Query 009655
Match_columns 529
No_of_seqs 328 out of 1287
Neff 4.5
Searched_HMMs 46136
Date Thu Mar 28 15:44:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009655.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009655hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd06160 S2P-M50_like_2 Unchara 100.0 3.1E-31 6.8E-36 253.2 19.2 177 252-477 3-181 (183)
2 cd06164 S2P-M50_SpoIVFB_CBS Sp 99.9 2.2E-25 4.7E-30 219.1 21.1 134 277-448 37-170 (227)
3 cd06161 S2P-M50_SpoIVFB SpoIVF 99.9 1.1E-23 2.4E-28 204.0 19.1 129 280-448 25-153 (208)
4 cd06163 S2P-M50_PDZ_RseP-like 99.9 6.7E-21 1.4E-25 182.2 15.2 112 287-445 3-145 (182)
5 cd05709 S2P-M50 Site-2 proteas 99.8 7.2E-21 1.6E-25 178.5 13.4 139 287-449 2-156 (180)
6 cd06159 S2P-M50_PDZ_Arch Uncha 99.8 3.7E-19 8E-24 179.0 18.5 119 282-447 107-228 (263)
7 PF02163 Peptidase_M50: Peptid 99.8 4.2E-19 9.1E-24 167.5 10.9 127 288-444 2-157 (192)
8 cd06162 S2P-M50_PDZ_SREBP Ster 99.8 8.8E-18 1.9E-22 170.1 15.9 114 288-449 130-250 (277)
9 cd06158 S2P-M50_like_1 Unchara 99.8 3.5E-18 7.5E-23 163.0 11.0 134 288-451 4-159 (181)
10 TIGR00054 RIP metalloprotease 99.5 9.4E-14 2E-18 147.6 16.4 79 288-367 9-119 (420)
11 PRK10779 zinc metallopeptidase 99.5 1.3E-13 2.7E-18 147.6 15.2 83 284-367 6-119 (449)
12 COG1994 SpoIVFB Zn-dependent p 99.3 1.7E-11 3.7E-16 120.9 14.7 131 281-451 40-178 (230)
13 COG0750 Predicted membrane-ass 98.9 1.6E-09 3.5E-14 111.9 5.9 242 165-448 82-338 (375)
14 PF13398 Peptidase_M50B: Pepti 97.4 0.00053 1.2E-08 66.8 8.1 65 294-366 23-88 (200)
15 COG0750 Predicted membrane-ass 96.2 0.016 3.5E-07 60.2 8.0 82 286-367 6-120 (375)
16 KOG2921 Intramembrane metallop 95.9 0.0069 1.5E-07 65.0 3.8 82 283-367 120-206 (484)
17 PF11667 DUF3267: Protein of u 71.7 2 4.3E-05 38.0 1.2 69 293-368 4-72 (111)
18 PF00413 Peptidase_M10: Matrix 62.7 4.5 9.7E-05 36.6 1.7 21 294-314 106-126 (154)
19 cd04279 ZnMc_MMP_like_1 Zinc-d 59.8 5.5 0.00012 36.8 1.8 22 293-314 104-125 (156)
20 PF13485 Peptidase_MA_2: Pepti 50.0 13 0.00028 31.5 2.4 18 295-312 27-44 (128)
21 cd04268 ZnMc_MMP_like Zinc-dep 49.7 11 0.00023 34.6 1.9 21 292-312 93-113 (165)
22 cd04278 ZnMc_MMP Zinc-dependen 49.6 7.5 0.00016 36.0 0.9 23 293-315 107-129 (157)
23 PTZ00429 beta-adaptin; Provisi 49.3 15 0.00032 43.2 3.4 32 75-106 608-639 (746)
24 PF05572 Peptidase_M43: Pregna 49.0 8.5 0.00019 36.4 1.2 14 294-307 70-83 (154)
25 KOG1832 HIV-1 Vpr-binding prot 44.3 22 0.00048 42.8 3.7 18 5-22 1354-1371(1516)
26 PF07423 DUF1510: Protein of u 44.1 17 0.00036 36.8 2.4 54 171-228 159-213 (217)
27 PF01435 Peptidase_M48: Peptid 43.8 16 0.00035 34.8 2.2 12 294-305 90-101 (226)
28 PF06114 DUF955: Domain of unk 42.0 16 0.00035 30.7 1.7 17 295-311 44-60 (122)
29 PF11085 YqhR: Conserved membr 41.7 2.4E+02 0.0052 27.9 9.7 100 415-520 33-153 (173)
30 cd04277 ZnMc_serralysin_like Z 41.1 15 0.00032 34.9 1.5 22 294-315 114-135 (186)
31 PF14247 DUF4344: Domain of un 40.6 28 0.00061 35.2 3.4 25 289-314 88-112 (220)
32 PF01434 Peptidase_M41: Peptid 40.5 22 0.00049 35.0 2.7 19 294-312 29-47 (213)
33 smart00235 ZnMc Zinc-dependent 40.1 15 0.00032 33.1 1.3 20 296-315 89-108 (140)
34 cd00203 ZnMc Zinc-dependent me 39.6 15 0.00033 33.5 1.2 21 292-312 95-115 (167)
35 PF13582 Reprolysin_3: Metallo 38.6 16 0.00034 32.0 1.2 14 295-308 109-122 (124)
36 PF12315 DUF3633: Protein of u 37.5 24 0.00051 35.7 2.3 29 282-313 84-112 (212)
37 PF13574 Reprolysin_2: Metallo 36.3 19 0.0004 34.4 1.3 21 293-313 111-131 (173)
38 PF14891 Peptidase_M91: Effect 36.3 23 0.0005 33.8 2.0 17 293-309 103-119 (174)
39 PF13688 Reprolysin_5: Metallo 35.2 19 0.00041 34.2 1.2 21 293-313 142-162 (196)
40 PF02031 Peptidase_M7: Strepto 33.3 26 0.00056 33.0 1.7 10 296-305 80-89 (132)
41 cd04327 ZnMc_MMP_like_3 Zinc-d 33.0 24 0.00052 34.2 1.5 20 294-313 93-112 (198)
42 cd04269 ZnMc_adamalysin_II_lik 30.7 33 0.00072 32.6 2.1 20 293-312 131-150 (194)
43 cd04270 ZnMc_TACE_like Zinc-de 30.3 32 0.00069 34.7 1.9 18 292-309 166-183 (244)
44 PRK03001 M48 family peptidase; 30.2 32 0.00069 35.3 2.0 12 294-305 125-136 (283)
45 PRK03982 heat shock protein Ht 29.3 34 0.00074 35.2 2.0 12 294-305 126-137 (288)
46 PF10263 SprT-like: SprT-like 29.1 40 0.00086 30.9 2.2 19 292-310 59-77 (157)
47 PF09471 Peptidase_M64: IgA Pe 28.8 24 0.00053 36.4 0.8 14 294-307 217-230 (264)
48 COG2856 Predicted Zn peptidase 28.7 31 0.00066 34.7 1.5 16 296-311 75-90 (213)
49 cd04267 ZnMc_ADAM_like Zinc-de 28.4 26 0.00056 33.2 0.9 20 293-312 133-152 (192)
50 smart00731 SprT SprT homologue 28.2 35 0.00077 31.6 1.7 17 293-309 59-75 (146)
51 PF13583 Reprolysin_4: Metallo 28.1 30 0.00066 34.0 1.3 18 295-312 139-156 (206)
52 COG0830 UreF Urease accessory 27.9 64 0.0014 32.9 3.6 32 414-445 157-188 (229)
53 PRK12462 phosphoserine aminotr 26.9 97 0.0021 33.5 5.0 63 151-221 12-76 (364)
54 PF12388 Peptidase_M57: Dual-a 26.5 33 0.00072 34.6 1.3 27 288-314 128-154 (211)
55 COG0501 HtpX Zn-dependent prot 25.6 44 0.00095 33.6 2.0 12 294-305 158-169 (302)
56 PF01447 Peptidase_M4: Thermol 25.5 44 0.00096 31.7 1.9 12 295-306 137-148 (150)
57 PRK04897 heat shock protein Ht 25.5 43 0.00094 34.8 2.0 12 294-305 138-149 (298)
58 TIGR01241 FtsH_fam ATP-depende 25.1 38 0.00082 37.4 1.5 17 295-311 313-329 (495)
59 PLN02452 phosphoserine transam 25.1 1.2E+02 0.0025 32.6 5.1 63 151-221 15-79 (365)
60 COG3824 Predicted Zn-dependent 24.7 33 0.00072 32.1 0.8 14 292-305 108-121 (136)
61 COG5309 Exo-beta-1,3-glucanase 24.5 1.2E+02 0.0025 32.2 4.7 61 156-220 218-281 (305)
62 KOG0391 SNF2 family DNA-depend 24.2 75 0.0016 39.8 3.7 36 158-193 584-619 (1958)
63 PRK01345 heat shock protein Ht 24.0 48 0.001 34.9 2.0 12 294-305 125-136 (317)
64 PRK03072 heat shock protein Ht 23.4 50 0.0011 34.2 2.0 11 294-304 128-138 (288)
65 PF13699 DUF4157: Domain of un 23.3 48 0.001 28.2 1.5 12 295-306 63-74 (79)
66 PRK02391 heat shock protein Ht 23.0 52 0.0011 34.4 2.0 11 294-304 134-144 (296)
67 COG3091 SprT Zn-dependent meta 22.9 1.2E+02 0.0027 29.4 4.2 32 277-311 48-79 (156)
68 PRK05457 heat shock protein Ht 22.6 54 0.0012 34.0 2.0 11 294-304 135-145 (284)
69 PHA02456 zinc metallopeptidase 22.4 52 0.0011 30.5 1.6 19 297-315 83-101 (141)
70 PF01421 Reprolysin: Reprolysi 22.1 62 0.0013 31.0 2.2 22 291-312 129-150 (199)
71 KOG3320 40S ribosomal protein 22.0 1.2E+02 0.0027 30.1 4.1 27 195-221 74-100 (192)
72 PF04298 Zn_peptidase_2: Putat 21.8 54 0.0012 33.4 1.7 13 294-306 90-102 (222)
73 cd04927 ACT_ACR-like_2 Second 21.5 1.1E+02 0.0024 25.2 3.3 35 167-212 40-74 (76)
74 KOG1832 HIV-1 Vpr-binding prot 21.1 79 0.0017 38.4 3.1 11 154-164 1489-1499(1516)
75 PRK01265 heat shock protein Ht 20.9 60 0.0013 34.6 2.0 11 294-304 141-151 (324)
76 PRK02870 heat shock protein Ht 20.6 61 0.0013 34.7 2.0 11 294-304 174-184 (336)
77 PF01432 Peptidase_M3: Peptida 20.4 63 0.0014 35.0 2.0 20 295-314 244-263 (458)
78 TIGR01364 serC_1 phosphoserine 20.3 1.6E+02 0.0035 31.1 5.0 60 153-220 2-63 (349)
79 KOG2719 Metalloprotease [Gener 20.2 58 0.0013 36.1 1.7 14 293-306 280-293 (428)
80 PF08525 OapA_N: Opacity-assoc 20.1 1.2E+02 0.0026 21.5 2.7 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=3.1e-31 Score=253.23 Aligned_cols=177 Identities=40% Similarity=0.706 Sum_probs=147.9
Q ss_pred HHHHHHHHHHhhccccccccccccccchHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHcCCccccccccccceeeeeeeE
Q 009655 252 FGLVTVFTLLLRNVPALQSNLLSTFDNLNLLTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAI 331 (529)
Q Consensus 252 l~l~Tl~Tt~~~~~~~L~~~~~~~~~~~~~l~~glp~aL~L~~iL~iHElGH~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 LLVLTLLTTLLVGAWLSG-N--DVPGNPLLLLQGLPFALALLAILGIHEMGHYLAARRHGVKASLPYFIPFPFIGTFGAF 79 (183)
T ss_pred HHHHHHHHHHHHHHHHhc-c--cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCccceeeeehHhcCcEEEE
Confidence 456677776655421111 1 2236678889999999999999999999999999999999999999998779999999
Q ss_pred EeeccccCCcccceeeEecchhhHHHHHHHHHHHHhhcCCCCCCcccccccchhhhhhhhhhHHhhhccccCCCCCccch
Q 009655 332 TRIRNIVSKREDLLKVAAAGPLAGFSLGFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVN 411 (529)
Q Consensus 332 i~~~s~~~~RkalfdIAiAGPLAg~llAl~ll~iGl~l~~s~~~~~~v~~~~f~~s~L~g~la~l~LG~~l~~g~~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--hHHHHHHHH
Q 009655 412 PLVIWAWAGLLINAINSIPAGELDGGRIAFALWGRKASTRLTGVSIVLLGLSSLFSD--VTFYWVVLV 477 (529)
Q Consensus 412 PLa~agwinLvltafNLLPigpLDGGrIlrAllgrr~a~~i~~~~~~lLGl~~l~~~--~~l~W~lli 477 (529)
+..++|+|+++++|||+|++|||||||+++++++|.+.++++++.+++|+.++.++ .+++|+.++
T Consensus 115 -~~~~~~~nl~l~~fNLLPi~PLDGGril~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ 181 (183)
T cd06160 115 -LAVAGWVGLLVTALNLLPVGQLDGGHIVRALFGRRVAALIGIGLLVALGLLALYLSFSIWLLWALLL 181 (183)
T ss_pred -HHHHHHHHHHHHHHHhCCCCCcChHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence 12368999999999999999999999999999999999999999899998888765 455665443
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=99.94 E-value=2.2e-25 Score=219.15 Aligned_cols=134 Identities=30% Similarity=0.390 Sum_probs=112.0
Q ss_pred cchHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHcCCccccccccccceeeeeeeEEeeccccCCcccceeeEecchhhHH
Q 009655 277 DNLNLLTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAITRIRNIVSKREDLLKVAAAGPLAGF 356 (529)
Q Consensus 277 ~~~~~l~~glp~aL~L~~iL~iHElGH~laAr~~Gvk~s~P~FIP~i~LGtFGAvi~~~s~~~~RkalfdIAiAGPLAg~ 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 455678889999999999999999999999999999998 77888899999999888889999999999999999
Q ss_pred HHHHHHHHHHhhcCCCCCCcccccccchhhhhhhhhhHHhhhccccCCCCCccchHHHHHHHHHHHHHHHhhcCCCCCCh
Q 009655 357 SLGFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAINSIPAGELDG 436 (529)
Q Consensus 357 llAl~ll~iGl~l~~s~~~~~~v~~~~f~~s~L~g~la~l~LG~~l~~g~~v~lhPLa~agwinLvltafNLLPigpLDG 436 (529)
+++++++++....+... .+. ....+.+.+|+|+++++|||+|++||||
T Consensus 111 lla~i~~~l~~~~~~~~------------~~~--------------------~~~~~~~~~~~Nl~l~~fNLlP~~PLDG 158 (227)
T cd06164 111 VLALLFLLLSLALPGSG------------AGP--------------------LGVLLGYLALINLLLAVFNLLPAFPLDG 158 (227)
T ss_pred HHHHHHHHHHHHhcccc------------chH--------------------HHHHHHHHHHHHHHHHHHhCcCCCCCCh
Confidence 99998877665432110 000 0112446789999999999999999999
Q ss_pred HHHHHHHhhhhH
Q 009655 437 GRIAFALWGRKA 448 (529)
Q Consensus 437 GrIlrAllgrr~ 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=1.1e-23 Score=203.96 Aligned_cols=129 Identities=29% Similarity=0.433 Sum_probs=108.5
Q ss_pred HHHHhhHHHHHHHHHHHHHHHHHHHHHHHHcCCccccccccccceeeeeeeEEeeccccCCcccceeeEecchhhHHHHH
Q 009655 280 NLLTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAITRIRNIVSKREDLLKVAAAGPLAGFSLG 359 (529)
Q Consensus 280 ~~l~~glp~aL~L~~iL~iHElGH~laAr~~Gvk~s~P~FIP~i~LGtFGAvi~~~s~~~~RkalfdIAiAGPLAg~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 457788999999999999999999999999999998 78888999999998777789999999999999999999
Q ss_pred HHHHHHHhhcCCCCCCcccccccchhhhhhhhhhHHhhhccccCCCCCccchHHHHHHHHHHHHHHHhhcCCCCCChHHH
Q 009655 360 FVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAINSIPAGELDGGRI 439 (529)
Q Consensus 360 l~ll~iGl~l~~s~~~~~~v~~~~f~~s~L~g~la~l~LG~~l~~g~~v~lhPLa~agwinLvltafNLLPigpLDGGrI 439 (529)
+++.++....+.. + .....+.+.+++|+++++|||+|++|||||||
T Consensus 99 ~~~~~l~~~~~~~--------------~--------------------~~~~~~~~~~~~N~~l~lfNLlPi~pLDGg~i 144 (208)
T cd06161 99 GLFYLLYLLLPGG--------------G--------------------PLSSLLEFLAQVNLILGLFNLLPALPLDGGRV 144 (208)
T ss_pred HHHHHHHHHcccc--------------h--------------------HHHHHHHHHHHHHHHHHHHHccCCCCCChHHH
Confidence 8887665432210 0 00123456789999999999999999999999
Q ss_pred HHHHhhhhH
Q 009655 440 AFALWGRKA 448 (529)
Q Consensus 440 lrAllgrr~ 448 (529)
+++++.++.
T Consensus 145 l~~ll~~~~ 153 (208)
T cd06161 145 LRALLWRRT 153 (208)
T ss_pred HHHHHHHhc
Confidence 999987664
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=99.86 E-value=6.7e-21 Score=182.19 Aligned_cols=112 Identities=33% Similarity=0.458 Sum_probs=88.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCcccccccc---cc------------ceeeeeeeEEeeccccC------------
Q 009655 287 PGALVTALVIGVHELGHILAAKSTGVELGVPYFV---PS------------WQIGSFGAITRIRNIVS------------ 339 (529)
Q Consensus 287 p~aL~L~~iL~iHElGH~laAr~~Gvk~s~P~FI---P~------------i~LGtFGAvi~~~s~~~------------ 339 (529)
.+.+++.+++++||+||+++||++|+++.. +.| |. +.+.++|+++++++..+
T Consensus 3 ~~~i~l~~~v~iHElGH~~~Ar~~Gv~v~~-f~iGfGp~l~~~~~~~t~~~i~~iPlGGyv~~~~~~~~~~~~~~~~~~~ 81 (182)
T cd06163 3 AFILVLGILIFVHELGHFLVAKLFGVKVEE-FSIGFGPKLFSFKKGETEYSISAIPLGGYVKMLGEDPEEEADPEDDPRS 81 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCeeeE-eeeecCceeeeeecCCeEEEEEEEEeccEEEecCCCcccccccccchHH
Confidence 356677789999999999999999999872 111 21 34568999998864311
Q ss_pred ----CcccceeeEecchhhHHHHHHHHHHHHhhcCCCCCCcccccccchhhhhhhhhhHHhhhccccCCCCCccchHHHH
Q 009655 340 ----KREDLLKVAAAGPLAGFSLGFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVI 415 (529)
Q Consensus 340 ----~RkalfdIAiAGPLAg~llAl~ll~iGl~l~~s~~~~~~v~~~~f~~s~L~g~la~l~LG~~l~~g~~v~lhPLa~ 415 (529)
++++++.|++|||++|+++|++++++. +.+
T Consensus 82 f~~~~~~~ri~V~lAGP~~NlilA~i~~~~~----------------------------------------------~~~ 115 (182)
T cd06163 82 FNSKPVWQRILIVFAGPLANFLLAIVLFAVL----------------------------------------------LSF 115 (182)
T ss_pred HccCCcchhhhhhhhHHHHHHHHHHHHHHHH----------------------------------------------HHH
Confidence 467899999999999999998764321 124
Q ss_pred HHHHHHHHHHHhhcCCCCCChHHHHHHHhh
Q 009655 416 WAWAGLLINAINSIPAGELDGGRIAFALWG 445 (529)
Q Consensus 416 agwinLvltafNLLPigpLDGGrIlrAllg 445 (529)
..++|+.+++|||+|++||||||++++++.
T Consensus 116 ~~~~n~~l~~fNLlPippLDGg~il~~~~~ 145 (182)
T cd06163 116 LALLSINLGILNLLPIPALDGGHLLFLLIE 145 (182)
T ss_pred HHHHHHHHHHHHcCCCCCCCHHHHHHHHHH
Confidence 678999999999999999999999999985
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=7.2e-21 Score=178.53 Aligned_cols=139 Identities=28% Similarity=0.328 Sum_probs=100.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCcccc----ccccc-------cceeeeeeeEEeeccccC-----CcccceeeEec
Q 009655 287 PGALVTALVIGVHELGHILAAKSTGVELGV----PYFVP-------SWQIGSFGAITRIRNIVS-----KREDLLKVAAA 350 (529)
Q Consensus 287 p~aL~L~~iL~iHElGH~laAr~~Gvk~s~----P~FIP-------~i~LGtFGAvi~~~s~~~-----~RkalfdIAiA 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 356778889999999999999999998741 11111 122345699998877554 48999999999
Q ss_pred chhhHHHHHHHHHHHHhhcCCCCCCcccccccchhhhhhhhhhHHhhhccccCCCCCccchHHHHHHHHHHHHHHHhhcC
Q 009655 351 GPLAGFSLGFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAINSIP 430 (529)
Q Consensus 351 GPLAg~llAl~ll~iGl~l~~s~~~~~~v~~~~f~~s~L~g~la~l~LG~~l~~g~~v~lhPLa~agwinLvltafNLLP 430 (529)
||++|++++++++++.......... .. ..+ ......+.+.+++|+|+.+++|||+|
T Consensus 82 GPl~nllla~i~~~~~~~~~~~~~~----~~---~~~-----------------~~~~~~~~l~~~~~~n~~l~~fNLlP 137 (180)
T cd05709 82 GPLANLLLALLLLLLLLLLGGLPPA----PV---GQA-----------------ASSGLANLLAFLALINLNLAVFNLLP 137 (180)
T ss_pred hHHHHHHHHHHHHHHHHHHccCCcc----ch---hhh-----------------HHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 9999999999988776543221100 00 000 00111245667899999999999999
Q ss_pred CCCCChHHHHHHHhhhhHH
Q 009655 431 AGELDGGRIAFALWGRKAS 449 (529)
Q Consensus 431 igpLDGGrIlrAllgrr~a 449 (529)
++||||||++++++.++..
T Consensus 138 i~plDGg~il~~~l~~~~~ 156 (180)
T cd05709 138 IPPLDGGRILRALLEAIRG 156 (180)
T ss_pred CCCCChHHHHHHHHhHHHH
Confidence 9999999999999887754
No 6
>cd06159 S2P-M50_PDZ_Arch Uncharacterized Archaeal homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the S2P/M50 family of RIP proteases use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. In eukaryotic cells they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum stress responses. In prokaryotes they regulate such processes as sporulation, cell division, stress response, and cell differentiation. This group appears to be limited to Archaeal S2P/M50s homologs with additional putative N-terminal transmembrane spanning regions, relative to the core protein, and either one or two PDZ domains present.
Probab=99.82 E-value=3.7e-19 Score=178.98 Aligned_cols=119 Identities=26% Similarity=0.325 Sum_probs=93.5
Q ss_pred HHhhHHHHHHHHHHHHHHHHHHHHHHHHcCCccccccccccceeeeeeeEEeecccc---CCcccceeeEecchhhHHHH
Q 009655 282 LTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAITRIRNIV---SKREDLLKVAAAGPLAGFSL 358 (529)
Q Consensus 282 l~~glp~aL~L~~iL~iHElGH~laAr~~Gvk~s~P~FIP~i~LGtFGAvi~~~s~~---~~RkalfdIAiAGPLAg~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 34566677788899999999999999999999983111 01123588999886544 46789999999999999999
Q ss_pred HHHHHHHHhhcCCCCCCcccccccchhhhhhhhhhHHhhhccccCCCCCccchHHHHHHHHHHHHHHHhhcCCCCCChHH
Q 009655 359 GFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAINSIPAGELDGGR 438 (529)
Q Consensus 359 Al~ll~iGl~l~~s~~~~~~v~~~~f~~s~L~g~la~l~LG~~l~~g~~v~lhPLa~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 12457899999999999999999999
Q ss_pred HHHHHhhhh
Q 009655 439 IAFALWGRK 447 (529)
Q Consensus 439 IlrAllgrr 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=99.79 E-value=4.2e-19 Score=167.45 Aligned_cols=127 Identities=28% Similarity=0.345 Sum_probs=80.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCccccccc----cc------c----ceeeeeeeE---------------Eeecccc
Q 009655 288 GALVTALVIGVHELGHILAAKSTGVELGVPYF----VP------S----WQIGSFGAI---------------TRIRNIV 338 (529)
Q Consensus 288 ~aL~L~~iL~iHElGH~laAr~~Gvk~s~P~F----IP------~----i~LGtFGAv---------------i~~~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 01 0 011122322 2222234
Q ss_pred CCcccceeeEecchhhHHHHHHHHHHHHhhcCCCCCCcccccccchhhhhhhhhhHHhhhccccCCCCCccchHHHHHHH
Q 009655 339 SKREDLLKVAAAGPLAGFSLGFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAW 418 (529)
Q Consensus 339 ~~RkalfdIAiAGPLAg~llAl~ll~iGl~l~~s~~~~~~v~~~~f~~s~L~g~la~l~LG~~l~~g~~v~lhPLa~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 567889999999999999999888766543221000 01122356678899
Q ss_pred HHHHHHHHhhcCCCCCChHHHHHHHh
Q 009655 419 AGLLINAINSIPAGELDGGRIAFALW 444 (529)
Q Consensus 419 inLvltafNLLPigpLDGGrIlrAll 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=8.8e-18 Score=170.09 Aligned_cols=114 Identities=25% Similarity=0.226 Sum_probs=90.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCccccccccccceeeee----eeEEeeccc---cCCcccceeeEecchhhHHHHHH
Q 009655 288 GALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSF----GAITRIRNI---VSKREDLLKVAAAGPLAGFSLGF 360 (529)
Q Consensus 288 ~aL~L~~iL~iHElGH~laAr~~Gvk~s~P~FIP~i~LGtF----GAvi~~~s~---~~~RkalfdIAiAGPLAg~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 3466788999999999999999999998 5544444 899988433 23567799999999999999998
Q ss_pred HHHHHHhhcCCCCCCcccccccchhhhhhhhhhHHhhhccccCCCCCccchHHHHHHHHHHHHHHHhhcCCCCCChHHHH
Q 009655 361 VLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAINSIPAGELDGGRIA 440 (529)
Q Consensus 361 ~ll~iGl~l~~s~~~~~~v~~~~f~~s~L~g~la~l~LG~~l~~g~~v~lhPLa~agwinLvltafNLLPigpLDGGrIl 440 (529)
+++++.+. .-+.+..++|+.+++|||+|+.|||||||+
T Consensus 204 i~~~l~~~------------------------------------------~~l~~la~iNl~lavfNLlP~~pLDGg~il 241 (277)
T cd06162 204 VGYLLLIE------------------------------------------TFLKYLISLSGALAVINAVPCFALDGQWIL 241 (277)
T ss_pred HHHHHHHH------------------------------------------HHHHHHHHHHHHHHHhhcCCCCCCChHHHH
Confidence 77653210 012346789999999999999999999999
Q ss_pred HHHhhhhHH
Q 009655 441 FALWGRKAS 449 (529)
Q Consensus 441 rAllgrr~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=99.76 E-value=3.5e-18 Score=163.01 Aligned_cols=134 Identities=25% Similarity=0.295 Sum_probs=90.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCcccc----ccccc-------------cceeeeeeeEEeec-----cccCCcccce
Q 009655 288 GALVTALVIGVHELGHILAAKSTGVELGV----PYFVP-------------SWQIGSFGAITRIR-----NIVSKREDLL 345 (529)
Q Consensus 288 ~aL~L~~iL~iHElGH~laAr~~Gvk~s~----P~FIP-------------~i~LGtFGAvi~~~-----s~~~~Rkalf 345 (529)
..++++.++..||+||+++|+++|+++.. -.+-| ...+.. +++.+.. ...++|++++
T Consensus 4 ~~~~~~~~i~~HE~aHa~~A~~~Gd~t~~~~Grltlnp~~hid~~g~l~~~~~~~~~-~G~a~p~~~~~~~~~~~r~~~~ 82 (181)
T cd06158 4 VIIAVLLAITLHEFAHAYVAYRLGDPTARRAGRLTLNPLAHIDPIGTIILPLLLPFL-FGWAKPVPVNPRNFKNPRRGML 82 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCcHHHHcCceecCcHHhcCcchHHHHHHHHHhC-eEEecccccChHhhcccHhhHh
Confidence 45567789999999999999999999862 11112 111112 3343322 2234578899
Q ss_pred eeEecchhhHHHHHHHHHHHHhhcCCCCCCcccccccchhhhhhhhhhHHhhhccccCCCCCccchHHHHHHHHHHHHHH
Q 009655 346 KVAAAGPLAGFSLGFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINA 425 (529)
Q Consensus 346 dIAiAGPLAg~llAl~ll~iGl~l~~s~~~~~~v~~~~f~~s~L~g~la~l~LG~~l~~g~~v~lhPLa~agwinLvlta 425 (529)
.|++|||++|+++++++.++........+ ...+.+ ...+....++|+.+++
T Consensus 83 ~valAGP~~n~~la~i~~~~~~~~~~~~~---------~~~~~l--------------------~~~~~~~~~~Ni~l~l 133 (181)
T cd06158 83 LVSLAGPLSNLLLALLFALLLRLLPAFGG---------VVASFL--------------------FLMLAYGVLINLVLAV 133 (181)
T ss_pred hhhhhhHHHHHHHHHHHHHHHHHhccccc---------hhhHHH--------------------HHHHHHHHHHHHHHHH
Confidence 99999999999999887655443221100 000110 1123456789999999
Q ss_pred HhhcCCCCCChHHHHHHHhhhhHHHH
Q 009655 426 INSIPAGELDGGRIAFALWGRKASTR 451 (529)
Q Consensus 426 fNLLPigpLDGGrIlrAllgrr~a~~ 451 (529)
|||+|++|||||||+++++.++....
T Consensus 134 fNLlPipPLDG~~il~~~l~~~~~~~ 159 (181)
T cd06158 134 FNLLPIPPLDGSKILAALLPRRLAEA 159 (181)
T ss_pred HHhCCCCCCChHHHHHHHcchhHHHH
Confidence 99999999999999999998876543
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=99.55 E-value=9.4e-14 Score=147.65 Aligned_cols=79 Identities=27% Similarity=0.463 Sum_probs=60.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCcccccccc---c------------cceeeeeeeEEeeccc---------------
Q 009655 288 GALVTALVIGVHELGHILAAKSTGVELGVPYFV---P------------SWQIGSFGAITRIRNI--------------- 337 (529)
Q Consensus 288 ~aL~L~~iL~iHElGH~laAr~~Gvk~s~P~FI---P------------~i~LGtFGAvi~~~s~--------------- 337 (529)
+.+.+.+++++||+||+++||++|+++.. |.| | .+.+.++|+++++...
T Consensus 9 ~~~~~~~~v~~HE~gH~~~a~~~g~~v~~-FsiGfGp~l~~~~~~~tey~i~~~plGg~v~~~g~~~~~~~~~~~~~~~~ 87 (420)
T TIGR00054 9 SILALAVLIFVHELGHFLAARLCGIKVER-FSIGFGPKILKFKKNGTEYAISLIPLGGYVKMKGLDKEMEVKPPETDGDL 87 (420)
T ss_pred HHHHHHHHHHHHhHHHHHHHHHcCCEEEE-EEEccCchheEEecCCeEEEEEEecCcceEeeccCCcccccCCcchhhhh
Confidence 35567778999999999999999999862 111 2 1346789999998411
Q ss_pred --cCCcccceeeEecchhhHHHHHHHHHHHHh
Q 009655 338 --VSKREDLLKVAAAGPLAGFSLGFVLFLVGF 367 (529)
Q Consensus 338 --~~~RkalfdIAiAGPLAg~llAl~ll~iGl 367 (529)
..+.++++.|++|||++|+++|++++++.+
T Consensus 88 f~~~~~~~r~~i~~aGp~~N~~~a~~~~~~~~ 119 (420)
T TIGR00054 88 FNNKSVFQKAIIIFAGPLANFIFAIFVYIFIS 119 (420)
T ss_pred hccCCHHHHHHhhhcccHHHHHHHHHHHHHHH
Confidence 035678899999999999999998876544
No 11
>PRK10779 zinc metallopeptidase RseP; Provisional
Probab=99.52 E-value=1.3e-13 Score=147.60 Aligned_cols=83 Identities=22% Similarity=0.371 Sum_probs=62.1
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHcCCcccccccc---cc-------------ceeeeeeeEEeeccc----------
Q 009655 284 NGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFV---PS-------------WQIGSFGAITRIRNI---------- 337 (529)
Q Consensus 284 ~glp~aL~L~~iL~iHElGH~laAr~~Gvk~s~P~FI---P~-------------i~LGtFGAvi~~~s~---------- 337 (529)
..+.+.+++..++++||+||+++||++|+++.. |.| |. +-+.++|++.+|...
T Consensus 6 ~i~~fil~l~~li~vHElGHfl~Ar~~gv~V~~-FsiGfGp~l~~~~~~~~Tey~i~~iPlGGyVk~~~e~~~~~~~~~~ 84 (449)
T PRK10779 6 NLAAFIVALGVLITVHEFGHFWVARRCGVRVER-FSIGFGKALWRRTDRQGTEYVIALIPLGGYVKMLDERVEPVAPELR 84 (449)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcCCeeeE-EEeecChhHeeEecCCCcEEEEEEEcCCCeeecCCCCCCcCChhhh
Confidence 344466677778999999999999999999983 111 21 235678999987532
Q ss_pred -----cCCcccceeeEecchhhHHHHHHHHHHHHh
Q 009655 338 -----VSKREDLLKVAAAGPLAGFSLGFVLFLVGF 367 (529)
Q Consensus 338 -----~~~RkalfdIAiAGPLAg~llAl~ll~iGl 367 (529)
..+.++++.|.+|||++|+++|++++.+-+
T Consensus 85 ~~~f~~k~~~~R~~i~~AGp~~N~ila~~~~~~~~ 119 (449)
T PRK10779 85 HHAFNNKTVGQRAAIIAAGPIANFIFAIFAYWLVF 119 (449)
T ss_pred hhhhccCCHHHhhhhhhhhHHHHHHHHHHHHHHHH
Confidence 123578899999999999999988865544
No 12
>COG1994 SpoIVFB Zn-dependent proteases [General function prediction only]
Probab=99.34 E-value=1.7e-11 Score=120.88 Aligned_cols=131 Identities=24% Similarity=0.307 Sum_probs=86.1
Q ss_pred HHHhhHHHHHHHHHHHHHHHHHHHHHHHHcCCccccccccccceeeeeeeEEeeccccCCcccceeeEec--------ch
Q 009655 281 LLTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAITRIRNIVSKREDLLKVAAA--------GP 352 (529)
Q Consensus 281 ~l~~glp~aL~L~~iL~iHElGH~laAr~~Gvk~s~P~FIP~i~LGtFGAvi~~~s~~~~RkalfdIAiA--------GP 352 (529)
.+.++....++++..+..||+||...++++|++.. .+.++.+|++..++..+.+.+..+.+..+ ||
T Consensus 40 ~~~~~~~~~~~l~~rl~l~~~gh~~~~~~~~~~l~------~~~i~~~~g~~~~~~~~v~~~~~~~~~~~g~lvs~algp 113 (230)
T COG1994 40 SLGDGTAAFVGLAHRLVLHPLGHSDEAGRLGLKLL------LALLFGFGGFGFLKPVPVNPRGEFLIRLAGPLVSLALGP 113 (230)
T ss_pred HHhhhHHHHHHHhHHHhhhHhhHHHHHHHHHHHHH------HHHHHhccceeeecCcCcCHHHHhhhhccchhHHHHHHH
Confidence 34555555555777999999999999999999987 54444477777777666565555555544 55
Q ss_pred hhHHHHHHHHHHHHhhcCCCCCCcccccccchhhhhhhhhhHHhhhccccCCCCCccchHHHHHHHHHHHHHHHhhcCCC
Q 009655 353 LAGFSLGFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAINSIPAG 432 (529)
Q Consensus 353 LAg~llAl~ll~iGl~l~~s~~~~~~v~~~~f~~s~L~g~la~l~LG~~l~~g~~v~lhPLa~agwinLvltafNLLPig 432 (529)
+.|+++++++ ... .+.. ...+ +...-+...+.+|+++++|||+|++
T Consensus 114 l~ni~la~~~-~~~--~~~~-----------~~~~--------------------~~~~~~~~la~~Nl~L~lFNLiPi~ 159 (230)
T COG1994 114 LTNIALAVLG-LLA--LSLF-----------LYHS--------------------VLFAFLAALALVNLVLALFNLLPIP 159 (230)
T ss_pred HHHHHHHHHH-HHh--hccc-----------ccch--------------------hHHHHHHHHHHHHHHHHHHhCCCCC
Confidence 5555544433 000 0000 0000 0011223467799999999999999
Q ss_pred CCChHHHHHHHhhhhHHHH
Q 009655 433 ELDGGRIAFALWGRKASTR 451 (529)
Q Consensus 433 pLDGGrIlrAllgrr~a~~ 451 (529)
||||||++|+++.++...+
T Consensus 160 PLDGg~vlr~~~~~~~~~~ 178 (230)
T COG1994 160 PLDGGRVLRALLPRRYGAA 178 (230)
T ss_pred CCChHHHHHHHccHHHHHH
Confidence 9999999999988876533
No 13
>COG0750 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]
Probab=98.90 E-value=1.6e-09 Score=111.88 Aligned_cols=242 Identities=13% Similarity=0.048 Sum_probs=138.5
Q ss_pred cccccceeeeccccccCceEEEEeccCCchHHHHHHHHHHHHhhhCCceEEEEEecCCCCCcEEEEEeCCCCCCCCCChh
Q 009655 165 QVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFGDQYKLFLLVNPEDDKPVAVVVPRKTLQPETTAVP 244 (529)
Q Consensus 165 ~~Fg~dtF~~t~~~~~~~gvi~rGnLR~~~e~~y~~l~~~l~~~fGd~y~lfl~~~~~~~kPv~~vvP~~~~~p~~~~~~ 244 (529)
.+++.++|+.....+ ...+++.|.+.......+..+...+ ..|..+ ...|+.. + .. ..
T Consensus 82 ~~~~~~~f~~~~~~~-~~~~~~~Gp~~n~i~~~~~~~~~~~--~~G~~~---------~~~~~~~---~--v~---~~-- 139 (375)
T COG0750 82 PEPRPRAFNAKSVWQ-RIAIVFAGPLFNFILAIVLFVVLFF--VIGLVP---------VASPVVG---E--VA---PK-- 139 (375)
T ss_pred cCcchhhhhcccccc-hhheeechHHHHHHHHHHHHHhhhe--Eeeeee---------eccCeee---e--cC---CC--
Confidence 588899999999999 9999999999988766655544433 223111 1122211 0 00 00
Q ss_pred HHHHHHHHHHHHHHHHHhhccccccccccccccchHHHHh------hHHHHHHHHHHHHHH--HHHHHHHHHHcCCcccc
Q 009655 245 EWFAAGAFGLVTVFTLLLRNVPALQSNLLSTFDNLNLLTN------GLPGALVTALVIGVH--ELGHILAAKSTGVELGV 316 (529)
Q Consensus 245 ~~~~~~ll~l~Tl~Tt~~~~~~~L~~~~~~~~~~~~~l~~------glp~aL~L~~iL~iH--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 0111223334433322221 11222322221 22222 35677788 99999999988888888
Q ss_pred ccccccceeeeeeeEEe--eccccCC-----cccceeeEecchhhHHHHHHHHHHHHhhcCCCCCCcccccccchhhhhh
Q 009655 317 PYFVPSWQIGSFGAITR--IRNIVSK-----REDLLKVAAAGPLAGFSLGFVLFLVGFIFPPSDGIGIVVDASVFHESFL 389 (529)
Q Consensus 317 P~FIP~i~LGtFGAvi~--~~s~~~~-----RkalfdIAiAGPLAg~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-AVEKTGRLVKLTLKMLK----KLITGDLSLKNL 281 (375)
T ss_pred cceec-cCCCCEEEEeeeeeeeeccCCCCccceeeeccCHHHHHHH-HHHHHHHHHHHHHHHHH----Hheecccccccc
Confidence 98877 45555555443 3344444 788999999999994 33333333433321000 000011122222
Q ss_pred hhhhHHhhhccccCCCCCccchHHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHhhhhH
Q 009655 390 AGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAINSIPAGELDGGRIAFALWGRKA 448 (529)
Q Consensus 390 ~g~la~l~LG~~l~~g~~v~lhPLa~agwinLvltafNLLPigpLDGGrIlrAllgrr~ 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 22221111111100 1235689999999999999999999999999999999986654
No 14
>PF13398 Peptidase_M50B: Peptidase M50B-like
Probab=97.40 E-value=0.00053 Score=66.83 Aligned_cols=65 Identities=31% Similarity=0.274 Sum_probs=52.9
Q ss_pred HHHHHHHHHHHHHHHHcCCccccccccccceeee-eeeEEeeccccCCcccceeeEecchhhHHHHHHHHHHHH
Q 009655 294 LVIGVHELGHILAAKSTGVELGVPYFVPSWQIGS-FGAITRIRNIVSKREDLLKVAAAGPLAGFSLGFVLFLVG 366 (529)
Q Consensus 294 ~iL~iHElGH~laAr~~Gvk~s~P~FIP~i~LGt-FGAvi~~~s~~~~RkalfdIAiAGPLAg~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 4588999999999999999998 665554 466777766 6666789999999999999887776655
No 15
>COG0750 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]
Probab=96.16 E-value=0.016 Score=60.19 Aligned_cols=82 Identities=27% Similarity=0.385 Sum_probs=54.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHcCCccccccc--cc-------c------ceeeeeeeEEeeccccC-----------
Q 009655 286 LPGALVTALVIGVHELGHILAAKSTGVELGVPYF--VP-------S------WQIGSFGAITRIRNIVS----------- 339 (529)
Q Consensus 286 lp~aL~L~~iL~iHElGH~laAr~~Gvk~s~P~F--IP-------~------i~LGtFGAvi~~~s~~~----------- 339 (529)
+.+.+.+...+.+||+||+|.||++|+++..... -| . +...++|++.++.....
T Consensus 6 i~~i~~~~~lv~~he~gh~~~a~~~~~~v~~f~ig~g~~l~~~~~~~~~~~~i~~~plggyv~~~~~~~~~~~~~~~~~~ 85 (375)
T COG0750 6 IAFIIALGVLVFVHELGHFWVARRCGVKVERFSIGFGPKLFSRKDKGGTEYVLSAIPLGGYVKMLGEDAEEVVLKGPEPR 85 (375)
T ss_pred HHHHHHHHHHHHHHHHhhHHHHHhcCceeEEEEeccCcceEEEEcCCceEEEEeecCccceEEEecCccccccccccCcc
Confidence 3345566678899999999999999999984211 12 0 12335666655532211
Q ss_pred -------CcccceeeEecchhhHHHHHHHHHHHHh
Q 009655 340 -------KREDLLKVAAAGPLAGFSLGFVLFLVGF 367 (529)
Q Consensus 340 -------~RkalfdIAiAGPLAg~llAl~ll~iGl 367 (529)
+-...+.+.+|||+.|++.++...+...
T Consensus 86 ~~~f~~~~~~~~~~~~~~Gp~~n~i~~~~~~~~~~ 120 (375)
T COG0750 86 PRAFNAKSVWQRIAIVFAGPLFNFILAIVLFVVLF 120 (375)
T ss_pred hhhhhcccccchhheeechHHHHHHHHHHHHHhhh
Confidence 1123678999999999998877766554
No 16
>KOG2921 consensus Intramembrane metalloprotease (sterol-regulatory element-binding protein (SREBP) protease) [Posttranslational modification, protein turnover, chaperones]
Probab=95.88 E-value=0.0069 Score=64.96 Aligned_cols=82 Identities=28% Similarity=0.313 Sum_probs=54.0
Q ss_pred HhhHHHH-HHHHHHHHHHHHHHHHHHHHcCCccccccccccceeeeeeeEEeeccc----cCCcccceeeEecchhhHHH
Q 009655 283 TNGLPGA-LVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAITRIRNI----VSKREDLLKVAAAGPLAGFS 357 (529)
Q Consensus 283 ~~glp~a-L~L~~iL~iHElGH~laAr~~Gvk~s~P~FIP~i~LGtFGAvi~~~s~----~~~RkalfdIAiAGPLAg~l 357 (529)
+.+++|. ..++..+.+||+||+|||.+.|+++. +|=-++..---||++.+... .+. -....|.-||-.-||+
T Consensus 120 l~~I~yf~t~lvi~~vvHElGHalAA~segV~vn--gfgIfi~aiyPgafvdl~~dhLqsl~~-fr~LrIfcAGIWHNfv 196 (484)
T KOG2921|consen 120 LSGIAYFLTSLVITVVVHELGHALAAASEGVQVN--GFGIFIAAIYPGAFVDLDNDHLQSLPS-FRALRIFCAGIWHNFV 196 (484)
T ss_pred cccchhhhhhHHHHHHHHHhhHHHHHHhcCceee--eeEEEEEEEcCchhhhhhhhHHhhcch-HHHHHHHhhhHHHHHH
Confidence 3445544 45667889999999999999999998 21001111123667665432 122 2346899999999999
Q ss_pred HHHHHHHHHh
Q 009655 358 LGFVLFLVGF 367 (529)
Q Consensus 358 lAl~ll~iGl 367 (529)
+|+++.+.-.
T Consensus 197 fallc~lal~ 206 (484)
T KOG2921|consen 197 FALLCVLALF 206 (484)
T ss_pred HHHHHHHHHH
Confidence 9988765544
No 17
>PF11667 DUF3267: Protein of unknown function (DUF3267); InterPro: IPR021683 This family of proteins has no known function.
Probab=71.75 E-value=2 Score=37.96 Aligned_cols=69 Identities=20% Similarity=0.186 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHHHHHHHcCCccccccccccceeeeeeeEEeeccccCCcccceeeEecchhhHHHHHHHHHHHHhh
Q 009655 293 ALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAITRIRNIVSKREDLLKVAAAGPLAGFSLGFVLFLVGFI 368 (529)
Q Consensus 293 ~~iL~iHElGH~laAr~~Gvk~s~P~FIP~i~LGtFGAvi~~~s~~~~RkalfdIAiAGPLAg~llAl~ll~iGl~ 368 (529)
+..+.+||+-|++..+.+|.+....+- +....+-.+.. .+ .+-.|..+.+...-|. ++++++.++++..
T Consensus 4 ~~~~~~HEliH~l~~~~~~~~~~~~~g---~~~~~~~~~~~-~~-~~~sk~~~~i~~l~P~--ivl~~~~~~~~~~ 72 (111)
T PF11667_consen 4 IVLIPLHELIHGLFFKLFGKKPKVKFG---FKWKLGPFYAT-CN-EPISKWRFIIILLAPF--IVLTILPLILGFF 72 (111)
T ss_pred EeeHHHHHHHHHHHHHHhCCCCceEEE---EEeeeEEEEEe-cC-cEEeHHHHHHHHHHHH--HHHHHHHHHHHHH
Confidence 345789999999999999996531110 00011111222 22 2323455666666675 4555555555444
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=62.72 E-value=4.5 Score=36.60 Aligned_cols=21 Identities=24% Similarity=0.436 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHHHHHcCCcc
Q 009655 294 LVIGVHELGHILAAKSTGVEL 314 (529)
Q Consensus 294 ~iL~iHElGH~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 468899999997655444433
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=59.82 E-value=5.5 Score=36.78 Aligned_cols=22 Identities=32% Similarity=0.364 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHHHHHHHcCCcc
Q 009655 293 ALVIGVHELGHILAAKSTGVEL 314 (529)
Q Consensus 293 ~~iL~iHElGH~laAr~~Gvk~ 314 (529)
+..+++||+||.+=.++...+.
T Consensus 104 ~~~~~~HEiGHaLGL~H~~~~~ 125 (156)
T cd04279 104 LQAIALHELGHALGLWHHSDRP 125 (156)
T ss_pred HHHHHHHHhhhhhcCCCCCCCc
Confidence 4578899999999888887776
No 20
>PF13485 Peptidase_MA_2: Peptidase MA superfamily
Probab=50.04 E-value=13 Score=31.53 Aligned_cols=18 Identities=28% Similarity=0.233 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHHHHcCC
Q 009655 295 VIGVHELGHILAAKSTGV 312 (529)
Q Consensus 295 iL~iHElGH~laAr~~Gv 312 (529)
-+++||++|.|.....+-
T Consensus 27 ~~l~HE~~H~~~~~~~~~ 44 (128)
T PF13485_consen 27 RVLAHELAHQWFGNYFGG 44 (128)
T ss_pred HHHHHHHHHHHHHHHcCC
Confidence 688999999999999763
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=49.73 E-value=11 Score=34.60 Aligned_cols=21 Identities=29% Similarity=0.300 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHHHHHHHcCC
Q 009655 292 TALVIGVHELGHILAAKSTGV 312 (529)
Q Consensus 292 L~~iL~iHElGH~laAr~~Gv 312 (529)
-....++||+||++=-.+-.-
T Consensus 93 ~~~~~~~HEiGHaLGL~H~~~ 113 (165)
T cd04268 93 RLRNTAEHELGHALGLRHNFA 113 (165)
T ss_pred HHHHHHHHHHHHHhcccccCc
Confidence 446788999999976655554
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=49.56 E-value=7.5 Score=36.01 Aligned_cols=23 Identities=22% Similarity=0.358 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHHHHHHHcCCccc
Q 009655 293 ALVIGVHELGHILAAKSTGVELG 315 (529)
Q Consensus 293 ~~iL~iHElGH~laAr~~Gvk~s 315 (529)
+..+++||+||++=-.+-..+.+
T Consensus 107 ~~~~~~HEiGHaLGL~H~~~~~~ 129 (157)
T cd04278 107 LFSVAAHEIGHALGLGHSSDPDS 129 (157)
T ss_pred HHHHHHHHhccccccCCCCCCcC
Confidence 45688999999986655444443
No 23
>PTZ00429 beta-adaptin; Provisional
Probab=49.27 E-value=15 Score=43.20 Aligned_cols=32 Identities=28% Similarity=0.251 Sum_probs=15.9
Q ss_pred ChhhhhcccCCCCCCCCCCcccCCCCCCCccC
Q 009655 75 NDKEKEVHDGQENQPATASDQEDDKSQPDSQL 106 (529)
Q Consensus 75 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 106 (529)
.|||++|+++.++.|++.++..++++..++++
T Consensus 608 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 639 (746)
T PTZ00429 608 LDEEDTEDDDAVELPSTPSMGTQDGSPAPSAA 639 (746)
T ss_pred cccccccchhhccCCCCCCCCCCCCCCCcccc
Confidence 34444444455555666555555544443443
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=48.96 E-value=8.5 Score=36.40 Aligned_cols=14 Identities=36% Similarity=0.344 Sum_probs=10.7
Q ss_pred HHHHHHHHHHHHHH
Q 009655 294 LVIGVHELGHILAA 307 (529)
Q Consensus 294 ~iL~iHElGH~laA 307 (529)
.-.++||+||++=-
T Consensus 70 g~TltHEvGH~LGL 83 (154)
T PF05572_consen 70 GKTLTHEVGHWLGL 83 (154)
T ss_dssp SHHHHHHHHHHTT-
T ss_pred ccchhhhhhhhhcc
Confidence 46889999998643
No 25
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=44.29 E-value=22 Score=42.77 Aligned_cols=18 Identities=28% Similarity=0.366 Sum_probs=8.6
Q ss_pred cccccccccCCCCccccc
Q 009655 5 TTFRGNLSLLPHCSSCCD 22 (529)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~ 22 (529)
+||-|.-..+--|++-.+
T Consensus 1354 aTi~v~R~~~Dlct~~~D 1371 (1516)
T KOG1832|consen 1354 ATIPVDRCLLDLCTEPTD 1371 (1516)
T ss_pred eeeecccchhhhhcCCcc
Confidence 444444444455555433
No 26
>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=44.06 E-value=17 Score=36.76 Aligned_cols=54 Identities=26% Similarity=0.338 Sum_probs=38.2
Q ss_pred eeeeccccccCceEEEEeccCCchHHHHHHHHHHHHhhhCCceEEEEEec-CCCCCcEE
Q 009655 171 TFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFGDQYKLFLLVN-PEDDKPVA 228 (529)
Q Consensus 171 tF~~t~~~~~~~gvi~rGnLR~~~e~~y~~l~~~l~~~fGd~y~lfl~~~-~~~~kPv~ 228 (529)
..|+|++..-.=-+.|.||= |.|.++|.+|+.+=. +++|+|++==- .++=||+-
T Consensus 159 is~atgi~~~~mi~w~ign~-G~~~~a~gtVs~k~~---~~~YrV~i~WVd~eGWkP~k 213 (217)
T PF07423_consen 159 ISYATGISEDNMIVWFIGNN-GSPQKAIGTVSDKDT---GKKYRVYIEWVDNEGWKPVK 213 (217)
T ss_pred HHHhhCCChhheEEEhhhcC-CcccceeEEeccCCC---CceEEEEEEEecCCCcccee
Confidence 36889988777789999996 777999999876533 57899974221 12227764
No 27
>PF01435 Peptidase_M48: Peptidase family M48 This is family M48 in the peptidase classification. ; InterPro: IPR001915 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M48 (Ste24 endopeptidase family, clan M-); members of both subfamily are represented. The members of this set of proteins are mostly described as probable protease htpX homologue (3.4.24 from EC) or CAAX prenyl protease 1, which proteolytically removes the C-terminal three residues of farnesylated proteins. They are integral membrane proteins associated with the endoplasmic reticulum and Golgi, binding one zinc ion per subunit. In Saccharomyces cerevisiae (Baker's yeast) Ste24p is required for the first NH2-terminal proteolytic processing event within the a-factor precursor, which takes place after COOH-terminal CAAX modification is complete. The Ste24p contains multiple predicted membrane spans, a zinc metalloprotease motif (HEXXH), and a COOH-terminal ER retrieval signal (KKXX). The HEXXH protease motif is critical for Ste24p activity, since Ste24p fails to function when conserved residues within this motif are mutated. The Ste24p homologues occur in a diverse group of organisms, including Escherichia coli, Schizosaccharomyces pombe (Fission yeast), Haemophilus influenzae, and Homo sapiens (Human), which indicates that the gene is highly conserved throughout evolution. Ste24p and the proteins related to it define a subfamily of proteins that are likely to function as intracellular, membrane-associated zinc metalloproteases []. HtpX is a zinc-dependent endoprotease member of the membrane-localized proteolytic system in E. coli, which participates in the proteolytic quality control of membrane proteins in conjunction with FtsH, a membrane-bound and ATP-dependent protease. Biochemical characterisation revealed that HtpX undergoes self-degradation upon cell disruption or membrane solubilization. It can also degraded casein and cleaves solubilized membrane proteins, for example, SecY []. Expression of HtpX in the plasma membrane is under the control of CpxR, with the metalloproteinase active site of HtpX located on the cytosolic side of the membrane. This suggests a potential role for HtpX in the response to mis-folded proteins [].; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis, 0016020 membrane; PDB: 3CQB_A 3C37_B.
Probab=43.83 E-value=16 Score=34.83 Aligned_cols=12 Identities=50% Similarity=0.717 Sum_probs=10.3
Q ss_pred HHHHHHHHHHHH
Q 009655 294 LVIGVHELGHIL 305 (529)
Q Consensus 294 ~iL~iHElGH~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 468899999986
No 28
>PF06114 DUF955: Domain of unknown function (DUF955); InterPro: IPR010359 This is a family of bacterial and viral proteins with undetermined function. A conserved H-E-X-X-H motif is suggestive of a catalytic active site and shows similarity to IPR001915 from INTERPRO.; PDB: 3DTE_A 3DTK_A 3DTI_A.
Probab=41.98 E-value=16 Score=30.71 Aligned_cols=17 Identities=41% Similarity=0.542 Sum_probs=12.6
Q ss_pred HHHHHHHHHHHHHHHcC
Q 009655 295 VIGVHELGHILAAKSTG 311 (529)
Q Consensus 295 iL~iHElGH~laAr~~G 311 (529)
..++||+||++.-....
T Consensus 44 f~laHELgH~~~~~~~~ 60 (122)
T PF06114_consen 44 FTLAHELGHILLHHGDE 60 (122)
T ss_dssp HHHHHHHHHHHHHH-HH
T ss_pred HHHHHHHHHHHhhhccc
Confidence 46789999999766554
No 29
>PF11085 YqhR: Conserved membrane protein YqhR; InterPro: IPR024563 This family of proteins is conserved in the Bacillaceae family of the Firmicutes. Their function is not known.
Probab=41.67 E-value=2.4e+02 Score=27.86 Aligned_cols=100 Identities=21% Similarity=0.365 Sum_probs=53.7
Q ss_pred HHHHHHHHHHHHhhcCCCCCChHHHHHHHh-hhhHHHHHH-HHHHHHHHHHHHh----h--------hh-------HHHH
Q 009655 415 IWAWAGLLINAINSIPAGELDGGRIAFALW-GRKASTRLT-GVSIVLLGLSSLF----S--------DV-------TFYW 473 (529)
Q Consensus 415 ~agwinLvltafNLLPigpLDGGrIlrAll-grr~a~~i~-~~~~~lLGl~~l~----~--------~~-------~l~W 473 (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 4566777888899999999 78888764 332233333 1222222222211 1 11 1234
Q ss_pred HHHHHHHHhCCCCCCCCCCCCCChhHHHHHHHHHHHHHHhhcccCCC
Q 009655 474 VVLVFFLQRGPIAPLSEEITDPDDKYIALGVLVLFLGLLVCLPYPFP 520 (529)
Q Consensus 474 ~llilfl~rgp~~P~~nevt~~~~~r~~lg~~~l~l~ll~llP~P~~ 520 (529)
+++ |...+|..|..+.+.+++..-.. .-+.+.+.-=+|+=+-++
T Consensus 110 ~iv--F~~lnP~fp~~~~~~~l~~nTii-T~~CiyiLyGlFIGYSIs 153 (173)
T PF11085_consen 110 AIV--FFVLNPIFPMIKPVTELDWNTII-TTLCIYILYGLFIGYSIS 153 (173)
T ss_pred HHH--HHHhcccccCChhhhhCchhHHH-HHHHHHHHHHHHhceeeh
Confidence 333 33457888888888888855543 333444444444444443
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=41.05 E-value=15 Score=34.92 Aligned_cols=22 Identities=32% Similarity=0.451 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHHHHHHcCCccc
Q 009655 294 LVIGVHELGHILAAKSTGVELG 315 (529)
Q Consensus 294 ~iL~iHElGH~laAr~~Gvk~s 315 (529)
.-.++||+||.+=-++-+....
T Consensus 114 ~~t~~HEiGHaLGL~H~~~~~~ 135 (186)
T cd04277 114 YQTIIHEIGHALGLEHPGDYNG 135 (186)
T ss_pred HHHHHHHHHHHhcCCCCCcCCC
Confidence 4678999999987666555443
No 31
>PF14247 DUF4344: Domain of unknown function (DUF4344)
Probab=40.58 E-value=28 Score=35.19 Aligned_cols=25 Identities=32% Similarity=0.406 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcc
Q 009655 289 ALVTALVIGVHELGHILAAKSTGVEL 314 (529)
Q Consensus 289 aL~L~~iL~iHElGH~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 556667788999999998753 4444
No 32
>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=40.53 E-value=22 Score=34.97 Aligned_cols=19 Identities=32% Similarity=0.261 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHHHHHHcCC
Q 009655 294 LVIGVHELGHILAAKSTGV 312 (529)
Q Consensus 294 ~iL~iHElGH~laAr~~Gv 312 (529)
-.+.+||.||+++|...+-
T Consensus 29 ~~~A~HEAGhAvva~~l~~ 47 (213)
T PF01434_consen 29 RRIAYHEAGHAVVAYLLPP 47 (213)
T ss_dssp HHHHHHHHHHHHHHHHSSS
T ss_pred HHHHHHHHHHHHHHHHhcc
Confidence 3678999999999999873
No 33
>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=40.11 E-value=15 Score=33.09 Aligned_cols=20 Identities=30% Similarity=0.441 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHHHcCCccc
Q 009655 296 IGVHELGHILAAKSTGVELG 315 (529)
Q Consensus 296 L~iHElGH~laAr~~Gvk~s 315 (529)
+++||+||++=..+-..+..
T Consensus 89 ~~~HEigHaLGl~H~~~~~d 108 (140)
T smart00235 89 VAAHELGHALGLYHEQSRSD 108 (140)
T ss_pred cHHHHHHHHhcCCcCCCCCc
Confidence 78999999986665554443
No 34
>cd00203 ZnMc Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease.
Probab=39.57 E-value=15 Score=33.54 Aligned_cols=21 Identities=29% Similarity=0.219 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHHHHHHHcCC
Q 009655 292 TALVIGVHELGHILAAKSTGV 312 (529)
Q Consensus 292 L~~iL~iHElGH~laAr~~Gv 312 (529)
....+++||+||.+=.++-.-
T Consensus 95 ~~~~~~~HElGH~LGl~H~~~ 115 (167)
T cd00203 95 EGAQTIAHELGHALGFYHDHD 115 (167)
T ss_pred cchhhHHHHHHHHhCCCccCc
Confidence 345788999999987665544
No 35
>PF13582 Reprolysin_3: Metallo-peptidase family M12B Reprolysin-like; PDB: 3P24_C.
Probab=38.62 E-value=16 Score=32.00 Aligned_cols=14 Identities=36% Similarity=0.423 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHHHH
Q 009655 295 VIGVHELGHILAAK 308 (529)
Q Consensus 295 iL~iHElGH~laAr 308 (529)
..++||+||.+=+.
T Consensus 109 ~~~~HEiGH~lGl~ 122 (124)
T PF13582_consen 109 DTFAHEIGHNLGLN 122 (124)
T ss_dssp THHHHHHHHHTT--
T ss_pred eEeeehhhHhcCCC
Confidence 67899999986443
No 36
>PF12315 DUF3633: Protein of unknown function (DUF3633); InterPro: IPR022087 This domain family is found in bacteria and eukaryotes, and is approximately 210 amino acids in length. The family is found in association with PF00412 from PFAM.
Probab=37.47 E-value=24 Score=35.69 Aligned_cols=29 Identities=31% Similarity=0.339 Sum_probs=20.1
Q ss_pred HHhhHHHHHHHHHHHHHHHHHHHHHHHHcCCc
Q 009655 282 LTNGLPGALVTALVIGVHELGHILAAKSTGVE 313 (529)
Q Consensus 282 l~~glp~aL~L~~iL~iHElGH~laAr~~Gvk 313 (529)
++.|+|-. ++.++++||++|+|. |..|.+
T Consensus 84 vl~GLPrl--l~gsiLAHE~mHa~L-rl~g~~ 112 (212)
T PF12315_consen 84 VLYGLPRL--LTGSILAHELMHAWL-RLNGFP 112 (212)
T ss_pred EECCCCHH--HHhhHHHHHHHHHHh-cccCCC
Confidence 34456643 447899999999998 455544
No 37
>PF13574 Reprolysin_2: Metallo-peptidase family M12B Reprolysin-like; PDB: 1KAP_P 1JIW_P 1AKL_A 1OM7_A 1OM8_A 1O0T_A 1OM6_A 1H71_P 1O0Q_A 1OMJ_A ....
Probab=36.29 E-value=19 Score=34.38 Aligned_cols=21 Identities=33% Similarity=0.286 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHHHHHHHcCCc
Q 009655 293 ALVIGVHELGHILAAKSTGVE 313 (529)
Q Consensus 293 ~~iL~iHElGH~laAr~~Gvk 313 (529)
-.-.++||+||.+=|.+-+-.
T Consensus 111 ~~~~~aHElGH~lGa~Hd~~~ 131 (173)
T PF13574_consen 111 GIDTFAHELGHQLGAPHDFDN 131 (173)
T ss_dssp HHHHHHHHHHHHHT---SSSS
T ss_pred eeeeehhhhHhhcCCCCCCCC
Confidence 345689999999999887764
No 38
>PF14891 Peptidase_M91: Effector protein
Probab=36.26 E-value=23 Score=33.83 Aligned_cols=17 Identities=29% Similarity=0.288 Sum_probs=13.8
Q ss_pred HHHHHHHHHHHHHHHHH
Q 009655 293 ALVIGVHELGHILAAKS 309 (529)
Q Consensus 293 ~~iL~iHElGH~laAr~ 309 (529)
-++++.|||+|++-...
T Consensus 103 p~v~L~HEL~HA~~~~~ 119 (174)
T PF14891_consen 103 PFVVLYHELIHAYDYMN 119 (174)
T ss_pred HHHHHHHHHHHHHHHHC
Confidence 36788999999997654
No 39
>PF13688 Reprolysin_5: Metallo-peptidase family M12; PDB: 2FV5_B 3EWJ_A 3KME_A 3L0T_B 1BKC_E 3G42_D 2I47_D 2FV9_B 3LEA_A 1ZXC_B ....
Probab=35.16 E-value=19 Score=34.18 Aligned_cols=21 Identities=33% Similarity=0.414 Sum_probs=13.3
Q ss_pred HHHHHHHHHHHHHHHHHcCCc
Q 009655 293 ALVIGVHELGHILAAKSTGVE 313 (529)
Q Consensus 293 ~~iL~iHElGH~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 357889999999999876654
No 40
>PF02031 Peptidase_M7: Streptomyces extracellular neutral proteinase (M7) family; InterPro: IPR000013 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M7 (snapalysin family, clan MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA. With a molecular weight of around 16kDa, Streptomyces extracellular neutral protease is one of the smallest known proteases []; it is capable of hydrolysing milk proteins []. The enzyme is synthesised as a proenzyme with a signal peptide, a propeptide and an active domain that contains the conserved HEXXH motif characteristic of metalloproteases. Although family M7 shows active site sequence similarity to other members, it differs in one major respect: the third zinc ligand appears to be an aspartate residue rather than the usual histidine.; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis, 0005576 extracellular region; PDB: 1C7K_A 1KUH_A.
Probab=33.33 E-value=26 Score=33.01 Aligned_cols=10 Identities=80% Similarity=1.291 Sum_probs=8.8
Q ss_pred HHHHHHHHHH
Q 009655 296 IGVHELGHIL 305 (529)
Q Consensus 296 L~iHElGH~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 7799999986
No 41
>cd04327 ZnMc_MMP_like_3 Zinc-dependent metalloprotease; MMP_like sub-family 3. A group of bacterial and fungal metalloproteinase domains similar to matrix metalloproteinases and astacin.
Probab=32.99 E-value=24 Score=34.20 Aligned_cols=20 Identities=25% Similarity=0.302 Sum_probs=13.8
Q ss_pred HHHHHHHHHHHHHHHHcCCc
Q 009655 294 LVIGVHELGHILAAKSTGVE 313 (529)
Q Consensus 294 ~iL~iHElGH~laAr~~Gvk 313 (529)
...++||+||++=-.+-.-+
T Consensus 93 ~~~i~HElgHaLG~~HEh~r 112 (198)
T cd04327 93 SRVVLHEFGHALGFIHEHQS 112 (198)
T ss_pred HHHHHHHHHHHhcCcccccC
Confidence 35778999999765544433
No 42
>cd04269 ZnMc_adamalysin_II_like Zinc-dependent metalloprotease; adamalysin_II_like subfamily. Adamalysin II is a snake venom zinc endopeptidase. This subfamily contains other snake venom metalloproteinases, as well as membrane-anchored metalloproteases belonging to the ADAM family. ADAMs (A Disintegrin And Metalloprotease) are glycoproteins, which play roles in cell signaling, cell fusion, and cell-cell interactions.
Probab=30.69 E-value=33 Score=32.64 Aligned_cols=20 Identities=35% Similarity=0.350 Sum_probs=15.4
Q ss_pred HHHHHHHHHHHHHHHHHcCC
Q 009655 293 ALVIGVHELGHILAAKSTGV 312 (529)
Q Consensus 293 ~~iL~iHElGH~laAr~~Gv 312 (529)
.+.+++||+||-+=+.+-+.
T Consensus 131 ~a~~~AHElGH~lG~~HD~~ 150 (194)
T cd04269 131 FAVTMAHELGHNLGMEHDDG 150 (194)
T ss_pred HHHHHHHHHHhhcCCCcCCC
Confidence 45788999999987775544
No 43
>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=30.26 E-value=32 Score=34.72 Aligned_cols=18 Identities=28% Similarity=0.503 Sum_probs=14.4
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 009655 292 TALVIGVHELGHILAAKS 309 (529)
Q Consensus 292 L~~iL~iHElGH~laAr~ 309 (529)
.++..++||+||-+=+.+
T Consensus 166 ~~a~t~AHElGHnlGm~H 183 (244)
T cd04270 166 ESDLVTAHELGHNFGSPH 183 (244)
T ss_pred HHHHHHHHHHHHhcCCCC
Confidence 456789999999987764
No 44
>PRK03001 M48 family peptidase; Provisional
Probab=30.17 E-value=32 Score=35.31 Aligned_cols=12 Identities=33% Similarity=0.426 Sum_probs=10.0
Q ss_pred HHHHHHHHHHHH
Q 009655 294 LVIGVHELGHIL 305 (529)
Q Consensus 294 ~iL~iHElGH~l 305 (529)
..+++||+||.-
T Consensus 125 ~aVlAHElgHi~ 136 (283)
T PRK03001 125 RGVMAHELAHVK 136 (283)
T ss_pred HHHHHHHHHHHh
Confidence 468899999974
No 45
>PRK03982 heat shock protein HtpX; Provisional
Probab=29.27 E-value=34 Score=35.21 Aligned_cols=12 Identities=42% Similarity=0.362 Sum_probs=9.9
Q ss_pred HHHHHHHHHHHH
Q 009655 294 LVIGVHELGHIL 305 (529)
Q Consensus 294 ~iL~iHElGH~l 305 (529)
..++.||+||.-
T Consensus 126 ~AVlAHElgHi~ 137 (288)
T PRK03982 126 EGVIAHELTHIK 137 (288)
T ss_pred HHHHHHHHHHHH
Confidence 468899999974
No 46
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=29.09 E-value=40 Score=30.94 Aligned_cols=19 Identities=21% Similarity=0.123 Sum_probs=14.8
Q ss_pred HHHHHHHHHHHHHHHHHHc
Q 009655 292 TALVIGVHELGHILAAKST 310 (529)
Q Consensus 292 L~~iL~iHElGH~laAr~~ 310 (529)
.+.-.++|||.|+++-...
T Consensus 59 ~~~~tL~HEm~H~~~~~~~ 77 (157)
T PF10263_consen 59 ELIDTLLHEMAHAAAYVFG 77 (157)
T ss_pred HHHHHHHHHHHHHHhhhcc
Confidence 4456889999999996553
No 47
>PF09471 Peptidase_M64: IgA Peptidase M64; InterPro: IPR019026 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This is a family of highly selective metallo-endopeptidases belonging to the MEROPS peptidase family M64 (IgA peptidase, clan MA). The primary structure of the Clostridium ramosum IgA peptidase shows no significant overall similarity to any other known metallo-endopeptidase []. ; PDB: 3P1V_A 4DF9_D.
Probab=28.77 E-value=24 Score=36.41 Aligned_cols=14 Identities=36% Similarity=0.596 Sum_probs=10.8
Q ss_pred HHHHHHHHHHHHHH
Q 009655 294 LVIGVHELGHILAA 307 (529)
Q Consensus 294 ~iL~iHElGH~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 46789999998753
No 48
>COG2856 Predicted Zn peptidase [Amino acid transport and metabolism]
Probab=28.73 E-value=31 Score=34.72 Aligned_cols=16 Identities=38% Similarity=0.463 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHHHHcC
Q 009655 296 IGVHELGHILAAKSTG 311 (529)
Q Consensus 296 L~iHElGH~laAr~~G 311 (529)
.++||+||++.=+.-.
T Consensus 75 tlAHELGH~llH~~~~ 90 (213)
T COG2856 75 TLAHELGHALLHTDLN 90 (213)
T ss_pred HHHHHHhHHHhccccc
Confidence 5689999998654433
No 49
>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=28.41 E-value=26 Score=33.24 Aligned_cols=20 Identities=40% Similarity=0.531 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHHHHHHHcCC
Q 009655 293 ALVIGVHELGHILAAKSTGV 312 (529)
Q Consensus 293 ~~iL~iHElGH~laAr~~Gv 312 (529)
.+.+++||+||.+=+.+-+.
T Consensus 133 ~~~~~aHElGH~lG~~HD~~ 152 (192)
T cd04267 133 TALTMAHELGHNLGAEHDGG 152 (192)
T ss_pred ehhhhhhhHHhhcCCcCCCC
Confidence 35688999999998877654
No 50
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=28.23 E-value=35 Score=31.60 Aligned_cols=17 Identities=24% Similarity=-0.021 Sum_probs=13.9
Q ss_pred HHHHHHHHHHHHHHHHH
Q 009655 293 ALVIGVHELGHILAAKS 309 (529)
Q Consensus 293 ~~iL~iHElGH~laAr~ 309 (529)
+.-++.|||.|+++-..
T Consensus 59 l~~~l~HEm~H~~~~~~ 75 (146)
T smart00731 59 LRETLLHELCHAALYLF 75 (146)
T ss_pred HHhhHHHHHHHHHHHHh
Confidence 34588999999999864
No 51
>PF13583 Reprolysin_4: Metallo-peptidase family M12B Reprolysin-like
Probab=28.13 E-value=30 Score=33.97 Aligned_cols=18 Identities=28% Similarity=0.237 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHHHHHcCC
Q 009655 295 VIGVHELGHILAAKSTGV 312 (529)
Q Consensus 295 iL~iHElGH~laAr~~Gv 312 (529)
-.++||+||.+=|++-+-
T Consensus 139 ~~~aHEiGH~lGl~H~~~ 156 (206)
T PF13583_consen 139 QTFAHEIGHNLGLRHDFD 156 (206)
T ss_pred hHHHHHHHHHhcCCCCcc
Confidence 348899999998887766
No 52
>COG0830 UreF Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]
Probab=27.88 E-value=64 Score=32.92 Aligned_cols=32 Identities=31% Similarity=0.348 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHHHhhcCCCCCChHHHHHHHhh
Q 009655 414 VIWAWAGLLINAINSIPAGELDGGRIAFALWG 445 (529)
Q Consensus 414 a~agwinLvltafNLLPigpLDGGrIlrAllg 445 (529)
.++.-.|++.++.=|+|.||+||=||+..+-.
T Consensus 157 lya~~~~lv~aavRlipLgQ~~gq~il~~l~~ 188 (229)
T COG0830 157 LYAWASNLVSAAVRLIPLGQLDGQKILAQLEP 188 (229)
T ss_pred HHHHHHHHHHHHHHhcccCcHHHHHHHHHhhH
Confidence 34555699999999999999999999998843
No 53
>PRK12462 phosphoserine aminotransferase; Provisional
Probab=26.93 E-value=97 Score=33.49 Aligned_cols=63 Identities=13% Similarity=0.201 Sum_probs=43.4
Q ss_pred cCCCCHhHHHHhhccccccceeeeccccccCceEEEEeccCCchHHHHHHHHHHHHhhhC--CceEEEEEecC
Q 009655 151 YIRIPKETIDILKDQVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFG--DQYKLFLLVNP 221 (529)
Q Consensus 151 ~~~i~~ed~~~ik~~~Fg~dtF~~t~~~~~~~gvi~rGnLR~~~e~~y~~l~~~l~~~fG--d~y~lfl~~~~ 221 (529)
+..+|+|.++++++++.-|.. -+-+++=.+---.+=.+.|++.+++|+++|+ |.|.+++++-.
T Consensus 12 Pa~lp~~Vl~~~~~~~~~~~~--------~g~si~eisHRs~~F~~i~~~~~~~Lr~Ll~~P~~y~Vlfl~Gg 76 (364)
T PRK12462 12 PGALPDTVLEQVRQAVVELPE--------TGLSVLGMSHRSSWFSSLLAQAEADLRDLLGIPDEYGVVFLQGG 76 (364)
T ss_pred CcCCCHHHHHHHHHHHhcccc--------cCccccccccccHHHHHHHHHHHHHHHHHhCCCCCCeEEEEecc
Confidence 458999999999985543321 1123333333234568899999999999998 68988766654
No 54
>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=26.49 E-value=33 Score=34.57 Aligned_cols=27 Identities=19% Similarity=0.146 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCcc
Q 009655 288 GALVTALVIGVHELGHILAAKSTGVEL 314 (529)
Q Consensus 288 ~aL~L~~iL~iHElGH~laAr~~Gvk~ 314 (529)
+..-+..-++.||+||.+=-|+-.+..
T Consensus 128 ~~~~~~~hvi~HEiGH~IGfRHTD~~~ 154 (211)
T PF12388_consen 128 YSVNVIEHVITHEIGHCIGFRHTDYFN 154 (211)
T ss_pred CchhHHHHHHHHHhhhhccccccCcCC
Confidence 344456679999999999887765444
No 55
>COG0501 HtpX Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]
Probab=25.58 E-value=44 Score=33.58 Aligned_cols=12 Identities=50% Similarity=0.672 Sum_probs=9.6
Q ss_pred HHHHHHHHHHHH
Q 009655 294 LVIGVHELGHIL 305 (529)
Q Consensus 294 ~iL~iHElGH~l 305 (529)
..++.||+||..
T Consensus 158 ~aVlaHElgHi~ 169 (302)
T COG0501 158 EAVLAHELGHIK 169 (302)
T ss_pred HHHHHHHHHHHh
Confidence 358899999963
No 56
>PF01447 Peptidase_M4: Thermolysin metallopeptidase, catalytic domain This Prosite motif covers only the active site. This is family M4 in the peptidase classification. ; InterPro: IPR013856 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases that belong to the MEROPS peptidase family M4 (thermolysin family, clan MA(E)). The protein fold of the peptidase domain of thermolysin, is the type example for members of the clan MA. The thermolysin family is composed only of secreted eubacterial endopeptidases. The zinc-binding residues are H-142, H-146 and E-166, with E-143 acting as the catalytic residue. Thermolysin also contains 4 calcium-binding sites, which contribute to its unusual thermostability. The family also includes enzymes from a number of pathogens, including Legionella and Listeria, and the protein pseudolysin, all with a substrate specificity for an aromatic residue in the P1' position. Three-dimensional structure analysis has shown that the enzymes undergo a hinge-bend motion during catalysis. Pseudolysin has a broader specificity, acting on large molecules such as elastin and collagen, possibly due to its wider active site cleft []. This entry represents a domain found in peptidase M4 family members.; GO: 0004222 metalloendopeptidase activity; PDB: 3NQX_A 3NQZ_B 3NQY_B 1BQB_A 1U4G_A 1EZM_A 3DBK_A 1ESP_A 1NPC_A 1LND_E ....
Probab=25.49 E-value=44 Score=31.68 Aligned_cols=12 Identities=33% Similarity=0.373 Sum_probs=10.1
Q ss_pred HHHHHHHHHHHH
Q 009655 295 VIGVHELGHILA 306 (529)
Q Consensus 295 iL~iHElGH~la 306 (529)
=++.|||+|.++
T Consensus 137 DVvaHEltHGVt 148 (150)
T PF01447_consen 137 DVVAHELTHGVT 148 (150)
T ss_dssp HHHHHHHHHHHH
T ss_pred ceeeeccccccc
Confidence 377899999986
No 57
>PRK04897 heat shock protein HtpX; Provisional
Probab=25.46 E-value=43 Score=34.80 Aligned_cols=12 Identities=33% Similarity=0.274 Sum_probs=9.7
Q ss_pred HHHHHHHHHHHH
Q 009655 294 LVIGVHELGHIL 305 (529)
Q Consensus 294 ~iL~iHElGH~l 305 (529)
..++.||+||.-
T Consensus 138 ~aVlAHElgHi~ 149 (298)
T PRK04897 138 EGVIGHEISHIR 149 (298)
T ss_pred HHHHHHHHHHHh
Confidence 468899999963
No 58
>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=25.13 E-value=38 Score=37.41 Aligned_cols=17 Identities=29% Similarity=0.442 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHHcC
Q 009655 295 VIGVHELGHILAAKSTG 311 (529)
Q Consensus 295 iL~iHElGH~laAr~~G 311 (529)
.+..||.||++++..++
T Consensus 313 ~~A~hEaGhAlv~~~l~ 329 (495)
T TIGR01241 313 LVAYHEAGHALVGLLLK 329 (495)
T ss_pred HHHHHHHhHHHHHHhcC
Confidence 67899999999998874
No 59
>PLN02452 phosphoserine transaminase
Probab=25.11 E-value=1.2e+02 Score=32.59 Aligned_cols=63 Identities=10% Similarity=0.228 Sum_probs=45.0
Q ss_pred cCCCCHhHHHHhhccccccceeeeccccccCceEEEEeccCCchHHHHHHHHHHHHhhhC--CceEEEEEecC
Q 009655 151 YIRIPKETIDILKDQVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFG--DQYKLFLLVNP 221 (529)
Q Consensus 151 ~~~i~~ed~~~ik~~~Fg~dtF~~t~~~~~~~gvi~rGnLR~~~e~~y~~l~~~l~~~fG--d~y~lfl~~~~ 221 (529)
+..+|++.+++++.+.+-|. .-+-+++-.+---.+=.++++.++++|++.++ +.|.+++++-.
T Consensus 15 P~~lp~~Vl~~~~~~~~~~~--------~~g~s~~~~sHRs~~f~~i~~~~~~~L~~l~~~p~~y~v~~l~Gs 79 (365)
T PLN02452 15 PATLPANVLAKAQAELYNWE--------GSGMSVMEMSHRGKEFLSIIQKAEADLRELLDIPDNYEVLFLQGG 79 (365)
T ss_pred CCCCCHHHHHHHHHHHhccc--------ccCccccccCCCchHHHHHHHHHHHHHHHHhCCCCCceEEEEeCc
Confidence 56899999999998655443 22334444444444567999999999999997 67988766544
No 60
>COG3824 Predicted Zn-dependent protease [General function prediction only]
Probab=24.70 E-value=33 Score=32.15 Aligned_cols=14 Identities=29% Similarity=0.558 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHHHH
Q 009655 292 TALVIGVHELGHIL 305 (529)
Q Consensus 292 L~~iL~iHElGH~l 305 (529)
.+..+++||+||.+
T Consensus 108 ~vthvliHEIgHhF 121 (136)
T COG3824 108 QVTHVLIHEIGHHF 121 (136)
T ss_pred Hhhhhhhhhhhhhc
Confidence 56788999999975
No 61
>COG5309 Exo-beta-1,3-glucanase [Carbohydrate transport and metabolism]
Probab=24.45 E-value=1.2e+02 Score=32.25 Aligned_cols=61 Identities=16% Similarity=0.312 Sum_probs=43.0
Q ss_pred HhHHHHhhcccccc-ceeeeccccccCceEEEEeccCC--chHHHHHHHHHHHHhhhCCceEEEEEec
Q 009655 156 KETIDILKDQVFGF-DTFFVTNQEPYEGGVLFKGNLRG--QAAKTYEKISTRMKNKFGDQYKLFLLVN 220 (529)
Q Consensus 156 ~ed~~~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 688999999 6666 99999998755555555555443 3466778888888874 6 66665553
No 62
>KOG0391 consensus SNF2 family DNA-dependent ATPase [General function prediction only]
Probab=24.20 E-value=75 Score=39.81 Aligned_cols=36 Identities=22% Similarity=0.195 Sum_probs=20.8
Q ss_pred HHHHhhccccccceeeeccccccCceEEEEeccCCc
Q 009655 158 TIDILKDQVFGFDTFFVTNQEPYEGGVLFKGNLRGQ 193 (529)
Q Consensus 158 d~~~ik~~~Fg~dtF~~t~~~~~~~gvi~rGnLR~~ 193 (529)
||+..-+++-+-.-=-+|.+-..+---+.|||||.-
T Consensus 584 dIaavae~~qpKgytl~tTqVktpvPsLLrGqLReY 619 (1958)
T KOG0391|consen 584 DIAAVAEAIQPKGYTLVTTQVKTPVPSLLRGQLREY 619 (1958)
T ss_pred hHHHHHHhhCccceeeeeeeeccCchHHHHHHHHHH
Confidence 444443333333323455555667777999999963
No 63
>PRK01345 heat shock protein HtpX; Provisional
Probab=24.01 E-value=48 Score=34.95 Aligned_cols=12 Identities=33% Similarity=0.454 Sum_probs=10.1
Q ss_pred HHHHHHHHHHHH
Q 009655 294 LVIGVHELGHIL 305 (529)
Q Consensus 294 ~iL~iHElGH~l 305 (529)
..++.||+||.-
T Consensus 125 ~aVlAHElgHi~ 136 (317)
T PRK01345 125 AGVMAHELAHVK 136 (317)
T ss_pred HHHHHHHHHHHH
Confidence 468899999975
No 64
>PRK03072 heat shock protein HtpX; Provisional
Probab=23.40 E-value=50 Score=34.21 Aligned_cols=11 Identities=36% Similarity=0.395 Sum_probs=9.2
Q ss_pred HHHHHHHHHHH
Q 009655 294 LVIGVHELGHI 304 (529)
Q Consensus 294 ~iL~iHElGH~ 304 (529)
..++.||+||.
T Consensus 128 ~aVlAHElgHi 138 (288)
T PRK03072 128 RGVLGHELSHV 138 (288)
T ss_pred HHHHHHHHHHH
Confidence 46889999995
No 65
>PF13699 DUF4157: Domain of unknown function (DUF4157)
Probab=23.28 E-value=48 Score=28.16 Aligned_cols=12 Identities=33% Similarity=0.650 Sum_probs=10.1
Q ss_pred HHHHHHHHHHHH
Q 009655 295 VIGVHELGHILA 306 (529)
Q Consensus 295 iL~iHElGH~la 306 (529)
.++.||++|.+.
T Consensus 63 ~llaHEl~Hv~Q 74 (79)
T PF13699_consen 63 ALLAHELAHVVQ 74 (79)
T ss_pred hhHhHHHHHHHh
Confidence 578999999875
No 66
>PRK02391 heat shock protein HtpX; Provisional
Probab=23.02 E-value=52 Score=34.37 Aligned_cols=11 Identities=36% Similarity=0.582 Sum_probs=9.1
Q ss_pred HHHHHHHHHHH
Q 009655 294 LVIGVHELGHI 304 (529)
Q Consensus 294 ~iL~iHElGH~ 304 (529)
..++.||+||.
T Consensus 134 ~aVlaHElgHi 144 (296)
T PRK02391 134 EAVLAHELSHV 144 (296)
T ss_pred HHHHHHHHHHH
Confidence 36889999995
No 67
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=22.85 E-value=1.2e+02 Score=29.37 Aligned_cols=32 Identities=25% Similarity=0.176 Sum_probs=22.3
Q ss_pred cchHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHcC
Q 009655 277 DNLNLLTNGLPGALVTALVIGVHELGHILAAKSTG 311 (529)
Q Consensus 277 ~~~~~l~~glp~aL~L~~iL~iHElGH~laAr~~G 311 (529)
-||.++.+ ....++.-++-||++|+.+=..+|
T Consensus 48 lNP~ll~e---n~~~f~~~vV~HELaHl~ly~~~g 79 (156)
T COG3091 48 LNPKLLEE---NGEDFIEQVVPHELAHLHLYQEFG 79 (156)
T ss_pred cCHHHHHH---ccHHHHHHHHHHHHHHHHHHHHcC
Confidence 35655443 333455668899999999988877
No 68
>PRK05457 heat shock protein HtpX; Provisional
Probab=22.56 E-value=54 Score=34.01 Aligned_cols=11 Identities=36% Similarity=0.573 Sum_probs=9.2
Q ss_pred HHHHHHHHHHH
Q 009655 294 LVIGVHELGHI 304 (529)
Q Consensus 294 ~iL~iHElGH~ 304 (529)
..++.||+||.
T Consensus 135 ~aVlAHElgHi 145 (284)
T PRK05457 135 EAVLAHEISHI 145 (284)
T ss_pred HHHHHHHHHHH
Confidence 46889999996
No 69
>PHA02456 zinc metallopeptidase motif-containing protein
Probab=22.40 E-value=52 Score=30.54 Aligned_cols=19 Identities=26% Similarity=0.305 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHHcCCccc
Q 009655 297 GVHELGHILAAKSTGVELG 315 (529)
Q Consensus 297 ~iHElGH~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 5799999999999997554
No 70
>PF01421 Reprolysin: Reprolysin (M12B) family zinc metalloprotease This Prosite motif covers only the active site.; InterPro: IPR001590 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M12, subfamily M12B (adamalysin family, clan (MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA and the predicted active site residues for members of this family and thermolysin occur in the motif HEXXH []. The adamalysins are zinc dependent endopeptidases found in snake venom. There are some mammalian proteins such as P78325 from SWISSPROT, and fertilin Q28472 from SWISSPROT. Fertilin and closely related proteins appear to not have some active site residues and may not be active enzymes. CD156 (also called ADAM8 (3.4.24 from EC) or MS2 human) has been implicated in extravasation of leukocytes. CD molecules are leucocyte antigens on cell surfaces. CD antigens nomenclature is updated at Protein Reviews On The Web (http://prow.nci.nih.gov/). ; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 2E3X_A 2W15_A 2W14_A 2W13_A 2W12_A 1ND1_A 3K7L_A 2DW2_A 2DW0_B 2DW1_A ....
Probab=22.12 E-value=62 Score=30.98 Aligned_cols=22 Identities=41% Similarity=0.499 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHHHHHHcCC
Q 009655 291 VTALVIGVHELGHILAAKSTGV 312 (529)
Q Consensus 291 ~L~~iL~iHElGH~laAr~~Gv 312 (529)
..++.+++||+||-+=+.+-+.
T Consensus 129 ~~~a~~~AHelGH~lGm~HD~~ 150 (199)
T PF01421_consen 129 LSFAVIIAHELGHNLGMPHDGD 150 (199)
T ss_dssp HHHHHHHHHHHHHHTT---TTT
T ss_pred HHHHHHHHHHHHHhcCCCCCCC
Confidence 3456788999999887777666
No 71
>KOG3320 consensus 40S ribosomal protein S7 [Translation, ribosomal structure and biogenesis]
Probab=21.99 E-value=1.2e+02 Score=30.09 Aligned_cols=27 Identities=15% Similarity=0.321 Sum_probs=20.7
Q ss_pred HHHHHHHHHHHHhhhCCceEEEEEecC
Q 009655 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 72
>PF04298 Zn_peptidase_2: Putative neutral zinc metallopeptidase; InterPro: IPR007395 Members of this family of bacterial proteins are described as hypothetical proteins or zinc-dependent proteases. The majority have a HExxH zinc-binding motif characteristic of neutral zinc metallopeptidases, however there is no evidence to support their function as metallopeptidases.
Probab=21.81 E-value=54 Score=33.40 Aligned_cols=13 Identities=31% Similarity=0.805 Sum_probs=10.7
Q ss_pred HHHHHHHHHHHHH
Q 009655 294 LVIGVHELGHILA 306 (529)
Q Consensus 294 ~iL~iHElGH~la 306 (529)
..+.+||.||++.
T Consensus 90 vaVAAHEvGHAiQ 102 (222)
T PF04298_consen 90 VAVAAHEVGHAIQ 102 (222)
T ss_pred HHHHHHHHhHHHh
Confidence 3578999999875
No 73
>cd04927 ACT_ACR-like_2 Second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=21.46 E-value=1.1e+02 Score=25.19 Aligned_cols=35 Identities=23% Similarity=0.314 Sum_probs=25.0
Q ss_pred cccceeeeccccccCceEEEEeccCCchHHHHHHHHHHHHhhhCCc
Q 009655 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 457999997531 11 244567788999999999864
No 74
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=21.05 E-value=79 Score=38.42 Aligned_cols=11 Identities=18% Similarity=0.124 Sum_probs=4.6
Q ss_pred CCHhHHHHhhc
Q 009655 154 IPKETIDILKD 164 (529)
Q Consensus 154 i~~ed~~~ik~ 164 (529)
.++||=-.+++
T Consensus 1489 ~Dee~~~~~~d 1499 (1516)
T KOG1832|consen 1489 EDEEDDGEMQD 1499 (1516)
T ss_pred cchhhhhhhhc
Confidence 34444444444
No 75
>PRK01265 heat shock protein HtpX; Provisional
Probab=20.95 E-value=60 Score=34.59 Aligned_cols=11 Identities=45% Similarity=0.827 Sum_probs=9.2
Q ss_pred HHHHHHHHHHH
Q 009655 294 LVIGVHELGHI 304 (529)
Q Consensus 294 ~iL~iHElGH~ 304 (529)
..++.||+||+
T Consensus 141 ~aVlAHElgHi 151 (324)
T PRK01265 141 KAVAGHELGHL 151 (324)
T ss_pred HHHHHHHHHHH
Confidence 36889999996
No 76
>PRK02870 heat shock protein HtpX; Provisional
Probab=20.64 E-value=61 Score=34.66 Aligned_cols=11 Identities=45% Similarity=0.673 Sum_probs=9.5
Q ss_pred HHHHHHHHHHH
Q 009655 294 LVIGVHELGHI 304 (529)
Q Consensus 294 ~iL~iHElGH~ 304 (529)
..++.||+||.
T Consensus 174 ~aVlAHELgHi 184 (336)
T PRK02870 174 QAVMAHELSHI 184 (336)
T ss_pred HHHHHHHHHHH
Confidence 46889999998
No 77
>PF01432 Peptidase_M3: Peptidase family M3 This Prosite motif covers only the active site. This family belongs to family M3 of the peptidase classification.; InterPro: IPR001567 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M3 (clan MA(E)), subfamilies M3A and M3B. The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA. The Thimet oligopeptidase family, is a large family of archaeal, bacterial and eukaryotic oligopeptidases that cleave medium sized peptides. The group contains: mitochondrial intermediate peptidase (3.4.24.59 from EC) Neurolysin, mitochondrial precursor, (3.4.24.16 from EC) Thimet oligopeptidase (3.4.24.15 from EC) Dipeptidyl carboxypeptidase (3.4.15.5 from EC) Oligopeptidase A (3.4.24.70 from EC) Oligoendopeptidase F ; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 2QR4_B 3CE2_A 1Y79_1 2H1J_A 2H1N_A 2O36_A 1S4B_P 2O3E_A 1I1I_P.
Probab=20.39 E-value=63 Score=35.02 Aligned_cols=20 Identities=20% Similarity=0.288 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHHHHHcCCcc
Q 009655 295 VIGVHELGHILAAKSTGVEL 314 (529)
Q Consensus 295 iL~iHElGH~laAr~~Gvk~ 314 (529)
..++||+||++-...-+.+.
T Consensus 244 ~tLfHE~GHa~H~~ls~~~~ 263 (458)
T PF01432_consen 244 ETLFHEFGHAMHSLLSRTKY 263 (458)
T ss_dssp HHHHHHHHHHHHHHHCCCSS
T ss_pred HHHHHHHhHHHHHHHhcccc
Confidence 56799999999888776654
No 78
>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=20.29 E-value=1.6e+02 Score=31.07 Aligned_cols=60 Identities=10% Similarity=0.208 Sum_probs=40.6
Q ss_pred CCCHhHHHHhhccccccceeeeccccccCceEEEEeccCCchHHHHHHHHHHHHhhhC--CceEEEEEec
Q 009655 153 RIPKETIDILKDQVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFG--DQYKLFLLVN 220 (529)
Q Consensus 153 ~i~~ed~~~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 368899999999 444433 33345555554444556999999999999988 4576654443
No 79
>KOG2719 consensus Metalloprotease [General function prediction only]
Probab=20.15 E-value=58 Score=36.14 Aligned_cols=14 Identities=36% Similarity=0.491 Sum_probs=11.1
Q ss_pred HHHHHHHHHHHHHH
Q 009655 293 ALVIGVHELGHILA 306 (529)
Q Consensus 293 ~~iL~iHElGH~la 306 (529)
+.++++||+||+--
T Consensus 280 l~AVl~HELGHW~~ 293 (428)
T KOG2719|consen 280 LVAVLAHELGHWKL 293 (428)
T ss_pred HHHHHHHHhhHHHH
Confidence 35788999999854
No 80
>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=20.06 E-value=1.2e+02 Score=21.45 Aligned_cols=21 Identities=24% Similarity=0.078 Sum_probs=15.6
Q ss_pred hhHHHHHHHHHHHHHHhhccc
Q 009655 497 DKYIALGVLVLFLGLLVCLPY 517 (529)
Q Consensus 497 ~~r~~lg~~~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 347777788877777888775
Done!