Query 009660
Match_columns 529
No_of_seqs 322 out of 1239
Neff 4.6
Searched_HMMs 46136
Date Thu Mar 28 15:48:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009660.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009660hhsearch_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 4E-31 8.6E-36 252.6 18.8 176 252-476 3-180 (183)
2 cd06164 S2P-M50_SpoIVFB_CBS Sp 99.9 3.8E-25 8.3E-30 217.5 20.4 134 277-448 37-170 (227)
3 cd06161 S2P-M50_SpoIVFB SpoIVF 99.9 1.6E-23 3.4E-28 203.1 18.6 129 280-448 25-153 (208)
4 cd06163 S2P-M50_PDZ_RseP-like 99.9 8.5E-21 1.8E-25 181.6 14.7 113 287-445 3-145 (182)
5 cd05709 S2P-M50 Site-2 proteas 99.8 6E-21 1.3E-25 179.2 12.9 140 287-450 2-157 (180)
6 cd06159 S2P-M50_PDZ_Arch Uncha 99.8 4.2E-19 9E-24 178.7 18.2 119 282-447 107-228 (263)
7 PF02163 Peptidase_M50: Peptid 99.8 6.8E-19 1.5E-23 166.2 11.3 127 288-444 2-157 (192)
8 cd06162 S2P-M50_PDZ_SREBP Ster 99.8 8.5E-18 1.8E-22 170.2 15.3 114 288-449 130-250 (277)
9 cd06158 S2P-M50_like_1 Unchara 99.8 5E-18 1.1E-22 162.0 11.7 135 288-451 4-159 (181)
10 TIGR00054 RIP metalloprotease 99.5 1.7E-13 3.7E-18 145.7 16.4 79 288-366 9-118 (420)
11 PRK10779 zinc metallopeptidase 99.5 2.4E-13 5.3E-18 145.6 15.2 82 285-366 7-118 (449)
12 COG1994 SpoIVFB Zn-dependent p 99.3 2.2E-11 4.8E-16 120.2 13.9 128 282-449 41-176 (230)
13 COG0750 Predicted membrane-ass 98.9 1.7E-09 3.8E-14 111.7 5.2 242 165-448 82-338 (375)
14 PF13398 Peptidase_M50B: Pepti 97.3 0.00066 1.4E-08 66.2 8.1 65 294-366 23-88 (200)
15 COG0750 Predicted membrane-ass 96.2 0.013 2.9E-07 60.9 7.9 81 287-367 7-120 (375)
16 KOG2921 Intramembrane metallop 95.4 0.012 2.6E-07 63.2 3.5 80 284-366 121-205 (484)
17 PF11667 DUF3267: Protein of u 69.2 1.8 4E-05 38.2 0.5 69 293-368 4-72 (111)
18 PF00413 Peptidase_M10: Matrix 61.0 5 0.00011 36.3 1.7 21 294-314 106-126 (154)
19 cd04279 ZnMc_MMP_like_1 Zinc-d 58.7 5.9 0.00013 36.6 1.8 22 293-314 104-125 (156)
20 PF13485 Peptidase_MA_2: Pepti 49.9 13 0.00029 31.5 2.4 18 295-312 27-44 (128)
21 cd04268 ZnMc_MMP_like Zinc-dep 48.8 11 0.00024 34.5 1.9 21 292-312 93-113 (165)
22 cd04278 ZnMc_MMP Zinc-dependen 48.6 7.9 0.00017 35.9 0.9 23 293-315 107-129 (157)
23 PF07423 DUF1510: Protein of u 48.6 14 0.00029 37.4 2.6 55 171-229 159-214 (217)
24 PF05572 Peptidase_M43: Pregna 48.2 8.9 0.00019 36.3 1.2 13 294-306 70-82 (154)
25 KOG1832 HIV-1 Vpr-binding prot 46.1 19 0.0004 43.3 3.4 17 5-21 1354-1370(1516)
26 PF01435 Peptidase_M48: Peptid 43.4 16 0.00036 34.8 2.2 12 294-305 90-101 (226)
27 PF06114 DUF955: Domain of unk 41.7 16 0.00035 30.7 1.7 16 296-311 45-60 (122)
28 PF14247 DUF4344: Domain of un 40.4 28 0.00061 35.1 3.4 25 289-314 88-112 (220)
29 PF01434 Peptidase_M41: Peptid 40.2 21 0.00046 35.2 2.4 18 295-312 30-47 (213)
30 cd04277 ZnMc_serralysin_like Z 39.5 16 0.00035 34.7 1.5 22 294-315 114-135 (186)
31 cd00203 ZnMc Zinc-dependent me 38.7 16 0.00034 33.4 1.2 21 292-312 95-115 (167)
32 smart00235 ZnMc Zinc-dependent 38.7 16 0.00035 32.9 1.3 19 296-314 89-107 (140)
33 PF13582 Reprolysin_3: Metallo 37.4 17 0.00037 31.8 1.2 13 295-307 109-121 (124)
34 PF12315 DUF3633: Protein of u 35.9 26 0.00056 35.4 2.3 28 283-313 85-112 (212)
35 PF14891 Peptidase_M91: Effect 35.1 25 0.00054 33.6 2.0 16 294-309 104-119 (174)
36 PF13574 Reprolysin_2: Metallo 34.9 20 0.00044 34.1 1.3 20 294-313 112-131 (173)
37 PF13688 Reprolysin_5: Metallo 34.6 19 0.00042 34.1 1.2 21 293-313 142-162 (196)
38 PF02031 Peptidase_M7: Strepto 32.7 27 0.00058 32.9 1.7 10 296-305 80-89 (132)
39 PTZ00429 beta-adaptin; Provisi 32.5 43 0.00093 39.5 3.7 33 71-103 607-639 (746)
40 cd04327 ZnMc_MMP_like_3 Zinc-d 31.1 31 0.00068 33.4 2.0 20 294-313 93-112 (198)
41 PRK03001 M48 family peptidase; 30.4 31 0.00068 35.4 2.0 12 294-305 125-136 (283)
42 PRK11037 hypothetical protein; 30.3 1.2E+02 0.0027 26.4 5.1 65 150-215 4-81 (83)
43 PF11085 YqhR: Conserved membr 30.1 5.2E+02 0.011 25.6 10.0 102 415-521 33-154 (173)
44 cd04270 ZnMc_TACE_like Zinc-de 30.0 32 0.0007 34.7 1.9 18 292-309 166-183 (244)
45 cd04269 ZnMc_adamalysin_II_lik 29.9 35 0.00076 32.5 2.1 20 293-312 131-150 (194)
46 PRK03982 heat shock protein Ht 29.9 33 0.00071 35.3 2.0 12 294-305 126-137 (288)
47 PHA02456 zinc metallopeptidase 29.6 32 0.0007 31.9 1.6 19 297-315 83-101 (141)
48 PF09471 Peptidase_M64: IgA Pe 29.3 24 0.00051 36.5 0.8 14 294-307 217-230 (264)
49 COG2856 Predicted Zn peptidase 29.0 30 0.00065 34.8 1.5 16 296-311 75-90 (213)
50 PRK12462 phosphoserine aminotr 28.8 91 0.002 33.7 5.2 67 147-221 8-76 (364)
51 cd04267 ZnMc_ADAM_like Zinc-de 28.2 26 0.00057 33.2 0.9 20 293-312 133-152 (192)
52 PF10263 SprT-like: SprT-like 28.1 42 0.00091 30.8 2.2 19 292-310 59-77 (157)
53 smart00731 SprT SprT homologue 27.2 38 0.00082 31.4 1.7 16 294-309 60-75 (146)
54 PF13583 Reprolysin_4: Metallo 26.7 33 0.00072 33.7 1.3 18 296-313 140-157 (206)
55 COG0501 HtpX Zn-dependent prot 26.3 42 0.0009 33.7 2.0 11 295-305 159-169 (302)
56 PLN02452 phosphoserine transam 26.1 1.2E+02 0.0025 32.6 5.3 68 146-221 10-79 (365)
57 PRK04897 heat shock protein Ht 26.0 42 0.00091 34.9 2.0 12 294-305 138-149 (298)
58 COG5309 Exo-beta-1,3-glucanase 26.0 1E+02 0.0022 32.6 4.7 61 156-220 218-281 (305)
59 KOG3320 40S ribosomal protein 25.8 94 0.002 30.9 4.1 27 195-221 74-100 (192)
60 PF12388 Peptidase_M57: Dual-a 25.7 35 0.00076 34.4 1.3 27 288-314 128-154 (211)
61 KOG0391 SNF2 family DNA-depend 25.0 81 0.0018 39.5 4.2 21 173-193 599-619 (1958)
62 PF01447 Peptidase_M4: Thermol 24.7 47 0.001 31.5 1.9 11 296-306 138-148 (150)
63 COG0830 UreF Urease accessory 24.5 82 0.0018 32.2 3.6 31 415-445 158-188 (229)
64 PF13699 DUF4157: Domain of un 24.5 44 0.00095 28.4 1.5 12 295-306 63-74 (79)
65 PRK01345 heat shock protein Ht 24.3 47 0.001 35.0 2.0 12 294-305 125-136 (317)
66 PRK03072 heat shock protein Ht 23.7 49 0.0011 34.3 2.0 11 294-304 128-138 (288)
67 COG3824 Predicted Zn-dependent 23.5 36 0.00078 31.9 0.8 14 292-305 108-121 (136)
68 PRK02391 heat shock protein Ht 23.4 50 0.0011 34.5 2.0 10 295-304 135-144 (296)
69 PRK05457 heat shock protein Ht 23.0 52 0.0011 34.1 2.0 11 294-304 135-145 (284)
70 TIGR01651 CobT cobaltochelatas 22.5 1.6E+02 0.0035 34.1 5.8 9 200-208 338-346 (600)
71 cd04927 ACT_ACR-like_2 Second 22.3 1.1E+02 0.0023 25.3 3.4 35 167-212 40-74 (76)
72 PF10692 DUF2498: Protein of u 22.0 1.5E+02 0.0032 25.9 4.1 64 151-215 4-80 (82)
73 KOG2719 Metalloprotease [Gener 21.7 51 0.0011 36.5 1.7 15 293-307 280-294 (428)
74 PF01421 Reprolysin: Reprolysi 21.4 65 0.0014 30.8 2.2 21 292-312 130-150 (199)
75 PRK01265 heat shock protein Ht 21.3 59 0.0013 34.7 2.0 10 295-304 142-151 (324)
76 PRK02870 heat shock protein Ht 21.2 59 0.0013 34.8 2.0 11 294-304 174-184 (336)
77 TIGR01241 FtsH_fam ATP-depende 21.0 45 0.00096 36.9 1.1 18 295-312 313-330 (495)
78 PF04298 Zn_peptidase_2: Putat 20.8 58 0.0013 33.1 1.7 12 295-306 91-102 (222)
79 COG5495 Uncharacterized conser 20.5 61 0.0013 33.7 1.8 38 154-213 128-165 (289)
80 PRK04860 hypothetical protein; 20.3 94 0.002 29.9 3.0 21 291-311 61-81 (160)
81 TIGR01364 serC_1 phosphoserine 20.1 1.7E+02 0.0036 30.9 5.1 60 153-220 2-63 (349)
82 PF08525 OapA_N: Opacity-assoc 20.0 1.2E+02 0.0027 21.4 2.8 21 497-517 9-29 (30)
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=4e-31 Score=252.63 Aligned_cols=176 Identities=40% Similarity=0.723 Sum_probs=147.0
Q ss_pred HHHHHHHHHHhhcccccccchhccccchHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHcCCccCCccccccceeeccceE
Q 009660 252 FGLVTVFTLLLRNVPALQSNLLSTFDNLNLLTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAI 331 (529)
Q Consensus 252 ~~l~Tl~Tt~~ag~~~L~~~~~~~~~~~~~l~~glp~aL~Ll~iL~vHElGH~laAr~~Gvk~s~P~FIP~i~LgtFGAv 331 (529)
++++|+.+....+.- .+.+ +..++++.+..+++++++++.++++||+||+++||++|+|++.++++|...+|++|++
T Consensus 3 ~~~~s~~~~~~~~~~-~~~~--~~~~~~~~~~~~~~~~l~l~~~l~iHElgH~~~A~~~G~~~~~~~l~P~~~~G~~G~~ 79 (183)
T cd06160 3 LLVLTLLTTLLVGAW-LSGN--DVPGNPLLLLQGLPFALALLAILGIHEMGHYLAARRHGVKASLPYFIPFPFIGTFGAF 79 (183)
T ss_pred HHHHHHHHHHHHHHH-Hhcc--cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCccceeeeehHhcCcEEEE
Confidence 456677766655421 1111 2336778888999999999999999999999999999999999999998779999999
Q ss_pred EeeccccCCccceeeeeecchhhHHHHHHHHHHhhhccCCCCCccccccccchhhhhhhhhHHHHhhccccCCCCCccch
Q 009660 332 TRIRNIVSKREDLLKVAAAGPLAGFSLGFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVN 411 (529)
Q Consensus 332 ir~~s~~~~RkalfdIAlAGPLAg~llAl~ll~iGl~l~~s~~~~~~v~~~~f~~s~Llg~la~l~LG~~l~~~~~v~lh 411 (529)
+++++..++|+++++|++|||++|+++++++++++
T Consensus 80 ~~~~~~~~~~~~~~~IalAGPl~nl~lali~~~~~--------------------------------------------- 114 (183)
T cd06160 80 IRMRSPIPNRKALFDIALAGPLAGLLLALPVLIIG--------------------------------------------- 114 (183)
T ss_pred EEecCCCCChhHhehhhhhHHHHHHHHHHHHHHHH---------------------------------------------
Confidence 99998888999999999999999999988775543
Q ss_pred HHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHhhhhHHHHHHHHHHHHHHHHHHhhh--hhHHHHHH
Q 009660 412 PLVIWAWAGLLINAINSIPAGELDGGRIAFALWGRKASTRLTGVSIVLLGLSSLFSD--VTFYWVVL 476 (529)
Q Consensus 412 PL~~agwinLvltafNLLPigPLDGGrIl~Allgrr~a~~i~~~~~ilLGl~~l~~~--~~l~W~il 476 (529)
+..++|+|+++++|||+|++|||||||+++++++|.+.++++++.+++|+.++.++ .+++|+.+
T Consensus 115 -~~~~~~~nl~l~~fNLLPi~PLDGGril~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~ 180 (183)
T cd06160 115 -LAVAGWVGLLVTALNLLPVGQLDGGHIVRALFGRRVAALIGIGLLVALGLLALYLSFSIWLLWALL 180 (183)
T ss_pred -HHHHHHHHHHHHHHHhCCCCCcChHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHH
Confidence 12468999999999999999999999999999999999999999888888888765 45555543
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=3.8e-25 Score=217.52 Aligned_cols=134 Identities=31% Similarity=0.406 Sum_probs=111.3
Q ss_pred cchHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHcCCccCCccccccceeeccceEEeeccccCCccceeeeeecchhhHH
Q 009660 277 DNLNLLTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAITRIRNIVSKREDLLKVAAAGPLAGF 356 (529)
Q Consensus 277 ~~~~~l~~glp~aL~Ll~iL~vHElGH~laAr~~Gvk~s~P~FIP~i~LgtFGAvir~~s~~~~RkalfdIAlAGPLAg~ 356 (529)
.+...+..|+.++++++.++++||+||+++||++|+++. .+.+.+||+++++++...++++++.|++|||++|+
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 67788899999999888889999999999999999
Q ss_pred HHHHHHHHhhhccCCCCCccccccccchhhhhhhhhHHHHhhccccCCCCCccchHHHHHHHHHHHHHHHhhcCCCCCCh
Q 009660 357 SLGFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAINSIPAGELDG 436 (529)
Q Consensus 357 llAl~ll~iGl~l~~s~~~~~~v~~~~f~~s~Llg~la~l~LG~~l~~~~~v~lhPL~~agwinLvltafNLLPigPLDG 436 (529)
+++++++++....+... .+.+ ...+.+.+|+|+++++|||+|++||||
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 99998877665432110 0000 122456789999999999999999999
Q ss_pred HHHHHHHhhhhH
Q 009660 437 GRIAFALWGRKA 448 (529)
Q Consensus 437 GrIl~Allgrr~ 448 (529)
|||+++++.++.
T Consensus 159 gril~~ll~~~~ 170 (227)
T cd06164 159 GRVLRALLWRRT 170 (227)
T ss_pred HHHHHHHHHHhc
Confidence 999999987654
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=1.6e-23 Score=203.08 Aligned_cols=129 Identities=29% Similarity=0.430 Sum_probs=107.9
Q ss_pred HHHHhhHHHHHHHHHHHHHHHHHHHHHHHHcCCccCCccccccceeeccceEEeeccccCCccceeeeeecchhhHHHHH
Q 009660 280 NLLTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAITRIRNIVSKREDLLKVAAAGPLAGFSLG 359 (529)
Q Consensus 280 ~~l~~glp~aL~Ll~iL~vHElGH~laAr~~Gvk~s~P~FIP~i~LgtFGAvir~~s~~~~RkalfdIAlAGPLAg~llA 359 (529)
..+..++.+++.++.++++||+||+++||++|+++. .+.+.+||+++++++...+|++++.|++|||++|++++
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 457788999999999999999999999999999997 77888899999998777789999999999999999999
Q ss_pred HHHHHhhhccCCCCCccccccccchhhhhhhhhHHHHhhccccCCCCCccchHHHHHHHHHHHHHHHhhcCCCCCChHHH
Q 009660 360 FVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAINSIPAGELDGGRI 439 (529)
Q Consensus 360 l~ll~iGl~l~~s~~~~~~v~~~~f~~s~Llg~la~l~LG~~l~~~~~v~lhPL~~agwinLvltafNLLPigPLDGGrI 439 (529)
+++.++....+.. +. ....+.+.+++|+++++|||+|+.|||||||
T Consensus 99 ~~~~~l~~~~~~~--------------~~--------------------~~~~~~~~~~~N~~l~lfNLlPi~pLDGg~i 144 (208)
T cd06161 99 GLFYLLYLLLPGG--------------GP--------------------LSSLLEFLAQVNLILGLFNLLPALPLDGGRV 144 (208)
T ss_pred HHHHHHHHHcccc--------------hH--------------------HHHHHHHHHHHHHHHHHHHccCCCCCChHHH
Confidence 9887655432110 00 0123456789999999999999999999999
Q ss_pred HHHHhhhhH
Q 009660 440 AFALWGRKA 448 (529)
Q Consensus 440 l~Allgrr~ 448 (529)
+++++.++.
T Consensus 145 l~~ll~~~~ 153 (208)
T cd06161 145 LRALLWRRT 153 (208)
T ss_pred HHHHHHHhc
Confidence 999987764
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=8.5e-21 Score=181.56 Aligned_cols=113 Identities=34% Similarity=0.438 Sum_probs=88.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCccCC-c-ccccc------------ceeeccceEEeeccccC-------------
Q 009660 287 PGALVTALVIGVHELGHILAAKSTGVELGV-P-YFVPS------------WQIGSFGAITRIRNIVS------------- 339 (529)
Q Consensus 287 p~aL~Ll~iL~vHElGH~laAr~~Gvk~s~-P-~FIP~------------i~LgtFGAvir~~s~~~------------- 339 (529)
.+.+++..++++||+||+++||++|+|+.. . -|=|. +.+.++|+++++++..+
T Consensus 3 ~~~i~l~~~v~iHElGH~~~Ar~~Gv~v~~f~iGfGp~l~~~~~~~t~~~i~~iPlGGyv~~~~~~~~~~~~~~~~~~~f 82 (182)
T cd06163 3 AFILVLGILIFVHELGHFLVAKLFGVKVEEFSIGFGPKLFSFKKGETEYSISAIPLGGYVKMLGEDPEEEADPEDDPRSF 82 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCeeeEeeeecCceeeeeecCCeEEEEEEEEeccEEEecCCCcccccccccchHHH
Confidence 355667778999999999999999999863 0 01121 23567999999864321
Q ss_pred ---CccceeeeeecchhhHHHHHHHHHHhhhccCCCCCccccccccchhhhhhhhhHHHHhhccccCCCCCccchHHHHH
Q 009660 340 ---KREDLLKVAAAGPLAGFSLGFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIW 416 (529)
Q Consensus 340 ---~RkalfdIAlAGPLAg~llAl~ll~iGl~l~~s~~~~~~v~~~~f~~s~Llg~la~l~LG~~l~~~~~v~lhPL~~a 416 (529)
++++++.|++|||++|+++|++++++. +.+.
T Consensus 83 ~~~~~~~ri~V~lAGP~~NlilA~i~~~~~----------------------------------------------~~~~ 116 (182)
T cd06163 83 NSKPVWQRILIVFAGPLANFLLAIVLFAVL----------------------------------------------LSFL 116 (182)
T ss_pred ccCCcchhhhhhhhHHHHHHHHHHHHHHHH----------------------------------------------HHHH
Confidence 467899999999999999998764321 1245
Q ss_pred HHHHHHHHHHhhcCCCCCChHHHHHHHhh
Q 009660 417 AWAGLLINAINSIPAGELDGGRIAFALWG 445 (529)
Q Consensus 417 gwinLvltafNLLPigPLDGGrIl~Allg 445 (529)
.++|+.+++|||+|++||||||++++++.
T Consensus 117 ~~~n~~l~~fNLlPippLDGg~il~~~~~ 145 (182)
T cd06163 117 ALLSINLGILNLLPIPALDGGHLLFLLIE 145 (182)
T ss_pred HHHHHHHHHHHcCCCCCCCHHHHHHHHHH
Confidence 78999999999999999999999999985
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=6e-21 Score=179.22 Aligned_cols=140 Identities=28% Similarity=0.307 Sum_probs=100.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCccCC----ccccc-------cceeeccceEEeeccccC-----Cccceeeeeec
Q 009660 287 PGALVTALVIGVHELGHILAAKSTGVELGV----PYFVP-------SWQIGSFGAITRIRNIVS-----KREDLLKVAAA 350 (529)
Q Consensus 287 p~aL~Ll~iL~vHElGH~laAr~~Gvk~s~----P~FIP-------~i~LgtFGAvir~~s~~~-----~RkalfdIAlA 350 (529)
.+.++++.++.+||+||+++||++|+++.. ..+.| .+.+.++|+++++.+... +|++++.|++|
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 356678889999999999999999998741 11112 122345699998877654 48899999999
Q ss_pred chhhHHHHHHHHHHhhhccCCCCCccccccccchhhhhhhhhHHHHhhccccCCCCCccchHHHHHHHHHHHHHHHhhcC
Q 009660 351 GPLAGFSLGFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAINSIP 430 (529)
Q Consensus 351 GPLAg~llAl~ll~iGl~l~~s~~~~~~v~~~~f~~s~Llg~la~l~LG~~l~~~~~v~lhPL~~agwinLvltafNLLP 430 (529)
||++|++++++++.+....+..... ....-.. ....+.+.+++|+|+.+++|||+|
T Consensus 82 GPl~nllla~i~~~~~~~~~~~~~~----~~~~~~~--------------------~~~~~~l~~~~~~n~~l~~fNLlP 137 (180)
T cd05709 82 GPLANLLLALLLLLLLLLLGGLPPA----PVGQAAS--------------------SGLANLLAFLALINLNLAVFNLLP 137 (180)
T ss_pred hHHHHHHHHHHHHHHHHHHccCCcc----chhhhHH--------------------HHHHHHHHHHHHHHHHHHHHHhCC
Confidence 9999999999987765543221000 0000000 011245678899999999999999
Q ss_pred CCCCChHHHHHHHhhhhHHH
Q 009660 431 AGELDGGRIAFALWGRKAST 450 (529)
Q Consensus 431 igPLDGGrIl~Allgrr~a~ 450 (529)
++||||||++++++.++..+
T Consensus 138 i~plDGg~il~~~l~~~~~~ 157 (180)
T cd05709 138 IPPLDGGRILRALLEAIRGR 157 (180)
T ss_pred CCCCChHHHHHHHHhHHHHH
Confidence 99999999999999887643
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=4.2e-19 Score=178.69 Aligned_cols=119 Identities=26% Similarity=0.325 Sum_probs=93.6
Q ss_pred HHhhHHHHHHHHHHHHHHHHHHHHHHHHcCCccCCccccccceeeccceEEeecccc---CCccceeeeeecchhhHHHH
Q 009660 282 LTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAITRIRNIV---SKREDLLKVAAAGPLAGFSL 358 (529)
Q Consensus 282 l~~glp~aL~Ll~iL~vHElGH~laAr~~Gvk~s~P~FIP~i~LgtFGAvir~~s~~---~~RkalfdIAlAGPLAg~ll 358 (529)
....+.+.++++.++.+||+||+++||++|+++..-.+ .+.+.++||++++++.. .++++++.|++|||++|+++
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 33556667788889999999999999999999983211 01123588999886544 46789999999999999999
Q ss_pred HHHHHHhhhccCCCCCccccccccchhhhhhhhhHHHHhhccccCCCCCccchHHHHHHHHHHHHHHHhhcCCCCCChHH
Q 009660 359 GFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAINSIPAGELDGGR 438 (529)
Q Consensus 359 Al~ll~iGl~l~~s~~~~~~v~~~~f~~s~Llg~la~l~LG~~l~~~~~v~lhPL~~agwinLvltafNLLPigPLDGGr 438 (529)
|++++++.. +.+..|+|+.+++|||+|+.||||||
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 987654321 22457899999999999999999999
Q ss_pred HHHHHhhhh
Q 009660 439 IAFALWGRK 447 (529)
Q Consensus 439 Il~Allgrr 447 (529)
++++++..+
T Consensus 220 il~~ll~~~ 228 (263)
T cd06159 220 VFRDLLEAL 228 (263)
T ss_pred HHHHHHHHH
Confidence 999997554
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=166.18 Aligned_cols=127 Identities=28% Similarity=0.345 Sum_probs=80.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCccCCccc----ccc----------ceeeccceE---------------Eeecccc
Q 009660 288 GALVTALVIGVHELGHILAAKSTGVELGVPYF----VPS----------WQIGSFGAI---------------TRIRNIV 338 (529)
Q Consensus 288 ~aL~Ll~iL~vHElGH~laAr~~Gvk~s~P~F----IP~----------i~LgtFGAv---------------ir~~s~~ 338 (529)
+.++++.++.+||+||+++|+++|+|+..... .+. +.+.++|++ ...+...
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 35677889999999999999999999975421 110 001122322 2222234
Q ss_pred CCccceeeeeecchhhHHHHHHHHHHhhhccCCCCCccccccccchhhhhhhhhHHHHhhccccCCCCCccchHHHHHHH
Q 009660 339 SKREDLLKVAAAGPLAGFSLGFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAW 418 (529)
Q Consensus 339 ~~RkalfdIAlAGPLAg~llAl~ll~iGl~l~~s~~~~~~v~~~~f~~s~Llg~la~l~LG~~l~~~~~v~lhPL~~agw 418 (529)
.+|++.+.|++|||++|++++++++.+......... ......+.+.+++|
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 567889999999999999999988776554221100 01112356778999
Q ss_pred HHHHHHHHhhcCCCCCChHHHHHHHh
Q 009660 419 AGLLINAINSIPAGELDGGRIAFALW 444 (529)
Q Consensus 419 inLvltafNLLPigPLDGGrIl~All 444 (529)
+|+.++++||+|++||||||++++++
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=8.5e-18 Score=170.22 Aligned_cols=114 Identities=25% Similarity=0.235 Sum_probs=89.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCccCCccccccceeecc----ceEEeeccc---cCCccceeeeeecchhhHHHHHH
Q 009660 288 GALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSF----GAITRIRNI---VSKREDLLKVAAAGPLAGFSLGF 360 (529)
Q Consensus 288 ~aL~Ll~iL~vHElGH~laAr~~Gvk~s~P~FIP~i~LgtF----GAvir~~s~---~~~RkalfdIAlAGPLAg~llAl 360 (529)
+.++++.++.+||+||+++|+++|+++. .+.+..| ||+++..+. ..++++++.|+.|||++|+++|+
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 3456788999999999999999999998 4333333 899998443 23567789999999999999998
Q ss_pred HHHHhhhccCCCCCccccccccchhhhhhhhhHHHHhhccccCCCCCccchHHHHHHHHHHHHHHHhhcCCCCCChHHHH
Q 009660 361 VLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAINSIPAGELDGGRIA 440 (529)
Q Consensus 361 ~ll~iGl~l~~s~~~~~~v~~~~f~~s~Llg~la~l~LG~~l~~~~~v~lhPL~~agwinLvltafNLLPigPLDGGrIl 440 (529)
+++++.+ . ..+.+..++|+.+++|||+|+.|||||||+
T Consensus 204 i~~~l~~-----------------~-------------------------~~l~~la~iNl~lavfNLlP~~pLDGg~il 241 (277)
T cd06162 204 VGYLLLI-----------------E-------------------------TFLKYLISLSGALAVINAVPCFALDGQWIL 241 (277)
T ss_pred HHHHHHH-----------------H-------------------------HHHHHHHHHHHHHHHhhcCCCCCCChHHHH
Confidence 7754321 0 012356789999999999999999999999
Q ss_pred HHHhhhhHH
Q 009660 441 FALWGRKAS 449 (529)
Q Consensus 441 ~Allgrr~a 449 (529)
++++.++..
T Consensus 242 ~~ll~~~~~ 250 (277)
T cd06162 242 STFLEATLV 250 (277)
T ss_pred HHHHHHHhC
Confidence 999766543
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=99.75 E-value=5e-18 Score=162.03 Aligned_cols=135 Identities=25% Similarity=0.308 Sum_probs=91.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCccCC----cccccc--------ce--ee--ccceEEeec-----cccCCccceee
Q 009660 288 GALVTALVIGVHELGHILAAKSTGVELGV----PYFVPS--------WQ--IG--SFGAITRIR-----NIVSKREDLLK 346 (529)
Q Consensus 288 ~aL~Ll~iL~vHElGH~laAr~~Gvk~s~----P~FIP~--------i~--Lg--tFGAvir~~-----s~~~~Rkalfd 346 (529)
..++++.++.+||+||+++|+++|+++.. -.+.|. +. +. ..+++++.. ...++|++++.
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 44567779999999999999999999862 223331 00 11 023454432 22346688999
Q ss_pred eeecchhhHHHHHHHHHHhhhccCCCCCccccccccchhhhhhhhhHHHHhhccccCCCCCccchHHHHHHHHHHHHHHH
Q 009660 347 VAAAGPLAGFSLGFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAI 426 (529)
Q Consensus 347 IAlAGPLAg~llAl~ll~iGl~l~~s~~~~~~v~~~~f~~s~Llg~la~l~LG~~l~~~~~v~lhPL~~agwinLvltaf 426 (529)
|++|||++|+++++++.++........+ ...+.+ ...+.+..++|+.+++|
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 9999999999999887655443211100 001111 12234567899999999
Q ss_pred hhcCCCCCChHHHHHHHhhhhHHHH
Q 009660 427 NSIPAGELDGGRIAFALWGRKASTR 451 (529)
Q Consensus 427 NLLPigPLDGGrIl~Allgrr~a~~ 451 (529)
||+|++|||||||+++++.++....
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=99.53 E-value=1.7e-13 Score=145.74 Aligned_cols=79 Identities=28% Similarity=0.463 Sum_probs=59.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCccCC-cc-cccc------------ceeeccceEEeeccc----------------
Q 009660 288 GALVTALVIGVHELGHILAAKSTGVELGV-PY-FVPS------------WQIGSFGAITRIRNI---------------- 337 (529)
Q Consensus 288 ~aL~Ll~iL~vHElGH~laAr~~Gvk~s~-P~-FIP~------------i~LgtFGAvir~~s~---------------- 337 (529)
+.+.+.+++++||+||+++||++|+++.. .. |=|. +-+.++|+++++...
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 35566678899999999999999999862 11 1121 336789999998411
Q ss_pred -cCCccceeeeeecchhhHHHHHHHHHHhh
Q 009660 338 -VSKREDLLKVAAAGPLAGFSLGFVLFLVG 366 (529)
Q Consensus 338 -~~~RkalfdIAlAGPLAg~llAl~ll~iG 366 (529)
..+.++++.|.+|||++|+++|++++++.
T Consensus 89 ~~~~~~~r~~i~~aGp~~N~~~a~~~~~~~ 118 (420)
T TIGR00054 89 NNKSVFQKAIIIFAGPLANFIFAIFVYIFI 118 (420)
T ss_pred ccCCHHHHHHhhhcccHHHHHHHHHHHHHH
Confidence 03557889999999999999999887644
No 11
>PRK10779 zinc metallopeptidase RseP; Provisional
Probab=99.50 E-value=2.4e-13 Score=145.56 Aligned_cols=82 Identities=21% Similarity=0.293 Sum_probs=60.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHcCCccCCc--ccccc-------------ceeeccceEEeeccc------------
Q 009660 285 GLPGALVTALVIGVHELGHILAAKSTGVELGVP--YFVPS-------------WQIGSFGAITRIRNI------------ 337 (529)
Q Consensus 285 glp~aL~Ll~iL~vHElGH~laAr~~Gvk~s~P--~FIP~-------------i~LgtFGAvir~~s~------------ 337 (529)
.+.+.+++..++++||+||+++||++|+|+..= -|=|. +-+-++|++.+|...
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 344666677788999999999999999999731 11121 235678999987532
Q ss_pred ---cCCccceeeeeecchhhHHHHHHHHHHhh
Q 009660 338 ---VSKREDLLKVAAAGPLAGFSLGFVLFLVG 366 (529)
Q Consensus 338 ---~~~RkalfdIAlAGPLAg~llAl~ll~iG 366 (529)
.++.++++.|.+|||++|+++|++++.+-
T Consensus 87 ~f~~k~~~~R~~i~~AGp~~N~ila~~~~~~~ 118 (449)
T PRK10779 87 AFNNKTVGQRAAIIAAGPIANFIFAIFAYWLV 118 (449)
T ss_pred hhccCCHHHhhhhhhhhHHHHHHHHHHHHHHH
Confidence 13357889999999999999999886543
No 12
>COG1994 SpoIVFB Zn-dependent proteases [General function prediction only]
Probab=99.32 E-value=2.2e-11 Score=120.17 Aligned_cols=128 Identities=26% Similarity=0.317 Sum_probs=84.3
Q ss_pred HHhhHHHHHHHHHHHHHHHHHHHHHHHHcCCccCCccccccceeeccceEEeeccccCCccceee-------eeec-chh
Q 009660 282 LTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAITRIRNIVSKREDLLK-------VAAA-GPL 353 (529)
Q Consensus 282 l~~glp~aL~Ll~iL~vHElGH~laAr~~Gvk~s~P~FIP~i~LgtFGAvir~~s~~~~Rkalfd-------IAlA-GPL 353 (529)
+.++....++++..+..||+||...++++|.+.. .+.++.+|++..++..+.+.+..+. ++.| ||+
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 4455555555777899999999999999999886 4444346777777665555544444 4555 666
Q ss_pred hHHHHHHHHHHhhhccCCCCCccccccccchhhhhhhhhHHHHhhccccCCCCCccchHHHHHHHHHHHHHHHhhcCCCC
Q 009660 354 AGFSLGFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAINSIPAGE 433 (529)
Q Consensus 354 Ag~llAl~ll~iGl~l~~s~~~~~~v~~~~f~~s~Llg~la~l~LG~~l~~~~~v~lhPL~~agwinLvltafNLLPigP 433 (529)
.|+.+++++ .... +.. ...+. ...-+...+.+|+++++|||+|++|
T Consensus 115 ~ni~la~~~-~~~~--~~~-----------~~~~~--------------------~~~~~~~la~~Nl~L~lFNLiPi~P 160 (230)
T COG1994 115 TNIALAVLG-LLAL--SLF-----------LYHSV--------------------LFAFLAALALVNLVLALFNLLPIPP 160 (230)
T ss_pred HHHHHHHHH-HHhh--ccc-----------ccchh--------------------HHHHHHHHHHHHHHHHHHhCCCCCC
Confidence 666555443 1100 000 00000 0112235567899999999999999
Q ss_pred CChHHHHHHHhhhhHH
Q 009660 434 LDGGRIAFALWGRKAS 449 (529)
Q Consensus 434 LDGGrIl~Allgrr~a 449 (529)
|||||++++++.++..
T Consensus 161 LDGg~vlr~~~~~~~~ 176 (230)
T COG1994 161 LDGGRVLRALLPRRYG 176 (230)
T ss_pred CChHHHHHHHccHHHH
Confidence 9999999999888765
No 13
>COG0750 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]
Probab=98.87 E-value=1.7e-09 Score=111.73 Aligned_cols=242 Identities=14% Similarity=0.057 Sum_probs=138.1
Q ss_pred cccccceeeeccccccCceEEEEeccCCchHHHHHHHHHHHHhHhCCceEEEEEecCCCCCCEEEEEcCCCCCCCCCChh
Q 009660 165 QVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFGDQYKLFLLVNPEDDKPVAVVVPRKTLQPETTAVP 244 (529)
Q Consensus 165 ~~Fg~dtF~~t~~~~~~~gvi~rGnLR~~~e~~y~~l~~~l~~~fGd~y~lfl~~~~~~~kPv~~v~P~~~~~p~~~~~~ 244 (529)
.+++.++|+.....+ ...+++.|.+.......+..+...+ ..|..+ ...|+.. + ....
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 9999999999987766665544433 223111 1122211 0 0000
Q ss_pred HHHHHHHHHHHHHHHHHhhcccccccchhccccchHHHHh------hHHHHHHHHHHHHHH--HHHHHHHHHHcCCccCC
Q 009660 245 EWFAAGAFGLVTVFTLLLRNVPALQSNLLSTFDNLNLLTN------GLPGALVTALVIGVH--ELGHILAAKSTGVELGV 316 (529)
Q Consensus 245 ~~~~~~l~~l~Tl~Tt~~ag~~~L~~~~~~~~~~~~~l~~------glp~aL~Ll~iL~vH--ElGH~laAr~~Gvk~s~ 316 (529)
..+..+.+..|...+..|- +...+++.... +.++. .+.+.+.| +..|..+++.++.....
T Consensus 140 ---------s~a~~a~l~~Gd~iv~~~~-~~i~~~~~~~~~~~~~~~~~~~--~~~i~~~~~~~~~~~~~~~~~~~~~~~ 207 (375)
T COG0750 140 ---------SAAALAGLRPGDRIVAVDG-EKVASWDDVRRLLVAAAGDVFN--LLTILVIRLDGEAHAVAAEIIKSLGLT 207 (375)
T ss_pred ---------CHHHHcCCCCCCEEEeECC-EEccCHHHHHHHHHhccCCccc--ceEEEEEeccceeeeccccceeeEeee
Confidence 0112223344433333221 11222322222 22222 34567788 99999999988888888
Q ss_pred ccccccceeeccceEEe--eccccCC-----ccceeeeeecchhhHHHHHHHHHHhhhccCCCCCccccccccchhhhhh
Q 009660 317 PYFVPSWQIGSFGAITR--IRNIVSK-----REDLLKVAAAGPLAGFSLGFVLFLVGFIFPPSDGIGIVVDASVFHESFL 389 (529)
Q Consensus 317 P~FIP~i~LgtFGAvir--~~s~~~~-----RkalfdIAlAGPLAg~llAl~ll~iGl~l~~s~~~~~~v~~~~f~~s~L 389 (529)
|+++| ...+..++.++ ..+..++ ++...++..+++++. .+.-...++++.+... .......++.+.+
T Consensus 208 P~~~~-~~~~~~~~~i~~~~i~~~p~~~~~~~~~~~~~~~~~~i~~-~v~~~~~~~~~~~~~l----~~~~~~~~~~~~l 281 (375)
T COG0750 208 PVVIP-LKPGDKIVAVDVGAIGLSPNGEPDVGKVLVKYGPLEAVGL-AVEKTGRLVKLTLKML----KKLITGDLSLKNL 281 (375)
T ss_pred cceec-cCCCCEEEEeeeeeeeeccCCCCccceeeeccCHHHHHHH-HHHHHHHHHHHHHHHH----HHheecccccccc
Confidence 98876 44555555443 3344444 788999999999993 3333333333322100 0000111112222
Q ss_pred hhhHHHHhhccccCCCCCccchHHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHhhhhH
Q 009660 390 AGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAINSIPAGELDGGRIAFALWGRKA 448 (529)
Q Consensus 390 lg~la~l~LG~~l~~~~~v~lhPL~~agwinLvltafNLLPigPLDGGrIl~Allgrr~ 448 (529)
.+.+.....+.... .....+++.+++|+|+.++++||+|+++|||||++++++.+..
T Consensus 282 ~Gpi~i~~~~~~~~--~~~~~~~l~~~~~lsi~lg~lNllP~p~LDGG~i~~~~~e~~~ 338 (375)
T COG0750 282 SGPIGIAKIAGAAA--SLGLINLLFFLALLSINLGILNLLPIPPLDGGHLLFYLLEALR 338 (375)
T ss_pred cCceehhhhhhHHH--hhHHHHHHHHHHHHHHHHHHHhccCCCccCccHHHHHHHHHHh
Confidence 22111111111000 1234689999999999999999999999999999999986654
No 14
>PF13398 Peptidase_M50B: Peptidase M50B-like
Probab=97.35 E-value=0.00066 Score=66.21 Aligned_cols=65 Identities=31% Similarity=0.274 Sum_probs=51.9
Q ss_pred HHHHHHHHHHHHHHHHcCCccCCccccccceeec-cceEEeeccccCCccceeeeeecchhhHHHHHHHHHHhh
Q 009660 294 LVIGVHELGHILAAKSTGVELGVPYFVPSWQIGS-FGAITRIRNIVSKREDLLKVAAAGPLAGFSLGFVLFLVG 366 (529)
Q Consensus 294 ~iL~vHElGH~laAr~~Gvk~s~P~FIP~i~Lgt-FGAvir~~s~~~~RkalfdIAlAGPLAg~llAl~ll~iG 366 (529)
....+||+||+++|...|-|+. .+.+.+ -++.+..+. +++...+.++.|||++..+++..++..+
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 554433 466777666 5666789999999999999887776555
No 15
>COG0750 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]
Probab=96.24 E-value=0.013 Score=60.87 Aligned_cols=81 Identities=28% Similarity=0.402 Sum_probs=53.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCccCCcc--ccc-------c------ceeeccceEEeeccccC------------
Q 009660 287 PGALVTALVIGVHELGHILAAKSTGVELGVPY--FVP-------S------WQIGSFGAITRIRNIVS------------ 339 (529)
Q Consensus 287 p~aL~Ll~iL~vHElGH~laAr~~Gvk~s~P~--FIP-------~------i~LgtFGAvir~~s~~~------------ 339 (529)
.+.+.+...+.+||+||+|.||++|+++.... |-| . +...+.|++.++.....
T Consensus 7 ~~i~~~~~lv~~he~gh~~~a~~~~~~v~~f~ig~g~~l~~~~~~~~~~~~i~~~plggyv~~~~~~~~~~~~~~~~~~~ 86 (375)
T COG0750 7 AFIIALGVLVFVHELGHFWVARRCGVKVERFSIGFGPKLFSRKDKGGTEYVLSAIPLGGYVKMLGEDAEEVVLKGPEPRP 86 (375)
T ss_pred HHHHHHHHHHHHHHHhhHHHHHhcCceeEEEEeccCcceEEEEcCCceEEEEeecCccceEEEecCccccccccccCcch
Confidence 34555666889999999999999999997421 112 0 12345666665532211
Q ss_pred ------CccceeeeeecchhhHHHHHHHHHHhhh
Q 009660 340 ------KREDLLKVAAAGPLAGFSLGFVLFLVGF 367 (529)
Q Consensus 340 ------~RkalfdIAlAGPLAg~llAl~ll~iGl 367 (529)
+-...+.+-++||+.|++.++...+...
T Consensus 87 ~~f~~~~~~~~~~~~~~Gp~~n~i~~~~~~~~~~ 120 (375)
T COG0750 87 RAFNAKSVWQRIAIVFAGPLFNFILAIVLFVVLF 120 (375)
T ss_pred hhhhcccccchhheeechHHHHHHHHHHHHHhhh
Confidence 1123678999999999998877765543
No 16
>KOG2921 consensus Intramembrane metalloprotease (sterol-regulatory element-binding protein (SREBP) protease) [Posttranslational modification, protein turnover, chaperones]
Probab=95.41 E-value=0.012 Score=63.17 Aligned_cols=80 Identities=28% Similarity=0.303 Sum_probs=52.4
Q ss_pred hhHHHH-HHHHHHHHHHHHHHHHHHHHcCCccCCccccccceeeccceEEeeccc----cCCccceeeeeecchhhHHHH
Q 009660 284 NGLPGA-LVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAITRIRNI----VSKREDLLKVAAAGPLAGFSL 358 (529)
Q Consensus 284 ~glp~a-L~Ll~iL~vHElGH~laAr~~Gvk~s~P~FIP~i~LgtFGAvir~~s~----~~~RkalfdIAlAGPLAg~ll 358 (529)
.+++|. ..++..+.+||+||+|||.+.|+++.. |--.+..--=||++.+... .+.- ....|.=||-.-||++
T Consensus 121 ~~I~yf~t~lvi~~vvHElGHalAA~segV~vng--fgIfi~aiyPgafvdl~~dhLqsl~~f-r~LrIfcAGIWHNfvf 197 (484)
T KOG2921|consen 121 SGIAYFLTSLVITVVVHELGHALAAASEGVQVNG--FGIFIAAIYPGAFVDLDNDHLQSLPSF-RALRIFCAGIWHNFVF 197 (484)
T ss_pred ccchhhhhhHHHHHHHHHhhHHHHHHhcCceeee--eEEEEEEEcCchhhhhhhhHHhhcchH-HHHHHHhhhHHHHHHH
Confidence 345544 456668889999999999999999972 1001111123566655432 2222 2457889999999999
Q ss_pred HHHHHHhh
Q 009660 359 GFVLFLVG 366 (529)
Q Consensus 359 Al~ll~iG 366 (529)
|+++.+.-
T Consensus 198 allc~lal 205 (484)
T KOG2921|consen 198 ALLCVLAL 205 (484)
T ss_pred HHHHHHHH
Confidence 98886543
No 17
>PF11667 DUF3267: Protein of unknown function (DUF3267); InterPro: IPR021683 This family of proteins has no known function.
Probab=69.22 E-value=1.8 Score=38.16 Aligned_cols=69 Identities=22% Similarity=0.222 Sum_probs=37.0
Q ss_pred HHHHHHHHHHHHHHHHHcCCccCCccccccceeeccceEEeeccccCCccceeeeeecchhhHHHHHHHHHHhhhc
Q 009660 293 ALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAITRIRNIVSKREDLLKVAAAGPLAGFSLGFVLFLVGFI 368 (529)
Q Consensus 293 l~iL~vHElGH~laAr~~Gvk~s~P~FIP~i~LgtFGAvir~~s~~~~RkalfdIAlAGPLAg~llAl~ll~iGl~ 368 (529)
+..+.+||+-|++..+.+|.+.... | .+....+-.+.. .+ .+-.|..+.+...-|+ ++++++.++++..
T Consensus 4 ~~~~~~HEliH~l~~~~~~~~~~~~-~--g~~~~~~~~~~~-~~-~~~sk~~~~i~~l~P~--ivl~~~~~~~~~~ 72 (111)
T PF11667_consen 4 IVLIPLHELIHGLFFKLFGKKPKVK-F--GFKWKLGPFYAT-CN-EPISKWRFIIILLAPF--IVLTILPLILGFF 72 (111)
T ss_pred EeeHHHHHHHHHHHHHHhCCCCceE-E--EEEeeeEEEEEe-cC-cEEeHHHHHHHHHHHH--HHHHHHHHHHHHH
Confidence 3456899999999999999966311 1 000011111222 22 2333455666666675 4555555554443
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=61.04 E-value=5 Score=36.30 Aligned_cols=21 Identities=24% Similarity=0.436 Sum_probs=14.5
Q ss_pred HHHHHHHHHHHHHHHHcCCcc
Q 009660 294 LVIGVHELGHILAAKSTGVEL 314 (529)
Q Consensus 294 ~iL~vHElGH~laAr~~Gvk~ 314 (529)
..+++||+||++=-..-..+-
T Consensus 106 ~~v~~HEiGHaLGL~H~~~~~ 126 (154)
T PF00413_consen 106 QSVAIHEIGHALGLDHSNDPN 126 (154)
T ss_dssp HHHHHHHHHHHTTBESSSSTT
T ss_pred hhhhhhccccccCcCcCCCcc
Confidence 357899999997655444433
No 19
>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=58.74 E-value=5.9 Score=36.60 Aligned_cols=22 Identities=32% Similarity=0.364 Sum_probs=18.4
Q ss_pred HHHHHHHHHHHHHHHHHcCCcc
Q 009660 293 ALVIGVHELGHILAAKSTGVEL 314 (529)
Q Consensus 293 l~iL~vHElGH~laAr~~Gvk~ 314 (529)
+..+++||+||.+=.+....+.
T Consensus 104 ~~~~~~HEiGHaLGL~H~~~~~ 125 (156)
T cd04279 104 LQAIALHELGHALGLWHHSDRP 125 (156)
T ss_pred HHHHHHHHhhhhhcCCCCCCCc
Confidence 4578999999999888887776
No 20
>PF13485 Peptidase_MA_2: Peptidase MA superfamily
Probab=49.91 E-value=13 Score=31.52 Aligned_cols=18 Identities=28% Similarity=0.233 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHHHHcCC
Q 009660 295 VIGVHELGHILAAKSTGV 312 (529)
Q Consensus 295 iL~vHElGH~laAr~~Gv 312 (529)
-+++||++|.+.....+-
T Consensus 27 ~~l~HE~~H~~~~~~~~~ 44 (128)
T PF13485_consen 27 RVLAHELAHQWFGNYFGG 44 (128)
T ss_pred HHHHHHHHHHHHHHHcCC
Confidence 578999999999999773
No 21
>cd04268 ZnMc_MMP_like Zinc-dependent metalloprotease, MMP_like subfamily. This group contains matrix metalloproteinases (MMPs), serralysins, and the astacin_like family of proteases.
Probab=48.82 E-value=11 Score=34.47 Aligned_cols=21 Identities=29% Similarity=0.300 Sum_probs=15.3
Q ss_pred HHHHHHHHHHHHHHHHHHcCC
Q 009660 292 TALVIGVHELGHILAAKSTGV 312 (529)
Q Consensus 292 Ll~iL~vHElGH~laAr~~Gv 312 (529)
-....++||+||++=-+.-.-
T Consensus 93 ~~~~~~~HEiGHaLGL~H~~~ 113 (165)
T cd04268 93 RLRNTAEHELGHALGLRHNFA 113 (165)
T ss_pred HHHHHHHHHHHHHhcccccCc
Confidence 345788999999976655544
No 22
>cd04278 ZnMc_MMP Zinc-dependent metalloprotease, matrix metalloproteinase (MMP) sub-family. MMPs are responsible for a great deal of pericellular proteolysis of extracellular matrix and cell surface molecules, playing crucial roles in morphogenesis, cell fate specification, cell migration, tissue repair, tumorigenesis, gain or loss of tissue-specific functions, and apoptosis. In many instances, they are anchored to cell membranes via trans-membrane domains, and their activity is controlled via TIMPs (tissue inhibitors of metalloproteinases).
Probab=48.56 E-value=7.9 Score=35.85 Aligned_cols=23 Identities=22% Similarity=0.358 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHHHHHHHcCCccC
Q 009660 293 ALVIGVHELGHILAAKSTGVELG 315 (529)
Q Consensus 293 l~iL~vHElGH~laAr~~Gvk~s 315 (529)
+..+++||+||++=-..-..+.+
T Consensus 107 ~~~~~~HEiGHaLGL~H~~~~~~ 129 (157)
T cd04278 107 LFSVAAHEIGHALGLGHSSDPDS 129 (157)
T ss_pred HHHHHHHHhccccccCCCCCCcC
Confidence 45678999999987655444443
No 23
>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=48.55 E-value=14 Score=37.39 Aligned_cols=55 Identities=27% Similarity=0.353 Sum_probs=39.1
Q ss_pred eeeeccccccCceEEEEeccCCchHHHHHHHHHHHHhHhCCceEEEEEec-CCCCCCEEE
Q 009660 171 TFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFGDQYKLFLLVN-PEDDKPVAV 229 (529)
Q Consensus 171 tF~~t~~~~~~~gvi~rGnLR~~~e~~y~~l~~~l~~~fGd~y~lfl~~~-~~~~kPv~~ 229 (529)
..|+|++..-.=-+.|.||= |.|.++|.+|+.+=. +++|+|++==- .++=||+-+
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 36899988877889999996 777999999886533 57899974222 222277743
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=48.20 E-value=8.9 Score=36.28 Aligned_cols=13 Identities=38% Similarity=0.401 Sum_probs=10.5
Q ss_pred HHHHHHHHHHHHH
Q 009660 294 LVIGVHELGHILA 306 (529)
Q Consensus 294 ~iL~vHElGH~la 306 (529)
.-.++||+||++=
T Consensus 70 g~TltHEvGH~LG 82 (154)
T PF05572_consen 70 GKTLTHEVGHWLG 82 (154)
T ss_dssp SHHHHHHHHHHTT
T ss_pred ccchhhhhhhhhc
Confidence 3678999999864
No 25
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=46.12 E-value=19 Score=43.34 Aligned_cols=17 Identities=24% Similarity=0.296 Sum_probs=7.4
Q ss_pred cccccccccCCCCcccc
Q 009660 5 TTFRGNLSLLPHCSSCC 21 (529)
Q Consensus 5 ~~~~~~~~~~~~~~~~~ 21 (529)
+||-|.-..+--|++-.
T Consensus 1354 aTi~v~R~~~Dlct~~~ 1370 (1516)
T KOG1832|consen 1354 ATIPVDRCLLDLCTEPT 1370 (1516)
T ss_pred eeeecccchhhhhcCCc
Confidence 34444444444455433
No 26
>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=43.44 E-value=16 Score=34.79 Aligned_cols=12 Identities=50% Similarity=0.717 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHH
Q 009660 294 LVIGVHELGHIL 305 (529)
Q Consensus 294 ~iL~vHElGH~l 305 (529)
..++.||+||+.
T Consensus 90 ~aVlaHElgH~~ 101 (226)
T PF01435_consen 90 AAVLAHELGHIK 101 (226)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 368999999986
No 27
>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=41.74 E-value=16 Score=30.70 Aligned_cols=16 Identities=44% Similarity=0.574 Sum_probs=12.2
Q ss_pred HHHHHHHHHHHHHHcC
Q 009660 296 IGVHELGHILAAKSTG 311 (529)
Q Consensus 296 L~vHElGH~laAr~~G 311 (529)
.++||+||++.-....
T Consensus 45 ~laHELgH~~~~~~~~ 60 (122)
T PF06114_consen 45 TLAHELGHILLHHGDE 60 (122)
T ss_dssp HHHHHHHHHHHHH-HH
T ss_pred HHHHHHHHHHhhhccc
Confidence 5789999999766553
No 28
>PF14247 DUF4344: Domain of unknown function (DUF4344)
Probab=40.35 E-value=28 Score=35.14 Aligned_cols=25 Identities=32% Similarity=0.406 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcc
Q 009660 289 ALVTALVIGVHELGHILAAKSTGVEL 314 (529)
Q Consensus 289 aL~Ll~iL~vHElGH~laAr~~Gvk~ 314 (529)
++..+..++.||+||++...+ ++++
T Consensus 88 ~~~~~~~~l~HE~GHAlI~~~-~lPv 112 (220)
T PF14247_consen 88 AIGNVLFTLYHELGHALIDDL-DLPV 112 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHHh-cCCc
Confidence 555666789999999998753 3443
No 29
>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=40.16 E-value=21 Score=35.17 Aligned_cols=18 Identities=33% Similarity=0.316 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHHHHHcCC
Q 009660 295 VIGVHELGHILAAKSTGV 312 (529)
Q Consensus 295 iL~vHElGH~laAr~~Gv 312 (529)
.+.+||.||+++|..++-
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 30
>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=39.45 E-value=16 Score=34.67 Aligned_cols=22 Identities=32% Similarity=0.451 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHHHHHHcCCccC
Q 009660 294 LVIGVHELGHILAAKSTGVELG 315 (529)
Q Consensus 294 ~iL~vHElGH~laAr~~Gvk~s 315 (529)
...++||+||.+=-++-+....
T Consensus 114 ~~t~~HEiGHaLGL~H~~~~~~ 135 (186)
T cd04277 114 YQTIIHEIGHALGLEHPGDYNG 135 (186)
T ss_pred HHHHHHHHHHHhcCCCCCcCCC
Confidence 4678999999987665555443
No 31
>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=38.70 E-value=16 Score=33.41 Aligned_cols=21 Identities=29% Similarity=0.219 Sum_probs=15.4
Q ss_pred HHHHHHHHHHHHHHHHHHcCC
Q 009660 292 TALVIGVHELGHILAAKSTGV 312 (529)
Q Consensus 292 Ll~iL~vHElGH~laAr~~Gv 312 (529)
....+++||+||.+=.+.-..
T Consensus 95 ~~~~~~~HElGH~LGl~H~~~ 115 (167)
T cd00203 95 EGAQTIAHELGHALGFYHDHD 115 (167)
T ss_pred cchhhHHHHHHHHhCCCccCc
Confidence 345678999999987665544
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=38.68 E-value=16 Score=32.88 Aligned_cols=19 Identities=32% Similarity=0.462 Sum_probs=13.9
Q ss_pred HHHHHHHHHHHHHHcCCcc
Q 009660 296 IGVHELGHILAAKSTGVEL 314 (529)
Q Consensus 296 L~vHElGH~laAr~~Gvk~ 314 (529)
+++||+||++-...-..+.
T Consensus 89 ~~~HEigHaLGl~H~~~~~ 107 (140)
T smart00235 89 VAAHELGHALGLYHEQSRS 107 (140)
T ss_pred cHHHHHHHHhcCCcCCCCC
Confidence 7899999998655444443
No 33
>PF13582 Reprolysin_3: Metallo-peptidase family M12B Reprolysin-like; PDB: 3P24_C.
Probab=37.44 E-value=17 Score=31.83 Aligned_cols=13 Identities=38% Similarity=0.434 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHHH
Q 009660 295 VIGVHELGHILAA 307 (529)
Q Consensus 295 iL~vHElGH~laA 307 (529)
..++||+||.+=+
T Consensus 109 ~~~~HEiGH~lGl 121 (124)
T PF13582_consen 109 DTFAHEIGHNLGL 121 (124)
T ss_dssp THHHHHHHHHTT-
T ss_pred eEeeehhhHhcCC
Confidence 6789999998644
No 34
>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=35.91 E-value=26 Score=35.40 Aligned_cols=28 Identities=32% Similarity=0.330 Sum_probs=19.7
Q ss_pred HhhHHHHHHHHHHHHHHHHHHHHHHHHcCCc
Q 009660 283 TNGLPGALVTALVIGVHELGHILAAKSTGVE 313 (529)
Q Consensus 283 ~~glp~aL~Ll~iL~vHElGH~laAr~~Gvk 313 (529)
+.|+|-. ++.++++||++|+|. |..|.+
T Consensus 85 l~GLPrl--l~gsiLAHE~mHa~L-rl~g~~ 112 (212)
T PF12315_consen 85 LYGLPRL--LTGSILAHELMHAWL-RLNGFP 112 (212)
T ss_pred ECCCCHH--HHhhHHHHHHHHHHh-cccCCC
Confidence 4456643 456899999999998 455544
No 35
>PF14891 Peptidase_M91: Effector protein
Probab=35.08 E-value=25 Score=33.63 Aligned_cols=16 Identities=31% Similarity=0.299 Sum_probs=13.1
Q ss_pred HHHHHHHHHHHHHHHH
Q 009660 294 LVIGVHELGHILAAKS 309 (529)
Q Consensus 294 ~iL~vHElGH~laAr~ 309 (529)
++++.|||+|++-...
T Consensus 104 ~v~L~HEL~HA~~~~~ 119 (174)
T PF14891_consen 104 FVVLYHELIHAYDYMN 119 (174)
T ss_pred HHHHHHHHHHHHHHHC
Confidence 5789999999987654
No 36
>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=34.85 E-value=20 Score=34.14 Aligned_cols=20 Identities=35% Similarity=0.291 Sum_probs=13.9
Q ss_pred HHHHHHHHHHHHHHHHcCCc
Q 009660 294 LVIGVHELGHILAAKSTGVE 313 (529)
Q Consensus 294 ~iL~vHElGH~laAr~~Gvk 313 (529)
.-.++||+||.+=|..-+..
T Consensus 112 ~~~~aHElGH~lGa~Hd~~~ 131 (173)
T PF13574_consen 112 IDTFAHELGHQLGAPHDFDN 131 (173)
T ss_dssp HHHHHHHHHHHHT---SSSS
T ss_pred eeeehhhhHhhcCCCCCCCC
Confidence 35689999999999887764
No 37
>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=34.58 E-value=19 Score=34.09 Aligned_cols=21 Identities=33% Similarity=0.414 Sum_probs=13.1
Q ss_pred HHHHHHHHHHHHHHHHHcCCc
Q 009660 293 ALVIGVHELGHILAAKSTGVE 313 (529)
Q Consensus 293 l~iL~vHElGH~laAr~~Gvk 313 (529)
-.+.++||+||-+=|..=+..
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 346889999999999876654
No 38
>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=32.68 E-value=27 Score=32.89 Aligned_cols=10 Identities=80% Similarity=1.291 Sum_probs=8.8
Q ss_pred HHHHHHHHHH
Q 009660 296 IGVHELGHIL 305 (529)
Q Consensus 296 L~vHElGH~l 305 (529)
+.+||+||.+
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 39
>PTZ00429 beta-adaptin; Provisional
Probab=32.51 E-value=43 Score=39.52 Aligned_cols=33 Identities=27% Similarity=0.252 Sum_probs=17.3
Q ss_pred CChhhhhcccCCCCCCCCCCcccCCCCCCCccC
Q 009660 71 NNDKEKEVHDGQENQPATASDQEDDKSQPDSQL 103 (529)
Q Consensus 71 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 103 (529)
+.||||+|+++.++.|++.++..++++..++++
T Consensus 607 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 639 (746)
T PTZ00429 607 ELDEEDTEDDDAVELPSTPSMGTQDGSPAPSAA 639 (746)
T ss_pred ccccccccchhhccCCCCCCCCCCCCCCCcccc
Confidence 344455555555566666666555554444444
No 40
>cd04327 ZnMc_MMP_like_3 Zinc-dependent metalloprotease; MMP_like sub-family 3. A group of bacterial and fungal metalloproteinase domains similar to matrix metalloproteinases and astacin.
Probab=31.09 E-value=31 Score=33.43 Aligned_cols=20 Identities=25% Similarity=0.302 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHHHHHHcCCc
Q 009660 294 LVIGVHELGHILAAKSTGVE 313 (529)
Q Consensus 294 ~iL~vHElGH~laAr~~Gvk 313 (529)
...++||+||++=...-.-+
T Consensus 93 ~~~i~HElgHaLG~~HEh~r 112 (198)
T cd04327 93 SRVVLHEFGHALGFIHEHQS 112 (198)
T ss_pred HHHHHHHHHHHhcCcccccC
Confidence 35788999999865544333
No 41
>PRK03001 M48 family peptidase; Provisional
Probab=30.44 E-value=31 Score=35.38 Aligned_cols=12 Identities=33% Similarity=0.426 Sum_probs=10.0
Q ss_pred HHHHHHHHHHHH
Q 009660 294 LVIGVHELGHIL 305 (529)
Q Consensus 294 ~iL~vHElGH~l 305 (529)
.++++||+||+-
T Consensus 125 ~aVlAHElgHi~ 136 (283)
T PRK03001 125 RGVMAHELAHVK 136 (283)
T ss_pred HHHHHHHHHHHh
Confidence 368899999974
No 42
>PRK11037 hypothetical protein; Provisional
Probab=30.27 E-value=1.2e+02 Score=26.38 Aligned_cols=65 Identities=18% Similarity=0.366 Sum_probs=42.8
Q ss_pred ccCCCCHhHH-----HHhhccccccceeeeccccccCceEEEEeccC-------C-chHHHHHHHHHHHHhHhCCceEE
Q 009660 150 EYIRIPKETI-----DILKDQVFGFDTFFVTNQEPYEGGVLFKGNLR-------G-QAAKTYEKISTRMKNKFGDQYKL 215 (529)
Q Consensus 150 ~~~~i~~edl-----~~ik~~~Fg~dtF~~t~~~~~~~gvi~rGnLR-------~-~~e~~y~~l~~~l~~~fGd~y~l 215 (529)
+..+|++++| +.||+.===+..-.+|++|-.++..+|||..= + +.-.||. +=+-|.-.+..+|+|
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 2233443 334455566777876
No 43
>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=30.06 E-value=5.2e+02 Score=25.57 Aligned_cols=102 Identities=22% Similarity=0.385 Sum_probs=55.3
Q ss_pred HHHHHHHHHHHHhhcCCCCCChHHHHHHHh-hhhHHHHHHH-HHHHHHHHHHHhh------------hh------hHHHH
Q 009660 415 IWAWAGLLINAINSIPAGELDGGRIAFALW-GRKASTRLTG-VSIVLLGLSSLFS------------DV------TFYWV 474 (529)
Q Consensus 415 ~agwinLvltafNLLPigPLDGGrIl~All-grr~a~~i~~-~~~ilLGl~~l~~------------~~------~l~W~ 474 (529)
+.+-+..+.-.||.-+++| +-+++-.+ |......++. +.++++|+.++.. +. ...|.
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 4455777888999999999 77887764 3333333332 2233333322211 11 12222
Q ss_pred HHHHHHHhCCCCCCCcCCCCCChhHHHHHHHHHHHHHHhhcccCCCC
Q 009660 475 VLVFFLQRGPIAPLSEEITDPDDKYIALGVLVLFLGLLVCLPYPFPF 521 (529)
Q Consensus 475 ililfl~rgp~~P~~nevt~~~~~r~~lg~l~l~l~ll~llP~P~~~ 521 (529)
.+ +|..-+|..|....+.+++..-.. .-+.+.+.-=+|+-+-+++
T Consensus 110 ~i-vF~~lnP~fp~~~~~~~l~~nTii-T~~CiyiLyGlFIGYSIsf 154 (173)
T PF11085_consen 110 AI-VFFVLNPIFPMIKPVTELDWNTII-TTLCIYILYGLFIGYSISF 154 (173)
T ss_pred HH-HHHHhcccccCChhhhhCchhHHH-HHHHHHHHHHHHhceeehh
Confidence 22 334468888988888888765543 3344444444554444443
No 44
>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=30.04 E-value=32 Score=34.69 Aligned_cols=18 Identities=28% Similarity=0.503 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 009660 292 TALVIGVHELGHILAAKS 309 (529)
Q Consensus 292 Ll~iL~vHElGH~laAr~ 309 (529)
.++..++||+||-+=+..
T Consensus 166 ~~a~t~AHElGHnlGm~H 183 (244)
T cd04270 166 ESDLVTAHELGHNFGSPH 183 (244)
T ss_pred HHHHHHHHHHHHhcCCCC
Confidence 456789999999987763
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=29.90 E-value=35 Score=32.51 Aligned_cols=20 Identities=35% Similarity=0.350 Sum_probs=15.3
Q ss_pred HHHHHHHHHHHHHHHHHcCC
Q 009660 293 ALVIGVHELGHILAAKSTGV 312 (529)
Q Consensus 293 l~iL~vHElGH~laAr~~Gv 312 (529)
.+.+++||+||-+=+..-+.
T Consensus 131 ~a~~~AHElGH~lG~~HD~~ 150 (194)
T cd04269 131 FAVTMAHELGHNLGMEHDDG 150 (194)
T ss_pred HHHHHHHHHHhhcCCCcCCC
Confidence 35788999999987775544
No 46
>PRK03982 heat shock protein HtpX; Provisional
Probab=29.86 E-value=33 Score=35.34 Aligned_cols=12 Identities=42% Similarity=0.362 Sum_probs=9.8
Q ss_pred HHHHHHHHHHHH
Q 009660 294 LVIGVHELGHIL 305 (529)
Q Consensus 294 ~iL~vHElGH~l 305 (529)
.++++||+||.-
T Consensus 126 ~AVlAHElgHi~ 137 (288)
T PRK03982 126 EGVIAHELTHIK 137 (288)
T ss_pred HHHHHHHHHHHH
Confidence 367899999974
No 47
>PHA02456 zinc metallopeptidase motif-containing protein
Probab=29.57 E-value=32 Score=31.86 Aligned_cols=19 Identities=26% Similarity=0.305 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHHcCCccC
Q 009660 297 GVHELGHILAAKSTGVELG 315 (529)
Q Consensus 297 ~vHElGH~laAr~~Gvk~s 315 (529)
+.||++|.|.-|.||.-..
T Consensus 83 L~HEL~H~WQ~RsYG~i~P 101 (141)
T PHA02456 83 LAHELNHAWQFRTYGLVQP 101 (141)
T ss_pred HHHHHHHHHhhhccceeee
Confidence 5799999999999997553
No 48
>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=29.30 E-value=24 Score=36.52 Aligned_cols=14 Identities=36% Similarity=0.596 Sum_probs=10.7
Q ss_pred HHHHHHHHHHHHHH
Q 009660 294 LVIGVHELGHILAA 307 (529)
Q Consensus 294 ~iL~vHElGH~laA 307 (529)
.-+++||+||.++-
T Consensus 217 ~~v~vHE~GHsf~~ 230 (264)
T PF09471_consen 217 KQVVVHEFGHSFGG 230 (264)
T ss_dssp HHHHHHHHHHHTT-
T ss_pred cceeeeeccccccc
Confidence 35789999998754
No 49
>COG2856 Predicted Zn peptidase [Amino acid transport and metabolism]
Probab=29.03 E-value=30 Score=34.78 Aligned_cols=16 Identities=38% Similarity=0.463 Sum_probs=11.9
Q ss_pred HHHHHHHHHHHHHHcC
Q 009660 296 IGVHELGHILAAKSTG 311 (529)
Q Consensus 296 L~vHElGH~laAr~~G 311 (529)
.++||+||++.=+...
T Consensus 75 tlAHELGH~llH~~~~ 90 (213)
T COG2856 75 TLAHELGHALLHTDLN 90 (213)
T ss_pred HHHHHHhHHHhccccc
Confidence 4789999998755443
No 50
>PRK12462 phosphoserine aminotransferase; Provisional
Probab=28.83 E-value=91 Score=33.69 Aligned_cols=67 Identities=12% Similarity=0.160 Sum_probs=45.9
Q ss_pred CccccCCCCHhHHHHhhccccccceeeeccccccCceEEEEeccCCchHHHHHHHHHHHHhHhC--CceEEEEEecC
Q 009660 147 QLDEYIRIPKETIDILKDQVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFG--DQYKLFLLVNP 221 (529)
Q Consensus 147 ~~~~~~~i~~edl~~ik~~~Fg~dtF~~t~~~~~~~gvi~rGnLR~~~e~~y~~l~~~l~~~fG--d~y~lfl~~~~ 221 (529)
....|..+|+|.++++++++.-|. .-+-+++=.+---.+=.+.|++.+++|+++|+ |.|.+++++-.
T Consensus 8 F~aGPa~lp~~Vl~~~~~~~~~~~--------~~g~si~eisHRs~~F~~i~~~~~~~Lr~Ll~~P~~y~Vlfl~Gg 76 (364)
T PRK12462 8 FSGGPGALPDTVLEQVRQAVVELP--------ETGLSVLGMSHRSSWFSSLLAQAEADLRDLLGIPDEYGVVFLQGG 76 (364)
T ss_pred ecCCCcCCCHHHHHHHHHHHhccc--------ccCccccccccccHHHHHHHHHHHHHHHHHhCCCCCCeEEEEecc
Confidence 456788999999999997543322 11113333333234568899999999999998 68988776654
No 51
>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=28.18 E-value=26 Score=33.21 Aligned_cols=20 Identities=40% Similarity=0.531 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHHHHHcCC
Q 009660 293 ALVIGVHELGHILAAKSTGV 312 (529)
Q Consensus 293 l~iL~vHElGH~laAr~~Gv 312 (529)
.+.+++||+||.+=+.+-+.
T Consensus 133 ~~~~~aHElGH~lG~~HD~~ 152 (192)
T cd04267 133 TALTMAHELGHNLGAEHDGG 152 (192)
T ss_pred ehhhhhhhHHhhcCCcCCCC
Confidence 34689999999998877654
No 52
>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=28.09 E-value=42 Score=30.77 Aligned_cols=19 Identities=21% Similarity=0.123 Sum_probs=14.8
Q ss_pred HHHHHHHHHHHHHHHHHHc
Q 009660 292 TALVIGVHELGHILAAKST 310 (529)
Q Consensus 292 Ll~iL~vHElGH~laAr~~ 310 (529)
.+.-.++|||.|+++-...
T Consensus 59 ~~~~tL~HEm~H~~~~~~~ 77 (157)
T PF10263_consen 59 ELIDTLLHEMAHAAAYVFG 77 (157)
T ss_pred HHHHHHHHHHHHHHhhhcc
Confidence 4446789999999996663
No 53
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=27.17 E-value=38 Score=31.40 Aligned_cols=16 Identities=25% Similarity=0.003 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHHHHHH
Q 009660 294 LVIGVHELGHILAAKS 309 (529)
Q Consensus 294 ~iL~vHElGH~laAr~ 309 (529)
.-++.|||+|+++-..
T Consensus 60 ~~~l~HEm~H~~~~~~ 75 (146)
T smart00731 60 RETLLHELCHAALYLF 75 (146)
T ss_pred HhhHHHHHHHHHHHHh
Confidence 4578999999999875
No 54
>PF13583 Reprolysin_4: Metallo-peptidase family M12B Reprolysin-like
Probab=26.70 E-value=33 Score=33.69 Aligned_cols=18 Identities=28% Similarity=0.215 Sum_probs=14.8
Q ss_pred HHHHHHHHHHHHHHcCCc
Q 009660 296 IGVHELGHILAAKSTGVE 313 (529)
Q Consensus 296 L~vHElGH~laAr~~Gvk 313 (529)
.++||+||.+=|++-+-.
T Consensus 140 ~~aHEiGH~lGl~H~~~~ 157 (206)
T PF13583_consen 140 TFAHEIGHNLGLRHDFDY 157 (206)
T ss_pred HHHHHHHHHhcCCCCccc
Confidence 488999999988877663
No 55
>COG0501 HtpX Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]
Probab=26.27 E-value=42 Score=33.75 Aligned_cols=11 Identities=55% Similarity=0.818 Sum_probs=9.2
Q ss_pred HHHHHHHHHHH
Q 009660 295 VIGVHELGHIL 305 (529)
Q Consensus 295 iL~vHElGH~l 305 (529)
.++.||+||..
T Consensus 159 aVlaHElgHi~ 169 (302)
T COG0501 159 AVLAHELGHIK 169 (302)
T ss_pred HHHHHHHHHHh
Confidence 57899999963
No 56
>PLN02452 phosphoserine transaminase
Probab=26.09 E-value=1.2e+02 Score=32.63 Aligned_cols=68 Identities=9% Similarity=0.187 Sum_probs=47.8
Q ss_pred CCccccCCCCHhHHHHhhccccccceeeeccccccCceEEEEeccCCchHHHHHHHHHHHHhHhC--CceEEEEEecC
Q 009660 146 QQLDEYIRIPKETIDILKDQVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFG--DQYKLFLLVNP 221 (529)
Q Consensus 146 ~~~~~~~~i~~edl~~ik~~~Fg~dtF~~t~~~~~~~gvi~rGnLR~~~e~~y~~l~~~l~~~fG--d~y~lfl~~~~ 221 (529)
.....|..+|++.+++++.+.+-|. .-+-+++-.+---.+=.++++.++++|++.++ |.|.+++++-.
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 57
>PRK04897 heat shock protein HtpX; Provisional
Probab=25.98 E-value=42 Score=34.93 Aligned_cols=12 Identities=33% Similarity=0.274 Sum_probs=9.6
Q ss_pred HHHHHHHHHHHH
Q 009660 294 LVIGVHELGHIL 305 (529)
Q Consensus 294 ~iL~vHElGH~l 305 (529)
..+++||+||.-
T Consensus 138 ~aVlAHElgHi~ 149 (298)
T PRK04897 138 EGVIGHEISHIR 149 (298)
T ss_pred HHHHHHHHHHHh
Confidence 367899999963
No 58
>COG5309 Exo-beta-1,3-glucanase [Carbohydrate transport and metabolism]
Probab=25.98 E-value=1e+02 Score=32.61 Aligned_cols=61 Identities=16% Similarity=0.312 Sum_probs=43.1
Q ss_pred HhHHHHhhcccccc-ceeeeccccccCceEEEEeccCC--chHHHHHHHHHHHHhHhCCceEEEEEec
Q 009660 156 KETIDILKDQVFGF-DTFFVTNQEPYEGGVLFKGNLRG--QAAKTYEKISTRMKNKFGDQYKLFLLVN 220 (529)
Q Consensus 156 ~edl~~ik~~~Fg~-dtF~~t~~~~~~~gvi~rGnLR~--~~e~~y~~l~~~l~~~fGd~y~lfl~~~ 220 (529)
.|.++++|. .||= .+||+||+-.--.|--+-++.-. +..+.++++..+|++. | |.+|+++-
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 99999998755555555454443 3466778888888874 7 66665553
No 59
>KOG3320 consensus 40S ribosomal protein S7 [Translation, ribosomal structure and biogenesis]
Probab=25.80 E-value=94 Score=30.86 Aligned_cols=27 Identities=15% Similarity=0.321 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHHhHhCCceEEEEEecC
Q 009660 195 AKTYEKISTRMKNKFGDQYKLFLLVNP 221 (529)
Q Consensus 195 e~~y~~l~~~l~~~fGd~y~lfl~~~~ 221 (529)
.+.|.+|...||.+|+|+|.+|+.+..
T Consensus 74 qki~~~LvreleKKF~gk~Vifia~Rr 100 (192)
T KOG3320|consen 74 QKIQVRLVRELEKKFSGKHVIFIAQRR 100 (192)
T ss_pred HHHHHHHHHHHHHhcCCceEEEEEeee
Confidence 455556666999999999999876654
No 60
>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=25.72 E-value=35 Score=34.40 Aligned_cols=27 Identities=19% Similarity=0.146 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCcc
Q 009660 288 GALVTALVIGVHELGHILAAKSTGVEL 314 (529)
Q Consensus 288 ~aL~Ll~iL~vHElGH~laAr~~Gvk~ 314 (529)
+..-+..-+++||+||.+=-|+-....
T Consensus 128 ~~~~~~~hvi~HEiGH~IGfRHTD~~~ 154 (211)
T PF12388_consen 128 YSVNVIEHVITHEIGHCIGFRHTDYFN 154 (211)
T ss_pred CchhHHHHHHHHHhhhhccccccCcCC
Confidence 344456678999999999887755443
No 61
>KOG0391 consensus SNF2 family DNA-dependent ATPase [General function prediction only]
Probab=25.00 E-value=81 Score=39.52 Aligned_cols=21 Identities=33% Similarity=0.358 Sum_probs=15.1
Q ss_pred eeccccccCceEEEEeccCCc
Q 009660 173 FVTNQEPYEGGVLFKGNLRGQ 193 (529)
Q Consensus 173 ~~t~~~~~~~gvi~rGnLR~~ 193 (529)
-+|.+-..+---+.|||||.-
T Consensus 599 l~tTqVktpvPsLLrGqLReY 619 (1958)
T KOG0391|consen 599 LVTTQVKTPVPSLLRGQLREY 619 (1958)
T ss_pred eeeeeeccCchHHHHHHHHHH
Confidence 345555667777999999963
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=24.70 E-value=47 Score=31.52 Aligned_cols=11 Identities=36% Similarity=0.495 Sum_probs=9.7
Q ss_pred HHHHHHHHHHH
Q 009660 296 IGVHELGHILA 306 (529)
Q Consensus 296 L~vHElGH~la 306 (529)
++.||++|.++
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
>COG0830 UreF Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]
Probab=24.50 E-value=82 Score=32.19 Aligned_cols=31 Identities=32% Similarity=0.340 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHhhcCCCCCChHHHHHHHhh
Q 009660 415 IWAWAGLLINAINSIPAGELDGGRIAFALWG 445 (529)
Q Consensus 415 ~agwinLvltafNLLPigPLDGGrIl~Allg 445 (529)
++.-.|++.++.=|+|.||+||=+|+..+-.
T Consensus 158 ya~~~~lv~aavRlipLgQ~~gq~il~~l~~ 188 (229)
T COG0830 158 YAWASNLVSAAVRLIPLGQLDGQKILAQLEP 188 (229)
T ss_pred HHHHHHHHHHHHHhcccCcHHHHHHHHHhhH
Confidence 3444699999999999999999999998844
No 64
>PF13699 DUF4157: Domain of unknown function (DUF4157)
Probab=24.45 E-value=44 Score=28.37 Aligned_cols=12 Identities=33% Similarity=0.650 Sum_probs=10.1
Q ss_pred HHHHHHHHHHHH
Q 009660 295 VIGVHELGHILA 306 (529)
Q Consensus 295 iL~vHElGH~la 306 (529)
.++.||++|.+-
T Consensus 63 ~llaHEl~Hv~Q 74 (79)
T PF13699_consen 63 ALLAHELAHVVQ 74 (79)
T ss_pred hhHhHHHHHHHh
Confidence 478999999874
No 65
>PRK01345 heat shock protein HtpX; Provisional
Probab=24.34 E-value=47 Score=35.03 Aligned_cols=12 Identities=33% Similarity=0.454 Sum_probs=10.0
Q ss_pred HHHHHHHHHHHH
Q 009660 294 LVIGVHELGHIL 305 (529)
Q Consensus 294 ~iL~vHElGH~l 305 (529)
..++.||+||.-
T Consensus 125 ~aVlAHElgHi~ 136 (317)
T PRK01345 125 AGVMAHELAHVK 136 (317)
T ss_pred HHHHHHHHHHHH
Confidence 368899999985
No 66
>PRK03072 heat shock protein HtpX; Provisional
Probab=23.72 E-value=49 Score=34.29 Aligned_cols=11 Identities=36% Similarity=0.395 Sum_probs=9.2
Q ss_pred HHHHHHHHHHH
Q 009660 294 LVIGVHELGHI 304 (529)
Q Consensus 294 ~iL~vHElGH~ 304 (529)
..++.||+||.
T Consensus 128 ~aVlAHElgHi 138 (288)
T PRK03072 128 RGVLGHELSHV 138 (288)
T ss_pred HHHHHHHHHHH
Confidence 36789999995
No 67
>COG3824 Predicted Zn-dependent protease [General function prediction only]
Probab=23.49 E-value=36 Score=31.89 Aligned_cols=14 Identities=29% Similarity=0.558 Sum_probs=11.7
Q ss_pred HHHHHHHHHHHHHH
Q 009660 292 TALVIGVHELGHIL 305 (529)
Q Consensus 292 Ll~iL~vHElGH~l 305 (529)
.+..+++||+||.+
T Consensus 108 ~vthvliHEIgHhF 121 (136)
T COG3824 108 QVTHVLIHEIGHHF 121 (136)
T ss_pred Hhhhhhhhhhhhhc
Confidence 55688999999975
No 68
>PRK02391 heat shock protein HtpX; Provisional
Probab=23.38 E-value=50 Score=34.46 Aligned_cols=10 Identities=40% Similarity=0.733 Sum_probs=8.7
Q ss_pred HHHHHHHHHH
Q 009660 295 VIGVHELGHI 304 (529)
Q Consensus 295 iL~vHElGH~ 304 (529)
.++.||+||.
T Consensus 135 aVlaHElgHi 144 (296)
T PRK02391 135 AVLAHELSHV 144 (296)
T ss_pred HHHHHHHHHH
Confidence 6789999995
No 69
>PRK05457 heat shock protein HtpX; Provisional
Probab=23.03 E-value=52 Score=34.13 Aligned_cols=11 Identities=36% Similarity=0.573 Sum_probs=9.2
Q ss_pred HHHHHHHHHHH
Q 009660 294 LVIGVHELGHI 304 (529)
Q Consensus 294 ~iL~vHElGH~ 304 (529)
..++.||+||.
T Consensus 135 ~aVlAHElgHi 145 (284)
T PRK05457 135 EAVLAHEISHI 145 (284)
T ss_pred HHHHHHHHHHH
Confidence 36789999996
No 70
>TIGR01651 CobT cobaltochelatase, CobT subunit. This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit, with a MW ~70 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobS (TIGR01650) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobT gene product, the P. denitrificans gene symbol is not used in the name of this model.
Probab=22.46 E-value=1.6e+02 Score=34.10 Aligned_cols=9 Identities=11% Similarity=0.707 Sum_probs=3.8
Q ss_pred HHHHHHHhH
Q 009660 200 KISTRMKNK 208 (529)
Q Consensus 200 ~l~~~l~~~ 208 (529)
+|.++|+..
T Consensus 338 rLA~~Lqr~ 346 (600)
T TIGR01651 338 RLANRLQRR 346 (600)
T ss_pred HHHHHHHHH
Confidence 344444443
No 71
>cd04927 ACT_ACR-like_2 Second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=22.30 E-value=1.1e+02 Score=25.32 Aligned_cols=35 Identities=23% Similarity=0.314 Sum_probs=25.1
Q ss_pred cccceeeeccccccCceEEEEeccCCchHHHHHHHHHHHHhHhCCc
Q 009660 167 FGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFGDQ 212 (529)
Q Consensus 167 Fg~dtF~~t~~~~~~~gvi~rGnLR~~~e~~y~~l~~~l~~~fGd~ 212 (529)
.-+||||+++.. |+ ...++..+++++.|++.+|+-
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 72
>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=22.00 E-value=1.5e+02 Score=25.90 Aligned_cols=64 Identities=16% Similarity=0.309 Sum_probs=36.5
Q ss_pred cCCCCHhHH-----HHhhccccccceeeeccccccCceEEEEeccC----Cch----HHHHHHHHHHHHhHhCCceEE
Q 009660 151 YIRIPKETI-----DILKDQVFGFDTFFVTNQEPYEGGVLFKGNLR----GQA----AKTYEKISTRMKNKFGDQYKL 215 (529)
Q Consensus 151 ~~~i~~edl-----~~ik~~~Fg~dtF~~t~~~~~~~gvi~rGnLR----~~~----e~~y~~l~~~l~~~fGd~y~l 215 (529)
.-+|++++| +.||+.===+..-.+|++|-.++..+|||+.= |-| -.||. +=+-|.-.+.++|.|
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 345566677888976
No 73
>KOG2719 consensus Metalloprotease [General function prediction only]
Probab=21.74 E-value=51 Score=36.54 Aligned_cols=15 Identities=33% Similarity=0.452 Sum_probs=11.5
Q ss_pred HHHHHHHHHHHHHHH
Q 009660 293 ALVIGVHELGHILAA 307 (529)
Q Consensus 293 l~iL~vHElGH~laA 307 (529)
+.++++||+||+---
T Consensus 280 l~AVl~HELGHW~~~ 294 (428)
T KOG2719|consen 280 LVAVLAHELGHWKLN 294 (428)
T ss_pred HHHHHHHHhhHHHHh
Confidence 357899999998543
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=21.43 E-value=65 Score=30.83 Aligned_cols=21 Identities=43% Similarity=0.494 Sum_probs=14.2
Q ss_pred HHHHHHHHHHHHHHHHHHcCC
Q 009660 292 TALVIGVHELGHILAAKSTGV 312 (529)
Q Consensus 292 Ll~iL~vHElGH~laAr~~Gv 312 (529)
.++.+++||+||.+=+..-+.
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 445778999999887777666
No 75
>PRK01265 heat shock protein HtpX; Provisional
Probab=21.26 E-value=59 Score=34.67 Aligned_cols=10 Identities=50% Similarity=0.979 Sum_probs=8.8
Q ss_pred HHHHHHHHHH
Q 009660 295 VIGVHELGHI 304 (529)
Q Consensus 295 iL~vHElGH~ 304 (529)
.++.||+||+
T Consensus 142 aVlAHElgHi 151 (324)
T PRK01265 142 AVAGHELGHL 151 (324)
T ss_pred HHHHHHHHHH
Confidence 5789999996
No 76
>PRK02870 heat shock protein HtpX; Provisional
Probab=21.16 E-value=59 Score=34.79 Aligned_cols=11 Identities=45% Similarity=0.673 Sum_probs=9.4
Q ss_pred HHHHHHHHHHH
Q 009660 294 LVIGVHELGHI 304 (529)
Q Consensus 294 ~iL~vHElGH~ 304 (529)
..++.||+||.
T Consensus 174 ~aVlAHELgHi 184 (336)
T PRK02870 174 QAVMAHELSHI 184 (336)
T ss_pred HHHHHHHHHHH
Confidence 36789999998
No 77
>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH. HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.
Probab=21.03 E-value=45 Score=36.87 Aligned_cols=18 Identities=28% Similarity=0.364 Sum_probs=15.4
Q ss_pred HHHHHHHHHHHHHHHcCC
Q 009660 295 VIGVHELGHILAAKSTGV 312 (529)
Q Consensus 295 iL~vHElGH~laAr~~Gv 312 (529)
.+..||.||++++..++.
T Consensus 313 ~~A~hEaGhAlv~~~l~~ 330 (495)
T TIGR01241 313 LVAYHEAGHALVGLLLKD 330 (495)
T ss_pred HHHHHHHhHHHHHHhcCC
Confidence 578999999999998753
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=20.75 E-value=58 Score=33.15 Aligned_cols=12 Identities=33% Similarity=0.822 Sum_probs=10.3
Q ss_pred HHHHHHHHHHHH
Q 009660 295 VIGVHELGHILA 306 (529)
Q Consensus 295 iL~vHElGH~la 306 (529)
.+.+||.||++.
T Consensus 91 aVAAHEvGHAiQ 102 (222)
T PF04298_consen 91 AVAAHEVGHAIQ 102 (222)
T ss_pred HHHHHHHhHHHh
Confidence 578999999875
No 79
>COG5495 Uncharacterized conserved protein [Function unknown]
Probab=20.47 E-value=61 Score=33.73 Aligned_cols=38 Identities=24% Similarity=0.330 Sum_probs=25.5
Q ss_pred CCHhHHHHhhccccccceeeeccccccCceEEEEeccCCchHHHHHHHHHHHHhHhCCce
Q 009660 154 IPKETIDILKDQVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFGDQY 213 (529)
Q Consensus 154 i~~edl~~ik~~~Fg~dtF~~t~~~~~~~gvi~rGnLR~~~e~~y~~l~~~l~~~fGd~y 213 (529)
=.+||+++||++||++ |+.+ ++.-.|-++|...+|.+|
T Consensus 128 gl~edl~rl~d~~~~i-----~eaD-----------------~~g~ai~q~la~emgg~~ 165 (289)
T COG5495 128 GLDEDLSRLKDTIFGI-----TEAD-----------------DVGYAIVQSLALEMGGEP 165 (289)
T ss_pred CCHHHHHhCcccEEEe-----eccc-----------------ccccHHHHHHHHHhCCCc
Confidence 3579999999988765 3333 333346666777777776
No 80
>PRK04860 hypothetical protein; Provisional
Probab=20.34 E-value=94 Score=29.92 Aligned_cols=21 Identities=29% Similarity=0.284 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHHHHHHcC
Q 009660 291 VTALVIGVHELGHILAAKSTG 311 (529)
Q Consensus 291 ~Ll~iL~vHElGH~laAr~~G 311 (529)
..+.-++.||++|+++=..+|
T Consensus 61 ~~l~~~v~HEl~H~~~~~~~g 81 (160)
T PRK04860 61 AFIDEVVPHELAHLLVYQLFG 81 (160)
T ss_pred HHHHhHHHHHHHHHHHHHHcC
Confidence 344567899999999999988
No 81
>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=20.12 E-value=1.7e+02 Score=30.90 Aligned_cols=60 Identities=10% Similarity=0.208 Sum_probs=40.3
Q ss_pred CCCHhHHHHhhccccccceeeeccccccCceEEEEeccCCchHHHHHHHHHHHHhHhC--CceEEEEEec
Q 009660 153 RIPKETIDILKDQVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFG--DQYKLFLLVN 220 (529)
Q Consensus 153 ~i~~edl~~ik~~~Fg~dtF~~t~~~~~~~gvi~rGnLR~~~e~~y~~l~~~l~~~fG--d~y~lfl~~~ 220 (529)
..|.+.++++++ ||.+.- .-.-|..-.+.--.+-.+.|++++++|++.|+ ++|.++++..
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 444332 33345555554444556999999999999988 4566655543
No 82
>PF08525 OapA_N: Opacity-associated protein A N-terminal motif; InterPro: IPR013731 This domain is found in the Haemophilus influenzae opacity-associated protein (OapA). It is required for efficient nasopharyngeal mucosal colonisation, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [, ]. This motif occurs at the N terminus of these proteins. It contains a conserved histidine followed by a run of hydrophobic residues. Many of the proteins in this entry are unassigned peptidases belonging to MEROPS peptidase family M23B.
Probab=20.03 E-value=1.2e+02 Score=21.38 Aligned_cols=21 Identities=24% Similarity=0.078 Sum_probs=15.5
Q ss_pred hhHHHHHHHHHHHHHHhhccc
Q 009660 497 DKYIALGVLVLFLGLLVCLPY 517 (529)
Q Consensus 497 ~~r~~lg~l~l~l~ll~llP~ 517 (529)
.-|+++++++.++.++.+.|.
T Consensus 9 ~Hr~~l~~l~~v~l~ll~~Ps 29 (30)
T PF08525_consen 9 LHRRALIALSAVVLVLLLWPS 29 (30)
T ss_pred HHHHHHHHHHHHHHHHHhccC
Confidence 346777777777777888775
Done!