVLaHEiaHv~~rH~~ 317 (325)
.+++.+..||+||++|.......
T Consensus 20 ~~~~~~~~~l~HE~~H~~~~~~~ 42 (128)
T PF13485_consen 20 SDEDWLDRVLAHELAHQWFGNYF 42 (128)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHc
Confidence 57888899999999999876654
No 29
>PF10026 DUF2268: Predicted Zn-dependent protease (DUF2268); InterPro: IPR018728 This domain, found in various hypothetical bacterial proteins, as well as predicted zinc dependent proteases, has no known function.
Probab=87.16 E-value=1.1 Score=40.73 Aligned_cols=32 Identities=28% Similarity=0.373 Sum_probs=25.4
Q ss_pred CeEEEcHhHHhhcCCHHHHHHHHHHHHHHHhcCc
Q 020494 282 GKIVVFTGLLEHFRTDAEIATIIGHEDGNGSRLY 315 (325)
Q Consensus 282 G~I~V~tGLL~~~~~ddELAaVLaHEiaHv~~rH 315 (325)
|+|+++- +..-.+.++|.++||||.-|+..-.
T Consensus 49 ~~i~l~~--~~~~~~~~~l~~~iaHE~hH~~r~~ 80 (195)
T PF10026_consen 49 GYIFLFL--LPNDYSLEELPALIAHEYHHNCRYE 80 (195)
T ss_pred CEEEEEe--cCCcccHHHHHHHHHHHHHHHHHHh
Confidence 5788775 4544588999999999999997544
No 30
>COG1451 Predicted metal-dependent hydrolase [General function prediction only]
Probab=85.91 E-value=1.5 Score=41.22 Aligned_cols=49 Identities=16% Similarity=0.090 Sum_probs=38.4
Q ss_pred EEEEeCCCCcEEEeCCCeEEEcHhHHhhcCCHHHHHHHHHHHHHHHhcCcH
Q 020494 266 VLVVNEPVINAFCLPGGKIVVFTGLLEHFRTDAEIATIIGHEDGNGSRLYR 316 (325)
Q Consensus 266 v~Vv~~~~~NAfalpgG~I~V~tGLL~~~~~ddELAaVLaHEiaHv~~rH~ 316 (325)
+.+-+-...-+-|...|.|.++.-|.. ..++.|..|+.||++|....++
T Consensus 143 ~~ik~~k~~WGScs~~~~i~~~~~l~~--~p~~~i~YVvvHELaHLke~nH 191 (223)
T COG1451 143 IKLKNMKRRWGSCSKAGEIRFNWRLVM--APEEVIDYVVVHELAHLKEKNH 191 (223)
T ss_pred eeeeeccceeeeecCCCcEEeehhhhc--CCHHHHHHHHHHHHHHHhhhhc
Confidence 333355567788888898888887776 3899999999999999986654
No 31
>COG2856 Predicted Zn peptidase [Amino acid transport and metabolism]
Probab=83.74 E-value=1 Score=42.10 Aligned_cols=30 Identities=13% Similarity=0.026 Sum_probs=23.3
Q ss_pred CeEEEcHhHHhhcCCHHHHHHHHHHHHHHHhcCcH
Q 020494 282 GKIVVFTGLLEHFRTDAEIATIIGHEDGNGSRLYR 316 (325)
Q Consensus 282 G~I~V~tGLL~~~~~ddELAaVLaHEiaHv~~rH~ 316 (325)
+.|++++- .+++.-.++||||+||++++-.
T Consensus 59 ~~I~iN~n-----~~~~r~rFtlAHELGH~llH~~ 88 (213)
T COG2856 59 PVIYINAN-----NSLERKRFTLAHELGHALLHTD 88 (213)
T ss_pred ceEEEeCC-----CCHHHHHHHHHHHHhHHHhccc
Confidence 57777653 3777888999999999987644
No 32
>COG2321 Predicted metalloprotease [General function prediction only]
Probab=82.38 E-value=1.2 Score=43.54 Aligned_cols=39 Identities=23% Similarity=0.372 Sum_probs=30.9
Q ss_pred EEEeCC-CeEEEcHhHHhhcC------CHHHHHHHHHHHHHHHhcC
Q 020494 276 AFCLPG-GKIVVFTGLLEHFR------TDAEIATIIGHEDGNGSRL 314 (325)
Q Consensus 276 Afalpg-G~I~V~tGLL~~~~------~ddELAaVLaHEiaHv~~r 314 (325)
-|-+|+ .++++...+++.|+ .|=.-|.|+|||++|++.+
T Consensus 136 PFYCP~D~kvYlDlsFf~~m~~~fga~GdfAqaYViAHEVGHHVQn 181 (295)
T COG2321 136 PFYCPADTKVYLDLSFFDEMKTKFGASGDFAQAYVIAHEVGHHVQN 181 (295)
T ss_pred CeecCCCceEEEehhHHHHHHHHhcCCccHHHHHHHHhhhhHHHHH
Confidence 455566 79999999999875 4556679999999998764
No 33
>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=81.32 E-value=1 Score=37.98 Aligned_cols=21 Identities=14% Similarity=0.150 Sum_probs=16.6
Q ss_pred CHHHHHHHHHHHHHHHh-cCcH
Q 020494 296 TDAEIATIIGHEDGNGS-RLYR 316 (325)
Q Consensus 296 ~ddELAaVLaHEiaHv~-~rH~ 316 (325)
+..++..|+.|||||++ +.|.
T Consensus 101 ~~~~~~~v~~HEiGHaLGL~H~ 122 (154)
T PF00413_consen 101 SGNDLQSVAIHEIGHALGLDHS 122 (154)
T ss_dssp SSEEHHHHHHHHHHHHTTBESS
T ss_pred hhhhhhhhhhhccccccCcCcC
Confidence 55578899999999995 4554
No 34
>PRK04860 hypothetical protein; Provisional
Probab=81.13 E-value=1.7 Score=38.90 Aligned_cols=34 Identities=21% Similarity=0.068 Sum_probs=27.6
Q ss_pred CCeEEEcHhHHhhcCCHHHHHHHHHHHHHHHhcCc
Q 020494 281 GGKIVVFTGLLEHFRTDAEIATIIGHEDGNGSRLY 315 (325)
Q Consensus 281 gG~I~V~tGLL~~~~~ddELAaVLaHEiaHv~~rH 315 (325)
.+.|-++--++..- .+++|..||.||++|+....
T Consensus 45 ~~~I~~Np~ll~~~-~~~~l~~~v~HEl~H~~~~~ 78 (160)
T PRK04860 45 SNEIRLNPVLLLEN-QQAFIDEVVPHELAHLLVYQ 78 (160)
T ss_pred cCCeeeCHHHHhhC-cHHHHHhHHHHHHHHHHHHH
Confidence 36677887777764 89999999999999987653
No 35
>PF10463 Peptidase_U49: Peptidase U49; InterPro: IPR019504 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. The peptidases families associated with clan U- have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported. This entry contains peptidases belonging to MEROPS peptidase family U49 (Lit peptidase, clan U-). The Lit peptidase from Escherichia coli functions in bacterial cell death in response to infection by Enterobacteria phage T4. Following binding of Gol peptide to domains II and III of elongation factor Tu, the Lit peptidase cleaves domain I of the elongation factor. This prevents binding of guanine nucleotides, shuts down translation and leads to cell death.
Probab=77.93 E-value=1.4 Score=41.10 Aligned_cols=20 Identities=25% Similarity=0.026 Sum_probs=17.5
Q ss_pred HHHHHHHHHHHHHhcCcHHh
Q 020494 299 EIATIIGHEDGNGSRLYRAA 318 (325)
Q Consensus 299 ELAaVLaHEiaHv~~rH~~~ 318 (325)
.++.+|.||++|+..+|...
T Consensus 100 A~~fil~HE~~Hv~~~h~~~ 119 (206)
T PF10463_consen 100 AIAFILLHELAHVVLGHEGD 119 (206)
T ss_pred HHHHHHHHHHHHHHHcCccc
Confidence 47899999999999999754
No 36
>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=77.91 E-value=1.4 Score=37.84 Aligned_cols=20 Identities=20% Similarity=0.167 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHHHHHh-cCcH
Q 020494 297 DAEIATIIGHEDGNGS-RLYR 316 (325)
Q Consensus 297 ddELAaVLaHEiaHv~-~rH~ 316 (325)
..++..|+.|||||++ ++|.
T Consensus 101 ~~~~~~~~~HEiGHaLGL~H~ 121 (156)
T cd04279 101 AENLQAIALHELGHALGLWHH 121 (156)
T ss_pred chHHHHHHHHHhhhhhcCCCC
Confidence 5679999999999987 3443
No 37
>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=76.58 E-value=5.9 Score=34.82 Aligned_cols=47 Identities=19% Similarity=0.033 Sum_probs=24.6
Q ss_pred CCeEEEEEeCCC-CcEEEeCC--CeEEEcHhHHhhcCCHHHHHHHHHHHHHHHh
Q 020494 262 LNWEVLVVNEPV-INAFCLPG--GKIVVFTGLLEHFRTDAEIATIIGHEDGNGS 312 (325)
Q Consensus 262 ~~w~v~Vv~~~~-~NAfalpg--G~I~V~tGLL~~~~~ddELAaVLaHEiaHv~ 312 (325)
.+..++..+++. .=|...+. |.|++-+.--+.- +.+. |.+||+||++
T Consensus 40 a~~~~~~~~~~~~sya~~~g~G~G~I~l~~~~~qgy---~~~R-IaaHE~GHiL 89 (132)
T PF02031_consen 40 ADIRYYEGNDPRGSYASTDGLGSGYIFLDYQQNQGY---NSTR-IAAHELGHIL 89 (132)
T ss_dssp -SEEEEEE--TT--EEEE-SSS-EEEEEEHHHHHHS----HHH-HHHHHHHHHH
T ss_pred CcEEEEEecCCCCcccccCCCCcEEEEechHHhhCC---ccce-eeeehhcccc
Confidence 456666655443 33555554 4666655433322 2222 8899999996
No 38
>COG3590 PepO Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]
Probab=76.54 E-value=0.52 Score=50.04 Aligned_cols=86 Identities=28% Similarity=0.364 Sum_probs=49.2
Q ss_pred ccccchHHHHHHhhhcccc--ccccc-ccCCCCCCeEEEEEeCCCCcEEEeCC-CeEEEcHhHHh--hcC-------CHH
Q 020494 232 DEILDDKWVQQSRKKGQEK--GLQSA-TSHLDGLNWEVLVVNEPVINAFCLPG-GKIVVFTGLLE--HFR-------TDA 298 (325)
Q Consensus 232 ~~ll~D~~v~~~~~~g~~~--~~~~~-~s~l~~~~w~v~Vv~~~~~NAfalpg-G~I~V~tGLL~--~~~-------~dd 298 (325)
.++-+|..+.+.++..+.. ..+.+ ...++...|.. .-..+|||.-|+ +.|++-.+||. ... |=-
T Consensus 409 L~~~~~sl~~N~~r~~~~~~~~~l~K~~kPVDr~eW~M---~pq~VNAYYnp~~N~IVFPAAILQ~PFfd~ea~~a~NYG 485 (654)
T COG3590 409 LEIKRDSLYGNVLRASAFNHAHELSKIGKPVDRDEWEM---PPQTVNAYYNPQKNEIVFPAAILQAPFFDPEADSAANYG 485 (654)
T ss_pred hccCchhHHHHHHHHHHHHHhhhHHHhCCCCchhhcCC---CHHHhhhhcCCCCceEeeeHHhcCCCCCCCCcchhhccc
Confidence 3344566666666532110 00000 12234445543 122599999998 46777777775 221 223
Q ss_pred HHHHHHHHHHHHHhcCcHHhhh
Q 020494 299 EIATIIGHEDGNGSRLYRAAFD 320 (325)
Q Consensus 299 ELAaVLaHEiaHv~~rH~~~~~ 320 (325)
.|-+||||||+|.--.-.++++
T Consensus 486 gIGaVIgHEI~HgFDdqGakfD 507 (654)
T COG3590 486 GIGAVIGHEIGHGFDDQGAKFD 507 (654)
T ss_pred CccceehhhhcccccCCccccC
Confidence 5789999999998776666543
No 39
>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=76.11 E-value=1.9 Score=36.77 Aligned_cols=19 Identities=26% Similarity=0.347 Sum_probs=15.5
Q ss_pred CHHHHHHHHHHHHHHHhcC
Q 020494 296 TDAEIATIIGHEDGNGSRL 314 (325)
Q Consensus 296 ~ddELAaVLaHEiaHv~~r 314 (325)
+.+.+.+|+.|||||.+--
T Consensus 90 ~~~~~~~~~~HEiGHaLGL 108 (165)
T cd04268 90 SGARLRNTAEHELGHALGL 108 (165)
T ss_pred HHHHHHHHHHHHHHHHhcc
Confidence 3467899999999999853
No 40
>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=75.42 E-value=1.9 Score=40.59 Aligned_cols=30 Identities=23% Similarity=0.226 Sum_probs=20.4
Q ss_pred EEEcHhHHhhcC-----CHHHHHHHHHHHHHHHhc
Q 020494 284 IVVFTGLLEHFR-----TDAEIATIIGHEDGNGSR 313 (325)
Q Consensus 284 I~V~tGLL~~~~-----~ddELAaVLaHEiaHv~~ 313 (325)
++..+||..... .....+.++||||||..-
T Consensus 146 ~~~n~gl~t~~~~~~~~~~~~~a~t~AHElGHnlG 180 (244)
T cd04270 146 KYLNTGLTTTVNYGKRVPTKESDLVTAHELGHNFG 180 (244)
T ss_pred eeeecceEeeeccCCccchhHHHHHHHHHHHHhcC
Confidence 455667664221 245678999999999875
No 41
>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=74.82 E-value=2.3 Score=39.24 Aligned_cols=32 Identities=19% Similarity=0.464 Sum_probs=24.9
Q ss_pred CeEEEcHhHHhhcCC------HHHHHHHHHHHHHHHhc
Q 020494 282 GKIVVFTGLLEHFRT------DAEIATIIGHEDGNGSR 313 (325)
Q Consensus 282 G~I~V~tGLL~~~~~------ddELAaVLaHEiaHv~~ 313 (325)
+.|.++++.+..... -+-|..+++||+||.+-
T Consensus 92 a~V~l~~~~~~~~~~~~~~~~~~~~~~~~~he~gh~lG 129 (197)
T cd04276 92 ADVILYSGFLRQDQLWYEDLLAASLRYLLAHEVGHTLG 129 (197)
T ss_pred EEEEeCchhhccchhHHHHHHHHHHHHHHHHHHHHHhc
Confidence 678899999876432 25588999999999873
No 42
>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=72.41 E-value=2.7 Score=37.34 Aligned_cols=16 Identities=25% Similarity=0.200 Sum_probs=14.0
Q ss_pred HHHHHHHHHHHHHHHh
Q 020494 297 DAEIATIIGHEDGNGS 312 (325)
Q Consensus 297 ddELAaVLaHEiaHv~ 312 (325)
-...|.++||||||..
T Consensus 128 ~~~~a~~~AHElGH~l 143 (194)
T cd04269 128 LLLFAVTMAHELGHNL 143 (194)
T ss_pred hHHHHHHHHHHHHhhc
Confidence 4577999999999987
No 43
>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=71.99 E-value=3.3 Score=36.99 Aligned_cols=17 Identities=35% Similarity=0.476 Sum_probs=14.9
Q ss_pred CHHHHHHHHHHHHHHHh
Q 020494 296 TDAEIATIIGHEDGNGS 312 (325)
Q Consensus 296 ~ddELAaVLaHEiaHv~ 312 (325)
+...+|.++||||||.+
T Consensus 127 ~~~~~a~~~AHelGH~l 143 (199)
T PF01421_consen 127 SGLSFAVIIAHELGHNL 143 (199)
T ss_dssp SHHHHHHHHHHHHHHHT
T ss_pred hhHHHHHHHHHHHHHhc
Confidence 56788999999999986
No 44
>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=70.92 E-value=3.4 Score=36.53 Aligned_cols=18 Identities=22% Similarity=0.148 Sum_probs=14.2
Q ss_pred CHHHHHHHHHHHHHHHhc
Q 020494 296 TDAEIATIIGHEDGNGSR 313 (325)
Q Consensus 296 ~ddELAaVLaHEiaHv~~ 313 (325)
....-.-|+||||||..-
T Consensus 138 ~~~~~~~~~AHEiGH~lG 155 (196)
T PF13688_consen 138 PTYNGAITFAHEIGHNLG 155 (196)
T ss_dssp -HHHHHHHHHHHHHHHTT
T ss_pred CCCceehhhHHhHHHhcC
Confidence 456777899999999863
No 45
>PF06262 DUF1025: Possibl zinc metallo-peptidase; InterPro: IPR010428 This is a family of bacterial protein with undetermined function.; PDB: 3E11_A.
Probab=69.32 E-value=11 Score=31.20 Aligned_cols=40 Identities=25% Similarity=0.350 Sum_probs=25.7
Q ss_pred CeEEEcHhHHh-hcCCHHHHH----HHHHHHHHHHhcCcHHhhhh
Q 020494 282 GKIVVFTGLLE-HFRTDAEIA----TIIGHEDGNGSRLYRAAFDR 321 (325)
Q Consensus 282 G~I~V~tGLL~-~~~~ddELA----aVLaHEiaHv~~rH~~~~~~ 321 (325)
..|+||..=|. .+.+.+||+ -|+=||+||..--.-.+...
T Consensus 50 ~rI~lyR~pl~~~~~~~~eL~~~I~~tlvhEiah~fG~~~e~l~~ 94 (97)
T PF06262_consen 50 DRIVLYRRPLERRARSREELAELIRDTLVHEIAHHFGISDEDLDA 94 (97)
T ss_dssp EEEEEEHHHHHHT-SSHHHHHHHHHHHHHHHHHHHTT--HHHHHC
T ss_pred CEEEEehHHHHHHhCCHHHHHHHHHHHHHHHHHHHcCCCHHHhhh
Confidence 48888887665 667776665 56788888887655444433
No 46
>PF13582 Reprolysin_3: Metallo-peptidase family M12B Reprolysin-like; PDB: 3P24_C.
Probab=68.71 E-value=2.9 Score=34.14 Aligned_cols=11 Identities=27% Similarity=0.389 Sum_probs=10.2
Q ss_pred HHHHHHHHHHh
Q 020494 302 TIIGHEDGNGS 312 (325)
Q Consensus 302 aVLaHEiaHv~ 312 (325)
.+++|||||.+
T Consensus 109 ~~~~HEiGH~l 119 (124)
T PF13582_consen 109 DTFAHEIGHNL 119 (124)
T ss_dssp THHHHHHHHHT
T ss_pred eEeeehhhHhc
Confidence 89999999986
No 47
>PF14891 Peptidase_M91: Effector protein
Probab=68.41 E-value=3.1 Score=37.08 Aligned_cols=16 Identities=13% Similarity=-0.079 Sum_probs=13.0
Q ss_pred HHHHHHHHHHHHHHHh
Q 020494 297 DAEIATIIGHEDGNGS 312 (325)
Q Consensus 297 ddELAaVLaHEiaHv~ 312 (325)
+..=+.||+|||+|+.
T Consensus 100 ~~~p~v~L~HEL~HA~ 115 (174)
T PF14891_consen 100 PRPPFVVLYHELIHAY 115 (174)
T ss_pred hHHHHHHHHHHHHHHH
Confidence 4556789999999985
No 48
>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=68.14 E-value=2.5 Score=36.04 Aligned_cols=15 Identities=40% Similarity=0.375 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHHHHh
Q 020494 298 AEIATIIGHEDGNGS 312 (325)
Q Consensus 298 dELAaVLaHEiaHv~ 312 (325)
..++.+++|||||.+
T Consensus 94 ~~~~~~~~HElGH~L 108 (167)
T cd00203 94 KEGAQTIAHELGHAL 108 (167)
T ss_pred ccchhhHHHHHHHHh
Confidence 468899999999998
No 49
>cd04272 ZnMc_salivary_gland_MPs Zinc-dependent metalloprotease, salivary_gland_MPs. Metalloproteases secreted by the salivary glands of arthropods.
Probab=66.22 E-value=3.6 Score=37.61 Aligned_cols=14 Identities=14% Similarity=-0.173 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHHHh
Q 020494 299 EIATIIGHEDGNGS 312 (325)
Q Consensus 299 ELAaVLaHEiaHv~ 312 (325)
..+.++||||||.+
T Consensus 144 ~~~~~~AHElGH~l 157 (220)
T cd04272 144 YGVYTMTHELAHLL 157 (220)
T ss_pred ccHHHHHHHHHHHh
Confidence 45899999999987
No 50
>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=65.23 E-value=2.6 Score=37.30 Aligned_cols=16 Identities=25% Similarity=0.223 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHHHHHh
Q 020494 297 DAEIATIIGHEDGNGS 312 (325)
Q Consensus 297 ddELAaVLaHEiaHv~ 312 (325)
.-..+.++|||+||.+
T Consensus 130 ~~~~~~~~aHElGH~l 145 (192)
T cd04267 130 TLLTALTMAHELGHNL 145 (192)
T ss_pred ceeehhhhhhhHHhhc
Confidence 3467889999999987
No 51
>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=64.39 E-value=5.1 Score=35.45 Aligned_cols=43 Identities=28% Similarity=0.295 Sum_probs=23.3
Q ss_pred CCCcEEEeCCCeEEEcHhHHhhcCCHHHHHHHHHHHHHHHhcCc
Q 020494 272 PVINAFCLPGGKIVVFTGLLEHFRTDAEIATIIGHEDGNGSRLY 315 (325)
Q Consensus 272 ~~~NAfalpgG~I~V~tGLL~~~~~ddELAaVLaHEiaHv~~rH 315 (325)
+-.|||=- |..|+.-.|--..+..-..=.=|+||||+|.+-.|
T Consensus 108 ~~~NAfW~-g~~m~yGdG~~~~f~~~~~~lDVvaHEltHGVte~ 150 (150)
T PF01447_consen 108 NYNNAFWN-GSQMVYGDGDGQIFKPFASSLDVVAHELTHGVTEY 150 (150)
T ss_dssp STT-EEE--SSSEEEE---SSSBS-GGG-HHHHHHHHHHHHHHT
T ss_pred CccCcccc-CCEEEEECCCCcccccCccccceeeeccccccccC
Confidence 45899984 56777776654333211111239999999987654
No 52
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=64.28 E-value=7.4 Score=35.06 Aligned_cols=31 Identities=23% Similarity=0.182 Sum_probs=25.3
Q ss_pred CeEEEcHhHHhhcCCHHHHHHHHHHHHHHHhc
Q 020494 282 GKIVVFTGLLEHFRTDAEIATIIGHEDGNGSR 313 (325)
Q Consensus 282 G~I~V~tGLL~~~~~ddELAaVLaHEiaHv~~ 313 (325)
+.|-++-=++..- .+|.|..|+.||++|...
T Consensus 44 ~~I~lNP~ll~en-~~~f~~~vV~HELaHl~l 74 (156)
T COG3091 44 SEIRLNPKLLEEN-GEDFIEQVVPHELAHLHL 74 (156)
T ss_pred cccccCHHHHHHc-cHHHHHHHHHHHHHHHHH
Confidence 3666777777764 899999999999999864
No 53
>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=64.05 E-value=3.4 Score=35.67 Aligned_cols=20 Identities=15% Similarity=0.189 Sum_probs=15.2
Q ss_pred HHHHHHHHHHHHHHHh-cCcH
Q 020494 297 DAEIATIIGHEDGNGS-RLYR 316 (325)
Q Consensus 297 ddELAaVLaHEiaHv~-~rH~ 316 (325)
...+..|+.|||||++ +.|.
T Consensus 104 ~~~~~~~~~HEiGHaLGL~H~ 124 (157)
T cd04278 104 GTDLFSVAAHEIGHALGLGHS 124 (157)
T ss_pred cchHHHHHHHHhccccccCCC
Confidence 3458899999999986 3443
No 54
>KOG3624 consensus M13 family peptidase [Amino acid transport and metabolism]
Probab=63.65 E-value=4.8 Score=42.97 Aligned_cols=47 Identities=32% Similarity=0.427 Sum_probs=35.7
Q ss_pred CCcEEEeCC-CeEEEcHhHHhh----c-----CCHHHHHHHHHHHHHHHhcCcHHhh
Q 020494 273 VINAFCLPG-GKIVVFTGLLEH----F-----RTDAEIATIIGHEDGNGSRLYRAAF 319 (325)
Q Consensus 273 ~~NAfalpg-G~I~V~tGLL~~----~-----~~ddELAaVLaHEiaHv~~rH~~~~ 319 (325)
..|||-.|. +.|+|.-|+|+. . -+=.-+.+||||||+|..-.++.+.
T Consensus 481 ~~na~Y~~~~N~i~~pa~ilq~P~f~~~~P~~~nyg~iG~vigHEl~H~FD~~G~~~ 537 (687)
T KOG3624|consen 481 QVNAFYSPEKNEIVFPAGLLQPPFFDLSYPDYLNYGGIGFVIGHELTHGFDDQGRQY 537 (687)
T ss_pred eeeccccCCCceEEEehhcccCCCCCcccchhhhhHHHHHHHHHHHhhccccccccc
Confidence 478887665 678999999884 1 1556788999999999877666543
No 55
>TIGR02411 leuko_A4_hydro leukotriene A-4 hydrolase/aminopeptidase. Members of this family represent a distinctive subset within the zinc metallopeptidase family M1 (pfam01433). The majority of the members of pfam01433 are aminopeptidases, but the sequences in this family for which the function is known are leukotriene A-4 hydrolase. A dual epoxide hydrolase and aminopeptidase activity at the same active site is indicated. The physiological substrate for aminopeptidase activity is not known.
Probab=63.22 E-value=6 Score=42.09 Aligned_cols=30 Identities=17% Similarity=0.107 Sum_probs=21.4
Q ss_pred CeEEEcHhHHhhcCCHHHHHHHHHHHHHHHhcC
Q 020494 282 GKIVVFTGLLEHFRTDAEIATIIGHEDGNGSRL 314 (325)
Q Consensus 282 G~I~V~tGLL~~~~~ddELAaVLaHEiaHv~~r 314 (325)
|.++....++. .+.+++.|+||||||-=-+
T Consensus 264 ~ltf~~~~ll~---~d~s~~~viaHElAHqWfG 293 (601)
T TIGR02411 264 NLTFATPTLIA---GDRSNVDVIAHELAHSWSG 293 (601)
T ss_pred cceeecccccc---CChhhhhhHHHHHHhhccC
Confidence 36666666654 3456789999999997554
No 56
>PF01433 Peptidase_M1: Peptidase family M1 This is family M1 in the peptidase classification.; InterPro: IPR014782 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 M1 (clan MA(E)), the type example being aminopeptidase N from Homo sapiens (Human). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA. Membrane alanine aminopeptidase (3.4.11.2 from EC) is part of the HEXXH+E group; it consists entirely of aminopeptidases, spread across a wide variety of species []. Functional studies show that CD13/APN catalyzes the removal of single amino acids from the amino terminus of small peptides and probably plays a role in their final digestion; one family member (leukotriene-A4 hydrolase) is known to hydrolyse the epoxide leukotriene-A4 to form an inflammatory mediator []. This hydrolase has been shown to have aminopeptidase activity [], and the zinc ligands of the M1 family were identified by site-directed mutagenesis on this enzyme [] CD13 participates in trimming peptides bound to MHC class II molecules [] and cleaves MIP-1 chemokine, which alters target cell specificity from basophils to eosinophils []. CD13 acts as a receptor for specific strains of RNA viruses (coronaviruses) which cause a relatively large percentage of upper respiratory trace infections. 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: 0008237 metallopeptidase activity, 0008270 zinc ion binding; PDB: 2XQ0_A 2XPY_A 2XPZ_A 3SE6_B 3EBH_A 3EBG_A 3T8V_A 3Q44_A 3Q43_A 3EBI_A ....
Probab=62.19 E-value=9.6 Score=36.82 Aligned_cols=54 Identities=19% Similarity=0.018 Sum_probs=30.0
Q ss_pred CeEEEEEeCCCCcEEEeCCCeEEEcHhHHhhc--C---CHHHHHHHHHHHHHHHhcCcH
Q 020494 263 NWEVLVVNEPVINAFCLPGGKIVVFTGLLEHF--R---TDAEIATIIGHEDGNGSRLYR 316 (325)
Q Consensus 263 ~w~v~Vv~~~~~NAfalpgG~I~V~tGLL~~~--~---~ddELAaVLaHEiaHv~~rH~ 316 (325)
...+.++++-..+++.-+|-.++-...++..- . ...+++.||||||||.--+..
T Consensus 253 k~~~v~~p~~~~~~me~~g~i~~~~~~l~~~~~~~~~~~~~~~~~~iahElahqWfGn~ 311 (390)
T PF01433_consen 253 KLDIVAVPDFPFGGMENWGLITYRESYLLYDPDISTIGDKQEIASLIAHELAHQWFGNL 311 (390)
T ss_dssp EEEEEEEST-SSSEE--TTEEEEEGGGTS-STTTS-HHHHHHHHHHHHHHHHTTTBTTT
T ss_pred ceeEEEEeccccccccccccccccccccccCcccccchhhhhhHHHHHHHHHHHHhccC
Confidence 34555555333456665554444444444221 1 245789999999999877664
No 57
>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=61.91 E-value=4.5 Score=35.96 Aligned_cols=14 Identities=21% Similarity=0.119 Sum_probs=11.1
Q ss_pred HHHHHHHHHHHHhc
Q 020494 300 IATIIGHEDGNGSR 313 (325)
Q Consensus 300 LAaVLaHEiaHv~~ 313 (325)
-.-++||||||..-
T Consensus 111 ~~~~~aHElGH~lG 124 (173)
T PF13574_consen 111 GIDTFAHELGHQLG 124 (173)
T ss_dssp HHHHHHHHHHHHHT
T ss_pred eeeeehhhhHhhcC
Confidence 34569999999874
No 58
>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=60.44 E-value=5.9 Score=35.42 Aligned_cols=25 Identities=16% Similarity=0.125 Sum_probs=19.3
Q ss_pred CHHHHHHHHHHHHHHHhcCcHHhhh
Q 020494 296 TDAEIATIIGHEDGNGSRLYRAAFD 320 (325)
Q Consensus 296 ~ddELAaVLaHEiaHv~~rH~~~~~ 320 (325)
+=..|.+||||||.|..-.+....+
T Consensus 32 ~yg~lG~ilahel~hafd~~g~~~D 56 (206)
T PF01431_consen 32 NYGGLGFILAHELMHAFDPEGINYD 56 (206)
T ss_dssp HHHTHHHHHHHHHHHCTSTTGGGB-
T ss_pred HHHHHHHHHHHHHHHHHHHhHhhcC
Confidence 3345789999999999988877653
No 59
>PRK09672 phage exclusion protein Lit; Provisional
Probab=59.67 E-value=6.1 Score=39.09 Aligned_cols=19 Identities=21% Similarity=0.045 Sum_probs=17.5
Q ss_pred HHHHHHHHHHHHHhcCcHH
Q 020494 299 EIATIIGHEDGNGSRLYRA 317 (325)
Q Consensus 299 ELAaVLaHEiaHv~~rH~~ 317 (325)
.+|.|+-||++|+...|..
T Consensus 164 A~a~i~~HEiaHv~~~h~~ 182 (305)
T PRK09672 164 ALAWILLHEIAHVEFQHSS 182 (305)
T ss_pred HHHHHHHHHHHHHHhcccc
Confidence 4899999999999999986
No 60
>PF01457 Peptidase_M8: Leishmanolysin This Prosite motif covers only the active site. This is family M8 in the peptidase classification. ; InterPro: IPR001577 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 M8 (leishmanolysin 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. Leishmanolysin is an enzyme found in the eukaryotes including Leishmania and related parasitic protozoa []. The endopeptidase is the most abundant protein on the cell surface during the promastigote stage of the parasite, and is attached to the membrane by a glycosylphosphatidylinositol anchor []. In the amastigote form, the parasite lives in lysosomes of host macrophages, producing a form of the protease that has an acidic pH optimum []. This differs from most other metalloproteases and may be an adaptation to the environment in which the organism survives [].; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis, 0007155 cell adhesion, 0016020 membrane; PDB: 1LML_A.
Probab=58.80 E-value=9.5 Score=39.80 Aligned_cols=56 Identities=18% Similarity=0.237 Sum_probs=30.9
Q ss_pred CCCCCCeEEEEEeCCCC---cEEEeC-----C-----CeEEEcHhHHhhcCCHHHHHHHHHHHHHHHhcC
Q 020494 258 HLDGLNWEVLVVNEPVI---NAFCLP-----G-----GKIVVFTGLLEHFRTDAEIATIIGHEDGNGSRL 314 (325)
Q Consensus 258 ~l~~~~w~v~Vv~~~~~---NAfalp-----g-----G~I~V~tGLL~~~~~ddELAaVLaHEiaHv~~r 314 (325)
++++.+.-++|...|.. =|+|.| . |.|.+....|... ..+..--|+.|||+|++-=
T Consensus 156 gv~~~D~vlyV~~~~~~~~~~A~A~~C~~~~~~RP~~G~in~~p~~i~~~-~~~~~~~~~~HEi~HaLGF 224 (521)
T PF01457_consen 156 GVPNADFVLYVTARPSSSSTLAWAAPCQQDSDGRPIAGVININPSYIPSF-YFQEFFRTVIHEIAHALGF 224 (521)
T ss_dssp -EES-SEEEEEE----STT---EEEEEEE-TTS-EEEEEEE--GGG---S---HHHHHHHHHHHHHHTT-
T ss_pred CcCCccEEEEEEEeeccCCceEEEeehhhccCCCCeeEEEEEchhHccch-hhhcccceeeeeeeeeeee
Confidence 45677888888876643 366553 1 7888888777654 5677888999999999853
No 61
>TIGR02412 pepN_strep_liv aminopeptidase N, Streptomyces lividans type. This family is a subset of the members of the zinc metallopeptidase family M1 (pfam01433), with a single member characterized in Streptomyces lividans 66 and designated aminopeptidase N. The spectrum of activity may differ somewhat from the aminopeptidase N clade of E. coli and most other Proteobacteria, well separated phylogenetically within the M1 family. The M1 family also includes leukotriene A-4 hydrolase/aminopeptidase (with a bifunctional active site).
Probab=58.12 E-value=9.4 Score=42.07 Aligned_cols=45 Identities=22% Similarity=0.116 Sum_probs=26.2
Q ss_pred CCCcEEEeCC-CeEEEcHhHHhhcC-C---HHHHHHHHHHHHHHHhcCcH
Q 020494 272 PVINAFCLPG-GKIVVFTGLLEHFR-T---DAEIATIIGHEDGNGSRLYR 316 (325)
Q Consensus 272 ~~~NAfalpg-G~I~V~tGLL~~~~-~---ddELAaVLaHEiaHv~~rH~ 316 (325)
|..++.+|=+ |.|.+...++..-. + ...++.|++|||||.=-+..
T Consensus 254 P~f~~GaMEn~Glit~~e~~l~~~~~~~~~~~~~~~viaHElAHqWFGnl 303 (831)
T TIGR02412 254 PEFNAGAMENAGCVTFAENFLHRAEATRAEKENRAGVILHEMAHMWFGDL 303 (831)
T ss_pred CCCCCCcccccceeeechhhccCCcCCHHHHHHHHHHHHHHHHHHHhCCE
Confidence 4444333322 56666555553211 2 34578999999999876643
No 62
>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=57.91 E-value=7.3 Score=34.47 Aligned_cols=35 Identities=17% Similarity=-0.022 Sum_probs=21.9
Q ss_pred CeEEEcHhHHhhc-CCHHHHHHHHHHHHHHHhc-CcH
Q 020494 282 GKIVVFTGLLEHF-RTDAEIATIIGHEDGNGSR-LYR 316 (325)
Q Consensus 282 G~I~V~tGLL~~~-~~ddELAaVLaHEiaHv~~-rH~ 316 (325)
|.|.+........ ..-...-.|+.|||||++- .|.
T Consensus 94 g~i~~~~~~~~~~~~~g~~~~~t~~HEiGHaLGL~H~ 130 (186)
T cd04277 94 GDIWFNSSYDTNSDSPGSYGYQTIIHEIGHALGLEHP 130 (186)
T ss_pred ceeEEecCcccccCCCChhhHHHHHHHHHHHhcCCCC
Confidence 5666665543321 1234567899999999974 444
No 63
>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=57.84 E-value=5.3 Score=33.51 Aligned_cols=45 Identities=16% Similarity=0.101 Sum_probs=24.6
Q ss_pred CeEEEEEeCC--CC-cEEE-eCCCeEEEcHhHHhhcCCHHHHHHHHHHHHHHHhc
Q 020494 263 NWEVLVVNEP--VI-NAFC-LPGGKIVVFTGLLEHFRTDAEIATIIGHEDGNGSR 313 (325)
Q Consensus 263 ~w~v~Vv~~~--~~-NAfa-lpgG~I~V~tGLL~~~~~ddELAaVLaHEiaHv~~ 313 (325)
+-.|.+...+ .. -|++ .|+|.+-+..+ ..+. -.+|+.|||||++-
T Consensus 51 d~~I~f~~~~~~g~~~a~~g~~~g~~~~~~~--~~~~----~~~~~~HEigHaLG 99 (140)
T smart00235 51 DIYISFGKGDGSGCTLSHAGRPGGDQHFSLG--NGCI----NTGVAAHELGHALG 99 (140)
T ss_pred CeEEEEEECCCCCcceeeeecCCCceEEEcc--CCcC----CcccHHHHHHHHhc
Confidence 3445555544 23 2444 35676666431 1121 23599999999974
No 64
>KOG1047 consensus Bifunctional leukotriene A4 hydrolase/aminopeptidase LTA4H [Lipid transport and metabolism; Posttranslational modification, protein turnover, chaperones; Defense mechanisms; Amino acid transport and metabolism]
Probab=57.07 E-value=5.3 Score=42.61 Aligned_cols=29 Identities=24% Similarity=0.224 Sum_probs=22.7
Q ss_pred eEEEcHhHHhhcCCHHHHHHHHHHHHHHHhcC
Q 020494 283 KIVVFTGLLEHFRTDAEIATIIGHEDGNGSRL 314 (325)
Q Consensus 283 ~I~V~tGLL~~~~~ddELAaVLaHEiaHv~~r 314 (325)
..||+--||. -|.-|+.||||||||---+
T Consensus 274 ltF~TpTlla---GDrsl~~vIaHEIAHSWtG 302 (613)
T KOG1047|consen 274 LTFVTPTLLA---GDRSLVDVIAHEIAHSWTG 302 (613)
T ss_pred eeeecchhhc---CCcchhhHHHHHhhhhhcc
Confidence 5677776765 6778899999999996543
No 65
>PF14521 Aspzincin_M35: Lysine-specific metallo-endopeptidase ; PDB: 2X3C_A 2X3A_A 2X3B_A 1GE7_B 1GE6_A 1GE5_A 1G12_A.
Probab=57.05 E-value=14 Score=32.19 Aligned_cols=40 Identities=13% Similarity=0.078 Sum_probs=28.3
Q ss_pred CCCcEEEeCCC---eEEEcHhHHhhc-CCHHHHHHHHHHHHHHH
Q 020494 272 PVINAFCLPGG---KIVVFTGLLEHF-RTDAEIATIIGHEDGNG 311 (325)
Q Consensus 272 ~~~NAfalpgG---~I~V~tGLL~~~-~~ddELAaVLaHEiaHv 311 (325)
+..-|+|.|+. .|+|-..+...- ...+--+.+|-||++|.
T Consensus 64 ~~~~a~~~~~~~~~~IyLc~~F~~~p~~g~~Sk~~TLiHE~SHf 107 (148)
T PF14521_consen 64 NNTYAYVYPDSPTYTIYLCPAFFSAPTTGKDSKEGTLIHEWSHF 107 (148)
T ss_dssp SSSSEEE-TTST-TEEEE-HHHHHS-SSSTT-HHHHHHHHHHHS
T ss_pred cceEEEEECCCCceEEEEChhhcCCCCCCCCchHHHHHHhhhhh
Confidence 35678888985 599999888832 34567799999999993
No 66
>PF13583 Reprolysin_4: Metallo-peptidase family M12B Reprolysin-like
Probab=56.48 E-value=5.8 Score=36.36 Aligned_cols=15 Identities=20% Similarity=0.160 Sum_probs=11.2
Q ss_pred HHHHHHHHHHhc-CcH
Q 020494 302 TIIGHEDGNGSR-LYR 316 (325)
Q Consensus 302 aVLaHEiaHv~~-rH~ 316 (325)
-+++|||||.+- +|.
T Consensus 139 ~~~aHEiGH~lGl~H~ 154 (206)
T PF13583_consen 139 QTFAHEIGHNLGLRHD 154 (206)
T ss_pred hHHHHHHHHHhcCCCC
Confidence 459999999873 443
No 67
>PF14247 DUF4344: Domain of unknown function (DUF4344)
Probab=54.81 E-value=26 Score=33.12 Aligned_cols=51 Identities=16% Similarity=0.146 Sum_probs=36.6
Q ss_pred CeEEEEEeCCCCcEEEeCC-CeEEEcHhHHhhcC--------C--------HHHHHHHHHHHHHHHhc
Q 020494 263 NWEVLVVNEPVINAFCLPG-GKIVVFTGLLEHFR--------T--------DAEIATIIGHEDGNGSR 313 (325)
Q Consensus 263 ~w~v~Vv~~~~~NAfalpg-G~I~V~tGLL~~~~--------~--------ddELAaVLaHEiaHv~~ 313 (325)
+..|.+-.-.+.|||=-|. ..|.+-..+++... + .+-+..+|-||+||.+-
T Consensus 38 ~l~i~~~~CGe~nA~ydPe~~~I~iCYEf~~~~~~~f~~~~~~~~~~~~~~~~~~~~~l~HE~GHAlI 105 (220)
T PF14247_consen 38 DLTIRFAECGEDNAFYDPENRSITICYEFVDEILDRFAKANDPDEEYGQAAIGNVLFTLYHELGHALI 105 (220)
T ss_pred CeEEEEeecCCCCCccCCCCCEEEECHHHHHHHHHHHHhCCcCcchHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555555577899999996 68998887776332 1 23456789999999864
No 68
>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=54.50 E-value=4.6 Score=37.70 Aligned_cols=12 Identities=25% Similarity=0.371 Sum_probs=10.6
Q ss_pred HHHHHHHHHHhc
Q 020494 302 TIIGHEDGNGSR 313 (325)
Q Consensus 302 aVLaHEiaHv~~ 313 (325)
.++||||||.+-
T Consensus 147 ~t~AHElGHnLG 158 (228)
T cd04271 147 QVFAHEIGHTFG 158 (228)
T ss_pred eehhhhhhhhcC
Confidence 699999999983
No 69
>PF08325 WLM: WLM domain; InterPro: IPR013536 The WLM (WSS1-like metalloprotease) domain is a globular domain related to the zincin-like superfamily of Zn-dependent peptidase. Since the WLM domain contains all known active site residues of zincins, it is predicted to be a catalytically active peptidase domain. The WLM domain is a eukaryotic domain represented in plants, fungi, Plasmodium, and kinetoplastids. By contrast, it is absent in animals, Cryptosporidium, and Microsporidia, suggesting that it has been lost on multiple occasions during the evolution of eukaryotes. The WLM domain is found either in stand-alone form or in association with other domains such as the RanBP2 zinc finger , the ubiquitin domain, or the PUB/PUG domain. This domain could function as a specific de-SUMOylating domain of distinct protein complexes in the nucleus and the cytoplasm []. It has been suggested to form a segregated alpha/beta structure with eight helices and five strands. Proteins containign this domain include yeast WSS1 (a weak suppressor of the Ub-related protein SMT3), and various putative metalloproteases from plant and fungal species.
Probab=52.65 E-value=11 Score=34.48 Aligned_cols=21 Identities=14% Similarity=-0.048 Sum_probs=17.7
Q ss_pred CHHHHHHHHHHHHHHHhcCcH
Q 020494 296 TDAEIATIIGHEDGNGSRLYR 316 (325)
Q Consensus 296 ~ddELAaVLaHEiaHv~~rH~ 316 (325)
+-++|..||-||++|++...+
T Consensus 78 ~~~~i~~t~lHELaH~~~~~H 98 (186)
T PF08325_consen 78 PYETILGTMLHELAHNVHGPH 98 (186)
T ss_pred eHHHHHHHHHHHHHhcccCCc
Confidence 567999999999999986643
No 70
>PTZ00337 surface protease GP63; Provisional
Probab=52.19 E-value=27 Score=37.34 Aligned_cols=54 Identities=13% Similarity=0.132 Sum_probs=37.8
Q ss_pred cCCCCCCeEEEEEeCCC--CcEEEeCC----------CeEEEcHhHHhhcCCHHHHHHHHHHHHHHHhc
Q 020494 257 SHLDGLNWEVLVVNEPV--INAFCLPG----------GKIVVFTGLLEHFRTDAEIATIIGHEDGNGSR 313 (325)
Q Consensus 257 s~l~~~~w~v~Vv~~~~--~NAfalpg----------G~I~V~tGLL~~~~~ddELAaVLaHEiaHv~~ 313 (325)
.++.+.|..++|...|. .=|+|.|- |.|.+.-..|. +.++..-|+.|||+|++-
T Consensus 177 ~Gv~naD~vLyV~a~p~~~~~A~A~~C~~~~~~RPi~G~in~np~~i~---~~~~~~~v~~HEi~HALG 242 (567)
T PTZ00337 177 VGVAGADMILYANIFPTSGPAAWAIPCFLLDDGRPFAAAVNFDPRQIA---VTNGDVRVAAHELGHALG 242 (567)
T ss_pred CCccccceEEEEEeccCCCcceEEEEcccccCCCceEEEEEECHHHcc---chhHHHHHHHHHHHHHHc
Confidence 45667788888876554 23666532 67777765554 456777899999999984
No 71
>PF06861 BALF1: BALF1 protein; InterPro: IPR010677 Epstein-Barr virus (strain GD1) (HHV-4), a human tumour DNA virus and a prominent member of gamma-herpesviruses, encodes homologues of cellular antiapoptotic viral Bcl-2 proteins BALF1 and BHRF1. They protect the virus from apoptosis in its host cell during virus synthesis [, ]. The virus infects B lymphocytes to establish a latent infection and yield proliferating, growth-transformed B cells in vitro. Bcl-2 genes are essential for the initial evasion of apoptosis which allows it to establish a latent infection or cause cellular transformation, or both []. Bcl-2 family proteins can inhibit or induce programmed cell death in part by counteracting the activity of other BCL-2 family members. BALF1, inhibits the antiapoptotic activity of EBV BHRF1 and of KSBcl-2 in several transfected cell lines. BALF1 fails, however, to inhibit the cellular BCL-2 family member, BCL-x(L). Thus, BALF1 acts as a negative regulator of the survival function of BHRF1, similar to the counterbalance observed between cellular BCL-2 family members [].
Probab=52.17 E-value=9.5 Score=35.06 Aligned_cols=26 Identities=23% Similarity=0.269 Sum_probs=22.7
Q ss_pred hhcCCHHHHHHHHHHHHHHHhcCcHH
Q 020494 292 EHFRTDAEIATIIGHEDGNGSRLYRA 317 (325)
Q Consensus 292 ~~~~~ddELAaVLaHEiaHv~~rH~~ 317 (325)
..+.||.|-++|++|++||..++|-.
T Consensus 124 ~~l~~d~e~~s~v~~~lA~Fy~~~r~ 149 (182)
T PF06861_consen 124 RNLLNDHENASLVSHALAHFYLRYRR 149 (182)
T ss_pred HHhcCchHHHHHHHHHHHHHHHHHHH
Confidence 45679999999999999999999853
No 72
>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=51.41 E-value=9.6 Score=37.47 Aligned_cols=44 Identities=18% Similarity=0.277 Sum_probs=26.3
Q ss_pred eCCCCcEEEeC---CCeEEEcHhHHhhcCCHHHHHHHHHHHHHHHhcCcHH
Q 020494 270 NEPVINAFCLP---GGKIVVFTGLLEHFRTDAEIATIIGHEDGNGSRLYRA 317 (325)
Q Consensus 270 ~~~~~NAfalp---gG~I~V~tGLL~~~~~ddELAaVLaHEiaHv~~rH~~ 317 (325)
+.+..-|||.+ ++..+|.... -.+-++ ...|+||+||.++....
T Consensus 193 ~gK~~gaf~~~~~~~~~p~i~~n~---~~~~~~-v~tl~HE~GHa~h~~~~ 239 (427)
T cd06459 193 KGKRSGAYCTGLPPGKHPFILMNF---NGTLDD-VFTLAHELGHAFHSYLS 239 (427)
T ss_pred CCCCCCeecCCCCCCCCCeEEecC---CCChhh-HHHHHHHhhHHHHHHHH
Confidence 33456688865 3445553332 234444 45689999998865544
No 73
>cd04273 ZnMc_ADAMTS_like Zinc-dependent metalloprotease, ADAMTS_like subgroup. ADAMs (A Disintegrin And Metalloprotease) are glycoproteins, which play roles in cell signaling, cell fusion, and cell-cell interactions. This particular subfamily represents domain architectures that combine ADAM-like metalloproteinases with thrombospondin type-1 repeats. ADAMTS (a disintegrin and metalloproteinase with thrombospondin motifs) proteinases are inhibited by TIMPs (tissue inhibitors of metalloproteinases), and they play roles in coagulation, angiogenesis, development and progression of arthritis. They hydrolyze the von Willebrand factor precursor and various components of the extracellular matrix.
Probab=51.25 E-value=2.1 Score=38.74 Aligned_cols=13 Identities=38% Similarity=0.266 Sum_probs=11.6
Q ss_pred HHHHHHHHHHHHh
Q 020494 300 IATIIGHEDGNGS 312 (325)
Q Consensus 300 LAaVLaHEiaHv~ 312 (325)
.|.++||||||.+
T Consensus 140 ~a~~~aHElGH~L 152 (207)
T cd04273 140 SAFTIAHELGHVL 152 (207)
T ss_pred eEEeeeeechhhc
Confidence 4789999999987
No 74
>PF13402 M60-like: Peptidase M60-like family; PDB: 4FCA_A.
Probab=50.60 E-value=20 Score=33.87 Aligned_cols=51 Identities=14% Similarity=0.024 Sum_probs=29.3
Q ss_pred eEEEEEeCCCCc-EEEe-CCCeEEEcHhHHhhcCCHHHH---HHHHHHHHHHHhcC
Q 020494 264 WEVLVVNEPVIN-AFCL-PGGKIVVFTGLLEHFRTDAEI---ATIIGHEDGNGSRL 314 (325)
Q Consensus 264 w~v~Vv~~~~~N-Afal-pgG~I~V~tGLL~~~~~ddEL---AaVLaHEiaHv~~r 314 (325)
....++.+...+ +++. .|+.|....+..+.+-+.+.+ .=-+.||+||....
T Consensus 178 ~~~r~v~~v~~~~g~m~a~g~~i~~~~~~~~~~l~~~~~~~~~WG~~HE~GH~~Q~ 233 (307)
T PF13402_consen 178 PNNRFVFDVQISAGYMHASGYPIGFPPNWMNELLNPNPLRKGGWGPWHELGHNHQQ 233 (307)
T ss_dssp --EEEEEETT----SEEEETTEEEEETT--HHHH-HHHHHHH-HHHHHHHHHHH-B
T ss_pred ccceEEEeccccccceeecCCcEEeeCcHHhcccCHhHcCCCCeeehhhhhhhcCc
Confidence 444777777655 5555 677777777766655466665 33589999998764
No 75
>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=50.16 E-value=9.5 Score=36.17 Aligned_cols=16 Identities=19% Similarity=0.304 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHhcCcH
Q 020494 301 ATIIGHEDGNGSRLYR 316 (325)
Q Consensus 301 AaVLaHEiaHv~~rH~ 316 (325)
.+|=|||.||.+.++.
T Consensus 90 vaVAAHEvGHAiQ~a~ 105 (222)
T PF04298_consen 90 VAVAAHEVGHAIQHAE 105 (222)
T ss_pred HHHHHHHHhHHHhccc
Confidence 4789999999998874
No 76
>COG2738 Predicted Zn-dependent protease [General function prediction only]
Probab=48.81 E-value=9.5 Score=35.95 Aligned_cols=17 Identities=18% Similarity=0.231 Sum_probs=14.2
Q ss_pred HHHHHHHHHHHhcCcHH
Q 020494 301 ATIIGHEDGNGSRLYRA 317 (325)
Q Consensus 301 AaVLaHEiaHv~~rH~~ 317 (325)
.+|-|||+||.+.++.-
T Consensus 93 ~aVAAHEVGHAiQd~~~ 109 (226)
T COG2738 93 IAVAAHEVGHAIQDQED 109 (226)
T ss_pred HHHHHHHhhHHHhhhcc
Confidence 47899999999987753
No 77
>TIGR02414 pepN_proteo aminopeptidase N, Escherichia coli type. The M1 family of zinc metallopeptidases contains a number of distinct, well-separated clades of proteins with aminopeptidase activity. Several are designated aminopeptidase N, EC 3.4.11.2, after the Escherichia coli enzyme, suggesting a similar activity profile. This family consists of all aminopeptidases closely related to E. coli PepN and presumed to have similar (not identical) function. Nearly all are found in Proteobacteria, but members are found also in Cyanobacteria, plants, and apicomplexan parasites. This family differs greatly in sequence from the family of aminopeptidases typified by Streptomyces lividans PepN (TIGR02412), from the membrane bound aminopeptidase N family in animals, etc.
Probab=48.06 E-value=9.8 Score=42.43 Aligned_cols=17 Identities=24% Similarity=0.147 Sum_probs=13.9
Q ss_pred HHHHHHHHHHHHHhcCc
Q 020494 299 EIATIIGHEDGNGSRLY 315 (325)
Q Consensus 299 ELAaVLaHEiaHv~~rH 315 (325)
.++.|+|||++|.--+.
T Consensus 282 ~i~~VIaHElaHqWfGN 298 (863)
T TIGR02414 282 RIESVIAHEYFHNWTGN 298 (863)
T ss_pred HHHHHHHHHHHHHHhcc
Confidence 47899999999976554
No 78
>KOG1046 consensus Puromycin-sensitive aminopeptidase and related aminopeptidases [Amino acid transport and metabolism; Posttranslational modification, protein turnover, chaperones]
Probab=47.97 E-value=20 Score=39.97 Aligned_cols=49 Identities=18% Similarity=0.066 Sum_probs=28.7
Q ss_pred EEEeCCCCcEEEeCC-CeEEEcHhHHhhc------CCHHHHHHHHHHHHHHHhcCc
Q 020494 267 LVVNEPVINAFCLPG-GKIVVFTGLLEHF------RTDAEIATIIGHEDGNGSRLY 315 (325)
Q Consensus 267 ~Vv~~~~~NAfalpg-G~I~V~tGLL~~~------~~ddELAaVLaHEiaHv~~rH 315 (325)
-+|--|...+-||=+ |.|..-...|-.- .+...+|.|+|||+||.--+-
T Consensus 284 D~iavPdf~~GAMENwGLvtyre~~lL~~~~~ss~~~k~~va~vIaHElAHQWFGN 339 (882)
T KOG1046|consen 284 DLVAVPDFSAGAMENWGLVTYRETALLYDPQTSSSSNKQRVAEVIAHELAHQWFGN 339 (882)
T ss_pred cEEecCCccccchhcCcceeeeehhhccCCCcCcHHHHHHHHHHHHHHHHHHHhcC
Confidence 334444555555534 5554444433321 136779999999999976553
No 79
>PF10023 DUF2265: Predicted aminopeptidase (DUF2265); InterPro: IPR014553 This group represents a predicted aminopeptidase.
Probab=47.75 E-value=9.6 Score=38.23 Aligned_cols=17 Identities=35% Similarity=0.458 Sum_probs=15.8
Q ss_pred CHHHHHHHHHHHHHHHh
Q 020494 296 TDAEIATIIGHEDGNGS 312 (325)
Q Consensus 296 ~ddELAaVLaHEiaHv~ 312 (325)
+|.+||.+|=||++|..
T Consensus 161 ~~~~LA~LIfHELaHq~ 177 (337)
T PF10023_consen 161 PDGELARLIFHELAHQT 177 (337)
T ss_pred CchHHHHHHHHHHhhce
Confidence 89999999999999975
No 80
>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=47.11 E-value=6 Score=41.37 Aligned_cols=48 Identities=19% Similarity=0.166 Sum_probs=26.8
Q ss_pred EEEEeCCCCcEEEeCCC--eEEEcHhHHhhcCCHHHHHHHHHHHHHHHhcCcHH
Q 020494 266 VLVVNEPVINAFCLPGG--KIVVFTGLLEHFRTDAEIATIIGHEDGNGSRLYRA 317 (325)
Q Consensus 266 v~Vv~~~~~NAfalpgG--~I~V~tGLL~~~~~ddELAaVLaHEiaHv~~rH~~ 317 (325)
++--+.+..-|||.+.+ .-+| |+..-.+-+++ .+|+||+||.++....
T Consensus 346 ~~~r~gK~~Ga~~~~~~~~~p~i---l~N~~~~~~dv-~TLaHElGHa~H~~~~ 395 (591)
T TIGR00181 346 YAENKGKRSGAYSIGGYKVKPYI---LMNWDGTLNSV-FTLAHELGHSMHSYFS 395 (591)
T ss_pred ecCCCCCCCCcccCCCCCCCCeE---EEecCCCcchH-HHHHHHhhhHHHHHHH
Confidence 33334455779987542 2222 22222233333 5799999999876544
No 81
>COG0308 PepN Aminopeptidase N [Amino acid transport and metabolism]
Probab=46.67 E-value=16 Score=40.55 Aligned_cols=54 Identities=15% Similarity=0.068 Sum_probs=35.0
Q ss_pred CCeEEEEEeCCCCcEEEeCC-CeEEEcHhHHhhc--C----CHHHHHHHHHHHHHHHhcCc
Q 020494 262 LNWEVLVVNEPVINAFCLPG-GKIVVFTGLLEHF--R----TDAEIATIIGHEDGNGSRLY 315 (325)
Q Consensus 262 ~~w~v~Vv~~~~~NAfalpg-G~I~V~tGLL~~~--~----~ddELAaVLaHEiaHv~~rH 315 (325)
.+|...+|.-|..|+-+|=| |.|.+.+..+-.- . +-..++.|++||++|.--+-
T Consensus 262 y~l~~~~V~v~~f~~GaMEN~Gl~tf~~~~ll~~~~~at~~~~~~~~~viaHElaHqWfGn 322 (859)
T COG0308 262 YALPIDIVAVPDFSAGAMENWGLVTFREKYLLADPETATDSDYENVEEVIAHELAHQWFGN 322 (859)
T ss_pred CCCcccEEeccCCCCccccccceeEEeeeEEeeCcccchhHHHHHHHHHHHHHHhhhcccc
Confidence 34444677778888888866 6777766632211 0 11556779999999975543
No 82
>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=46.43 E-value=12 Score=35.25 Aligned_cols=26 Identities=27% Similarity=0.295 Sum_probs=18.7
Q ss_pred EEEcHhHHhhcCCHHHHHHHHHHHHHHHhcC
Q 020494 284 IVVFTGLLEHFRTDAEIATIIGHEDGNGSRL 314 (325)
Q Consensus 284 I~V~tGLL~~~~~ddELAaVLaHEiaHv~~r 314 (325)
|.|-.||=..+ ..+|||||+.|+.++
T Consensus 82 Ilvl~GLPrll-----~gsiLAHE~mHa~Lr 107 (212)
T PF12315_consen 82 ILVLYGLPRLL-----TGSILAHELMHAWLR 107 (212)
T ss_pred EEEECCCCHHH-----HhhHHHHHHHHHHhc
Confidence 55555554443 578999999999875
No 83
>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=45.55 E-value=15 Score=33.19 Aligned_cols=19 Identities=21% Similarity=0.349 Sum_probs=14.2
Q ss_pred HHHHHHHHHHHHHHhcCcH
Q 020494 298 AEIATIIGHEDGNGSRLYR 316 (325)
Q Consensus 298 dELAaVLaHEiaHv~~rH~ 316 (325)
....+|+-|||||++--.+
T Consensus 90 ~~~~~~i~HElgHaLG~~H 108 (198)
T cd04327 90 PEFSRVVLHEFGHALGFIH 108 (198)
T ss_pred hhHHHHHHHHHHHHhcCcc
Confidence 3456789999999986543
No 84
>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=44.08 E-value=13 Score=32.77 Aligned_cols=22 Identities=14% Similarity=0.082 Sum_probs=14.5
Q ss_pred CHHHHHHHHHHHHHHHh-cCcHH
Q 020494 296 TDAEIATIIGHEDGNGS-RLYRA 317 (325)
Q Consensus 296 ~ddELAaVLaHEiaHv~-~rH~~ 317 (325)
+.....-+|.||+||.+ +.|+.
T Consensus 65 ~~~~~g~TltHEvGH~LGL~HtF 87 (154)
T PF05572_consen 65 SQYNFGKTLTHEVGHWLGLYHTF 87 (154)
T ss_dssp TTS-SSHHHHHHHHHHTT---TT
T ss_pred Cccccccchhhhhhhhhcccccc
Confidence 45556799999999987 56654
No 85
>PRK14015 pepN aminopeptidase N; Provisional
Probab=42.60 E-value=16 Score=40.75 Aligned_cols=24 Identities=13% Similarity=0.153 Sum_probs=18.2
Q ss_pred cceEEeecceeeeecCCCCCCccc
Q 020494 72 KRYYYVDRYHVQHFRPRGPRKWLQ 95 (325)
Q Consensus 72 ~r~y~~~~~~~~hf~~rg~~~w~~ 95 (325)
.-+|..+.+-+-+|.|.|-|+|+.
T Consensus 112 ~Gly~s~~~~~TQ~Ep~gAR~~fP 135 (875)
T PRK14015 112 EGLYRSGGMFCTQCEAEGFRRITY 135 (875)
T ss_pred eeeEEECCEEEEeccccCcCCccc
Confidence 346665555678999999999886
No 86
>COG3824 Predicted Zn-dependent protease [General function prediction only]
Probab=38.87 E-value=23 Score=31.12 Aligned_cols=23 Identities=13% Similarity=0.199 Sum_probs=17.7
Q ss_pred CCCHHHHHHHHHHHHHHHHHHhc
Q 020494 132 LLSKAVERQLGESQFQQMKAAFK 154 (325)
Q Consensus 132 llS~~~E~~Lge~~y~qil~e~~ 154 (325)
-.|.+...+|+.++|.++=++|.
T Consensus 11 aps~~~fe~La~~A~d~lP~efr 33 (136)
T COG3824 11 APSLERFEELASDALDHLPQEFR 33 (136)
T ss_pred CCCHHHHHHHHHHHHHhCcHHHH
Confidence 46778888888888887777664
No 87
>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=37.33 E-value=22 Score=32.51 Aligned_cols=15 Identities=20% Similarity=0.220 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHHHhc
Q 020494 299 EIATIIGHEDGNGSR 313 (325)
Q Consensus 299 ELAaVLaHEiaHv~~ 313 (325)
=+.+|+-||+||...
T Consensus 37 l~~~v~iHElgH~~~ 51 (208)
T cd06161 37 LFLSVLLHELGHALV 51 (208)
T ss_pred HHHHHHHHHHHHHHH
Confidence 356899999999864
No 88
>PF09768 Peptidase_M76: Peptidase M76 family; InterPro: IPR019165 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 []. Mitochondrial inner membrane protease ATP23 has two roles in the assembly of mitochondrial ATPase. Firstly, it acts as a protease that removes the N-terminal 10 residues of mitochondrial ATPase CF(0) subunit 6 (ATP6) at the intermembrane space side. Secondly, it is involved in the correct assembly of the membrane-embedded ATPase CF(0) particle, probably mediating association of ATP6 with the subunit 9 ring [, ].; GO: 0004222 metalloendopeptidase activity
Probab=36.69 E-value=72 Score=29.06 Aligned_cols=48 Identities=15% Similarity=0.147 Sum_probs=30.5
Q ss_pred CCeEEEEEeCCCCcEEEeCCCeEEEcHhHHhhcCCHHHHHHHHHHHHHHHh
Q 020494 262 LNWEVLVVNEPVINAFCLPGGKIVVFTGLLEHFRTDAEIATIIGHEDGNGS 312 (325)
Q Consensus 262 ~~w~v~Vv~~~~~NAfalpgG~I~V~tGLL~~~~~ddELAaVLaHEiaHv~ 312 (325)
.......-++...-.|.-+...|+|-.. .+.+.+++.-+|+|||-|+.
T Consensus 36 ~~i~c~~C~~~~~Ggf~p~~~~I~lC~N---~~~~~~~l~~~l~HELIHay 83 (173)
T PF09768_consen 36 RHIKCEPCDSSVSGGFDPSKKGIVLCQN---RIRSQGHLEDTLTHELIHAY 83 (173)
T ss_pred CCeEEEECcCCCcCCccCCCCCEEEeeC---CCCCHHHHHHHHHHHHHHHH
Confidence 3344444444433444422556666543 34699999999999999985
No 89
>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=36.66 E-value=18 Score=37.72 Aligned_cols=44 Identities=18% Similarity=0.402 Sum_probs=26.1
Q ss_pred eCCCCcEEEeC--C-CeEEEcHhHHhhcCCHHHHHHHHHHHHHHHhcCcHH
Q 020494 270 NEPVINAFCLP--G-GKIVVFTGLLEHFRTDAEIATIIGHEDGNGSRLYRA 317 (325)
Q Consensus 270 ~~~~~NAfalp--g-G~I~V~tGLL~~~~~ddELAaVLaHEiaHv~~rH~~ 317 (325)
+.+...|||.+ . +.-+|+ +..-.+-+++ .+|+||+||..+....
T Consensus 308 ~gK~~Gayc~~~~~~~~P~I~---~Nf~~t~~dv-~TL~HElGHa~H~~~s 354 (549)
T TIGR02289 308 KGKAAGGYCTYLPKYKAPFIF---SNFNGTSGDI-DVLTHEAGHAFHVYES 354 (549)
T ss_pred CCCCCCcccCCCCCCCCcEEE---EeCCCChhHH-HHHHHHhhHHHHHHHh
Confidence 34457799874 2 333442 2333344444 5699999999866543
No 90
>PTZ00257 Glycoprotein GP63 (leishmanolysin); Provisional
Probab=35.57 E-value=72 Score=34.68 Aligned_cols=57 Identities=14% Similarity=0.200 Sum_probs=38.1
Q ss_pred cCCCCCCeEEEEEeCCC-Cc--EEEeCC----------CeEEEcHhHHhhcCCHHHHHHHHHHHHHHHhcC
Q 020494 257 SHLDGLNWEVLVVNEPV-IN--AFCLPG----------GKIVVFTGLLEHFRTDAEIATIIGHEDGNGSRL 314 (325)
Q Consensus 257 s~l~~~~w~v~Vv~~~~-~N--Afalpg----------G~I~V~tGLL~~~~~ddELAaVLaHEiaHv~~r 314 (325)
.++.+.|.-++|.-.|. .+ |+|.+- |.|.+.---+.. ..+.+..-|+.|||+|++-=
T Consensus 201 ~Gv~naD~vLYVta~P~~~~~lA~A~~C~~~~d~RPi~G~iNinp~~i~s-~~~~~~~rv~~HEi~HALGF 270 (622)
T PTZ00257 201 VGVSNADFVLYVASVPSEPGVLAWATTCQVFSDDHPAVGVMNIPAANIVS-RYDQGTTRTVTHEVAHALGF 270 (622)
T ss_pred CCccccCEEEEEEEecCCCCeeEEEEEeccccCCCceEEEEeeCHHHCCC-ccchHHHHHHHHHHHHHhcC
Confidence 34567888899887664 22 666531 667776554432 24566788999999999854
No 91
>KOG3658 consensus Tumor necrosis factor-alpha-converting enzyme (TACE/ADAM17) and related metalloproteases [Extracellular structures]
Probab=35.52 E-value=9.6 Score=41.51 Aligned_cols=50 Identities=20% Similarity=0.190 Sum_probs=33.9
Q ss_pred CeEEEEEeCCCCcEE--------EeC-CCeEEEcHhHHhhcC-----CHHHHHHHHHHHHHHHh
Q 020494 263 NWEVLVVNEPVINAF--------CLP-GGKIVVFTGLLEHFR-----TDAEIATIIGHEDGNGS 312 (325)
Q Consensus 263 ~w~v~Vv~~~~~NAf--------alp-gG~I~V~tGLL~~~~-----~ddELAaVLaHEiaHv~ 312 (325)
..-+.-|-+|..|+- -.+ |-+..++|||..... -..+.--|+||||||.-
T Consensus 341 tLGLAwVgsp~~~saGGIC~k~~~y~~G~~~sLNtGi~T~~NYg~~Vp~kvs~lt~AHEiGHNf 404 (764)
T KOG3658|consen 341 TLGLAWVGSPRSNSAGGICEKAYTYNEGKKRSLNTGISTSVNYGKRVPTKVSDLTLAHEIGHNF 404 (764)
T ss_pred eeeeEEeccCccCCCCcccccceeccCcceEEeecceeeeeecCCccCcchhheeehhhhcccc
Confidence 344555666544431 224 568999999998764 35667789999999974
No 92
>COG3864 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.81 E-value=44 Score=33.80 Aligned_cols=37 Identities=8% Similarity=-0.111 Sum_probs=31.4
Q ss_pred CCCeEEEcHhHHhhcCCHHHHHHHHHHHHHHHhcCcHH
Q 020494 280 PGGKIVVFTGLLEHFRTDAEIATIIGHEDGNGSRLYRA 317 (325)
Q Consensus 280 pgG~I~V~tGLL~~~~~ddELAaVLaHEiaHv~~rH~~ 317 (325)
.+=.++.+--++..| ..+++.+.|-||+-|+++.|..
T Consensus 50 ~~~~~y~NPei~~~~-p~~~~~aLl~HEV~Hi~l~Hi~ 86 (396)
T COG3864 50 SYFTMYFNPEIFLNC-PISEMKALLKHEVYHIMLNHIK 86 (396)
T ss_pred CceEEEeCHHHHccC-CHHHHHHHHHHHHHHHHHHHHH
Confidence 334677777787777 9999999999999999999986
No 93
>PF12725 DUF3810: Protein of unknown function (DUF3810); InterPro: IPR024294 This family of bacterial proteins is functionally uncharacterised. Proteins in this family are typically between 333 and 377 amino acids in length and contain a conserved HEXXH sequence motif that is characteristic of metallopeptidases. This family may therefore belong to an as yet uncharacterised family of peptidase enzymes.
Probab=33.88 E-value=23 Score=34.86 Aligned_cols=16 Identities=19% Similarity=0.081 Sum_probs=12.6
Q ss_pred HHHHHHHHHHHHHHHh
Q 020494 297 DAEIATIIGHEDGNGS 312 (325)
Q Consensus 297 ddELAaVLaHEiaHv~ 312 (325)
+-.+-++++|||||..
T Consensus 193 ~~~~P~T~~HElAHq~ 208 (318)
T PF12725_consen 193 PYSLPFTICHELAHQL 208 (318)
T ss_pred cccccHHHHHHHHHHh
Confidence 3456789999999975
No 94
>KOG3314 consensus Ku70-binding protein [Replication, recombination and repair]
Probab=31.90 E-value=44 Score=30.87 Aligned_cols=36 Identities=22% Similarity=0.280 Sum_probs=27.1
Q ss_pred CCCeEEEcHhHHhhcCCHHHHHHHHHHHHHHHhcCcHHh
Q 020494 280 PGGKIVVFTGLLEHFRTDAEIATIIGHEDGNGSRLYRAA 318 (325)
Q Consensus 280 pgG~I~V~tGLL~~~~~ddELAaVLaHEiaHv~~rH~~~ 318 (325)
||--|++-.- .+.+.+++.-|++||+-|..-.|-++
T Consensus 74 ~~~gIvlCqN---~l~~q~h~n~vv~HElIH~fDd~r~~ 109 (194)
T KOG3314|consen 74 PGRGIVLCQN---RLTIQDHVNQVVIHELIHAFDDCRAK 109 (194)
T ss_pred CCCceEEecc---ccchHHHHHHHHHHHHHHHHHhhhhh
Confidence 4433666553 44588999999999999998877665
No 95
>KOG3607 consensus Meltrins, fertilins and related Zn-dependent metalloproteinases of the ADAMs family [Posttranslational modification, protein turnover, chaperones]
Probab=31.46 E-value=28 Score=38.21 Aligned_cols=18 Identities=22% Similarity=0.274 Sum_probs=14.9
Q ss_pred CHHHHHHHHHHHHHHHhc
Q 020494 296 TDAEIATIIGHEDGNGSR 313 (325)
Q Consensus 296 ~ddELAaVLaHEiaHv~~ 313 (325)
+....|.||||||||.+-
T Consensus 319 ~~~~~a~v~AhelgH~lG 336 (716)
T KOG3607|consen 319 ILLAFAVVLAHELGHNLG 336 (716)
T ss_pred cchhHHHHHHHHHHhhcC
Confidence 456788999999999863
No 96
>PF09715 Plasmod_dom_1: Plasmodium protein of unknown function (Plasmod_dom_1); InterPro: IPR006410 These sequences represent an uncharacterised family consisting of a small number of hypothetical proteins of the malaria parasite Plasmodium falciparum (isolate 3D7).
Probab=29.65 E-value=22 Score=27.90 Aligned_cols=31 Identities=23% Similarity=0.490 Sum_probs=23.0
Q ss_pred hhhhhhHHHHHHHhhcccCCCCCCCcccccc
Q 020494 2 AYYRRAKAALDAFRNLSSKAVPKSPVQESCS 32 (325)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 (325)
++++|+|+.+|+|-++-+.-+=.++++...|
T Consensus 1 sFFKk~klvm~~fDnifidklId~~i~nk~s 31 (67)
T PF09715_consen 1 SFFKKAKLVMDIFDNIFIDKLIDNNIQNKSS 31 (67)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHccccccCCC
Confidence 4799999999999996554444566666555
No 97
>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=29.48 E-value=31 Score=34.80 Aligned_cols=18 Identities=17% Similarity=0.276 Sum_probs=14.1
Q ss_pred CHHHHHHHHHHHHHHHhcC
Q 020494 296 TDAEIATIIGHEDGNGSRL 314 (325)
Q Consensus 296 ~ddELAaVLaHEiaHv~~r 314 (325)
+-+++ ..|+||+||+++.
T Consensus 239 ~~~~v-~tLfHE~GHa~H~ 256 (458)
T PF01432_consen 239 SHDDV-ETLFHEFGHAMHS 256 (458)
T ss_dssp SHHHH-HHHHHHHHHHHHH
T ss_pred ChhhH-HHHHHHHhHHHHH
Confidence 55666 6799999999864
No 98
>COG1164 Oligoendopeptidase F [Amino acid transport and metabolism]
Probab=29.22 E-value=22 Score=37.97 Aligned_cols=53 Identities=13% Similarity=0.112 Sum_probs=32.3
Q ss_pred EEEEEeCCCCcEEEeCC---CeEEEcHhHHhhcCCHHHHHHHHHHHHHHHhcCcHHhhhh
Q 020494 265 EVLVVNEPVINAFCLPG---GKIVVFTGLLEHFRTDAEIATIIGHEDGNGSRLYRAAFDR 321 (325)
Q Consensus 265 ~v~Vv~~~~~NAfalpg---G~I~V~tGLL~~~~~ddELAaVLaHEiaHv~~rH~~~~~~ 321 (325)
++..-+.+..-|||.+. ++.+|. |....+... ..+|+||+||.++.......+
T Consensus 346 D~~~~~gKrsGaYs~~~~~~~~p~Il---mN~~gt~~d-V~TLaHElGHs~Hs~~s~~~q 401 (598)
T COG1164 346 DVYPRKGKRSGAYSIGFYKGDHPFIL---MNYDGTLRD-VFTLAHELGHSVHSYFSRKHQ 401 (598)
T ss_pred eccCCCCCCCCcccCCCCCCCCCeEE---EeCCCchhH-HHHHHHHccHHHHHHHHhccC
Confidence 33444455688999854 456663 233333333 367999999999876654443
No 99
>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=29.01 E-value=37 Score=31.76 Aligned_cols=15 Identities=27% Similarity=0.297 Sum_probs=12.2
Q ss_pred HHHHHHHHHHHHHhc
Q 020494 299 EIATIIGHEDGNGSR 313 (325)
Q Consensus 299 ELAaVLaHEiaHv~~ 313 (325)
=...|+-||+||...
T Consensus 52 l~~~v~iHElgH~~~ 66 (227)
T cd06164 52 LFASVLLHELGHSLV 66 (227)
T ss_pred HHHHHHHHHHHHHHH
Confidence 356899999999864
No 100
>COG4324 Predicted aminopeptidase [General function prediction only]
Probab=27.68 E-value=42 Score=33.35 Aligned_cols=46 Identities=24% Similarity=0.275 Sum_probs=28.1
Q ss_pred CCCeEEEEEeCCCCcEEEeCCCeEEEcHhHHhhc--CCHHHHHHHHHHHHHHHh
Q 020494 261 GLNWEVLVVNEPVINAFCLPGGKIVVFTGLLEHF--RTDAEIATIIGHEDGNGS 312 (325)
Q Consensus 261 ~~~w~v~Vv~~~~~NAfalpgG~I~V~tGLL~~~--~~ddELAaVLaHEiaHv~ 312 (325)
...|+|+|- .+.|++.=| ++..-||..+ .+|.+||..|-||++|..
T Consensus 162 aqG~DVyV~---Gv~AYSTLG---wFdDPlLstmlr~dd~~lA~LIFHELAHQk 209 (376)
T COG4324 162 AQGLDVYVS---GVTAYSTLG---WFDDPLLSTMLRQDDTYLASLIFHELAHQK 209 (376)
T ss_pred hcCCceeee---cccceeccc---ccccHHHHHHhcCChHHHHHHHHHHHhhhe
Confidence 344566653 345555433 2233344422 389999999999999964
No 101
>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=27.50 E-value=15 Score=35.42 Aligned_cols=12 Identities=33% Similarity=0.501 Sum_probs=10.4
Q ss_pred HHHHHHHHHHHh
Q 020494 301 ATIIGHEDGNGS 312 (325)
Q Consensus 301 AaVLaHEiaHv~ 312 (325)
..|++||+||.+
T Consensus 166 igv~~HE~gH~l 177 (286)
T TIGR03296 166 VGVIAHELGHDL 177 (286)
T ss_pred eeeeehhhhccc
Confidence 589999999954
No 102
>COG4900 Predicted metallopeptidase [General function prediction only]
Probab=27.29 E-value=51 Score=28.67 Aligned_cols=30 Identities=20% Similarity=0.128 Sum_probs=21.3
Q ss_pred eEEEcHhHHhhcCCHHHHHHHHHHHHHHHhc
Q 020494 283 KIVVFTGLLEHFRTDAEIATIIGHEDGNGSR 313 (325)
Q Consensus 283 ~I~V~tGLL~~~~~ddELAaVLaHEiaHv~~ 313 (325)
.|-+-+-=++.+ +-+|---|+.||+.|+-.
T Consensus 64 viEl~sekF~rL-s~~ekvKviiHEllHIP~ 93 (133)
T COG4900 64 VIELLSEKFKRL-SCAEKVKVIIHELLHIPA 93 (133)
T ss_pred eeeeehhhcCCC-ChHHHHHHHHHHHhcCcc
Confidence 344445555666 667777899999999864
No 103
>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=26.65 E-value=36 Score=34.93 Aligned_cols=19 Identities=21% Similarity=0.111 Sum_probs=13.8
Q ss_pred HHHHHHHHHHHHHHHhcCcH
Q 020494 297 DAEIATIIGHEDGNGSRLYR 316 (325)
Q Consensus 297 ddELAaVLaHEiaHv~~rH~ 316 (325)
-+++ ..|+||+||.++...
T Consensus 261 ~~~V-~TLfHEfGHalH~~l 279 (472)
T cd06455 261 HDEV-ETFFHEFGHVIHHLL 279 (472)
T ss_pred HHHH-HHHHHHHHHHHHHHh
Confidence 3554 568999999997543
No 104
>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=26.60 E-value=34 Score=35.99 Aligned_cols=46 Identities=15% Similarity=0.110 Sum_probs=24.4
Q ss_pred EEEEeCCCCcEEEeC--CC-eEEEcHhHHhhcCCHHHHHHHHHHHHHHHhcCc
Q 020494 266 VLVVNEPVINAFCLP--GG-KIVVFTGLLEHFRTDAEIATIIGHEDGNGSRLY 315 (325)
Q Consensus 266 v~Vv~~~~~NAfalp--gG-~I~V~tGLL~~~~~ddELAaVLaHEiaHv~~rH 315 (325)
++--+.+...|||.+ ++ .-+|.. ..-.+-+++ .+|+||+||.++..
T Consensus 342 ~~~r~gK~~Ga~~~~~~~~~~p~i~~---N~~~~~~~v-~TL~HE~GHa~H~~ 390 (587)
T TIGR02290 342 AEPRPGKRGGAFCTGFPPSKEPRVLM---NYDGSRRDV-STLAHELGHAYHSE 390 (587)
T ss_pred cCCCCCCCCCcccCCCCCCCCCEEEE---ecCCCchhH-HHHHHHhhHHHHHH
Confidence 333344556788854 22 222221 111233333 56999999999754
No 105
>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=26.29 E-value=45 Score=30.33 Aligned_cols=16 Identities=31% Similarity=0.121 Sum_probs=12.4
Q ss_pred HHHHHHHHHHHHHHhc
Q 020494 298 AEIATIIGHEDGNGSR 313 (325)
Q Consensus 298 dELAaVLaHEiaHv~~ 313 (325)
.=+..++.||+||...
T Consensus 39 ~l~~~l~iHElgH~~~ 54 (183)
T cd06160 39 ALLAILGIHEMGHYLA 54 (183)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3456788999999864
No 106
>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=25.99 E-value=41 Score=30.36 Aligned_cols=17 Identities=24% Similarity=0.305 Sum_probs=12.1
Q ss_pred HHHHHHHHHHHhcCcHH
Q 020494 301 ATIIGHEDGNGSRLYRA 317 (325)
Q Consensus 301 AaVLaHEiaHv~~rH~~ 317 (325)
.+++.|||+|++--.+.
T Consensus 80 ~~~i~HEl~HaLG~~HE 96 (191)
T PF01400_consen 80 VGTILHELGHALGFWHE 96 (191)
T ss_dssp HHHHHHHHHHHHTB--G
T ss_pred ccchHHHHHHHHhhhhh
Confidence 46899999999865443
No 107
>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=24.69 E-value=37 Score=31.43 Aligned_cols=17 Identities=24% Similarity=0.284 Sum_probs=13.1
Q ss_pred HHHHHHHHHHHhcCcHH
Q 020494 301 ATIIGHEDGNGSRLYRA 317 (325)
Q Consensus 301 AaVLaHEiaHv~~rH~~ 317 (325)
-+++.|||+|++-=++.
T Consensus 88 ~Gti~HEl~HaLGf~HE 104 (200)
T cd04281 88 FGIVVHELGHVIGFWHE 104 (200)
T ss_pred CchHHHHHHHHhcCcch
Confidence 37999999999865443
No 108
>TIGR01519 plasmod_dom_1 Plasmodium falciparum uncharacterized domain. This model represents an uncharacterized domain present in roughly eight hypothetical proteins of the malaria parasite Plasmodium falciparum.
Probab=24.49 E-value=33 Score=27.18 Aligned_cols=31 Identities=19% Similarity=0.379 Sum_probs=22.9
Q ss_pred hhhhhhHHHHHHHhhcccCCCCCCCcccccc
Q 020494 2 AYYRRAKAALDAFRNLSSKAVPKSPVQESCS 32 (325)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 (325)
++++|+|+.+|+|-++-+.-+=.++++...|
T Consensus 1 sFFKkaklvm~~fDnifidklid~~v~nk~S 31 (70)
T TIGR01519 1 SFFKRALLLMNIFDNIFIDKLIDNNVHNKGS 31 (70)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHccccccCCC
Confidence 4799999999999995444444566666655
No 109
>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=24.02 E-value=39 Score=30.84 Aligned_cols=16 Identities=31% Similarity=0.328 Sum_probs=12.5
Q ss_pred HHHHHHHHHHHhcCcH
Q 020494 301 ATIIGHEDGNGSRLYR 316 (325)
Q Consensus 301 AaVLaHEiaHv~~rH~ 316 (325)
-+++.||++|++-=.+
T Consensus 78 ~G~i~HEl~HaLG~~H 93 (182)
T cd04283 78 KGIIQHELLHALGFYH 93 (182)
T ss_pred cchHHHHHHHHhCCcc
Confidence 3789999999985443
No 110
>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=23.90 E-value=51 Score=31.76 Aligned_cols=33 Identities=24% Similarity=0.467 Sum_probs=20.4
Q ss_pred cEEEeCCCeEEE--cHhHHhhcCCHHHHHHHHHHHHHHHhc
Q 020494 275 NAFCLPGGKIVV--FTGLLEHFRTDAEIATIIGHEDGNGSR 313 (325)
Q Consensus 275 NAfalpgG~I~V--~tGLL~~~~~ddELAaVLaHEiaHv~~ 313 (325)
|.-.+||..+++ ..+++. =+.+|+-||+||...
T Consensus 97 ~~~~ipGv~~~i~~~~~~ia------L~isv~iHElgHa~~ 131 (263)
T cd06159 97 NVLVIPGVNIFIPLPYGIIA------LVVGVVVHELSHGIL 131 (263)
T ss_pred eeeccCCcchHHHHHHHHHH------HHHHHHHHHHHHHHH
Confidence 344567766543 222322 346899999999864
No 111
>PF07225 NDUF_B4: NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4); InterPro: IPR009866 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This family contains human NADH-ubiquinone oxidoreductase subunit NDUFB4 and related sequences.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0005739 mitochondrion
Probab=23.09 E-value=44 Score=29.09 Aligned_cols=37 Identities=24% Similarity=0.391 Sum_probs=23.8
Q ss_pred cce-EEeecceeeeecCCCCCCcccCCchhHHHHHHHHHHHHHHHh
Q 020494 72 KRY-YYVDRYHVQHFRPRGPRKWLQNPRTVFIVVVIGSGAFITLYL 116 (325)
Q Consensus 72 ~r~-y~~~~~~~~hf~~rg~~~w~~~~r~~~~~v~~g~g~~~~~y~ 116 (325)
-|| |...-..|.||.|.. |+.+++++.+++.++++|+
T Consensus 62 ~Rw~~a~~~~~y~~FRpTP--------ktsllg~~~~v~P~i~~~~ 99 (125)
T PF07225_consen 62 QRWAYARAVNIYEYFRPTP--------KTSLLGLGFGVVPLIFYYY 99 (125)
T ss_pred HHHHHHHHhCcccccccCc--------hHHHHHHHHHHHHHHHHHh
Confidence 567 555557899998864 7777776666654444443
No 112
>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=21.76 E-value=44 Score=32.46 Aligned_cols=20 Identities=20% Similarity=0.255 Sum_probs=14.4
Q ss_pred CHHHHHHHHHHHHHHHhcCcH
Q 020494 296 TDAEIATIIGHEDGNGSRLYR 316 (325)
Q Consensus 296 ~ddELAaVLaHEiaHv~~rH~ 316 (325)
+-+++. +|.||+||+++...
T Consensus 151 ~~~~v~-tl~HE~GHa~h~~l 170 (365)
T cd06258 151 GHDDIN-TLFHEFGHAVHFLL 170 (365)
T ss_pred CHHHHH-HHHHHHhHHHHHHH
Confidence 556654 57899999986543
No 113
>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=21.58 E-value=60 Score=31.73 Aligned_cols=15 Identities=27% Similarity=0.379 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHHhcC
Q 020494 300 IATIIGHEDGNGSRL 314 (325)
Q Consensus 300 LAaVLaHEiaHv~~r 314 (325)
+.+|+.||+||...-
T Consensus 135 ~isvvvHElgHal~A 149 (277)
T cd06162 135 LISGVVHEMGHGVAA 149 (277)
T ss_pred HHHHHHHHHHHHHHH
Confidence 568999999998753
No 114
>KOG1565 consensus Gelatinase A and related matrix metalloproteases [Posttranslational modification, protein turnover, chaperones; Extracellular structures]
Probab=21.48 E-value=37 Score=35.45 Aligned_cols=15 Identities=20% Similarity=0.350 Sum_probs=12.9
Q ss_pred HHHHHHHHHHHHHhc
Q 020494 299 EIATIIGHEDGNGSR 313 (325)
Q Consensus 299 ELAaVLaHEiaHv~~ 313 (325)
.|..|.+|||||.+-
T Consensus 210 ~l~~Va~HEiGH~LG 224 (469)
T KOG1565|consen 210 DLFLVAAHEIGHALG 224 (469)
T ss_pred hhHHHhhhhcccccc
Confidence 577899999999874
No 115
>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=20.59 E-value=48 Score=29.64 Aligned_cols=17 Identities=24% Similarity=0.176 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHhcCcHH
Q 020494 301 ATIIGHEDGNGSRLYRA 317 (325)
Q Consensus 301 AaVLaHEiaHv~~rH~~ 317 (325)
.+++.|||+|++-=++.
T Consensus 75 ~g~v~HE~~HalG~~HE 91 (180)
T cd04280 75 LGTIVHELMHALGFYHE 91 (180)
T ss_pred CchhHHHHHHHhcCcch
Confidence 47899999999866544
Done!