Query 009686
Match_columns 528
No_of_seqs 322 out of 1225
Neff 4.6
Searched_HMMs 46136
Date Thu Mar 28 16:07:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009686.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009686hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd06160 S2P-M50_like_2 Unchara 100.0 3.2E-31 6.9E-36 253.2 18.8 177 251-476 3-181 (183)
2 cd06164 S2P-M50_SpoIVFB_CBS Sp 99.9 5.5E-25 1.2E-29 216.4 20.5 134 276-447 37-170 (227)
3 cd06161 S2P-M50_SpoIVFB SpoIVF 99.9 2.1E-23 4.5E-28 202.2 18.9 129 279-447 25-153 (208)
4 cd06163 S2P-M50_PDZ_RseP-like 99.9 7.5E-21 1.6E-25 181.9 14.9 112 286-444 3-145 (182)
5 cd05709 S2P-M50 Site-2 proteas 99.8 8.3E-21 1.8E-25 178.2 13.2 139 286-448 2-156 (180)
6 cd06159 S2P-M50_PDZ_Arch Uncha 99.8 4.4E-19 9.5E-24 178.5 18.2 119 281-446 107-228 (263)
7 PF02163 Peptidase_M50: Peptid 99.8 6.8E-19 1.5E-23 166.1 10.8 127 287-443 2-157 (192)
8 cd06162 S2P-M50_PDZ_SREBP Ster 99.8 8.9E-18 1.9E-22 170.1 15.5 114 287-448 130-250 (277)
9 cd06158 S2P-M50_like_1 Unchara 99.8 2.9E-18 6.3E-23 163.6 10.7 135 287-450 4-159 (181)
10 TIGR00054 RIP metalloprotease 99.5 1.9E-13 4.1E-18 145.4 16.1 80 287-366 9-119 (420)
11 PRK10779 zinc metallopeptidase 99.5 1.8E-13 3.9E-18 146.5 15.0 83 284-366 7-119 (449)
12 COG1994 SpoIVFB Zn-dependent p 99.3 2.1E-11 4.5E-16 120.4 14.2 130 281-450 41-178 (230)
13 COG0750 Predicted membrane-ass 98.9 1.6E-09 3.5E-14 112.0 5.5 244 164-447 82-338 (375)
14 PF13398 Peptidase_M50B: Pepti 97.3 0.00069 1.5E-08 66.1 8.0 65 293-365 23-88 (200)
15 COG0750 Predicted membrane-ass 96.3 0.012 2.6E-07 61.2 7.9 82 285-366 6-120 (375)
16 KOG2921 Intramembrane metallop 96.2 0.0043 9.4E-08 66.4 3.9 82 282-366 120-206 (484)
17 PF11667 DUF3267: Protein of u 65.4 3.2 6.9E-05 36.6 1.2 22 292-313 4-25 (111)
18 PF00413 Peptidase_M10: Matrix 60.6 5.1 0.00011 36.2 1.7 21 293-313 106-126 (154)
19 PF07423 DUF1510: Protein of u 59.7 4.9 0.00011 40.5 1.5 55 170-228 159-214 (217)
20 cd04279 ZnMc_MMP_like_1 Zinc-d 58.1 6.1 0.00013 36.5 1.8 22 292-313 104-125 (156)
21 PF13485 Peptidase_MA_2: Pepti 51.2 12 0.00027 31.7 2.4 18 294-311 27-44 (128)
22 cd04268 ZnMc_MMP_like Zinc-dep 48.2 12 0.00025 34.4 1.9 21 291-311 93-113 (165)
23 KOG1832 HIV-1 Vpr-binding prot 48.1 18 0.00038 43.5 3.7 17 5-21 1354-1370(1516)
24 PF05572 Peptidase_M43: Pregna 48.0 9 0.0002 36.2 1.2 14 293-306 70-83 (154)
25 cd04278 ZnMc_MMP Zinc-dependen 48.0 8.2 0.00018 35.7 0.9 22 292-313 107-128 (157)
26 PTZ00429 beta-adaptin; Provisi 45.0 20 0.00042 42.2 3.5 33 71-103 607-639 (746)
27 PF01435 Peptidase_M48: Peptid 44.1 16 0.00034 34.9 2.2 12 293-304 90-101 (226)
28 PF06114 DUF955: Domain of unk 42.2 16 0.00034 30.8 1.7 16 295-310 45-60 (122)
29 PF11085 YqhR: Conserved membr 40.6 2.6E+02 0.0056 27.6 9.7 100 414-519 33-153 (173)
30 PF14247 DUF4344: Domain of un 39.9 29 0.00063 35.0 3.4 25 288-313 88-112 (220)
31 cd04277 ZnMc_serralysin_like Z 38.8 17 0.00037 34.5 1.5 22 293-314 114-135 (186)
32 smart00235 ZnMc Zinc-dependent 38.7 16 0.00035 32.9 1.3 20 295-314 89-108 (140)
33 PF01434 Peptidase_M41: Peptid 38.6 25 0.00054 34.6 2.7 18 294-311 30-47 (213)
34 cd00203 ZnMc Zinc-dependent me 38.3 16 0.00035 33.3 1.2 21 291-311 95-115 (167)
35 PF12315 DUF3633: Protein of u 37.9 23 0.0005 35.7 2.3 29 281-312 84-112 (212)
36 PF13582 Reprolysin_3: Metallo 37.4 17 0.00037 31.8 1.2 14 294-307 109-122 (124)
37 PF13574 Reprolysin_2: Metallo 37.3 18 0.00038 34.6 1.3 21 292-312 111-131 (173)
38 PF14891 Peptidase_M91: Effect 36.9 22 0.00048 33.9 2.0 16 293-308 104-119 (174)
39 PF13688 Reprolysin_5: Metallo 36.2 18 0.00038 34.4 1.2 21 292-312 142-162 (196)
40 PF02031 Peptidase_M7: Strepto 33.6 25 0.00055 33.0 1.7 10 295-304 80-89 (132)
41 cd04327 ZnMc_MMP_like_3 Zinc-d 31.2 27 0.00058 33.9 1.5 20 294-313 94-113 (198)
42 PRK03001 M48 family peptidase; 30.8 31 0.00067 35.4 2.0 12 293-304 125-136 (283)
43 PHA02456 zinc metallopeptidase 30.6 30 0.00065 32.0 1.6 18 296-313 83-100 (141)
44 PRK12462 phosphoserine aminotr 30.4 85 0.0018 33.9 5.2 68 145-220 7-76 (364)
45 cd04269 ZnMc_adamalysin_II_lik 30.3 34 0.00074 32.6 2.1 20 292-311 131-150 (194)
46 PRK03982 heat shock protein Ht 30.1 32 0.0007 35.4 2.0 12 293-304 126-137 (288)
47 KOG0391 SNF2 family DNA-depend 30.0 53 0.0011 41.0 3.8 21 172-192 599-619 (1958)
48 cd04270 ZnMc_TACE_like Zinc-de 29.8 33 0.00071 34.6 1.9 19 291-309 166-184 (244)
49 PRK11037 hypothetical protein; 29.5 1.3E+02 0.0028 26.3 5.1 65 149-214 4-81 (83)
50 PF10263 SprT-like: SprT-like 29.2 39 0.00085 31.0 2.2 19 291-309 59-77 (157)
51 COG2856 Predicted Zn peptidase 29.1 30 0.00065 34.8 1.5 16 295-310 75-90 (213)
52 cd04267 ZnMc_ADAM_like Zinc-de 28.3 26 0.00057 33.2 0.9 20 292-311 133-152 (192)
53 PF09471 Peptidase_M64: IgA Pe 28.1 25 0.00055 36.3 0.8 14 293-306 217-230 (264)
54 smart00731 SprT SprT homologue 28.1 36 0.00077 31.6 1.7 17 292-308 59-75 (146)
55 PF13583 Reprolysin_4: Metallo 27.4 32 0.00069 33.8 1.3 17 295-311 140-156 (206)
56 COG0501 HtpX Zn-dependent prot 26.7 40 0.00088 33.8 2.0 11 294-304 159-169 (302)
57 COG5309 Exo-beta-1,3-glucanase 26.5 1E+02 0.0022 32.6 4.8 61 155-219 218-281 (305)
58 PLN02452 phosphoserine transam 26.5 1.1E+02 0.0025 32.7 5.4 68 145-220 10-79 (365)
59 KOG0943 Predicted ubiquitin-pr 26.4 55 0.0012 40.8 3.2 13 50-62 1700-1712(3015)
60 PRK04897 heat shock protein Ht 26.2 41 0.00089 35.0 2.0 11 294-304 139-149 (298)
61 KOG3320 40S ribosomal protein 25.9 93 0.002 30.9 4.1 27 194-220 74-100 (192)
62 PF01447 Peptidase_M4: Thermol 25.5 44 0.00096 31.7 1.9 11 295-305 138-148 (150)
63 PF12388 Peptidase_M57: Dual-a 25.0 39 0.00084 34.1 1.5 27 287-313 128-154 (211)
64 PRK01345 heat shock protein Ht 24.5 46 0.001 35.1 2.0 12 293-304 125-136 (317)
65 PF13699 DUF4157: Domain of un 24.5 44 0.00095 28.4 1.5 12 294-305 63-74 (79)
66 COG0830 UreF Urease accessory 24.5 79 0.0017 32.3 3.5 31 414-444 158-188 (229)
67 PRK03072 heat shock protein Ht 24.1 48 0.001 34.4 2.0 11 293-303 128-138 (288)
68 PRK02391 heat shock protein Ht 23.9 49 0.0011 34.6 2.0 10 294-303 135-144 (296)
69 COG3824 Predicted Zn-dependent 23.6 36 0.00077 31.9 0.8 14 291-304 108-121 (136)
70 PRK05457 heat shock protein Ht 23.4 50 0.0011 34.2 2.0 10 294-303 136-145 (284)
71 PF10692 DUF2498: Protein of u 22.0 1.5E+02 0.0032 25.8 4.1 64 150-214 4-80 (82)
72 cd04927 ACT_ACR-like_2 Second 21.7 1.1E+02 0.0024 25.2 3.3 35 166-211 40-74 (76)
73 PRK01265 heat shock protein Ht 21.7 57 0.0012 34.8 2.0 10 294-303 142-151 (324)
74 PF01421 Reprolysin: Reprolysi 21.6 65 0.0014 30.9 2.2 21 291-311 130-150 (199)
75 PRK04860 hypothetical protein; 21.6 86 0.0019 30.2 3.0 21 290-310 61-81 (160)
76 KOG2719 Metalloprotease [Gener 21.5 52 0.0011 36.5 1.7 14 293-306 281-294 (428)
77 PRK02870 heat shock protein Ht 21.2 59 0.0013 34.8 2.0 11 293-303 174-184 (336)
78 PF04298 Zn_peptidase_2: Putat 21.2 56 0.0012 33.2 1.7 12 294-305 91-102 (222)
79 TIGR01364 serC_1 phosphoserine 20.8 1.6E+02 0.0036 31.0 5.2 60 152-219 2-63 (349)
80 COG3091 SprT Zn-dependent meta 20.6 1.4E+02 0.0031 28.9 4.2 31 277-310 49-79 (156)
81 PLN02829 Probable galacturonos 20.2 1.4E+02 0.0031 34.7 4.8 54 141-207 168-221 (639)
No 1
>cd06160 S2P-M50_like_2 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the S2P/M50 family of RIP proteases use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. In eukaryotic cells they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum stress responses. In prokaryotes they regulate such processes as sporulation, cell division, stress response, and cell differentiation. This group includes bacterial, eukaryotic, and Archaeal S2P/M50s homologs with additional putative N- and C-terminal transmembrane spanning regions, relative to the core protein, and no PDZ domains.
Probab=99.97 E-value=3.2e-31 Score=253.23 Aligned_cols=177 Identities=40% Similarity=0.706 Sum_probs=147.3
Q ss_pred HHHHHHHHHHHhcccccccchhhcccchHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHcCCccccccccccceeeecceE
Q 009686 251 FGLVTVFTLLLRNVPALQSNLLSTFDNLNLLTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAI 330 (528)
Q Consensus 251 ~~l~T~~T~~~a~~~~L~~~~~~~~~~~~~l~~glp~aL~Ll~iL~iHElGH~laArr~Gvk~s~P~FIP~i~LgtfGAv 330 (528)
++++|+.+....+.-... + +..++++.+..+++++++++.++++||+||+++||++|+|++.++++|...+|++|++
T Consensus 3 ~~~~s~~~~~~~~~~~~~-~--~~~~~~~~~~~~~~~~l~l~~~l~iHElgH~~~A~~~G~~~~~~~l~P~~~~G~~G~~ 79 (183)
T cd06160 3 LLVLTLLTTLLVGAWLSG-N--DVPGNPLLLLQGLPFALALLAILGIHEMGHYLAARRHGVKASLPYFIPFPFIGTFGAF 79 (183)
T ss_pred HHHHHHHHHHHHHHHHhc-c--cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCccceeeeehHhcCcEEEE
Confidence 456666666655421111 1 2236778888999999999999999999999999999999999999998779999999
Q ss_pred EeccccccCccceeeeEecchhhHHHHHHHHHHHHhhcCCCCCCcccccccchhhhhhhhhhHHhhhccccCCCCCccch
Q 009686 331 TRIRNIVSKREDLLKVAAAGPLAGFSLGFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVN 410 (528)
Q Consensus 331 i~~~s~~~~R~alfdIAiAGPLAg~llAl~llligl~l~~s~~~~~~v~~~~f~~s~L~g~la~l~LG~~l~~~~~v~lh 410 (528)
++.++..++|+++++|++|||++|+++++++++++
T Consensus 80 ~~~~~~~~~~~~~~~IalAGPl~nl~lali~~~~~--------------------------------------------- 114 (183)
T cd06160 80 IRMRSPIPNRKALFDIALAGPLAGLLLALPVLIIG--------------------------------------------- 114 (183)
T ss_pred EEecCCCCChhHhehhhhhHHHHHHHHHHHHHHHH---------------------------------------------
Confidence 99988888999999999999999999988775543
Q ss_pred HHHHHHHHHHHHHHHhhcCCCCCChHHHHHHhhhhhHHHHHHHHHHHHHHHHHHhhh--hhHHHHHHH
Q 009686 411 PLVIWAWAGLLINAINSIPAGELDGGRIAFALWGRKASTRLTGVSIVLLGLSSLFSD--VTFYWVVLV 476 (528)
Q Consensus 411 PL~~agwinLvltafNLLPigpLDGGrIl~Allgrr~a~~is~~~~~lLGl~~l~~~--~~l~W~lli 476 (528)
+..++|+|+++++|||+|++|||||||+++++++|++.++++++.+++|+.++.++ .+++|+.++
T Consensus 115 -~~~~~~~nl~l~~fNLLPi~PLDGGril~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ 181 (183)
T cd06160 115 -LAVAGWVGLLVTALNLLPVGQLDGGHIVRALFGRRVAALIGIGLLVALGLLALYLSFSIWLLWALLL 181 (183)
T ss_pred -HHHHHHHHHHHHHHHhCCCCCcChHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence 12468899999999999999999999999999999999999999899998888765 455555443
No 2
>cd06164 S2P-M50_SpoIVFB_CBS SpoIVFB Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50B), regulates intramembrane proteolysis (RIP), and is involved in the pro-sigmaK pathway of bacterial spore formation. In this subgroup, SpoIVFB (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain. SpoIVFB is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA (bypass-of-forespore A), and SpoIVB (sporulation protein, stage IV cell wall formation, B locus). SpoIVFB is negatively regulated by SpoIVFA and BofA and activated by SpoIVB. It is thought that SpoIVFB, SpoIVFA, and BofA are located in the mother-cell membrane that surrounds the forespore and that SpoIVB is secreted from the forespore into the space between the two where it activates SpoIVFB. It has been proposed tha
Probab=99.93 E-value=5.5e-25 Score=216.40 Aligned_cols=134 Identities=31% Similarity=0.406 Sum_probs=111.3
Q ss_pred cchHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHcCCccccccccccceeeecceEEeccccccCccceeeeEecchhhHH
Q 009686 276 DNLNLLTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAITRIRNIVSKREDLLKVAAAGPLAGF 355 (528)
Q Consensus 276 ~~~~~l~~glp~aL~Ll~iL~iHElGH~laArr~Gvk~s~P~FIP~i~LgtfGAvi~~~s~~~~R~alfdIAiAGPLAg~ 355 (528)
.+...+..|+.++++++.++++||+||+++||++|+++. .+.+.+||+++++++...++++++.|++|||++|+
T Consensus 37 ~~~~~~~~g~~~~~~l~~~v~iHElgH~~~A~~~G~~v~------~i~l~p~Gg~~~~~~~~~~~~~~~~IalAGPl~Nl 110 (227)
T cd06164 37 LGAVAWLLGLAAALLLFASVLLHELGHSLVARRYGIPVR------SITLFLFGGVARLEREPETPGQEFVIAIAGPLVSL 110 (227)
T ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCeEC------eEEEEeeeEEEEecCCCCCHHHHhhhhhhHHHHHH
Confidence 345667889999999999999999999999999999997 67888899999999888889999999999999999
Q ss_pred HHHHHHHHHHhhcCCCCCCcccccccchhhhhhhhhhHHhhhccccCCCCCccchHHHHHHHHHHHHHHHhhcCCCCCCh
Q 009686 356 SLGFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAINSIPAGELDG 435 (528)
Q Consensus 356 llAl~llligl~l~~s~~~~~~v~~~~f~~s~L~g~la~l~LG~~l~~~~~v~lhPL~~agwinLvltafNLLPigpLDG 435 (528)
+++++++++....+... .+.+ ...+.+.+|+|+++++|||+|++||||
T Consensus 111 lla~i~~~l~~~~~~~~------------~~~~--------------------~~~~~~~~~~Nl~l~~fNLlP~~PLDG 158 (227)
T cd06164 111 VLALLFLLLSLALPGSG------------AGPL--------------------GVLLGYLALINLLLAVFNLLPAFPLDG 158 (227)
T ss_pred HHHHHHHHHHHHhcccc------------chHH--------------------HHHHHHHHHHHHHHHHHhCcCCCCCCh
Confidence 99998887765432110 0000 012456789999999999999999999
Q ss_pred HHHHHHhhhhhH
Q 009686 436 GRIAFALWGRKA 447 (528)
Q Consensus 436 GrIl~Allgrr~ 447 (528)
|||+++++.++.
T Consensus 159 gril~~ll~~~~ 170 (227)
T cd06164 159 GRVLRALLWRRT 170 (227)
T ss_pred HHHHHHHHHHhc
Confidence 999999976654
No 3
>cd06161 S2P-M50_SpoIVFB SpoIVFB Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50B), regulates intramembrane proteolysis (RIP), and is involved in the pro-sigmaK pathway of bacterial spore formation. SpoIVFB (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA (bypass-of-forespore A), and SpoIVB (sporulation protein, stage IV cell wall formation, B locus). SpoIVFB is negatively regulated by SpoIVFA and BofA and activated by SpoIVB. It is thought that SpoIVFB, SpoIVFA, and BofA are located in the mother-cell membrane that surrounds the forespore and that SpoIVB is secreted from the forespore into the space between the two where it activates SpoIVFB.
Probab=99.91 E-value=2.1e-23 Score=202.21 Aligned_cols=129 Identities=29% Similarity=0.433 Sum_probs=107.8
Q ss_pred HHHHhhHHHHHHHHHHHHHHHHHHHHHHHHcCCccccccccccceeeecceEEeccccccCccceeeeEecchhhHHHHH
Q 009686 279 NLLTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAITRIRNIVSKREDLLKVAAAGPLAGFSLG 358 (528)
Q Consensus 279 ~~l~~glp~aL~Ll~iL~iHElGH~laArr~Gvk~s~P~FIP~i~LgtfGAvi~~~s~~~~R~alfdIAiAGPLAg~llA 358 (528)
..+..++.+++.++.++++||+||+++||++|+++. .+.+.+||+++++++...+|++++.|++|||++|++++
T Consensus 25 ~~~~~~~~~~l~l~~~v~iHElgH~~~A~~~G~~v~------~i~l~p~Gg~~~~~~~~~~~~~~~lIalAGPl~n~~la 98 (208)
T cd06161 25 VAWLLGLLEALLLFLSVLLHELGHALVARRYGIRVR------SITLLPFGGVAELEEEPETPKEEFVIALAGPLVSLLLA 98 (208)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcc------ceEEEeeeeeeeeccCCCChhHheeeeeehHHHHHHHH
Confidence 456788899999999999999999999999999997 78888899999998777789999999999999999999
Q ss_pred HHHHHHHhhcCCCCCCcccccccchhhhhhhhhhHHhhhccccCCCCCccchHHHHHHHHHHHHHHHhhcCCCCCChHHH
Q 009686 359 FVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAINSIPAGELDGGRI 438 (528)
Q Consensus 359 l~llligl~l~~s~~~~~~v~~~~f~~s~L~g~la~l~LG~~l~~~~~v~lhPL~~agwinLvltafNLLPigpLDGGrI 438 (528)
+++.++....+.. + .....+.+.+++|+++++|||+|+.|||||||
T Consensus 99 ~~~~~l~~~~~~~--------------~--------------------~~~~~~~~~~~~N~~l~lfNLlPi~pLDGg~i 144 (208)
T cd06161 99 GLFYLLYLLLPGG--------------G--------------------PLSSLLEFLAQVNLILGLFNLLPALPLDGGRV 144 (208)
T ss_pred HHHHHHHHHcccc--------------h--------------------HHHHHHHHHHHHHHHHHHHHccCCCCCChHHH
Confidence 9887665432110 0 00123456789999999999999999999999
Q ss_pred HHHhhhhhH
Q 009686 439 AFALWGRKA 447 (528)
Q Consensus 439 l~Allgrr~ 447 (528)
+++++.++.
T Consensus 145 l~~ll~~~~ 153 (208)
T cd06161 145 LRALLWRRT 153 (208)
T ss_pred HHHHHHHhc
Confidence 999976653
No 4
>cd06163 S2P-M50_PDZ_RseP-like RseP-like Site-2 proteases (S2P), zinc metalloproteases (MEROPS family M50A), cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. In Escherichia coli, the S2P homolog RseP is involved in the sigmaE pathway of extracytoplasmic stress responses. Also included in this group are such homologs as Bacillus subtilis YluC, Mycobacterium tuberculosis Rv2869c S2P, and Bordetella bronchiseptica HurP. Rv2869c S2P appears to have a role in the regulation of prokaryotic lipid biosynthesis and membrane composition and YluC of Bacillus has a role in transducing membrane stress. This group includes bacterial and eukaryotic S2P/M50s homologs with either one or two PDZ domains present. PDZ domains are believed to have a regulatory role. The RseP PDZ domain is required for the inhibitory reaction that prevents cleavage of its substrate, RseA.
Probab=99.85 E-value=7.5e-21 Score=181.90 Aligned_cols=112 Identities=33% Similarity=0.458 Sum_probs=88.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCcccccccc---cc------------ceeeecceEEecccccc------------
Q 009686 286 PGALVTALVIGVHELGHILAAKSTGVELGVPYFV---PS------------WQIGSFGAITRIRNIVS------------ 338 (528)
Q Consensus 286 p~aL~Ll~iL~iHElGH~laArr~Gvk~s~P~FI---P~------------i~LgtfGAvi~~~s~~~------------ 338 (528)
.+.+++.+++++||+||+++||++|+++.. +.| |. +.+.++|+++++++..+
T Consensus 3 ~~~i~l~~~v~iHElGH~~~Ar~~Gv~v~~-f~iGfGp~l~~~~~~~t~~~i~~iPlGGyv~~~~~~~~~~~~~~~~~~~ 81 (182)
T cd06163 3 AFILVLGILIFVHELGHFLVAKLFGVKVEE-FSIGFGPKLFSFKKGETEYSISAIPLGGYVKMLGEDPEEEADPEDDPRS 81 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCeeeE-eeeecCceeeeeecCCeEEEEEEEEeccEEEecCCCcccccccccchHH
Confidence 355667788999999999999999999862 111 21 23567999998864311
Q ss_pred ----CccceeeeEecchhhHHHHHHHHHHHHhhcCCCCCCcccccccchhhhhhhhhhHHhhhccccCCCCCccchHHHH
Q 009686 339 ----KREDLLKVAAAGPLAGFSLGFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVI 414 (528)
Q Consensus 339 ----~R~alfdIAiAGPLAg~llAl~llligl~l~~s~~~~~~v~~~~f~~s~L~g~la~l~LG~~l~~~~~v~lhPL~~ 414 (528)
++++++.|++|||++|+++|++++++. +.+
T Consensus 82 f~~~~~~~ri~V~lAGP~~NlilA~i~~~~~----------------------------------------------~~~ 115 (182)
T cd06163 82 FNSKPVWQRILIVFAGPLANFLLAIVLFAVL----------------------------------------------LSF 115 (182)
T ss_pred HccCCcchhhhhhhhHHHHHHHHHHHHHHHH----------------------------------------------HHH
Confidence 467899999999999999998664321 224
Q ss_pred HHHHHHHHHHHhhcCCCCCChHHHHHHhhh
Q 009686 415 WAWAGLLINAINSIPAGELDGGRIAFALWG 444 (528)
Q Consensus 415 agwinLvltafNLLPigpLDGGrIl~Allg 444 (528)
..++|+.+++|||+|++||||||++++++.
T Consensus 116 ~~~~n~~l~~fNLlPippLDGg~il~~~~~ 145 (182)
T cd06163 116 LALLSINLGILNLLPIPALDGGHLLFLLIE 145 (182)
T ss_pred HHHHHHHHHHHHcCCCCCCCHHHHHHHHHH
Confidence 578999999999999999999999999985
No 5
>cd05709 S2P-M50 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. The domain core structure appears to contain at least three transmembrane helices with a catalytic zinc atom coordinated by three conserved residues contained within the consensus sequence HExxH, together with a conserved aspartate residue. The S2P/M50 family of RIP proteases is widely distributed; in eukaryotic cells, they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum (ER) stress responses. In sterol-depleted mammalian cells, a two-step proteolytic process releases the N-terminal domains of sterol regulatory element-bindin
Probab=99.85 E-value=8.3e-21 Score=178.22 Aligned_cols=139 Identities=28% Similarity=0.328 Sum_probs=99.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCcccc----ccccc-------cceeeecceEEecccccc-----CccceeeeEec
Q 009686 286 PGALVTALVIGVHELGHILAAKSTGVELGV----PYFVP-------SWQIGSFGAITRIRNIVS-----KREDLLKVAAA 349 (528)
Q Consensus 286 p~aL~Ll~iL~iHElGH~laArr~Gvk~s~----P~FIP-------~i~LgtfGAvi~~~s~~~-----~R~alfdIAiA 349 (528)
.+.+++++++.+||+||+++||++|+++.. ..+.| .+.+.++|+++++.+... +|++++.|++|
T Consensus 2 ~~~~~~~i~i~iHE~gH~~~A~~~G~~~~~~~~~~~~~~~~~~~~~~~~~ip~gG~~~~~~~~~~~~~~~~~~~~~i~la 81 (180)
T cd05709 2 AFILALLISVTVHELGHALVARRLGVKVARFSGGFTLNPLKHGDPYGIILIPLGGYAKPVGENPRAFKKPRWQRLLVALA 81 (180)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHcCCCchheeeeEEECCcCCCCEehHHHHhccCeeccCCCChhhhccchhhhhhhhhh
Confidence 356678889999999999999999997741 11111 122345699998876554 48899999999
Q ss_pred chhhHHHHHHHHHHHHhhcCCCCCCcccccccchhhhhhhhhhHHhhhccccCCCCCccchHHHHHHHHHHHHHHHhhcC
Q 009686 350 GPLAGFSLGFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAINSIP 429 (528)
Q Consensus 350 GPLAg~llAl~llligl~l~~s~~~~~~v~~~~f~~s~L~g~la~l~LG~~l~~~~~v~lhPL~~agwinLvltafNLLP 429 (528)
||++|++++++++++.......... .. ..+ ......+.+.+.+|+|+.+++|||+|
T Consensus 82 GPl~nllla~i~~~~~~~~~~~~~~----~~---~~~-----------------~~~~~~~~l~~~~~~n~~l~~fNLlP 137 (180)
T cd05709 82 GPLANLLLALLLLLLLLLLGGLPPA----PV---GQA-----------------ASSGLANLLAFLALINLNLAVFNLLP 137 (180)
T ss_pred hHHHHHHHHHHHHHHHHHHccCCcc----ch---hhh-----------------HHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 9999999999988776543221000 00 000 00111245667899999999999999
Q ss_pred CCCCChHHHHHHhhhhhHH
Q 009686 430 AGELDGGRIAFALWGRKAS 448 (528)
Q Consensus 430 igpLDGGrIl~Allgrr~a 448 (528)
++||||||++++++.++..
T Consensus 138 i~plDGg~il~~~l~~~~~ 156 (180)
T cd05709 138 IPPLDGGRILRALLEAIRG 156 (180)
T ss_pred CCCCChHHHHHHHHhHHHH
Confidence 9999999999999887754
No 6
>cd06159 S2P-M50_PDZ_Arch Uncharacterized Archaeal homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the S2P/M50 family of RIP proteases use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. In eukaryotic cells they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum stress responses. In prokaryotes they regulate such processes as sporulation, cell division, stress response, and cell differentiation. This group appears to be limited to Archaeal S2P/M50s homologs with additional putative N-terminal transmembrane spanning regions, relative to the core protein, and either one or two PDZ domains present.
Probab=99.82 E-value=4.4e-19 Score=178.48 Aligned_cols=119 Identities=26% Similarity=0.325 Sum_probs=93.0
Q ss_pred HHhhHHHHHHHHHHHHHHHHHHHHHHHHcCCccccccccccceeeecceEEeccccc---cCccceeeeEecchhhHHHH
Q 009686 281 LTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAITRIRNIV---SKREDLLKVAAAGPLAGFSL 357 (528)
Q Consensus 281 l~~glp~aL~Ll~iL~iHElGH~laArr~Gvk~s~P~FIP~i~LgtfGAvi~~~s~~---~~R~alfdIAiAGPLAg~ll 357 (528)
....+.+.++++.++.+||+||+++||++|+++..--+ .+.+.++||++++++.. .++++++.|++|||++|+++
T Consensus 107 ~i~~~~~~iaL~isv~iHElgHa~~Ar~~G~~V~~iGl--~l~~ip~Gg~v~~~~~~~~~~~~~~~~~Ia~AGP~~Nlvl 184 (263)
T cd06159 107 FIPLPYGIIALVVGVVVHELSHGILARVEGIKVKSGGL--LLLIIPPGAFVEPDEEELNKADRRIRLRIFAAGVTANFVV 184 (263)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCEECchhH--HHHhhhcEEEEEecchhhccCChhheeeeeeehHHHHHHH
Confidence 33556667788889999999999999999999973111 01123478999886544 46789999999999999999
Q ss_pred HHHHHHHHhhcCCCCCCcccccccchhhhhhhhhhHHhhhccccCCCCCccchHHHHHHHHHHHHHHHhhcCCCCCChHH
Q 009686 358 GFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAINSIPAGELDGGR 437 (528)
Q Consensus 358 Al~llligl~l~~s~~~~~~v~~~~f~~s~L~g~la~l~LG~~l~~~~~v~lhPL~~agwinLvltafNLLPigpLDGGr 437 (528)
|++++++.. +.+..|+|+.+++|||+|+.||||||
T Consensus 185 a~i~~~l~~---------------------------------------------l~~~~~~N~~l~lFNLlP~~PLDGg~ 219 (263)
T cd06159 185 ALIAFALFF---------------------------------------------LYWIFWINFLLGLFNCLPAIPLDGGH 219 (263)
T ss_pred HHHHHHHHH---------------------------------------------HHHHHHHHHHHHHHhCCCCCCCChHH
Confidence 987754321 22457899999999999999999999
Q ss_pred HHHHhhhhh
Q 009686 438 IAFALWGRK 446 (528)
Q Consensus 438 Il~Allgrr 446 (528)
++++++..+
T Consensus 220 il~~ll~~~ 228 (263)
T cd06159 220 VFRDLLEAL 228 (263)
T ss_pred HHHHHHHHH
Confidence 999996544
No 7
>PF02163 Peptidase_M50: Peptidase family M50; InterPro: IPR008915 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This entry contains metallopeptidases belonging to MEROPS peptidase family M50 (S2P protease family, clan MM). Members of the M50 metallopeptidase family include: mammalian sterol-regulatory element binding protein (SREBP) site 2 protease, Escherichia coli protease EcfE, stage IV sporulation protein FB and various hypothetical bacterial and eukaryotic homologues. A number of proteins are classified as non-peptidase homologues as they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity.; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 3B4R_A 3ID4_A 3ID2_A 2ZPL_B 3ID1_A 2ZPM_A 3ID3_B 2HGA_A.
Probab=99.78 E-value=6.8e-19 Score=166.14 Aligned_cols=127 Identities=28% Similarity=0.345 Sum_probs=79.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCccccccc----ccc----------ceeeecceE---------------Eeccccc
Q 009686 287 GALVTALVIGVHELGHILAAKSTGVELGVPYF----VPS----------WQIGSFGAI---------------TRIRNIV 337 (528)
Q Consensus 287 ~aL~Ll~iL~iHElGH~laArr~Gvk~s~P~F----IP~----------i~LgtfGAv---------------i~~~s~~ 337 (528)
+.+++++++.+||+||+++|+++|+++..... .+. +.+.++|++ ...+...
T Consensus 2 ~~~~~~i~i~~HE~gH~~~a~~~G~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~g~~~~~G~~~~~~~~~~~~~~~~~ 81 (192)
T PF02163_consen 2 FILALLISIVLHELGHALAARLYGDKVPRFEGGFGLNIFSHRDGFTIWSIRLIPLGGYVGGFGWSNVNPFPAPISESFRK 81 (192)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHTTT--B--EEE------------------------------------------------
T ss_pred CcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccCC
Confidence 35677789999999999999999999975421 110 001122322 2222234
Q ss_pred cCccceeeeEecchhhHHHHHHHHHHHHhhcCCCCCCcccccccchhhhhhhhhhHHhhhccccCCCCCccchHHHHHHH
Q 009686 338 SKREDLLKVAAAGPLAGFSLGFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAW 417 (528)
Q Consensus 338 ~~R~alfdIAiAGPLAg~llAl~llligl~l~~s~~~~~~v~~~~f~~s~L~g~la~l~LG~~l~~~~~v~lhPL~~agw 417 (528)
.+|++.+.|++|||++|++++++++.+......... ......+.+.+++|
T Consensus 82 ~~~~~~~~i~laGp~~nllla~i~~~l~~~~~~~~~------------------------------~~~~~~~~~~~~~~ 131 (192)
T PF02163_consen 82 RSRWKRILIALAGPLANLLLAIIALLLLYLLSGSVG------------------------------WSSFFAEFLFFFAW 131 (192)
T ss_dssp --TTCHHHHHHHHHHHHHHHHHHHHHHTTS-------------------------------------EETTEEHHHHHHH
T ss_pred CCccceEEEEEEcHHHHHHHHHHHHHHHHHHhcccc------------------------------ccHHHHHHHHHHHH
Confidence 567889999999999999999888766543221000 01122345778899
Q ss_pred HHHHHHHHhhcCCCCCChHHHHHHhh
Q 009686 418 AGLLINAINSIPAGELDGGRIAFALW 443 (528)
Q Consensus 418 inLvltafNLLPigpLDGGrIl~All 443 (528)
+|+.++++||+|++||||||++++++
T Consensus 132 ~n~~l~~~NllPi~~lDG~~il~~l~ 157 (192)
T PF02163_consen 132 LNFILALFNLLPIPPLDGGRILRALL 157 (192)
T ss_dssp HHHHHHHHTTSSSSSSHHHHHHHHHH
T ss_pred HHHHHhhhhcccCCcCCHHHHHHHHH
Confidence 99999999999999999999999998
No 8
>cd06162 S2P-M50_PDZ_SREBP Sterol regulatory element-binding protein (SREBP) Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50A), regulates intramembrane proteolysis (RIP) of SREBP and is part of a signal transduction mechanism involved in sterol and lipid metabolism. In sterol-depleted mammalian cells, a two-step proteolytic process releases the N-terminal domains of SREBPs from membranes of the endoplasmic reticulum (ER). These domains translocate into the nucleus, where they activate genes of cholesterol and fatty acid biosynthesis. The first cleavage occurs at Site-1 within the ER lumen to generate an intermediate that is subsequently released from the membrane by cleavage at Site-2, which lies within the first transmembrane domain. It is the second proteolytic step that is carried out by the SREBP Site-2 protease (S2P) which is present in this CD family. This group appears to be limited to eumetazoan proteins and contains one PDZ domain.
Probab=99.76 E-value=8.9e-18 Score=170.05 Aligned_cols=114 Identities=25% Similarity=0.229 Sum_probs=89.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCccccccccccceeeec----ceEEecccc---ccCccceeeeEecchhhHHHHHH
Q 009686 287 GALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSF----GAITRIRNI---VSKREDLLKVAAAGPLAGFSLGF 359 (528)
Q Consensus 287 ~aL~Ll~iL~iHElGH~laArr~Gvk~s~P~FIP~i~Lgtf----GAvi~~~s~---~~~R~alfdIAiAGPLAg~llAl 359 (528)
+.++++.++.+||+||+++|+++|+++. .+.+..| ||+++..+. ..++++++.|+.|||++|+++|+
T Consensus 130 ~l~al~isvvvHElgHal~A~~~gi~V~------~iGl~l~~~~pGa~ve~~~e~~~~~~~~~~l~Ia~AGp~~NlvLa~ 203 (277)
T cd06162 130 YFTALLISGVVHEMGHGVAAVREQVRVN------GFGIFFFIIYPGAYVDLFTDHLNLISPVQQLRIFCAGVWHNFVLGL 203 (277)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCeec------eEEEeeeeccCeeEEeecccccccCChhhhhheehhhHHHHHHHHH
Confidence 4566788999999999999999999998 4444344 899987433 23567789999999999999998
Q ss_pred HHHHHHhhcCCCCCCcccccccchhhhhhhhhhHHhhhccccCCCCCccchHHHHHHHHHHHHHHHhhcCCCCCChHHHH
Q 009686 360 VLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAINSIPAGELDGGRIA 439 (528)
Q Consensus 360 ~llligl~l~~s~~~~~~v~~~~f~~s~L~g~la~l~LG~~l~~~~~v~lhPL~~agwinLvltafNLLPigpLDGGrIl 439 (528)
+++++.+. + -+.+..++|+.+++|||+|+.|||||||+
T Consensus 204 i~~~l~~~------------------~------------------------~l~~la~iNl~lavfNLlP~~pLDGg~il 241 (277)
T cd06162 204 VGYLLLIE------------------T------------------------FLKYLISLSGALAVINAVPCFALDGQWIL 241 (277)
T ss_pred HHHHHHHH------------------H------------------------HHHHHHHHHHHHHHhhcCCCCCCChHHHH
Confidence 77653210 0 13356789999999999999999999999
Q ss_pred HHhhhhhHH
Q 009686 440 FALWGRKAS 448 (528)
Q Consensus 440 ~Allgrr~a 448 (528)
++++.++..
T Consensus 242 ~~ll~~~~~ 250 (277)
T cd06162 242 STFLEATLV 250 (277)
T ss_pred HHHHHHHhC
Confidence 999765543
No 9
>cd06158 S2P-M50_like_1 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the S2P/M50 family of RIP proteases use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. In eukaryotic cells they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum stress responses. In prokaryotes they regulate such processes as sporulation, cell division, stress response, and cell differentiation. This group includes bacterial, eukaryotic, and Archaeal S2P/M50s homologs with a minimal core protein and no PDZ domains.
Probab=99.76 E-value=2.9e-18 Score=163.60 Aligned_cols=135 Identities=26% Similarity=0.325 Sum_probs=90.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCcccc----cccccc--------ce--ee--ecceEEec-----cccccCccceee
Q 009686 287 GALVTALVIGVHELGHILAAKSTGVELGV----PYFVPS--------WQ--IG--SFGAITRI-----RNIVSKREDLLK 345 (528)
Q Consensus 287 ~aL~Ll~iL~iHElGH~laArr~Gvk~s~----P~FIP~--------i~--Lg--tfGAvi~~-----~s~~~~R~alfd 345 (528)
..++++.++.+||+||+++|+++|+++.. -.+-|. +. +. ..+++.+. +...++|++++.
T Consensus 4 ~~~~~~~~i~~HE~aHa~~A~~~Gd~t~~~~Grltlnp~~hid~~g~l~~~~~~~~~~G~a~p~~~~~~~~~~~r~~~~~ 83 (181)
T cd06158 4 VIIAVLLAITLHEFAHAYVAYRLGDPTARRAGRLTLNPLAHIDPIGTIILPLLLPFLFGWAKPVPVNPRNFKNPRRGMLL 83 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCcHHHHcCceecCcHHhcCcchHHHHHHHHHhCeEEecccccChHhhcccHhhHhh
Confidence 44567789999999999999999999862 112221 00 00 02334332 222345788999
Q ss_pred eEecchhhHHHHHHHHHHHHhhcCCCCCCcccccccchhhhhhhhhhHHhhhccccCCCCCccchHHHHHHHHHHHHHHH
Q 009686 346 VAAAGPLAGFSLGFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAI 425 (528)
Q Consensus 346 IAiAGPLAg~llAl~llligl~l~~s~~~~~~v~~~~f~~s~L~g~la~l~LG~~l~~~~~v~lhPL~~agwinLvltaf 425 (528)
|++|||++|+++++++.++........+ ...+.+ ...+....++|+.+++|
T Consensus 84 valAGP~~n~~la~i~~~~~~~~~~~~~---------~~~~~l--------------------~~~~~~~~~~Ni~l~lf 134 (181)
T cd06158 84 VSLAGPLSNLLLALLFALLLRLLPAFGG---------VVASFL--------------------FLMLAYGVLINLVLAVF 134 (181)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHhccccc---------hhhHHH--------------------HHHHHHHHHHHHHHHHH
Confidence 9999999999999887665443211100 000111 01234567899999999
Q ss_pred hhcCCCCCChHHHHHHhhhhhHHHH
Q 009686 426 NSIPAGELDGGRIAFALWGRKASTR 450 (528)
Q Consensus 426 NLLPigpLDGGrIl~Allgrr~a~~ 450 (528)
||+|++|||||||+++++.++....
T Consensus 135 NLlPipPLDG~~il~~~l~~~~~~~ 159 (181)
T cd06158 135 NLLPIPPLDGSKILAALLPRRLAEA 159 (181)
T ss_pred HhCCCCCCChHHHHHHHcchhHHHH
Confidence 9999999999999999998876543
No 10
>TIGR00054 RIP metalloprotease RseP. A model that detects fragments as well matches a number of members of the PEPTIDASE FAMILY S2C. The region of match appears not to overlap the active site domain.
Probab=99.52 E-value=1.9e-13 Score=145.44 Aligned_cols=80 Identities=26% Similarity=0.413 Sum_probs=59.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCcccc-cccc-c------------cceeeecceEEecccc----------------
Q 009686 287 GALVTALVIGVHELGHILAAKSTGVELGV-PYFV-P------------SWQIGSFGAITRIRNI---------------- 336 (528)
Q Consensus 287 ~aL~Ll~iL~iHElGH~laArr~Gvk~s~-P~FI-P------------~i~LgtfGAvi~~~s~---------------- 336 (528)
+.+.+.+++++||+||+++||++|+++.. .... | .+.+.++|+++++...
T Consensus 9 ~~~~~~~~v~~HE~gH~~~a~~~g~~v~~FsiGfGp~l~~~~~~~tey~i~~~plGg~v~~~g~~~~~~~~~~~~~~~~f 88 (420)
T TIGR00054 9 SILALAVLIFVHELGHFLAARLCGIKVERFSIGFGPKILKFKKNGTEYAISLIPLGGYVKMKGLDKEMEVKPPETDGDLF 88 (420)
T ss_pred HHHHHHHHHHHHhHHHHHHHHHcCCEEEEEEEccCchheEEecCCeEEEEEEecCcceEeeccCCcccccCCcchhhhhh
Confidence 35566678899999999999999999861 1111 2 1336689999998411
Q ss_pred -ccCccceeeeEecchhhHHHHHHHHHHHHh
Q 009686 337 -VSKREDLLKVAAAGPLAGFSLGFVLFLVGF 366 (528)
Q Consensus 337 -~~~R~alfdIAiAGPLAg~llAl~llligl 366 (528)
..+.++++.|.+|||++|+++|++++++.+
T Consensus 89 ~~~~~~~r~~i~~aGp~~N~~~a~~~~~~~~ 119 (420)
T TIGR00054 89 NNKSVFQKAIIIFAGPLANFIFAIFVYIFIS 119 (420)
T ss_pred ccCCHHHHHHhhhcccHHHHHHHHHHHHHHH
Confidence 034577899999999999999998876543
No 11
>PRK10779 zinc metallopeptidase RseP; Provisional
Probab=99.51 E-value=1.8e-13 Score=146.51 Aligned_cols=83 Identities=20% Similarity=0.313 Sum_probs=60.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHcCCcccc-cccc-cc-------------ceeeecceEEecccc------------
Q 009686 284 GLPGALVTALVIGVHELGHILAAKSTGVELGV-PYFV-PS-------------WQIGSFGAITRIRNI------------ 336 (528)
Q Consensus 284 glp~aL~Ll~iL~iHElGH~laArr~Gvk~s~-P~FI-P~-------------i~LgtfGAvi~~~s~------------ 336 (528)
.+.+.+++.+++++||+||+++||++|+++.. .... |. +-+.++|++.+|...
T Consensus 7 i~~fil~l~~li~vHElGHfl~Ar~~gv~V~~FsiGfGp~l~~~~~~~~Tey~i~~iPlGGyVk~~~e~~~~~~~~~~~~ 86 (449)
T PRK10779 7 LAAFIVALGVLITVHEFGHFWVARRCGVRVERFSIGFGKALWRRTDRQGTEYVIALIPLGGYVKMLDERVEPVAPELRHH 86 (449)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHcCCeeeEEEeecChhHeeEecCCCcEEEEEEEcCCCeeecCCCCCCcCChhhhhh
Confidence 34466667778899999999999999999972 1111 10 235578999987432
Q ss_pred ---ccCccceeeeEecchhhHHHHHHHHHHHHh
Q 009686 337 ---VSKREDLLKVAAAGPLAGFSLGFVLFLVGF 366 (528)
Q Consensus 337 ---~~~R~alfdIAiAGPLAg~llAl~llligl 366 (528)
.++.++++.|.+|||++|+++|++++.+-+
T Consensus 87 ~f~~k~~~~R~~i~~AGp~~N~ila~~~~~~~~ 119 (449)
T PRK10779 87 AFNNKTVGQRAAIIAAGPIANFIFAIFAYWLVF 119 (449)
T ss_pred hhccCCHHHhhhhhhhhHHHHHHHHHHHHHHHH
Confidence 123578899999999999999998865543
No 12
>COG1994 SpoIVFB Zn-dependent proteases [General function prediction only]
Probab=99.32 E-value=2.1e-11 Score=120.35 Aligned_cols=130 Identities=25% Similarity=0.327 Sum_probs=84.7
Q ss_pred HHhhHHHHHHHHHHHHHHHHHHHHHHHHcCCccccccccccceeeecceEEeccccccCccceeee-------Eec-chh
Q 009686 281 LTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAITRIRNIVSKREDLLKV-------AAA-GPL 352 (528)
Q Consensus 281 l~~glp~aL~Ll~iL~iHElGH~laArr~Gvk~s~P~FIP~i~LgtfGAvi~~~s~~~~R~alfdI-------AiA-GPL 352 (528)
+.++....++++..+..||+||...++++|++.. .+.++.+|++..++..+.+.+..+.+ +.| ||+
T Consensus 41 ~~~~~~~~~~l~~rl~l~~~gh~~~~~~~~~~l~------~~~i~~~~g~~~~~~~~v~~~~~~~~~~~g~lvs~algpl 114 (230)
T COG1994 41 LGDGTAAFVGLAHRLVLHPLGHSDEAGRLGLKLL------LALLFGFGGFGFLKPVPVNPRGEFLIRLAGPLVSLALGPL 114 (230)
T ss_pred HhhhHHHHHHHhHHHhhhHhhHHHHHHHHHHHHH------HHHHHhccceeeecCcCcCHHHHhhhhccchhHHHHHHHH
Confidence 4555555555777899999999999999999986 44443467777776655555444444 444 555
Q ss_pred hHHHHHHHHHHHHhhcCCCCCCcccccccchhhhhhhhhhHHhhhccccCCCCCccchHHHHHHHHHHHHHHHhhcCCCC
Q 009686 353 AGFSLGFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAINSIPAGE 432 (528)
Q Consensus 353 Ag~llAl~llligl~l~~s~~~~~~v~~~~f~~s~L~g~la~l~LG~~l~~~~~v~lhPL~~agwinLvltafNLLPigp 432 (528)
.|+.+++++ .... +.. ...+.+ ..-+...+.+|+++++|||+|++|
T Consensus 115 ~ni~la~~~-~~~~--~~~-----------~~~~~~--------------------~~~~~~la~~Nl~L~lFNLiPi~P 160 (230)
T COG1994 115 TNIALAVLG-LLAL--SLF-----------LYHSVL--------------------FAFLAALALVNLVLALFNLLPIPP 160 (230)
T ss_pred HHHHHHHHH-HHhh--ccc-----------ccchhH--------------------HHHHHHHHHHHHHHHHHhCCCCCC
Confidence 555555443 0000 000 000000 111234577999999999999999
Q ss_pred CChHHHHHHhhhhhHHHH
Q 009686 433 LDGGRIAFALWGRKASTR 450 (528)
Q Consensus 433 LDGGrIl~Allgrr~a~~ 450 (528)
|||||++|+++.++....
T Consensus 161 LDGg~vlr~~~~~~~~~~ 178 (230)
T COG1994 161 LDGGRVLRALLPRRYGAA 178 (230)
T ss_pred CChHHHHHHHccHHHHHH
Confidence 999999999988876533
No 13
>COG0750 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]
Probab=98.89 E-value=1.6e-09 Score=111.96 Aligned_cols=244 Identities=14% Similarity=0.058 Sum_probs=137.9
Q ss_pred cccccceeeeccccccCceEEEEeccCChhHHHHHHHHHHHHhHhCCceEEEEEecCCCCCcEEEEEcCCCCCCCCCChh
Q 009686 164 QVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFGDQYKLFLLVNPEDDKPVAVVVPRKTLQPETTAVP 243 (528)
Q Consensus 164 ~~Fg~dtF~~t~~~~~~~gvi~rGnLR~~~e~~y~~l~~~l~~~fGd~y~lfl~~~~~~~kPv~~v~P~~~~~p~~~~~~ 243 (528)
.+++.++|+.....+ ...+++.|.+.......+..+...+ ..|..+ ...|+.. + ....
T Consensus 82 ~~~~~~~f~~~~~~~-~~~~~~~Gp~~n~i~~~~~~~~~~~--~~G~~~---------~~~~~~~---~--v~~~----- 139 (375)
T COG0750 82 PEPRPRAFNAKSVWQ-RIAIVFAGPLFNFILAIVLFVVLFF--VIGLVP---------VASPVVG---E--VAPK----- 139 (375)
T ss_pred cCcchhhhhcccccc-hhheeechHHHHHHHHHHHHHhhhe--Eeeeee---------eccCeee---e--cCCC-----
Confidence 588899999999999 9999999999988766665544433 223111 1122221 0 0000
Q ss_pred HHHHHHHHHHHHHHHHHHhcccccccchhhcccchHHHHhhHHHHHH----HHHHHHHH--HHHHHHHHHHcCCcccccc
Q 009686 244 EWFAAGAFGLVTVFTLLLRNVPALQSNLLSTFDNLNLLTNGLPGALV----TALVIGVH--ELGHILAAKSTGVELGVPY 317 (528)
Q Consensus 244 ~~~~~~l~~l~T~~T~~~a~~~~L~~~~~~~~~~~~~l~~glp~aL~----Ll~iL~iH--ElGH~laArr~Gvk~s~P~ 317 (528)
..+..+.+..|...+..+- +...+++..........+ .+.+.+.| +..|..+++.++.....|+
T Consensus 140 ---------s~a~~a~l~~Gd~iv~~~~-~~i~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~P~ 209 (375)
T COG0750 140 ---------SAAALAGLRPGDRIVAVDG-EKVASWDDVRRLLVAAAGDVFNLLTILVIRLDGEAHAVAAEIIKSLGLTPV 209 (375)
T ss_pred ---------CHHHHcCCCCCCEEEeECC-EEccCHHHHHHHHHhccCCcccceEEEEEeccceeeeccccceeeEeeecc
Confidence 0111223333433332221 112223222221211111 34567788 9999999998888888898
Q ss_pred ccccceeeecceEEe--ccccccC-----ccceeeeEecchhhHHHHHHHHHHHHhhcCCCCCCcccccccchhhhhhhh
Q 009686 318 FVPSWQIGSFGAITR--IRNIVSK-----REDLLKVAAAGPLAGFSLGFVLFLVGFIFPPSDGIGIVVDASVFHESFLAG 390 (528)
Q Consensus 318 FIP~i~LgtfGAvi~--~~s~~~~-----R~alfdIAiAGPLAg~llAl~llligl~l~~s~~~~~~v~~~~f~~s~L~g 390 (528)
++| ...+..++.++ ..+..++ ++...++..+++++. .+.-...++.+.+... .......+..+.+.+
T Consensus 210 ~~~-~~~~~~~~~i~~~~i~~~p~~~~~~~~~~~~~~~~~~i~~-~v~~~~~~~~~~~~~l----~~~~~~~~~~~~l~G 283 (375)
T COG0750 210 VIP-LKPGDKIVAVDVGAIGLSPNGEPDVGKVLVKYGPLEAVGL-AVEKTGRLVKLTLKML----KKLITGDLSLKNLSG 283 (375)
T ss_pred eec-cCCCCEEEEeeeeeeeeccCCCCccceeeeccCHHHHHHH-HHHHHHHHHHHHHHHH----HHheecccccccccC
Confidence 876 44555554443 3333444 788999999999993 3444444444332100 000011112222222
Q ss_pred hhHHhhhccccCCCCCccchHHHHHHHHHHHHHHHhhcCCCCCChHHHHHHhhhhhH
Q 009686 391 GFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAINSIPAGELDGGRIAFALWGRKA 447 (528)
Q Consensus 391 ~la~l~LG~~l~~~~~v~lhPL~~agwinLvltafNLLPigpLDGGrIl~Allgrr~ 447 (528)
.+.....+.... .....|++.+++|+|+.++++||+|+++|||||++++++.+..
T Consensus 284 pi~i~~~~~~~~--~~~~~~~l~~~~~lsi~lg~lNllP~p~LDGG~i~~~~~e~~~ 338 (375)
T COG0750 284 PIGIAKIAGAAA--SLGLINLLFFLALLSINLGILNLLPIPPLDGGHLLFYLLEALR 338 (375)
T ss_pred ceehhhhhhHHH--hhHHHHHHHHHHHHHHHHHHHhccCCCccCccHHHHHHHHHHh
Confidence 221111111100 1235689999999999999999999999999999999986654
No 14
>PF13398 Peptidase_M50B: Peptidase M50B-like
Probab=97.33 E-value=0.00069 Score=66.05 Aligned_cols=65 Identities=31% Similarity=0.274 Sum_probs=52.3
Q ss_pred HHHHHHHHHHHHHHHHcCCccccccccccceeee-cceEEeccccccCccceeeeEecchhhHHHHHHHHHHHH
Q 009686 293 LVIGVHELGHILAAKSTGVELGVPYFVPSWQIGS-FGAITRIRNIVSKREDLLKVAAAGPLAGFSLGFVLFLVG 365 (528)
Q Consensus 293 ~iL~iHElGH~laArr~Gvk~s~P~FIP~i~Lgt-fGAvi~~~s~~~~R~alfdIAiAGPLAg~llAl~lllig 365 (528)
....+||+||+++|...|-++. .+.+.+ -++.+..+. +++...+.++.|||++..+++..++..+
T Consensus 23 l~t~~HE~gHal~a~l~G~~v~------~i~l~~~~~G~~~~~~--~~~~~~~~i~~aGyl~~~l~g~~~~~~~ 88 (200)
T PF13398_consen 23 LVTFVHELGHALAALLTGGRVK------GIVLFPDGSGVTVSSG--PSGIGRFLIALAGYLGPALFGLLLLWLL 88 (200)
T ss_pred HHHHHHHHHHHHHHHHhCCCcc------eEEEEeCCCceEEEec--CCCcchhHHhcccchHHHHHHHHHHHHH
Confidence 3578999999999999999998 555544 466776665 5666789999999999999887776655
No 15
>COG0750 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]
Probab=96.29 E-value=0.012 Score=61.18 Aligned_cols=82 Identities=27% Similarity=0.385 Sum_probs=53.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHcCCccccccc--cc-------c------ceeeecceEEecccccc-----------
Q 009686 285 LPGALVTALVIGVHELGHILAAKSTGVELGVPYF--VP-------S------WQIGSFGAITRIRNIVS----------- 338 (528)
Q Consensus 285 lp~aL~Ll~iL~iHElGH~laArr~Gvk~s~P~F--IP-------~------i~LgtfGAvi~~~s~~~----------- 338 (528)
+.+.+.+...+.+||+||+|.||++|+++..... -| . +...+.|++.++.....
T Consensus 6 i~~i~~~~~lv~~he~gh~~~a~~~~~~v~~f~ig~g~~l~~~~~~~~~~~~i~~~plggyv~~~~~~~~~~~~~~~~~~ 85 (375)
T COG0750 6 IAFIIALGVLVFVHELGHFWVARRCGVKVERFSIGFGPKLFSRKDKGGTEYVLSAIPLGGYVKMLGEDAEEVVLKGPEPR 85 (375)
T ss_pred HHHHHHHHHHHHHHHHhhHHHHHhcCceeEEEEeccCcceEEEEcCCceEEEEeecCccceEEEecCccccccccccCcc
Confidence 3345556668899999999999999999973111 11 0 11335566655432111
Q ss_pred -------CccceeeeEecchhhHHHHHHHHHHHHh
Q 009686 339 -------KREDLLKVAAAGPLAGFSLGFVLFLVGF 366 (528)
Q Consensus 339 -------~R~alfdIAiAGPLAg~llAl~llligl 366 (528)
+-...+.+.+|||+.|++.++...+...
T Consensus 86 ~~~f~~~~~~~~~~~~~~Gp~~n~i~~~~~~~~~~ 120 (375)
T COG0750 86 PRAFNAKSVWQRIAIVFAGPLFNFILAIVLFVVLF 120 (375)
T ss_pred hhhhhcccccchhheeechHHHHHHHHHHHHHhhh
Confidence 1122678999999999998877766554
No 16
>KOG2921 consensus Intramembrane metalloprotease (sterol-regulatory element-binding protein (SREBP) protease) [Posttranslational modification, protein turnover, chaperones]
Probab=96.18 E-value=0.0043 Score=66.43 Aligned_cols=82 Identities=28% Similarity=0.313 Sum_probs=53.4
Q ss_pred HhhHHHH-HHHHHHHHHHHHHHHHHHHHcCCccccccccccceeeecceEEecccc----ccCccceeeeEecchhhHHH
Q 009686 282 TNGLPGA-LVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAITRIRNI----VSKREDLLKVAAAGPLAGFS 356 (528)
Q Consensus 282 ~~glp~a-L~Ll~iL~iHElGH~laArr~Gvk~s~P~FIP~i~LgtfGAvi~~~s~----~~~R~alfdIAiAGPLAg~l 356 (528)
+.+++|. ..+++.+.+||+||+|||.+.|+++. +|=-.+..--=||++.+... .+. -....|.-||-.-||+
T Consensus 120 l~~I~yf~t~lvi~~vvHElGHalAA~segV~vn--gfgIfi~aiyPgafvdl~~dhLqsl~~-fr~LrIfcAGIWHNfv 196 (484)
T KOG2921|consen 120 LSGIAYFLTSLVITVVVHELGHALAAASEGVQVN--GFGIFIAAIYPGAFVDLDNDHLQSLPS-FRALRIFCAGIWHNFV 196 (484)
T ss_pred cccchhhhhhHHHHHHHHHhhHHHHHHhcCceee--eeEEEEEEEcCchhhhhhhhHHhhcch-HHHHHHHhhhHHHHHH
Confidence 3455544 45666888999999999999999997 11000111112677655332 122 2245789999999999
Q ss_pred HHHHHHHHHh
Q 009686 357 LGFVLFLVGF 366 (528)
Q Consensus 357 lAl~llligl 366 (528)
+|+++.+.-.
T Consensus 197 fallc~lal~ 206 (484)
T KOG2921|consen 197 FALLCVLALF 206 (484)
T ss_pred HHHHHHHHHH
Confidence 9998866544
No 17
>PF11667 DUF3267: Protein of unknown function (DUF3267); InterPro: IPR021683 This family of proteins has no known function.
Probab=65.38 E-value=3.2 Score=36.62 Aligned_cols=22 Identities=36% Similarity=0.300 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHHHHHHcCCcc
Q 009686 292 ALVIGVHELGHILAAKSTGVEL 313 (528)
Q Consensus 292 l~iL~iHElGH~laArr~Gvk~ 313 (528)
+..+.+||+-|++..+.+|.+.
T Consensus 4 ~~~~~~HEliH~l~~~~~~~~~ 25 (111)
T PF11667_consen 4 IVLIPLHELIHGLFFKLFGKKP 25 (111)
T ss_pred EeeHHHHHHHHHHHHHHhCCCC
Confidence 3456899999999999999965
No 18
>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=60.62 E-value=5.1 Score=36.22 Aligned_cols=21 Identities=24% Similarity=0.436 Sum_probs=14.5
Q ss_pred HHHHHHHHHHHHHHHHcCCcc
Q 009686 293 LVIGVHELGHILAAKSTGVEL 313 (528)
Q Consensus 293 ~iL~iHElGH~laArr~Gvk~ 313 (528)
..+++||+||.+=-.+-..+-
T Consensus 106 ~~v~~HEiGHaLGL~H~~~~~ 126 (154)
T PF00413_consen 106 QSVAIHEIGHALGLDHSNDPN 126 (154)
T ss_dssp HHHHHHHHHHHTTBESSSSTT
T ss_pred hhhhhhccccccCcCcCCCcc
Confidence 357899999997655544433
No 19
>PF07423 DUF1510: Protein of unknown function (DUF1510); InterPro: IPR009988 This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.
Probab=59.66 E-value=4.9 Score=40.47 Aligned_cols=55 Identities=25% Similarity=0.385 Sum_probs=39.0
Q ss_pred eeeeccccccCceEEEEeccCChhHHHHHHHHHHHHhHhCCceEEEEEecCCCC-CcEEE
Q 009686 170 TFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFGDQYKLFLLVNPEDD-KPVAV 228 (528)
Q Consensus 170 tF~~t~~~~~~~gvi~rGnLR~~~e~~y~~l~~~l~~~fGd~y~lfl~~~~~~~-kPv~~ 228 (528)
..|+|++..-.=-+.|.||= |.|.++|.+|+.+=. +++|+|++==-...| ||+-+
T Consensus 159 is~atgi~~~~mi~w~ign~-G~~~~a~gtVs~k~~---~~~YrV~i~WVd~eGWkP~kv 214 (217)
T PF07423_consen 159 ISYATGISEDNMIVWFIGNN-GSPQKAIGTVSDKDT---GKKYRVYIEWVDNEGWKPVKV 214 (217)
T ss_pred HHHhhCCChhheEEEhhhcC-CcccceeEEeccCCC---CceEEEEEEEecCCCccceee
Confidence 36889988877889999996 777999999886533 578999743222122 77643
No 20
>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=58.13 E-value=6.1 Score=36.48 Aligned_cols=22 Identities=32% Similarity=0.364 Sum_probs=18.4
Q ss_pred HHHHHHHHHHHHHHHHHcCCcc
Q 009686 292 ALVIGVHELGHILAAKSTGVEL 313 (528)
Q Consensus 292 l~iL~iHElGH~laArr~Gvk~ 313 (528)
+..+++||+||.+=.+....+.
T Consensus 104 ~~~~~~HEiGHaLGL~H~~~~~ 125 (156)
T cd04279 104 LQAIALHELGHALGLWHHSDRP 125 (156)
T ss_pred HHHHHHHHhhhhhcCCCCCCCc
Confidence 4578999999999888887776
No 21
>PF13485 Peptidase_MA_2: Peptidase MA superfamily
Probab=51.17 E-value=12 Score=31.72 Aligned_cols=18 Identities=28% Similarity=0.233 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHHHHcCC
Q 009686 294 VIGVHELGHILAAKSTGV 311 (528)
Q Consensus 294 iL~iHElGH~laArr~Gv 311 (528)
-+++||++|.|.....+-
T Consensus 27 ~~l~HE~~H~~~~~~~~~ 44 (128)
T PF13485_consen 27 RVLAHELAHQWFGNYFGG 44 (128)
T ss_pred HHHHHHHHHHHHHHHcCC
Confidence 578999999999999763
No 22
>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=48.17 E-value=12 Score=34.35 Aligned_cols=21 Identities=29% Similarity=0.300 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHHHHHHHcCC
Q 009686 291 TALVIGVHELGHILAAKSTGV 311 (528)
Q Consensus 291 Ll~iL~iHElGH~laArr~Gv 311 (528)
-....++||+||.+=-++-.-
T Consensus 93 ~~~~~~~HEiGHaLGL~H~~~ 113 (165)
T cd04268 93 RLRNTAEHELGHALGLRHNFA 113 (165)
T ss_pred HHHHHHHHHHHHHhcccccCc
Confidence 345788999999986655554
No 23
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=48.14 E-value=18 Score=43.49 Aligned_cols=17 Identities=24% Similarity=0.296 Sum_probs=7.5
Q ss_pred cccccccccCCCCcccc
Q 009686 5 TTFRGNLSLLPHCSSCC 21 (528)
Q Consensus 5 ~~~~~~~~~~~~~~~~~ 21 (528)
+||-|.-..+--|++-.
T Consensus 1354 aTi~v~R~~~Dlct~~~ 1370 (1516)
T KOG1832|consen 1354 ATIPVDRCLLDLCTEPT 1370 (1516)
T ss_pred eeeecccchhhhhcCCc
Confidence 34444444444455433
No 24
>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=47.97 E-value=9 Score=36.23 Aligned_cols=14 Identities=36% Similarity=0.344 Sum_probs=10.5
Q ss_pred HHHHHHHHHHHHHH
Q 009686 293 LVIGVHELGHILAA 306 (528)
Q Consensus 293 ~iL~iHElGH~laA 306 (528)
.-.++||+||++=-
T Consensus 70 g~TltHEvGH~LGL 83 (154)
T PF05572_consen 70 GKTLTHEVGHWLGL 83 (154)
T ss_dssp SHHHHHHHHHHTT-
T ss_pred ccchhhhhhhhhcc
Confidence 36789999998643
No 25
>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=47.97 E-value=8.2 Score=35.75 Aligned_cols=22 Identities=23% Similarity=0.368 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHHHHHHcCCcc
Q 009686 292 ALVIGVHELGHILAAKSTGVEL 313 (528)
Q Consensus 292 l~iL~iHElGH~laArr~Gvk~ 313 (528)
+..+++||+||++=-..-..+.
T Consensus 107 ~~~~~~HEiGHaLGL~H~~~~~ 128 (157)
T cd04278 107 LFSVAAHEIGHALGLGHSSDPD 128 (157)
T ss_pred HHHHHHHHhccccccCCCCCCc
Confidence 4467899999998765544443
No 26
>PTZ00429 beta-adaptin; Provisional
Probab=44.98 E-value=20 Score=42.24 Aligned_cols=33 Identities=27% Similarity=0.252 Sum_probs=18.2
Q ss_pred CChhhhhcccCCCCCCCCcccccCCCCCCCccC
Q 009686 71 NNDKEKEVHDGQENQPATASDQEDDKSQPDSQL 103 (528)
Q Consensus 71 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 103 (528)
+.||||+|+++.++.+++.++..++++..++++
T Consensus 607 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 639 (746)
T PTZ00429 607 ELDEEDTEDDDAVELPSTPSMGTQDGSPAPSAA 639 (746)
T ss_pred ccccccccchhhccCCCCCCCCCCCCCCCcccc
Confidence 344455555555666666666555554444444
No 27
>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=44.14 E-value=16 Score=34.90 Aligned_cols=12 Identities=50% Similarity=0.717 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHH
Q 009686 293 LVIGVHELGHIL 304 (528)
Q Consensus 293 ~iL~iHElGH~l 304 (528)
..++.||+||+.
T Consensus 90 ~aVlaHElgH~~ 101 (226)
T PF01435_consen 90 AAVLAHELGHIK 101 (226)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 368999999986
No 28
>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=42.22 E-value=16 Score=30.76 Aligned_cols=16 Identities=44% Similarity=0.574 Sum_probs=12.2
Q ss_pred HHHHHHHHHHHHHHcC
Q 009686 295 IGVHELGHILAAKSTG 310 (528)
Q Consensus 295 L~iHElGH~laArr~G 310 (528)
.++||+||++.-....
T Consensus 45 ~laHELgH~~~~~~~~ 60 (122)
T PF06114_consen 45 TLAHELGHILLHHGDE 60 (122)
T ss_dssp HHHHHHHHHHHHH-HH
T ss_pred HHHHHHHHHHhhhccc
Confidence 5789999999866554
No 29
>PF11085 YqhR: Conserved membrane protein YqhR; InterPro: IPR024563 This family of proteins is conserved in the Bacillaceae family of the Firmicutes. Their function is not known.
Probab=40.55 E-value=2.6e+02 Score=27.65 Aligned_cols=100 Identities=21% Similarity=0.369 Sum_probs=54.2
Q ss_pred HHHHHHHHHHHHhhcCCCCCChHHHHHHhh-hhhHHHHHH-HHHHHHHHHHHHhh------------hh-------hHHH
Q 009686 414 IWAWAGLLINAINSIPAGELDGGRIAFALW-GRKASTRLT-GVSIVLLGLSSLFS------------DV-------TFYW 472 (528)
Q Consensus 414 ~agwinLvltafNLLPigpLDGGrIl~All-grr~a~~is-~~~~~lLGl~~l~~------------~~-------~l~W 472 (528)
+++-+..+.-.||.-+++| |-+++-.+ |.....+++ .+.++++|+.++.. +. ..+|
T Consensus 33 iWs~v~yl~y~f~FT~v~P---~~ll~Pf~~g~wk~t~~G~~igi~~~gv~Si~aAllY~~~l~k~~g~W~Gi~YG~~~W 109 (173)
T PF11085_consen 33 IWSLVRYLAYFFHFTEVGP---NFLLEPFALGDWKNTWLGNLIGIVFIGVFSIVAALLYYALLKKFKGPWPGILYGLAWW 109 (173)
T ss_pred HHHHHHHHHHHhccccccc---ChhhhhhhccchhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHHHH
Confidence 3455777788899999999 88888774 333333333 22233333322210 11 1234
Q ss_pred HHHHHHHHhCCCCCCCcCCCCCChhHHHHHHHHHHHHHHhhcccCCC
Q 009686 473 VVLVFFLQRGPIAPLSEEITDPDDKYIALGVLVLFLGLLVCLPYPFP 519 (528)
Q Consensus 473 ~llilfl~rg~~~P~~nevt~~~~~r~~lg~l~l~l~ll~llP~P~~ 519 (528)
++ +|..-+|..|....+.+++..-.. .-+.+.+.-=+|+-+-++
T Consensus 110 ~i--vF~~lnP~fp~~~~~~~l~~nTii-T~~CiyiLyGlFIGYSIs 153 (173)
T PF11085_consen 110 AI--VFFVLNPIFPMIKPVTELDWNTII-TTLCIYILYGLFIGYSIS 153 (173)
T ss_pred HH--HHHHhcccccCChhhhhCchhHHH-HHHHHHHHHHHHhceeeh
Confidence 33 333457888888888888765543 333444444444444333
No 30
>PF14247 DUF4344: Domain of unknown function (DUF4344)
Probab=39.86 E-value=29 Score=35.05 Aligned_cols=25 Identities=32% Similarity=0.417 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcc
Q 009686 288 ALVTALVIGVHELGHILAAKSTGVEL 313 (528)
Q Consensus 288 aL~Ll~iL~iHElGH~laArr~Gvk~ 313 (528)
++..+..++.||+||++... +++++
T Consensus 88 ~~~~~~~~l~HE~GHAlI~~-~~lPv 112 (220)
T PF14247_consen 88 AIGNVLFTLYHELGHALIDD-LDLPV 112 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHH-hcCCc
Confidence 55566678999999999875 34444
No 31
>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=38.78 E-value=17 Score=34.54 Aligned_cols=22 Identities=32% Similarity=0.451 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHHHHHHcCCccc
Q 009686 293 LVIGVHELGHILAAKSTGVELG 314 (528)
Q Consensus 293 ~iL~iHElGH~laArr~Gvk~s 314 (528)
...++||+||.+=-++-+....
T Consensus 114 ~~t~~HEiGHaLGL~H~~~~~~ 135 (186)
T cd04277 114 YQTIIHEIGHALGLEHPGDYNG 135 (186)
T ss_pred HHHHHHHHHHHhcCCCCCcCCC
Confidence 4678999999987766555443
No 32
>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=38.74 E-value=16 Score=32.88 Aligned_cols=20 Identities=30% Similarity=0.441 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHHHcCCccc
Q 009686 295 IGVHELGHILAAKSTGVELG 314 (528)
Q Consensus 295 L~iHElGH~laArr~Gvk~s 314 (528)
.++||+||++-...-..+..
T Consensus 89 ~~~HEigHaLGl~H~~~~~d 108 (140)
T smart00235 89 VAAHELGHALGLYHEQSRSD 108 (140)
T ss_pred cHHHHHHHHhcCCcCCCCCc
Confidence 78999999986665544443
No 33
>PF01434 Peptidase_M41: Peptidase family M41 This is family M41 in the peptidase classification. ; InterPro: IPR000642 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M41 (FtsH endopeptidase family, clan MA(E)). The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH. The peptidase M41 family belong to a larger family of zinc metalloproteases. This family includes the cell division protein FtsH, and the yeast mitochondrial respiratory chain complexes assembly protein, which is a putative ATP-dependent protease required for assembly of the mitochondrial respiratory chain and ATPase complexes. FtsH is an integral membrane protein, which seems to act as an ATP-dependent zinc metallopeptidase that binds one zinc ion.; GO: 0004222 metalloendopeptidase activity, 0005524 ATP binding, 0006508 proteolysis; PDB: 4EIW_C 2DHR_E 1IY1_A 1IY2_A 1IY0_A 1IXZ_A 2CE7_F 2CEA_F 3KDS_E 2QZ4_A ....
Probab=38.56 E-value=25 Score=34.63 Aligned_cols=18 Identities=33% Similarity=0.316 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHHHHHcCC
Q 009686 294 VIGVHELGHILAAKSTGV 311 (528)
Q Consensus 294 iL~iHElGH~laArr~Gv 311 (528)
.+.+||.||+++|...+-
T Consensus 30 ~~A~HEAGhAvva~~l~~ 47 (213)
T PF01434_consen 30 RIAYHEAGHAVVAYLLPP 47 (213)
T ss_dssp HHHHHHHHHHHHHHHSSS
T ss_pred HHHHHHHHHHHHHHHhcc
Confidence 578999999999999873
No 34
>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=38.29 E-value=16 Score=33.34 Aligned_cols=21 Identities=29% Similarity=0.219 Sum_probs=15.6
Q ss_pred HHHHHHHHHHHHHHHHHHcCC
Q 009686 291 TALVIGVHELGHILAAKSTGV 311 (528)
Q Consensus 291 Ll~iL~iHElGH~laArr~Gv 311 (528)
....+++||+||.+=.++-.-
T Consensus 95 ~~~~~~~HElGH~LGl~H~~~ 115 (167)
T cd00203 95 EGAQTIAHELGHALGFYHDHD 115 (167)
T ss_pred cchhhHHHHHHHHhCCCccCc
Confidence 345678999999987765544
No 35
>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=37.92 E-value=23 Score=35.75 Aligned_cols=29 Identities=31% Similarity=0.339 Sum_probs=20.0
Q ss_pred HHhhHHHHHHHHHHHHHHHHHHHHHHHHcCCc
Q 009686 281 LTNGLPGALVTALVIGVHELGHILAAKSTGVE 312 (528)
Q Consensus 281 l~~glp~aL~Ll~iL~iHElGH~laArr~Gvk 312 (528)
++.|+|-. ++.++++||++|+|. +..|.+
T Consensus 84 vl~GLPrl--l~gsiLAHE~mHa~L-rl~g~~ 112 (212)
T PF12315_consen 84 VLYGLPRL--LTGSILAHELMHAWL-RLNGFP 112 (212)
T ss_pred EECCCCHH--HHhhHHHHHHHHHHh-cccCCC
Confidence 34456643 446899999999998 455544
No 36
>PF13582 Reprolysin_3: Metallo-peptidase family M12B Reprolysin-like; PDB: 3P24_C.
Probab=37.36 E-value=17 Score=31.81 Aligned_cols=14 Identities=36% Similarity=0.423 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHHHH
Q 009686 294 VIGVHELGHILAAK 307 (528)
Q Consensus 294 iL~iHElGH~laAr 307 (528)
..++||+||.+=+.
T Consensus 109 ~~~~HEiGH~lGl~ 122 (124)
T PF13582_consen 109 DTFAHEIGHNLGLN 122 (124)
T ss_dssp THHHHHHHHHTT--
T ss_pred eEeeehhhHhcCCC
Confidence 67899999987543
No 37
>PF13574 Reprolysin_2: Metallo-peptidase family M12B Reprolysin-like; PDB: 1KAP_P 1JIW_P 1AKL_A 1OM7_A 1OM8_A 1O0T_A 1OM6_A 1H71_P 1O0Q_A 1OMJ_A ....
Probab=37.30 E-value=18 Score=34.55 Aligned_cols=21 Identities=33% Similarity=0.286 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHHHHHHHcCCc
Q 009686 292 ALVIGVHELGHILAAKSTGVE 312 (528)
Q Consensus 292 l~iL~iHElGH~laArr~Gvk 312 (528)
-.-.++||+||.+=|.+-+-.
T Consensus 111 ~~~~~aHElGH~lGa~Hd~~~ 131 (173)
T PF13574_consen 111 GIDTFAHELGHQLGAPHDFDN 131 (173)
T ss_dssp HHHHHHHHHHHHHT---SSSS
T ss_pred eeeeehhhhHhhcCCCCCCCC
Confidence 345689999999999887774
No 38
>PF14891 Peptidase_M91: Effector protein
Probab=36.87 E-value=22 Score=33.93 Aligned_cols=16 Identities=31% Similarity=0.299 Sum_probs=13.1
Q ss_pred HHHHHHHHHHHHHHHH
Q 009686 293 LVIGVHELGHILAAKS 308 (528)
Q Consensus 293 ~iL~iHElGH~laArr 308 (528)
++++.|||+|++-...
T Consensus 104 ~v~L~HEL~HA~~~~~ 119 (174)
T PF14891_consen 104 FVVLYHELIHAYDYMN 119 (174)
T ss_pred HHHHHHHHHHHHHHHC
Confidence 5789999999987654
No 39
>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=36.24 E-value=18 Score=34.38 Aligned_cols=21 Identities=33% Similarity=0.414 Sum_probs=13.1
Q ss_pred HHHHHHHHHHHHHHHHHcCCc
Q 009686 292 ALVIGVHELGHILAAKSTGVE 312 (528)
Q Consensus 292 l~iL~iHElGH~laArr~Gvk 312 (528)
-.+.++||+||-+=|.+=+..
T Consensus 142 ~~~~~AHEiGH~lGa~HD~~~ 162 (196)
T PF13688_consen 142 GAITFAHEIGHNLGAPHDGDY 162 (196)
T ss_dssp HHHHHHHHHHHHTT-----SS
T ss_pred eehhhHHhHHHhcCCCCCCCC
Confidence 347889999999999876654
No 40
>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=33.60 E-value=25 Score=33.03 Aligned_cols=10 Identities=80% Similarity=1.291 Sum_probs=8.9
Q ss_pred HHHHHHHHHH
Q 009686 295 IGVHELGHIL 304 (528)
Q Consensus 295 L~iHElGH~l 304 (528)
+.+||+||.+
T Consensus 80 IaaHE~GHiL 89 (132)
T PF02031_consen 80 IAAHELGHIL 89 (132)
T ss_dssp HHHHHHHHHH
T ss_pred eeeehhcccc
Confidence 6899999986
No 41
>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=31.19 E-value=27 Score=33.87 Aligned_cols=20 Identities=25% Similarity=0.298 Sum_probs=13.9
Q ss_pred HHHHHHHHHHHHHHHcCCcc
Q 009686 294 VIGVHELGHILAAKSTGVEL 313 (528)
Q Consensus 294 iL~iHElGH~laArr~Gvk~ 313 (528)
..++||+||++=..+-.-+.
T Consensus 94 ~~i~HElgHaLG~~HEh~rp 113 (198)
T cd04327 94 RVVLHEFGHALGFIHEHQSP 113 (198)
T ss_pred HHHHHHHHHHhcCcccccCC
Confidence 57889999998655444433
No 42
>PRK03001 M48 family peptidase; Provisional
Probab=30.80 E-value=31 Score=35.44 Aligned_cols=12 Identities=33% Similarity=0.426 Sum_probs=9.9
Q ss_pred HHHHHHHHHHHH
Q 009686 293 LVIGVHELGHIL 304 (528)
Q Consensus 293 ~iL~iHElGH~l 304 (528)
.++++||+||.-
T Consensus 125 ~aVlAHElgHi~ 136 (283)
T PRK03001 125 RGVMAHELAHVK 136 (283)
T ss_pred HHHHHHHHHHHh
Confidence 368899999974
No 43
>PHA02456 zinc metallopeptidase motif-containing protein
Probab=30.56 E-value=30 Score=32.03 Aligned_cols=18 Identities=28% Similarity=0.351 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHHHcCCcc
Q 009686 296 GVHELGHILAAKSTGVEL 313 (528)
Q Consensus 296 ~iHElGH~laArr~Gvk~ 313 (528)
+.||+.|.|.-|.||.-.
T Consensus 83 L~HEL~H~WQ~RsYG~i~ 100 (141)
T PHA02456 83 LAHELNHAWQFRTYGLVQ 100 (141)
T ss_pred HHHHHHHHHhhhccceee
Confidence 579999999999999755
No 44
>PRK12462 phosphoserine aminotransferase; Provisional
Probab=30.36 E-value=85 Score=33.92 Aligned_cols=68 Identities=12% Similarity=0.161 Sum_probs=46.5
Q ss_pred ccccccCCCCHhHHHHhhccccccceeeeccccccCceEEEEeccCChhHHHHHHHHHHHHhHhC--CceEEEEEecC
Q 009686 145 QQLDEYIRIPKETIDILKDQVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFG--DQYKLFLLVNP 220 (528)
Q Consensus 145 ~~~~~~~~i~~edl~~ik~~~Fg~dtF~~t~~~~~~~gvi~rGnLR~~~e~~y~~l~~~l~~~fG--d~y~lfl~~~~ 220 (528)
.....+..+|+|.++++++++.-|. .-+-+++=.+---.+=.+.|++.+++|+++|+ |.|.+++++-.
T Consensus 7 nF~aGPa~lp~~Vl~~~~~~~~~~~--------~~g~si~eisHRs~~F~~i~~~~~~~Lr~Ll~~P~~y~Vlfl~Gg 76 (364)
T PRK12462 7 NFSGGPGALPDTVLEQVRQAVVELP--------ETGLSVLGMSHRSSWFSSLLAQAEADLRDLLGIPDEYGVVFLQGG 76 (364)
T ss_pred eecCCCcCCCHHHHHHHHHHHhccc--------ccCccccccccccHHHHHHHHHHHHHHHHHhCCCCCCeEEEEecc
Confidence 3456788999999999997543332 11123333333334568999999999999998 68988766654
No 45
>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=30.30 E-value=34 Score=32.57 Aligned_cols=20 Identities=35% Similarity=0.350 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHHHHHHcCC
Q 009686 292 ALVIGVHELGHILAAKSTGV 311 (528)
Q Consensus 292 l~iL~iHElGH~laArr~Gv 311 (528)
.+.+++||+||-+=+.+-+.
T Consensus 131 ~a~~~AHElGH~lG~~HD~~ 150 (194)
T cd04269 131 FAVTMAHELGHNLGMEHDDG 150 (194)
T ss_pred HHHHHHHHHHhhcCCCcCCC
Confidence 35788999999987775554
No 46
>PRK03982 heat shock protein HtpX; Provisional
Probab=30.08 E-value=32 Score=35.38 Aligned_cols=12 Identities=42% Similarity=0.362 Sum_probs=9.8
Q ss_pred HHHHHHHHHHHH
Q 009686 293 LVIGVHELGHIL 304 (528)
Q Consensus 293 ~iL~iHElGH~l 304 (528)
.++++||+||.-
T Consensus 126 ~AVlAHElgHi~ 137 (288)
T PRK03982 126 EGVIAHELTHIK 137 (288)
T ss_pred HHHHHHHHHHHH
Confidence 367899999974
No 47
>KOG0391 consensus SNF2 family DNA-dependent ATPase [General function prediction only]
Probab=30.02 E-value=53 Score=41.01 Aligned_cols=21 Identities=33% Similarity=0.358 Sum_probs=15.1
Q ss_pred eeccccccCceEEEEeccCCh
Q 009686 172 FVTNQEPYEGGVLFKGNLRGQ 192 (528)
Q Consensus 172 ~~t~~~~~~~gvi~rGnLR~~ 192 (528)
-+|.+-..+---+.|||||.-
T Consensus 599 l~tTqVktpvPsLLrGqLReY 619 (1958)
T KOG0391|consen 599 LVTTQVKTPVPSLLRGQLREY 619 (1958)
T ss_pred eeeeeeccCchHHHHHHHHHH
Confidence 345555667777999999963
No 48
>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=29.84 E-value=33 Score=34.64 Aligned_cols=19 Identities=26% Similarity=0.476 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHHHHHc
Q 009686 291 TALVIGVHELGHILAAKST 309 (528)
Q Consensus 291 Ll~iL~iHElGH~laArr~ 309 (528)
++...++||+||-+=+.+=
T Consensus 166 ~~a~t~AHElGHnlGm~HD 184 (244)
T cd04270 166 ESDLVTAHELGHNFGSPHD 184 (244)
T ss_pred HHHHHHHHHHHHhcCCCCC
Confidence 4567899999999877643
No 49
>PRK11037 hypothetical protein; Provisional
Probab=29.53 E-value=1.3e+02 Score=26.29 Aligned_cols=65 Identities=18% Similarity=0.366 Sum_probs=42.7
Q ss_pred ccCCCCHhHH-----HHhhccccccceeeeccccccCceEEEEeccC-------C-hhHHHHHHHHHHHHhHhCCceEE
Q 009686 149 EYIRIPKETI-----DILKDQVFGFDTFFVTNQEPYEGGVLFKGNLR-------G-QAAKTYEKISTRMKNKFGDQYKL 214 (528)
Q Consensus 149 ~~~~i~~edl-----~~ik~~~Fg~dtF~~t~~~~~~~gvi~rGnLR-------~-~~e~~y~~l~~~l~~~fGd~y~l 214 (528)
+..+|++++| +.||+.===+..-.+|++|-.++..+|||..= + +...||. +=+-|.-.+..+|+|
T Consensus 4 ~~~~I~~~~LL~~AN~iI~~Hedyi~GM~a~~Veqk~~VLVFkGeyFLD~~GlPT~KtTAvFN-MFK~LAh~LS~~y~L 81 (83)
T PRK11037 4 ETQPIDRETLLLEANKIIREHEDYLAGMRATDVEQKNGVLVFRGEYFLDEQGLPTAKTTAVFN-MFKHLAHVLSEKYHL 81 (83)
T ss_pred CCcccCHHHHHHHHHHHHHhhHHHhcccccceeeeeCCEEEEecceeecCCCCCCccchHHHH-HHHHHHHHhCcceec
Confidence 4567888888 46665333344568999999999999999832 2 2234443 334455556667876
No 50
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=29.18 E-value=39 Score=30.96 Aligned_cols=19 Identities=21% Similarity=0.123 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHHHHHc
Q 009686 291 TALVIGVHELGHILAAKST 309 (528)
Q Consensus 291 Ll~iL~iHElGH~laArr~ 309 (528)
.+.-.++|||.|+++-..+
T Consensus 59 ~~~~tL~HEm~H~~~~~~~ 77 (157)
T PF10263_consen 59 ELIDTLLHEMAHAAAYVFG 77 (157)
T ss_pred HHHHHHHHHHHHHHhhhcc
Confidence 4446789999999996653
No 51
>COG2856 Predicted Zn peptidase [Amino acid transport and metabolism]
Probab=29.14 E-value=30 Score=34.79 Aligned_cols=16 Identities=38% Similarity=0.463 Sum_probs=12.0
Q ss_pred HHHHHHHHHHHHHHcC
Q 009686 295 IGVHELGHILAAKSTG 310 (528)
Q Consensus 295 L~iHElGH~laArr~G 310 (528)
.++||+||++.=+.-.
T Consensus 75 tlAHELGH~llH~~~~ 90 (213)
T COG2856 75 TLAHELGHALLHTDLN 90 (213)
T ss_pred HHHHHHhHHHhccccc
Confidence 4789999999755443
No 52
>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=28.34 E-value=26 Score=33.23 Aligned_cols=20 Identities=40% Similarity=0.531 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHHHHHHHcCC
Q 009686 292 ALVIGVHELGHILAAKSTGV 311 (528)
Q Consensus 292 l~iL~iHElGH~laArr~Gv 311 (528)
.+.+++||+||.+=+.+-+.
T Consensus 133 ~~~~~aHElGH~lG~~HD~~ 152 (192)
T cd04267 133 TALTMAHELGHNLGAEHDGG 152 (192)
T ss_pred ehhhhhhhHHhhcCCcCCCC
Confidence 34689999999998877654
No 53
>PF09471 Peptidase_M64: IgA Peptidase M64; InterPro: IPR019026 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This is a family of highly selective metallo-endopeptidases belonging to the MEROPS peptidase family M64 (IgA peptidase, clan MA). The primary structure of the Clostridium ramosum IgA peptidase shows no significant overall similarity to any other known metallo-endopeptidase []. ; PDB: 3P1V_A 4DF9_D.
Probab=28.12 E-value=25 Score=36.27 Aligned_cols=14 Identities=36% Similarity=0.596 Sum_probs=10.5
Q ss_pred HHHHHHHHHHHHHH
Q 009686 293 LVIGVHELGHILAA 306 (528)
Q Consensus 293 ~iL~iHElGH~laA 306 (528)
.-+++||+||.+.-
T Consensus 217 ~~v~vHE~GHsf~~ 230 (264)
T PF09471_consen 217 KQVVVHEFGHSFGG 230 (264)
T ss_dssp HHHHHHHHHHHTT-
T ss_pred cceeeeeccccccc
Confidence 35789999998753
No 54
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=28.10 E-value=36 Score=31.57 Aligned_cols=17 Identities=24% Similarity=-0.021 Sum_probs=13.8
Q ss_pred HHHHHHHHHHHHHHHHH
Q 009686 292 ALVIGVHELGHILAAKS 308 (528)
Q Consensus 292 l~iL~iHElGH~laArr 308 (528)
+.-++.|||+|+++-..
T Consensus 59 l~~~l~HEm~H~~~~~~ 75 (146)
T smart00731 59 LRETLLHELCHAALYLF 75 (146)
T ss_pred HHhhHHHHHHHHHHHHh
Confidence 34578999999999864
No 55
>PF13583 Reprolysin_4: Metallo-peptidase family M12B Reprolysin-like
Probab=27.42 E-value=32 Score=33.83 Aligned_cols=17 Identities=29% Similarity=0.280 Sum_probs=14.5
Q ss_pred HHHHHHHHHHHHHHcCC
Q 009686 295 IGVHELGHILAAKSTGV 311 (528)
Q Consensus 295 L~iHElGH~laArr~Gv 311 (528)
.++||+||.+=|++-+-
T Consensus 140 ~~aHEiGH~lGl~H~~~ 156 (206)
T PF13583_consen 140 TFAHEIGHNLGLRHDFD 156 (206)
T ss_pred HHHHHHHHHhcCCCCcc
Confidence 48899999999887776
No 56
>COG0501 HtpX Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]
Probab=26.74 E-value=40 Score=33.84 Aligned_cols=11 Identities=55% Similarity=0.818 Sum_probs=9.2
Q ss_pred HHHHHHHHHHH
Q 009686 294 VIGVHELGHIL 304 (528)
Q Consensus 294 iL~iHElGH~l 304 (528)
.++.||+||..
T Consensus 159 aVlaHElgHi~ 169 (302)
T COG0501 159 AVLAHELGHIK 169 (302)
T ss_pred HHHHHHHHHHh
Confidence 57899999963
No 57
>COG5309 Exo-beta-1,3-glucanase [Carbohydrate transport and metabolism]
Probab=26.47 E-value=1e+02 Score=32.63 Aligned_cols=61 Identities=16% Similarity=0.312 Sum_probs=43.2
Q ss_pred HhHHHHhhcccccc-ceeeeccccccCceEEEEeccCC--hhHHHHHHHHHHHHhHhCCceEEEEEec
Q 009686 155 KETIDILKDQVFGF-DTFFVTNQEPYEGGVLFKGNLRG--QAAKTYEKISTRMKNKFGDQYKLFLLVN 219 (528)
Q Consensus 155 ~edl~~ik~~~Fg~-dtF~~t~~~~~~~gvi~rGnLR~--~~e~~y~~l~~~l~~~fGd~y~lfl~~~ 219 (528)
.|.++++|. .||= .+||+||+-.--.|--+-++.-. +..+.++++..+|++. | |.+|+++-
T Consensus 218 ~~q~e~vqs-a~g~~k~~~v~EtGWPS~G~~~G~a~pS~anq~~~~~~i~~~~~~~-G--~d~fvfeA 281 (305)
T COG5309 218 LEQLERVQS-ACGTKKTVWVTETGWPSDGRTYGSAVPSVANQKIAVQEILNALRSC-G--YDVFVFEA 281 (305)
T ss_pred HHHHHHHHH-hcCCCccEEEeeccCCCCCCccCCcCCChhHHHHHHHHHHhhhhcc-C--ccEEEeee
Confidence 677999998 7776 99999998755555555555443 3466778888888874 7 66665553
No 58
>PLN02452 phosphoserine transaminase
Probab=26.47 E-value=1.1e+02 Score=32.65 Aligned_cols=68 Identities=9% Similarity=0.187 Sum_probs=48.1
Q ss_pred ccccccCCCCHhHHHHhhccccccceeeeccccccCceEEEEeccCChhHHHHHHHHHHHHhHhC--CceEEEEEecC
Q 009686 145 QQLDEYIRIPKETIDILKDQVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFG--DQYKLFLLVNP 220 (528)
Q Consensus 145 ~~~~~~~~i~~edl~~ik~~~Fg~dtF~~t~~~~~~~gvi~rGnLR~~~e~~y~~l~~~l~~~fG--d~y~lfl~~~~ 220 (528)
.....+..+|++.+++++.+.+-|. .-+-+++-.+---.+=.++++.++++|++.++ |.|.+++++-.
T Consensus 10 ~f~pGP~~lp~~Vl~~~~~~~~~~~--------~~g~s~~~~sHRs~~f~~i~~~~~~~L~~l~~~p~~y~v~~l~Gs 79 (365)
T PLN02452 10 NFSAGPATLPANVLAKAQAELYNWE--------GSGMSVMEMSHRGKEFLSIIQKAEADLRELLDIPDNYEVLFLQGG 79 (365)
T ss_pred eeeCCCCCCCHHHHHHHHHHHhccc--------ccCccccccCCCchHHHHHHHHHHHHHHHHhCCCCCceEEEEeCc
Confidence 3456788999999999987554432 22334444444444567999999999999997 67988766544
No 59
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=26.41 E-value=55 Score=40.85 Aligned_cols=13 Identities=23% Similarity=0.399 Sum_probs=8.3
Q ss_pred cccccceeEEeee
Q 009686 50 VSRKKRELICRVT 62 (528)
Q Consensus 50 ~~~~~~~~~~~~~ 62 (528)
+.-||||+...-|
T Consensus 1700 ptprrrrllsgnt 1712 (3015)
T KOG0943|consen 1700 PTPRRRRLLSGNT 1712 (3015)
T ss_pred CCchhhhhccCCc
Confidence 3557777776655
No 60
>PRK04897 heat shock protein HtpX; Provisional
Probab=26.18 E-value=41 Score=34.96 Aligned_cols=11 Identities=36% Similarity=0.383 Sum_probs=9.3
Q ss_pred HHHHHHHHHHH
Q 009686 294 VIGVHELGHIL 304 (528)
Q Consensus 294 iL~iHElGH~l 304 (528)
.+++||+||.-
T Consensus 139 aVlAHElgHi~ 149 (298)
T PRK04897 139 GVIGHEISHIR 149 (298)
T ss_pred HHHHHHHHHHh
Confidence 67899999963
No 61
>KOG3320 consensus 40S ribosomal protein S7 [Translation, ribosomal structure and biogenesis]
Probab=25.93 E-value=93 Score=30.89 Aligned_cols=27 Identities=15% Similarity=0.321 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHHhHhCCceEEEEEecC
Q 009686 194 AKTYEKISTRMKNKFGDQYKLFLLVNP 220 (528)
Q Consensus 194 e~~y~~l~~~l~~~fGd~y~lfl~~~~ 220 (528)
.+.|.+|.+.||.+|+|+|.+|+.+..
T Consensus 74 qki~~~LvreleKKF~gk~Vifia~Rr 100 (192)
T KOG3320|consen 74 QKIQVRLVRELEKKFSGKHVIFIAQRR 100 (192)
T ss_pred HHHHHHHHHHHHHhcCCceEEEEEeee
Confidence 455566667999999999999876654
No 62
>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=25.52 E-value=44 Score=31.68 Aligned_cols=11 Identities=36% Similarity=0.495 Sum_probs=9.8
Q ss_pred HHHHHHHHHHH
Q 009686 295 IGVHELGHILA 305 (528)
Q Consensus 295 L~iHElGH~la 305 (528)
+++|||+|.++
T Consensus 138 VvaHEltHGVt 148 (150)
T PF01447_consen 138 VVAHELTHGVT 148 (150)
T ss_dssp HHHHHHHHHHH
T ss_pred eeeeccccccc
Confidence 68999999986
No 63
>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=25.03 E-value=39 Score=34.09 Aligned_cols=27 Identities=19% Similarity=0.146 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCcc
Q 009686 287 GALVTALVIGVHELGHILAAKSTGVEL 313 (528)
Q Consensus 287 ~aL~Ll~iL~iHElGH~laArr~Gvk~ 313 (528)
+..-+..-+++||+||.+=-|+-.+..
T Consensus 128 ~~~~~~~hvi~HEiGH~IGfRHTD~~~ 154 (211)
T PF12388_consen 128 YSVNVIEHVITHEIGHCIGFRHTDYFN 154 (211)
T ss_pred CchhHHHHHHHHHhhhhccccccCcCC
Confidence 344456678999999999888765443
No 64
>PRK01345 heat shock protein HtpX; Provisional
Probab=24.50 E-value=46 Score=35.06 Aligned_cols=12 Identities=33% Similarity=0.454 Sum_probs=10.0
Q ss_pred HHHHHHHHHHHH
Q 009686 293 LVIGVHELGHIL 304 (528)
Q Consensus 293 ~iL~iHElGH~l 304 (528)
..+++||+||.-
T Consensus 125 ~aVlAHElgHi~ 136 (317)
T PRK01345 125 AGVMAHELAHVK 136 (317)
T ss_pred HHHHHHHHHHHH
Confidence 367899999985
No 65
>PF13699 DUF4157: Domain of unknown function (DUF4157)
Probab=24.46 E-value=44 Score=28.36 Aligned_cols=12 Identities=33% Similarity=0.650 Sum_probs=10.1
Q ss_pred HHHHHHHHHHHH
Q 009686 294 VIGVHELGHILA 305 (528)
Q Consensus 294 iL~iHElGH~la 305 (528)
.++.||++|.+.
T Consensus 63 ~llaHEl~Hv~Q 74 (79)
T PF13699_consen 63 ALLAHELAHVVQ 74 (79)
T ss_pred hhHhHHHHHHHh
Confidence 478999999875
No 66
>COG0830 UreF Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]
Probab=24.45 E-value=79 Score=32.28 Aligned_cols=31 Identities=32% Similarity=0.340 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHhhcCCCCCChHHHHHHhhh
Q 009686 414 IWAWAGLLINAINSIPAGELDGGRIAFALWG 444 (528)
Q Consensus 414 ~agwinLvltafNLLPigpLDGGrIl~Allg 444 (528)
++.-.|++.++.=|+|.||+||=||+..+-.
T Consensus 158 ya~~~~lv~aavRlipLgQ~~gq~il~~l~~ 188 (229)
T COG0830 158 YAWASNLVSAAVRLIPLGQLDGQKILAQLEP 188 (229)
T ss_pred HHHHHHHHHHHHHhcccCcHHHHHHHHHhhH
Confidence 3444699999999999999999999998843
No 67
>PRK03072 heat shock protein HtpX; Provisional
Probab=24.11 E-value=48 Score=34.37 Aligned_cols=11 Identities=36% Similarity=0.395 Sum_probs=9.2
Q ss_pred HHHHHHHHHHH
Q 009686 293 LVIGVHELGHI 303 (528)
Q Consensus 293 ~iL~iHElGH~ 303 (528)
..+++||+||.
T Consensus 128 ~aVlAHElgHi 138 (288)
T PRK03072 128 RGVLGHELSHV 138 (288)
T ss_pred HHHHHHHHHHH
Confidence 36789999995
No 68
>PRK02391 heat shock protein HtpX; Provisional
Probab=23.86 E-value=49 Score=34.56 Aligned_cols=10 Identities=40% Similarity=0.733 Sum_probs=8.7
Q ss_pred HHHHHHHHHH
Q 009686 294 VIGVHELGHI 303 (528)
Q Consensus 294 iL~iHElGH~ 303 (528)
.+++||+||.
T Consensus 135 aVlaHElgHi 144 (296)
T PRK02391 135 AVLAHELSHV 144 (296)
T ss_pred HHHHHHHHHH
Confidence 5789999995
No 69
>COG3824 Predicted Zn-dependent protease [General function prediction only]
Probab=23.64 E-value=36 Score=31.91 Aligned_cols=14 Identities=29% Similarity=0.558 Sum_probs=11.7
Q ss_pred HHHHHHHHHHHHHH
Q 009686 291 TALVIGVHELGHIL 304 (528)
Q Consensus 291 Ll~iL~iHElGH~l 304 (528)
.+..+++||+||.+
T Consensus 108 ~vthvliHEIgHhF 121 (136)
T COG3824 108 QVTHVLIHEIGHHF 121 (136)
T ss_pred Hhhhhhhhhhhhhc
Confidence 55688999999975
No 70
>PRK05457 heat shock protein HtpX; Provisional
Probab=23.43 E-value=50 Score=34.21 Aligned_cols=10 Identities=40% Similarity=0.723 Sum_probs=8.8
Q ss_pred HHHHHHHHHH
Q 009686 294 VIGVHELGHI 303 (528)
Q Consensus 294 iL~iHElGH~ 303 (528)
.+++||+||.
T Consensus 136 aVlAHElgHi 145 (284)
T PRK05457 136 AVLAHEISHI 145 (284)
T ss_pred HHHHHHHHHH
Confidence 6789999996
No 71
>PF10692 DUF2498: Protein of unknown function (DUF2498); InterPro: IPR019633 This entry represents proteins found in gammaproteobacteria, including YciN from Escherichia coli. Their function is not known. ; PDB: 3M92_A.
Probab=22.02 E-value=1.5e+02 Score=25.85 Aligned_cols=64 Identities=16% Similarity=0.309 Sum_probs=36.3
Q ss_pred cCCCCHhHH-----HHhhccccccceeeeccccccCceEEEEeccC----Chh----HHHHHHHHHHHHhHhCCceEE
Q 009686 150 YIRIPKETI-----DILKDQVFGFDTFFVTNQEPYEGGVLFKGNLR----GQA----AKTYEKISTRMKNKFGDQYKL 214 (528)
Q Consensus 150 ~~~i~~edl-----~~ik~~~Fg~dtF~~t~~~~~~~gvi~rGnLR----~~~----e~~y~~l~~~l~~~fGd~y~l 214 (528)
.-+|++++| +.||+.===+..-.+|++|-.++..+|||+.= |-| ..||. +=+-|.-.+.++|.|
T Consensus 4 ~~~I~~~~LL~~AN~iI~~Hddyi~GM~a~~Veqk~~VLVFkGeyFLD~~GlPT~KtTAvFN-mFK~LAh~LS~~y~L 80 (82)
T PF10692_consen 4 KQPISRQALLEIANQIIREHDDYIHGMRATSVEQKGDVLVFKGEYFLDEQGLPTAKTTAVFN-MFKHLAHVLSEKYHL 80 (82)
T ss_dssp SEEE-HHHHHHHHHHHHHHHHHHHTT--EEEEEECTTEEEEEE-----TTS---HHHHHHHH-HHHHHHHHHCCCEEE
T ss_pred CcccCHHHHHHHHHHHHHhhHhhhccccccceeeECCEEEEecceeecCCCCCCcchHHHHH-HHHHHHHHcCcceEe
Confidence 346777777 35554222233367899999999999999932 222 33443 344566667888976
No 72
>cd04927 ACT_ACR-like_2 Second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=21.74 E-value=1.1e+02 Score=25.24 Aligned_cols=35 Identities=23% Similarity=0.314 Sum_probs=25.0
Q ss_pred cccceeeeccccccCceEEEEeccCChhHHHHHHHHHHHHhHhCCc
Q 009686 166 FGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFGDQ 211 (528)
Q Consensus 166 Fg~dtF~~t~~~~~~~gvi~rGnLR~~~e~~y~~l~~~l~~~fGd~ 211 (528)
.-+||||+++.. |+ ...++..+++++.|++.+|+-
T Consensus 40 ~v~D~F~V~d~~---------~~--~~~~~~~~~l~~~L~~~L~~~ 74 (76)
T cd04927 40 RVLDLFFITDAR---------EL--LHTKKRREETYDYLRAVLGDS 74 (76)
T ss_pred EEEEEEEEeCCC---------CC--CCCHHHHHHHHHHHHHHHchh
Confidence 467999997531 11 244567788999999999864
No 73
>PRK01265 heat shock protein HtpX; Provisional
Probab=21.69 E-value=57 Score=34.76 Aligned_cols=10 Identities=50% Similarity=0.979 Sum_probs=8.8
Q ss_pred HHHHHHHHHH
Q 009686 294 VIGVHELGHI 303 (528)
Q Consensus 294 iL~iHElGH~ 303 (528)
.+++||+||+
T Consensus 142 aVlAHElgHi 151 (324)
T PRK01265 142 AVAGHELGHL 151 (324)
T ss_pred HHHHHHHHHH
Confidence 5789999996
No 74
>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=21.61 E-value=65 Score=30.86 Aligned_cols=21 Identities=43% Similarity=0.494 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHHHHHHHHcCC
Q 009686 291 TALVIGVHELGHILAAKSTGV 311 (528)
Q Consensus 291 Ll~iL~iHElGH~laArr~Gv 311 (528)
.++.+++||+||-+=+.+-+.
T Consensus 130 ~~a~~~AHelGH~lGm~HD~~ 150 (199)
T PF01421_consen 130 SFAVIIAHELGHNLGMPHDGD 150 (199)
T ss_dssp HHHHHHHHHHHHHTT---TTT
T ss_pred HHHHHHHHHHHHhcCCCCCCC
Confidence 445678999999987777666
No 75
>PRK04860 hypothetical protein; Provisional
Probab=21.59 E-value=86 Score=30.20 Aligned_cols=21 Identities=29% Similarity=0.284 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHHHHHHcC
Q 009686 290 VTALVIGVHELGHILAAKSTG 310 (528)
Q Consensus 290 ~Ll~iL~iHElGH~laArr~G 310 (528)
..+.-++.||++|+++=..+|
T Consensus 61 ~~l~~~v~HEl~H~~~~~~~g 81 (160)
T PRK04860 61 AFIDEVVPHELAHLLVYQLFG 81 (160)
T ss_pred HHHHhHHHHHHHHHHHHHHcC
Confidence 345567899999999999888
No 76
>KOG2719 consensus Metalloprotease [General function prediction only]
Probab=21.50 E-value=52 Score=36.47 Aligned_cols=14 Identities=36% Similarity=0.513 Sum_probs=11.1
Q ss_pred HHHHHHHHHHHHHH
Q 009686 293 LVIGVHELGHILAA 306 (528)
Q Consensus 293 ~iL~iHElGH~laA 306 (528)
.++++||+||+---
T Consensus 281 ~AVl~HELGHW~~~ 294 (428)
T KOG2719|consen 281 VAVLAHELGHWKLN 294 (428)
T ss_pred HHHHHHHhhHHHHh
Confidence 57899999998543
No 77
>PRK02870 heat shock protein HtpX; Provisional
Probab=21.24 E-value=59 Score=34.81 Aligned_cols=11 Identities=45% Similarity=0.673 Sum_probs=9.4
Q ss_pred HHHHHHHHHHH
Q 009686 293 LVIGVHELGHI 303 (528)
Q Consensus 293 ~iL~iHElGH~ 303 (528)
..+++||+||.
T Consensus 174 ~aVlAHELgHi 184 (336)
T PRK02870 174 QAVMAHELSHI 184 (336)
T ss_pred HHHHHHHHHHH
Confidence 36789999998
No 78
>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=21.19 E-value=56 Score=33.24 Aligned_cols=12 Identities=33% Similarity=0.822 Sum_probs=10.3
Q ss_pred HHHHHHHHHHHH
Q 009686 294 VIGVHELGHILA 305 (528)
Q Consensus 294 iL~iHElGH~la 305 (528)
.+.+||.||++.
T Consensus 91 aVAAHEvGHAiQ 102 (222)
T PF04298_consen 91 AVAAHEVGHAIQ 102 (222)
T ss_pred HHHHHHHhHHHh
Confidence 578999999875
No 79
>TIGR01364 serC_1 phosphoserine aminotransferase. This model represents the common form of the phosphoserine aminotransferase SerC. The phosphoserine aminotransferase of the archaeon Methanosarcina barkeri and putative phosphoserine aminotransferase of Mycobacterium tuberculosis are represented by separate models. All are members of the class V aminotransferases (pfam00266).
Probab=20.77 E-value=1.6e+02 Score=30.98 Aligned_cols=60 Identities=10% Similarity=0.208 Sum_probs=40.4
Q ss_pred CCCHhHHHHhhccccccceeeeccccccCceEEEEeccCChhHHHHHHHHHHHHhHhC--CceEEEEEec
Q 009686 152 RIPKETIDILKDQVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFG--DQYKLFLLVN 219 (528)
Q Consensus 152 ~i~~edl~~ik~~~Fg~dtF~~t~~~~~~~gvi~rGnLR~~~e~~y~~l~~~l~~~fG--d~y~lfl~~~ 219 (528)
..|.+.++++++ ||.+.- .-.-|..-.+.--.+-.+.|++++++|++.|+ ++|.++++..
T Consensus 2 ~~p~~v~~~~~~-------~~~~~~-~~~~~~~~~~hr~~~f~~~~~~~~~~l~~l~~~~~~~~v~~~~g 63 (349)
T TIGR01364 2 ALPEEVLEQAQK-------ELLNFN-GTGMSVMEISHRSKEFEAVANEAESDLRELLNIPDNYEVLFLQG 63 (349)
T ss_pred CCCHHHHHHHHH-------HHhCcc-CCCccccccCCCchHHHHHHHHHHHHHHHHhCCCCCceEEEEcC
Confidence 368899999998 444333 33345555555444556999999999999988 4566654443
No 80
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=20.59 E-value=1.4e+02 Score=28.89 Aligned_cols=31 Identities=26% Similarity=0.224 Sum_probs=21.6
Q ss_pred chHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHcC
Q 009686 277 NLNLLTNGLPGALVTALVIGVHELGHILAAKSTG 310 (528)
Q Consensus 277 ~~~~l~~glp~aL~Ll~iL~iHElGH~laArr~G 310 (528)
||.++.+ ....++.-++-||++|+.+=..+|
T Consensus 49 NP~ll~e---n~~~f~~~vV~HELaHl~ly~~~g 79 (156)
T COG3091 49 NPKLLEE---NGEDFIEQVVPHELAHLHLYQEFG 79 (156)
T ss_pred CHHHHHH---ccHHHHHHHHHHHHHHHHHHHHcC
Confidence 5654433 233455567899999999988877
No 81
>PLN02829 Probable galacturonosyltransferase
Probab=20.19 E-value=1.4e+02 Score=34.69 Aligned_cols=54 Identities=13% Similarity=0.247 Sum_probs=35.6
Q ss_pred CCCCccccccCCCCHhHHHHhhccccccceeeeccccccCceEEEEeccCChhHHHHHHHHHHHHhH
Q 009686 141 GVKPQQLDEYIRIPKETIDILKDQVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNK 207 (528)
Q Consensus 141 ~~~~~~~~~~~~i~~edl~~ik~~~Fg~dtF~~t~~~~~~~gvi~rGnLR~~~e~~y~~l~~~l~~~ 207 (528)
+.+.....+...++..-+++||+++|---+|. .+ .++++. ++-+..++.++++.
T Consensus 168 ~~~~~~~~~~~~~~d~~v~~lkDql~~AkaY~--~i----------ak~~~~-~~l~~el~~~i~e~ 221 (639)
T PLN02829 168 LTKTDKQTDQTVMPDARVRQLRDQLIKAKVYL--SL----------PATKAN-PHFTRELRLRIKEV 221 (639)
T ss_pred ccccccccccccCchHHHHHHHHHHHHHHHHH--HH----------hccCCc-HHHHHHHHHHHHHH
Confidence 44545556777888999999999998777763 11 223332 45556677777664
Done!