Query 015105
Match_columns 413
No_of_seqs 315 out of 1632
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 03:09:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015105.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015105hhsearch_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 2.6E-31 5.6E-36 246.7 19.0 177 136-361 3-181 (183)
2 cd06164 S2P-M50_SpoIVFB_CBS Sp 99.9 1.2E-24 2.5E-29 208.4 20.4 134 161-332 37-170 (227)
3 cd06161 S2P-M50_SpoIVFB SpoIVF 99.9 6.7E-23 1.5E-27 193.6 19.1 129 164-332 25-153 (208)
4 cd06163 S2P-M50_PDZ_RseP-like 99.8 1.6E-20 3.4E-25 174.5 14.8 113 171-329 3-145 (182)
5 cd05709 S2P-M50 Site-2 proteas 99.8 2.9E-20 6.2E-25 170.6 13.1 139 171-333 2-156 (180)
6 cd06159 S2P-M50_PDZ_Arch Uncha 99.8 1.9E-18 4.2E-23 168.9 18.1 120 166-332 107-229 (263)
7 cd06158 S2P-M50_like_1 Unchara 99.8 6.3E-19 1.4E-23 163.5 10.6 135 172-335 4-159 (181)
8 PF02163 Peptidase_M50: Peptid 99.8 1.1E-18 2.4E-23 161.1 10.3 127 172-328 2-157 (192)
9 cd06162 S2P-M50_PDZ_SREBP Ster 99.7 2.8E-17 6E-22 161.4 15.7 116 170-333 128-250 (277)
10 TIGR00054 RIP metalloprotease 99.5 4E-13 8.6E-18 139.4 14.5 81 171-251 8-119 (420)
11 PRK10779 zinc metallopeptidase 99.5 6.9E-13 1.5E-17 138.6 15.3 84 168-251 6-119 (449)
12 COG1994 SpoIVFB Zn-dependent p 99.3 1.6E-11 3.5E-16 117.9 10.1 128 166-333 41-176 (230)
13 COG0750 Predicted membrane-ass 98.9 2.2E-09 4.9E-14 108.5 5.5 244 49-332 82-338 (375)
14 PF13398 Peptidase_M50B: Pepti 97.3 0.00036 7.9E-09 65.9 5.1 65 178-250 23-88 (200)
15 KOG2921 Intramembrane metallop 96.1 0.0045 9.8E-08 63.9 3.5 83 167-251 120-206 (484)
16 COG0750 Predicted membrane-ass 95.9 0.025 5.3E-07 57.4 7.7 82 170-251 6-120 (375)
17 PF00413 Peptidase_M10: Matrix 61.0 4.9 0.00011 35.2 1.6 21 178-198 106-126 (154)
18 cd04279 ZnMc_MMP_like_1 Zinc-d 59.0 5.7 0.00012 35.4 1.7 22 177-198 104-125 (156)
19 PF11667 DUF3267: Protein of u 58.3 3.8 8.2E-05 34.9 0.4 68 177-252 4-72 (111)
20 PF05572 Peptidase_M43: Pregna 52.0 7.1 0.00015 35.6 1.1 15 178-192 70-84 (154)
21 cd04268 ZnMc_MMP_like Zinc-dep 50.2 15 0.00032 32.6 2.9 24 175-198 92-115 (165)
22 cd04278 ZnMc_MMP Zinc-dependen 48.0 8.1 0.00018 34.6 0.8 23 176-198 106-128 (157)
23 PF13485 Peptidase_MA_2: Pepti 48.0 15 0.00032 30.3 2.4 18 179-196 27-44 (128)
24 KOG3320 40S ribosomal protein 47.2 33 0.00072 32.4 4.7 26 80-105 75-100 (192)
25 PF06114 DUF955: Domain of unk 43.8 14 0.00031 30.1 1.6 17 179-195 44-60 (122)
26 PF01435 Peptidase_M48: Peptid 43.5 15 0.00033 34.0 2.0 12 178-189 90-101 (226)
27 cd04277 ZnMc_serralysin_like Z 42.4 14 0.00029 34.0 1.4 23 177-199 113-135 (186)
28 cd04927 ACT_ACR-like_2 Second 41.9 31 0.00066 27.4 3.2 35 51-96 40-74 (76)
29 PF13574 Reprolysin_2: Metallo 41.3 14 0.0003 34.0 1.3 21 177-197 111-131 (173)
30 PF13688 Reprolysin_5: Metallo 40.9 13 0.00029 34.1 1.1 22 176-197 141-162 (196)
31 smart00235 ZnMc Zinc-dependent 40.9 14 0.0003 32.1 1.2 20 180-199 89-108 (140)
32 cd00203 ZnMc Zinc-dependent me 39.9 15 0.00032 32.5 1.2 22 176-197 95-116 (167)
33 PF01434 Peptidase_M41: Peptid 39.8 23 0.00049 33.7 2.5 18 179-196 30-47 (213)
34 PF02031 Peptidase_M7: Strepto 36.8 21 0.00045 32.0 1.6 11 180-190 80-90 (132)
35 PF13582 Reprolysin_3: Metallo 35.5 16 0.00035 30.8 0.8 14 179-192 109-122 (124)
36 PF12315 DUF3633: Protein of u 35.1 26 0.00056 33.9 2.1 21 175-196 91-111 (212)
37 PF14247 DUF4344: Domain of un 34.4 41 0.00088 32.7 3.3 20 173-192 88-107 (220)
38 COG2856 Predicted Zn peptidase 34.2 22 0.00047 34.4 1.4 14 180-193 75-88 (213)
39 cd04327 ZnMc_MMP_like_3 Zinc-d 33.7 23 0.00049 33.2 1.5 21 178-198 93-113 (198)
40 cd04270 ZnMc_TACE_like Zinc-de 32.0 28 0.00061 33.8 1.9 18 176-193 166-183 (244)
41 cd04269 ZnMc_adamalysin_II_lik 31.6 27 0.00059 32.1 1.6 20 177-196 131-150 (194)
42 PF05265 DUF723: Protein of un 31.3 87 0.0019 24.5 4.0 36 81-119 4-39 (60)
43 PRK03001 M48 family peptidase; 30.9 30 0.00066 34.3 1.9 12 178-189 125-136 (283)
44 PF09471 Peptidase_M64: IgA Pe 30.4 22 0.00047 35.4 0.8 15 177-191 216-230 (264)
45 PRK03982 heat shock protein Ht 30.2 32 0.00069 34.2 1.9 11 179-189 127-137 (288)
46 cd04267 ZnMc_ADAM_like Zinc-de 30.1 23 0.0005 32.5 0.9 20 177-196 133-152 (192)
47 PHA02456 zinc metallopeptidase 30.1 31 0.00068 30.4 1.6 18 181-198 83-100 (141)
48 PF14891 Peptidase_M91: Effect 29.7 34 0.00075 31.4 1.9 18 177-194 103-120 (174)
49 PF12388 Peptidase_M57: Dual-a 29.1 27 0.0006 33.7 1.2 24 173-196 129-152 (211)
50 COG5495 Uncharacterized conser 29.0 38 0.00082 33.7 2.1 37 39-97 129-165 (289)
51 PF13583 Reprolysin_4: Metallo 28.8 19 0.00042 34.1 0.1 18 180-197 140-157 (206)
52 PF01447 Peptidase_M4: Thermol 28.5 36 0.00078 31.0 1.8 11 180-190 138-148 (150)
53 PRK04897 heat shock protein Ht 27.1 39 0.00084 33.9 1.9 11 179-189 139-149 (298)
54 PLN02452 phosphoserine transam 27.1 1.1E+02 0.0024 31.6 5.3 64 34-105 14-79 (365)
55 PRK12462 phosphoserine aminotr 26.7 1.1E+02 0.0023 31.9 5.1 64 34-105 11-76 (364)
56 PF04298 Zn_peptidase_2: Putat 26.7 38 0.00082 33.0 1.7 13 178-190 90-102 (222)
57 COG5309 Exo-beta-1,3-glucanase 26.7 98 0.0021 31.3 4.6 62 40-105 218-282 (305)
58 PF01990 ATP-synt_F: ATP synth 26.4 2.5E+02 0.0055 22.9 6.4 59 40-119 7-79 (95)
59 PF13699 DUF4157: Domain of un 25.5 41 0.00088 27.3 1.4 12 179-190 63-74 (79)
60 PF11711 Tim54: Inner membrane 24.9 1E+02 0.0022 32.5 4.5 65 6-73 114-179 (382)
61 PRK01345 heat shock protein Ht 24.9 45 0.00097 33.9 1.9 12 178-189 125-136 (317)
62 COG0501 HtpX Zn-dependent prot 24.8 46 0.00099 32.4 1.9 11 179-189 159-169 (302)
63 COG3824 Predicted Zn-dependent 24.7 33 0.00072 30.6 0.8 14 176-189 108-121 (136)
64 PRK03072 heat shock protein Ht 24.6 46 0.001 33.3 1.9 10 179-188 129-138 (288)
65 TIGR02500 type_III_yscD type I 24.5 2.1E+02 0.0047 29.9 6.9 38 63-100 302-339 (410)
66 PRK02391 heat shock protein Ht 24.4 47 0.001 33.4 1.9 10 179-188 135-144 (296)
67 PRK05457 heat shock protein Ht 24.2 48 0.001 33.1 1.9 10 179-188 136-145 (284)
68 COG0830 UreF Urease accessory 23.9 89 0.0019 30.6 3.7 32 298-329 157-188 (229)
69 smart00731 SprT SprT homologue 23.8 48 0.001 29.6 1.7 17 177-193 59-75 (146)
70 PRK01265 heat shock protein Ht 22.8 52 0.0011 33.7 1.9 10 179-188 142-151 (324)
71 PF10263 SprT-like: SprT-like 22.7 61 0.0013 28.7 2.1 19 176-194 59-77 (157)
72 PF01421 Reprolysin: Reprolysi 22.2 61 0.0013 29.9 2.1 21 176-196 130-150 (199)
73 PRK02870 heat shock protein Ht 22.1 55 0.0012 33.7 1.9 10 179-188 175-184 (336)
74 cd04272 ZnMc_salivary_gland_MP 21.9 54 0.0012 31.0 1.7 20 178-197 146-165 (220)
75 PF11085 YqhR: Conserved membr 21.7 6.9E+02 0.015 23.6 9.7 82 299-385 33-135 (173)
76 COG3091 SprT Zn-dependent meta 21.2 1.4E+02 0.003 27.6 4.1 31 162-195 49-79 (156)
77 PF04228 Zn_peptidase: Putativ 21.1 62 0.0013 32.7 2.0 15 179-193 172-186 (292)
78 KOG2719 Metalloprotease [Gener 20.7 55 0.0012 34.9 1.6 14 177-190 280-293 (428)
79 cd06459 M3B_Oligoendopeptidase 20.7 55 0.0012 33.6 1.7 16 179-194 224-239 (427)
80 PF01432 Peptidase_M3: Peptida 20.5 62 0.0013 34.0 2.0 21 178-198 243-263 (458)
81 cd04280 ZnMc_astacin_like Zinc 20.2 53 0.0011 30.4 1.2 22 179-200 76-97 (180)
82 PF05683 Fumerase_C: Fumarase 20.2 1.2E+02 0.0026 29.3 3.6 44 32-91 29-72 (205)
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=99.98 E-value=2.6e-31 Score=246.69 Aligned_cols=177 Identities=40% Similarity=0.725 Sum_probs=149.3
Q ss_pred HHHHHHHHHHhhcccccchhhhhhccchHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHcCCcccCccccccceeeeeeeE
Q 015105 136 FGLVTVFTLLLRNVPALQSNLLSTFDNLNLLTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAI 215 (413)
Q Consensus 136 ~~l~t~~t~~~~~~~~l~~~~~~~~~~~~~~~~gl~~al~l~~iL~iHElGH~laAr~~Gv~~~~P~fiP~~~Lg~fGav 215 (413)
++++|+.+....+. ..+.+ +..++.+.+..+++++++++.++.+||+||+++||++|+|++.++++|..++|++|++
T Consensus 3 ~~~~s~~~~~~~~~-~~~~~--~~~~~~~~~~~~~~~~l~l~~~l~iHElgH~~~A~~~G~~~~~~~l~P~~~~G~~G~~ 79 (183)
T cd06160 3 LLVLTLLTTLLVGA-WLSGN--DVPGNPLLLLQGLPFALALLAILGIHEMGHYLAARRHGVKASLPYFIPFPFIGTFGAF 79 (183)
T ss_pred HHHHHHHHHHHHHH-HHhcc--cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCccceeeeehHhcCcEEEE
Confidence 45667777665543 22222 3347788899999999999999999999999999999999999999998889999999
Q ss_pred EEccccccCccceeEEEecchhHHHHHHHHHHHHhhhcCCCCCccccccccchhhhhhHHHHHHHhhccccCCCCCccch
Q 015105 216 TRIRNIVSKREDLLKVAAAGPLAGFSLGFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVN 295 (413)
Q Consensus 216 i~~~~~~~~r~~lf~IaiAGPlag~lval~~l~~g~~l~~~~~~~~~~~~~~f~~s~L~g~la~l~LG~~l~~~~~v~~~ 295 (413)
++.++..++|+++++|++|||++|+++++++++++
T Consensus 80 ~~~~~~~~~~~~~~~IalAGPl~nl~lali~~~~~--------------------------------------------- 114 (183)
T cd06160 80 IRMRSPIPNRKALFDIALAGPLAGLLLALPVLIIG--------------------------------------------- 114 (183)
T ss_pred EEecCCCCChhHhehhhhhHHHHHHHHHHHHHHHH---------------------------------------------
Confidence 99999888999999999999999999988775543
Q ss_pred HHHHHHHHHHHHHHHhhcCCCCCchHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhhh--hHHHHHHHH
Q 015105 296 PLVIWAWAGLLINAINSIPAGELDGGRIAFALWGRKASTRLTGVSIVLLGLSSLFSD--VTFYWVVLV 361 (413)
Q Consensus 296 pl~~ag~~gl~ltafNLLPigpLDGGrIl~allg~r~~~~~~~~~~~llgl~~l~~~--~~l~W~ili 361 (413)
+..++|+|+++++|||+|++||||||++|+++++|.+.+.++.+.+++|+.++.++ .++.|..++
T Consensus 115 -~~~~~~~nl~l~~fNLLPi~PLDGGril~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ 181 (183)
T cd06160 115 -LAVAGWVGLLVTALNLLPVGQLDGGHIVRALFGRRVAALIGIGLLVALGLLALYLSFSIWLLWALLL 181 (183)
T ss_pred -HHHHHHHHHHHHHHHhCCCCCcChHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence 12468999999999999999999999999999999999999998888888887765 455555443
No 2
>cd06164 S2P-M50_SpoIVFB_CBS SpoIVFB Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50B), regulates intramembrane proteolysis (RIP), and is involved in the pro-sigmaK pathway of bacterial spore formation. In this subgroup, SpoIVFB (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain. SpoIVFB is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA (bypass-of-forespore A), and SpoIVB (sporulation protein, stage IV cell wall formation, B locus). SpoIVFB is negatively regulated by SpoIVFA and BofA and activated by SpoIVB. It is thought that SpoIVFB, SpoIVFA, and BofA are located in the mother-cell membrane that surrounds the forespore and that SpoIVB is secreted from the forespore into the space between the two where it activates SpoIVFB. It has been proposed tha
Probab=99.93 E-value=1.2e-24 Score=208.37 Aligned_cols=134 Identities=30% Similarity=0.390 Sum_probs=111.6
Q ss_pred cchHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHcCCcccCccccccceeeeeeeEEEccccccCccceeEEEecchhHHH
Q 015105 161 DNLNLLTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAITRIRNIVSKREDLLKVAAAGPLAGF 240 (413)
Q Consensus 161 ~~~~~~~~gl~~al~l~~iL~iHElGH~laAr~~Gv~~~~P~fiP~~~Lg~fGavi~~~~~~~~r~~lf~IaiAGPlag~ 240 (413)
.+...+..|+.++++++.++++||+||+++||++|+|++ .+.+.+||+++++++..+++++++.|++|||++|+
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 455667889999999999999999999999999999996 67788899999999988889999999999999999
Q ss_pred HHHHHHHHHhhhcCCCCCccccccccchhhhhhHHHHHHHhhccccCCCCCccchHHHHHHHHHHHHHHHhhcCCCCCch
Q 015105 241 SLGFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAINSIPAGELDG 320 (413)
Q Consensus 241 lval~~l~~g~~l~~~~~~~~~~~~~~f~~s~L~g~la~l~LG~~l~~~~~v~~~pl~~ag~~gl~ltafNLLPigpLDG 320 (413)
+++++++.+....+... ++. ....+.+.+|+|+++++|||+|++||||
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 0122457799999999999999999999
Q ss_pred HHHHHHhhhhHH
Q 015105 321 GRIAFALWGRKA 332 (413)
Q Consensus 321 GrIl~allg~r~ 332 (413)
||++++++.++.
T Consensus 159 gril~~ll~~~~ 170 (227)
T cd06164 159 GRVLRALLWRRT 170 (227)
T ss_pred HHHHHHHHHHhc
Confidence 999999987665
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=99.90 E-value=6.7e-23 Score=193.57 Aligned_cols=129 Identities=29% Similarity=0.433 Sum_probs=107.9
Q ss_pred HHHHhHHHHHHHHHHHHHHHHHHHHHHHHHcCCcccCccccccceeeeeeeEEEccccccCccceeEEEecchhHHHHHH
Q 015105 164 NLLTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAITRIRNIVSKREDLLKVAAAGPLAGFSLG 243 (413)
Q Consensus 164 ~~~~~gl~~al~l~~iL~iHElGH~laAr~~Gv~~~~P~fiP~~~Lg~fGavi~~~~~~~~r~~lf~IaiAGPlag~lva 243 (413)
..+..++.+++.++.++++||+||+++||++|+|++ .+.+.+||+.+++++...+|++++.|++|||++|++++
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 456788999999999999999999999999999985 67888899999998877788999999999999999999
Q ss_pred HHHHHHhhhcCCCCCccccccccchhhhhhHHHHHHHhhccccCCCCCccchHHHHHHHHHHHHHHHhhcCCCCCchHHH
Q 015105 244 FVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAINSIPAGELDGGRI 323 (413)
Q Consensus 244 l~~l~~g~~l~~~~~~~~~~~~~~f~~s~L~g~la~l~LG~~l~~~~~v~~~pl~~ag~~gl~ltafNLLPigpLDGGrI 323 (413)
+++..+....+.. + ...+.+...+++|+.+++|||+|++|||||||
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 8887655432110 0 01123457789999999999999999999999
Q ss_pred HHHhhhhHH
Q 015105 324 AFALWGRKA 332 (413)
Q Consensus 324 l~allg~r~ 332 (413)
+++++.++.
T Consensus 145 l~~ll~~~~ 153 (208)
T cd06161 145 LRALLWRRT 153 (208)
T ss_pred HHHHHHHhc
Confidence 999977664
No 4
>cd06163 S2P-M50_PDZ_RseP-like RseP-like Site-2 proteases (S2P), zinc metalloproteases (MEROPS family M50A), cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. In Escherichia coli, the S2P homolog RseP is involved in the sigmaE pathway of extracytoplasmic stress responses. Also included in this group are such homologs as Bacillus subtilis YluC, Mycobacterium tuberculosis Rv2869c S2P, and Bordetella bronchiseptica HurP. Rv2869c S2P appears to have a role in the regulation of prokaryotic lipid biosynthesis and membrane composition and YluC of Bacillus has a role in transducing membrane stress. This group includes bacterial and eukaryotic S2P/M50s homologs with either one or two PDZ domains present. PDZ domains are believed to have a regulatory role. The RseP PDZ domain is required for the inhibitory reaction that prevents cleavage of its substrate, RseA.
Probab=99.85 E-value=1.6e-20 Score=174.50 Aligned_cols=113 Identities=34% Similarity=0.429 Sum_probs=89.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCcccC--cccccc------------ceeeeeeeEEEcccccc-------------
Q 015105 171 PGALVTALVIGVHELGHILAAKSTGVELGV--PYFVPS------------WQIGSFGAITRIRNIVS------------- 223 (413)
Q Consensus 171 ~~al~l~~iL~iHElGH~laAr~~Gv~~~~--P~fiP~------------~~Lg~fGavi~~~~~~~------------- 223 (413)
.+.+++..++++||+||+++||++|+|+.. .-|-|. +.+-++|+++++++..+
T Consensus 3 ~~~i~l~~~v~iHElGH~~~Ar~~Gv~v~~f~iGfGp~l~~~~~~~t~~~i~~iPlGGyv~~~~~~~~~~~~~~~~~~~f 82 (182)
T cd06163 3 AFILVLGILIFVHELGHFLVAKLFGVKVEEFSIGFGPKLFSFKKGETEYSISAIPLGGYVKMLGEDPEEEADPEDDPRSF 82 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCeeeEeeeecCceeeeeecCCeEEEEEEEEeccEEEecCCCcccccccccchHHH
Confidence 356678889999999999999999999863 111121 34678999999865321
Q ss_pred ---CccceeEEEecchhHHHHHHHHHHHHhhhcCCCCCccccccccchhhhhhHHHHHHHhhccccCCCCCccchHHHHH
Q 015105 224 ---KREDLLKVAAAGPLAGFSLGFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIW 300 (413)
Q Consensus 224 ---~r~~lf~IaiAGPlag~lval~~l~~g~~l~~~~~~~~~~~~~~f~~s~L~g~la~l~LG~~l~~~~~v~~~pl~~a 300 (413)
++++++.|++|||++|+++|++++.+. +.+.
T Consensus 83 ~~~~~~~ri~V~lAGP~~NlilA~i~~~~~----------------------------------------------~~~~ 116 (182)
T cd06163 83 NSKPVWQRILIVFAGPLANFLLAIVLFAVL----------------------------------------------LSFL 116 (182)
T ss_pred ccCCcchhhhhhhhHHHHHHHHHHHHHHHH----------------------------------------------HHHH
Confidence 467889999999999999998764321 2256
Q ss_pred HHHHHHHHHHhhcCCCCCchHHHHHHhhh
Q 015105 301 AWAGLLINAINSIPAGELDGGRIAFALWG 329 (413)
Q Consensus 301 g~~gl~ltafNLLPigpLDGGrIl~allg 329 (413)
.++|+.+++|||+|++||||||++++++.
T Consensus 117 ~~~n~~l~~fNLlPippLDGg~il~~~~~ 145 (182)
T cd06163 117 ALLSINLGILNLLPIPALDGGHLLFLLIE 145 (182)
T ss_pred HHHHHHHHHHHcCCCCCCCHHHHHHHHHH
Confidence 78999999999999999999999999875
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=99.83 E-value=2.9e-20 Score=170.60 Aligned_cols=139 Identities=28% Similarity=0.307 Sum_probs=101.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCcccC----cccccc-------ceeeeeeeEEEcccccc-----CccceeEEEec
Q 015105 171 PGALVTALVIGVHELGHILAAKSTGVELGV----PYFVPS-------WQIGSFGAITRIRNIVS-----KREDLLKVAAA 234 (413)
Q Consensus 171 ~~al~l~~iL~iHElGH~laAr~~Gv~~~~----P~fiP~-------~~Lg~fGavi~~~~~~~-----~r~~lf~IaiA 234 (413)
.+.++++.++.+||+||+++||++|+|+.. ..+.|. +.+-++|++++.++... +|++++.|++|
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 356778889999999999999999998742 122221 22345799999877654 48899999999
Q ss_pred chhHHHHHHHHHHHHhhhcCCCCCccccccccchhhhhhHHHHHHHhhccccCCCCCccchHHHHHHHHHHHHHHHhhcC
Q 015105 235 GPLAGFSLGFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAINSIP 314 (413)
Q Consensus 235 GPlag~lval~~l~~g~~l~~~~~~~~~~~~~~f~~s~L~g~la~l~LG~~l~~~~~v~~~pl~~ag~~gl~ltafNLLP 314 (413)
||++|+++++++..+....+..... ...... +....+.+.+.+++|+.++++||+|
T Consensus 82 GPl~nllla~i~~~~~~~~~~~~~~----~~~~~~--------------------~~~~~~~l~~~~~~n~~l~~fNLlP 137 (180)
T cd05709 82 GPLANLLLALLLLLLLLLLGGLPPA----PVGQAA--------------------SSGLANLLAFLALINLNLAVFNLLP 137 (180)
T ss_pred hHHHHHHHHHHHHHHHHHHccCCcc----chhhhH--------------------HHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 9999999999988776543321100 000000 0011245678899999999999999
Q ss_pred CCCCchHHHHHHhhhhHHH
Q 015105 315 AGELDGGRIAFALWGRKAS 333 (413)
Q Consensus 315 igpLDGGrIl~allg~r~~ 333 (413)
++||||||++++++.++..
T Consensus 138 i~plDGg~il~~~l~~~~~ 156 (180)
T cd05709 138 IPPLDGGRILRALLEAIRG 156 (180)
T ss_pred CCCCChHHHHHHHHhHHHH
Confidence 9999999999999887764
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=99.80 E-value=1.9e-18 Score=168.91 Aligned_cols=120 Identities=26% Similarity=0.319 Sum_probs=94.8
Q ss_pred HHhHHHHHHHHHHHHHHHHHHHHHHHHHcCCcccCccccccceeeeeeeEEEccccc---cCccceeEEEecchhHHHHH
Q 015105 166 LTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAITRIRNIV---SKREDLLKVAAAGPLAGFSL 242 (413)
Q Consensus 166 ~~~gl~~al~l~~iL~iHElGH~laAr~~Gv~~~~P~fiP~~~Lg~fGavi~~~~~~---~~r~~lf~IaiAGPlag~lv 242 (413)
....+.+.+++..++.+||+||+++||++|+++..-.+ ...+.++|++++.++.. .++++++.|++|||++|+++
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 34566677788899999999999999999999974221 01123589999887654 56789999999999999999
Q ss_pred HHHHHHHhhhcCCCCCccccccccchhhhhhHHHHHHHhhccccCCCCCccchHHHHHHHHHHHHHHHhhcCCCCCchHH
Q 015105 243 GFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAINSIPAGELDGGR 322 (413)
Q Consensus 243 al~~l~~g~~l~~~~~~~~~~~~~~f~~s~L~g~la~l~LG~~l~~~~~v~~~pl~~ag~~gl~ltafNLLPigpLDGGr 322 (413)
|++++++.. +.+..|+|+.+++|||+|++||||||
T Consensus 185 a~i~~~l~~---------------------------------------------l~~~~~~N~~l~lFNLlP~~PLDGg~ 219 (263)
T cd06159 185 ALIAFALFF---------------------------------------------LYWIFWINFLLGLFNCLPAIPLDGGH 219 (263)
T ss_pred HHHHHHHHH---------------------------------------------HHHHHHHHHHHHHHhCCCCCCCChHH
Confidence 987754321 22557899999999999999999999
Q ss_pred HHHHhhhhHH
Q 015105 323 IAFALWGRKA 332 (413)
Q Consensus 323 Il~allg~r~ 332 (413)
++++++..+.
T Consensus 220 il~~ll~~~~ 229 (263)
T cd06159 220 VFRDLLEALL 229 (263)
T ss_pred HHHHHHHHHh
Confidence 9999865443
No 7
>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=99.78 E-value=6.3e-19 Score=163.50 Aligned_cols=135 Identities=27% Similarity=0.370 Sum_probs=94.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCccc----Cccccccceeeeee------------eEE-----EccccccCccceeE
Q 015105 172 GALVTALVIGVHELGHILAAKSTGVELG----VPYFVPSWQIGSFG------------AIT-----RIRNIVSKREDLLK 230 (413)
Q Consensus 172 ~al~l~~iL~iHElGH~laAr~~Gv~~~----~P~fiP~~~Lg~fG------------avi-----~~~~~~~~r~~lf~ 230 (413)
..++++.++..||+||+++|+++|+++. +.+++|.-+++++| +.. +.++..++|++++.
T Consensus 4 ~~~~~~~~i~~HE~aHa~~A~~~Gd~t~~~~Grltlnp~~hid~~g~l~~~~~~~~~~G~a~p~~~~~~~~~~~r~~~~~ 83 (181)
T cd06158 4 VIIAVLLAITLHEFAHAYVAYRLGDPTARRAGRLTLNPLAHIDPIGTIILPLLLPFLFGWAKPVPVNPRNFKNPRRGMLL 83 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCcHHHHcCceecCcHHhcCcchHHHHHHHHHhCeEEecccccChHhhcccHhhHhh
Confidence 4556788999999999999999999985 45666744433332 121 12223456688999
Q ss_pred EEecchhHHHHHHHHHHHHhhhcCCCCCccccccccchhhhhhHHHHHHHhhccccCCCCCccchHHHHHHHHHHHHHHH
Q 015105 231 VAAAGPLAGFSLGFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAI 310 (413)
Q Consensus 231 IaiAGPlag~lval~~l~~g~~l~~~~~~~~~~~~~~f~~s~L~g~la~l~LG~~l~~~~~v~~~pl~~ag~~gl~ltaf 310 (413)
|++|||++|+++++++...........+ ...+.+ ...+....++|+.+++|
T Consensus 84 valAGP~~n~~la~i~~~~~~~~~~~~~---------~~~~~l--------------------~~~~~~~~~~Ni~l~lf 134 (181)
T cd06158 84 VSLAGPLSNLLLALLFALLLRLLPAFGG---------VVASFL--------------------FLMLAYGVLINLVLAVF 134 (181)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHhccccc---------hhhHHH--------------------HHHHHHHHHHHHHHHHH
Confidence 9999999999999887655433221100 001111 11234567899999999
Q ss_pred hhcCCCCCchHHHHHHhhhhHHHHH
Q 015105 311 NSIPAGELDGGRIAFALWGRKASTR 335 (413)
Q Consensus 311 NLLPigpLDGGrIl~allg~r~~~~ 335 (413)
||+|++||||||++++++++|....
T Consensus 135 NLlPipPLDG~~il~~~l~~~~~~~ 159 (181)
T cd06158 135 NLLPIPPLDGSKILAALLPRRLAEA 159 (181)
T ss_pred HhCCCCCCChHHHHHHHcchhHHHH
Confidence 9999999999999999998876643
No 8
>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=99.77 E-value=1.1e-18 Score=161.11 Aligned_cols=127 Identities=29% Similarity=0.377 Sum_probs=80.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCcccCcc--c--ccc----------ceeeeeeeE---------------EEccccc
Q 015105 172 GALVTALVIGVHELGHILAAKSTGVELGVPY--F--VPS----------WQIGSFGAI---------------TRIRNIV 222 (413)
Q Consensus 172 ~al~l~~iL~iHElGH~laAr~~Gv~~~~P~--f--iP~----------~~Lg~fGav---------------i~~~~~~ 222 (413)
+.+++..++.+||+||+++|+++|+|+.... + .+. +..-++|++ .+.+...
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 4567888999999999999999999996541 1 111 011123332 2223335
Q ss_pred cCccceeEEEecchhHHHHHHHHHHHHhhhcCCCCCccccccccchhhhhhHHHHHHHhhccccCCCCCccchHHHHHHH
Q 015105 223 SKREDLLKVAAAGPLAGFSLGFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAW 302 (413)
Q Consensus 223 ~~r~~lf~IaiAGPlag~lval~~l~~g~~l~~~~~~~~~~~~~~f~~s~L~g~la~l~LG~~l~~~~~v~~~pl~~ag~ 302 (413)
.+|++.+.+++|||++|++++++++.+......... .+....+.+.++++
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 567889999999999999999888776543221100 01123356778999
Q ss_pred HHHHHHHHhhcCCCCCchHHHHHHhh
Q 015105 303 AGLLINAINSIPAGELDGGRIAFALW 328 (413)
Q Consensus 303 ~gl~ltafNLLPigpLDGGrIl~all 328 (413)
+|+.++++||+|++||||||++++++
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 99999999999999999999999987
No 9
>cd06162 S2P-M50_PDZ_SREBP Sterol regulatory element-binding protein (SREBP) Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50A), regulates intramembrane proteolysis (RIP) of SREBP and is part of a signal transduction mechanism involved in sterol and lipid metabolism. In sterol-depleted mammalian cells, a two-step proteolytic process releases the N-terminal domains of SREBPs from membranes of the endoplasmic reticulum (ER). These domains translocate into the nucleus, where they activate genes of cholesterol and fatty acid biosynthesis. The first cleavage occurs at Site-1 within the ER lumen to generate an intermediate that is subsequently released from the membrane by cleavage at Site-2, which lies within the first transmembrane domain. It is the second proteolytic step that is carried out by the SREBP Site-2 protease (S2P) which is present in this CD family. This group appears to be limited to eumetazoan proteins and contains one PDZ domain.
Probab=99.74 E-value=2.8e-17 Score=161.41 Aligned_cols=116 Identities=24% Similarity=0.209 Sum_probs=90.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHcCCcccCccccccceeeee----eeEEEcccc---ccCccceeEEEecchhHHHHH
Q 015105 170 LPGALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSF----GAITRIRNI---VSKREDLLKVAAAGPLAGFSL 242 (413)
Q Consensus 170 l~~al~l~~iL~iHElGH~laAr~~Gv~~~~P~fiP~~~Lg~f----Gavi~~~~~---~~~r~~lf~IaiAGPlag~lv 242 (413)
..+.++++.++.+||+||+++|+++|+++. ++.+..+ |++++.++. ..++++++.|+.|||++|+++
T Consensus 128 ~~~l~al~isvvvHElgHal~A~~~gi~V~------~iGl~l~~~~pGa~ve~~~e~~~~~~~~~~l~Ia~AGp~~NlvL 201 (277)
T cd06162 128 GYYFTALLISGVVHEMGHGVAAVREQVRVN------GFGIFFFIIYPGAYVDLFTDHLNLISPVQQLRIFCAGVWHNFVL 201 (277)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHcCCeec------eEEEeeeeccCeeEEeecccccccCChhhhhheehhhHHHHHHH
Confidence 334567888999999999999999999996 4444444 999998543 345677899999999999999
Q ss_pred HHHHHHHhhhcCCCCCccccccccchhhhhhHHHHHHHhhccccCCCCCccchHHHHHHHHHHHHHHHhhcCCCCCchHH
Q 015105 243 GFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAINSIPAGELDGGR 322 (413)
Q Consensus 243 al~~l~~g~~l~~~~~~~~~~~~~~f~~s~L~g~la~l~LG~~l~~~~~v~~~pl~~ag~~gl~ltafNLLPigpLDGGr 322 (413)
|++++++.+ . .-+.+.+++|+.+.++||+|++||||||
T Consensus 202 a~i~~~l~~-----------------~-------------------------~~l~~la~iNl~lavfNLlP~~pLDGg~ 239 (277)
T cd06162 202 GLVGYLLLI-----------------E-------------------------TFLKYLISLSGALAVINAVPCFALDGQW 239 (277)
T ss_pred HHHHHHHHH-----------------H-------------------------HHHHHHHHHHHHHHHhhcCCCCCCChHH
Confidence 987765320 0 0133567899999999999999999999
Q ss_pred HHHHhhhhHHH
Q 015105 323 IAFALWGRKAS 333 (413)
Q Consensus 323 Il~allg~r~~ 333 (413)
++++++.++..
T Consensus 240 il~~ll~~~~~ 250 (277)
T cd06162 240 ILSTFLEATLV 250 (277)
T ss_pred HHHHHHHHHhC
Confidence 99998765544
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=99.48 E-value=4e-13 Score=139.40 Aligned_cols=81 Identities=27% Similarity=0.420 Sum_probs=60.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCcccC--ccccc------------cceeeeeeeEEEcccc----c----------
Q 015105 171 PGALVTALVIGVHELGHILAAKSTGVELGV--PYFVP------------SWQIGSFGAITRIRNI----V---------- 222 (413)
Q Consensus 171 ~~al~l~~iL~iHElGH~laAr~~Gv~~~~--P~fiP------------~~~Lg~fGavi~~~~~----~---------- 222 (413)
.+.+.+.+++++||+||+++||++|+|+.. -.|=| .+.+-|+|+++++... .
T Consensus 8 ~~~~~~~~~v~~HE~gH~~~a~~~g~~v~~FsiGfGp~l~~~~~~~tey~i~~~plGg~v~~~g~~~~~~~~~~~~~~~~ 87 (420)
T TIGR00054 8 ASILALAVLIFVHELGHFLAARLCGIKVERFSIGFGPKILKFKKNGTEYAISLIPLGGYVKMKGLDKEMEVKPPETDGDL 87 (420)
T ss_pred HHHHHHHHHHHHHhHHHHHHHHHcCCEEEEEEEccCchheEEecCCeEEEEEEecCcceEeeccCCcccccCCcchhhhh
Confidence 345667788999999999999999999862 11222 1346789999999411 1
Q ss_pred ---cCccceeEEEecchhHHHHHHHHHHHHhh
Q 015105 223 ---SKREDLLKVAAAGPLAGFSLGFVLFLVGF 251 (413)
Q Consensus 223 ---~~r~~lf~IaiAGPlag~lval~~l~~g~ 251 (413)
.+.++++.|.+|||++|+++|++++.+.+
T Consensus 88 f~~~~~~~r~~i~~aGp~~N~~~a~~~~~~~~ 119 (420)
T TIGR00054 88 FNNKSVFQKAIIIFAGPLANFIFAIFVYIFIS 119 (420)
T ss_pred hccCCHHHHHHhhhcccHHHHHHHHHHHHHHH
Confidence 24577899999999999999988876543
No 11
>PRK10779 zinc metallopeptidase RseP; Provisional
Probab=99.47 E-value=6.9e-13 Score=138.59 Aligned_cols=84 Identities=23% Similarity=0.322 Sum_probs=62.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHcCCcccCc--cccc-------------cceeeeeeeEEEccccc----------
Q 015105 168 NGLPGALVTALVIGVHELGHILAAKSTGVELGVP--YFVP-------------SWQIGSFGAITRIRNIV---------- 222 (413)
Q Consensus 168 ~gl~~al~l~~iL~iHElGH~laAr~~Gv~~~~P--~fiP-------------~~~Lg~fGavi~~~~~~---------- 222 (413)
.-+.+.+++..++++||+||+++||++|+|+..= .|=| .+.+-|+|+++++.+..
T Consensus 6 ~i~~fil~l~~li~vHElGHfl~Ar~~gv~V~~FsiGfGp~l~~~~~~~~Tey~i~~iPlGGyVk~~~e~~~~~~~~~~~ 85 (449)
T PRK10779 6 NLAAFIVALGVLITVHEFGHFWVARRCGVRVERFSIGFGKALWRRTDRQGTEYVIALIPLGGYVKMLDERVEPVAPELRH 85 (449)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcCCeeeEEEeecChhHeeEecCCCcEEEEEEEcCCCeeecCCCCCCcCChhhhh
Confidence 3445666777888999999999999999999641 1222 13466899999985431
Q ss_pred -----cCccceeEEEecchhHHHHHHHHHHHHhh
Q 015105 223 -----SKREDLLKVAAAGPLAGFSLGFVLFLVGF 251 (413)
Q Consensus 223 -----~~r~~lf~IaiAGPlag~lval~~l~~g~ 251 (413)
.+.++++.|.+|||++|+++|++++..-+
T Consensus 86 ~~f~~k~~~~R~~i~~AGp~~N~ila~~~~~~~~ 119 (449)
T PRK10779 86 HAFNNKTVGQRAAIIAAGPIANFIFAIFAYWLVF 119 (449)
T ss_pred hhhccCCHHHhhhhhhhhHHHHHHHHHHHHHHHH
Confidence 23477899999999999999988765443
No 12
>COG1994 SpoIVFB Zn-dependent proteases [General function prediction only]
Probab=99.28 E-value=1.6e-11 Score=117.91 Aligned_cols=128 Identities=24% Similarity=0.293 Sum_probs=84.0
Q ss_pred HHhHHHHHHHHHHHHHHHHHHHHHHHHHcCCcccCccccccceeeeeeeEEEccccccCccceeEEE-------ec-chh
Q 015105 166 LTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAITRIRNIVSKREDLLKVA-------AA-GPL 237 (413)
Q Consensus 166 ~~~gl~~al~l~~iL~iHElGH~laAr~~Gv~~~~P~fiP~~~Lg~fGavi~~~~~~~~r~~lf~Ia-------iA-GPl 237 (413)
+.++......++..+..||+||...++++|.+.. ...++.+|++...+..+.+.+..+.+. .| ||+
T Consensus 41 ~~~~~~~~~~l~~rl~l~~~gh~~~~~~~~~~l~------~~~i~~~~g~~~~~~~~v~~~~~~~~~~~g~lvs~algpl 114 (230)
T COG1994 41 LGDGTAAFVGLAHRLVLHPLGHSDEAGRLGLKLL------LALLFGFGGFGFLKPVPVNPRGEFLIRLAGPLVSLALGPL 114 (230)
T ss_pred HhhhHHHHHHHhHHHhhhHhhHHHHHHHHHHHHH------HHHHHhccceeeecCcCcCHHHHhhhhccchhHHHHHHHH
Confidence 4455555555777899999999999999999885 333334677777776655555444444 44 555
Q ss_pred HHHHHHHHHHHHhhhcCCCCCccccccccchhhhhhHHHHHHHhhccccCCCCCccchHHHHHHHHHHHHHHHhhcCCCC
Q 015105 238 AGFSLGFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAINSIPAGE 317 (413)
Q Consensus 238 ag~lval~~l~~g~~l~~~~~~~~~~~~~~f~~s~L~g~la~l~LG~~l~~~~~v~~~pl~~ag~~gl~ltafNLLPigp 317 (413)
.|+.+++.+ ... .+.. .........+...+.+|+++++|||+|++|
T Consensus 115 ~ni~la~~~-~~~--~~~~-------------------------------~~~~~~~~~~~~la~~Nl~L~lFNLiPi~P 160 (230)
T COG1994 115 TNIALAVLG-LLA--LSLF-------------------------------LYHSVLFAFLAALALVNLVLALFNLLPIPP 160 (230)
T ss_pred HHHHHHHHH-HHh--hccc-------------------------------ccchhHHHHHHHHHHHHHHHHHHhCCCCCC
Confidence 555555443 110 0000 000001112335678999999999999999
Q ss_pred CchHHHHHHhhhhHHH
Q 015105 318 LDGGRIAFALWGRKAS 333 (413)
Q Consensus 318 LDGGrIl~allg~r~~ 333 (413)
|||||++|+++.++..
T Consensus 161 LDGg~vlr~~~~~~~~ 176 (230)
T COG1994 161 LDGGRVLRALLPRRYG 176 (230)
T ss_pred CChHHHHHHHccHHHH
Confidence 9999999999887765
No 13
>COG0750 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]
Probab=98.86 E-value=2.2e-09 Score=108.53 Aligned_cols=244 Identities=14% Similarity=0.075 Sum_probs=137.9
Q ss_pred cccccceeeeccccccCCeEEEEeccCCchHHHHHHHHHHHHhhhCCceEEEEeecCCCCCcEEEEecCCCCCCCCCCch
Q 015105 49 QVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFGDQYKLFLLVNPEDDKPVAVVVPRKTLQPETTAVP 128 (413)
Q Consensus 49 ~~f~~~tf~~t~~~~~~~gvi~rGnLr~~~~~~~~~l~~~l~~~~gd~y~lf~~~~~~~~kpv~~~~P~~~~~~~~~~~~ 128 (413)
.++..++|+..+..+ +..+++.|.+.......+..+.... ..|..+ ...|+.- +..... +
T Consensus 82 ~~~~~~~f~~~~~~~-~~~~~~~Gp~~n~i~~~~~~~~~~~--~~G~~~---------~~~~~~~-----~v~~~s---~ 141 (375)
T COG0750 82 PEPRPRAFNAKSVWQ-RIAIVFAGPLFNFILAIVLFVVLFF--VIGLVP---------VASPVVG-----EVAPKS---A 141 (375)
T ss_pred cCcchhhhhcccccc-hhheeechHHHHHHHHHHHHHhhhe--Eeeeee---------eccCeee-----ecCCCC---H
Confidence 588889999999998 8999999999887765555544332 222111 1112211 001110 0
Q ss_pred HHHHHHHHHHHHHHHHHhhcccccchhhhhhccchHHHHhHHHHHHH----HHHHHHHH--HHHHHHHHHHcCCcccCcc
Q 015105 129 EWFAAGAFGLVTVFTLLLRNVPALQSNLLSTFDNLNLLTNGLPGALV----TALVIGVH--ELGHILAAKSTGVELGVPY 202 (413)
Q Consensus 129 ~~~~~~l~~l~t~~t~~~~~~~~l~~~~~~~~~~~~~~~~gl~~al~----l~~iL~iH--ElGH~laAr~~Gv~~~~P~ 202 (413)
+..+.+..|...+..+- +...+.+..........+ .+.+.+.| |..|..+++.++.....|+
T Consensus 142 -----------a~~a~l~~Gd~iv~~~~-~~i~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~P~ 209 (375)
T COG0750 142 -----------AALAGLRPGDRIVAVDG-EKVASWDDVRRLLVAAAGDVFNLLTILVIRLDGEAHAVAAEIIKSLGLTPV 209 (375)
T ss_pred -----------HHHcCCCCCCEEEeECC-EEccCHHHHHHHHHhccCCcccceEEEEEeccceeeeccccceeeEeeecc
Confidence 11112333332222221 122233322221211111 35667788 9999999998888888898
Q ss_pred ccccceeeeeeeEEE--ccccccC-----ccceeEEEecchhHHHHHHHHHHHHhhhcCCCCCccccccccchhhhhhHH
Q 015105 203 FVPSWQIGSFGAITR--IRNIVSK-----REDLLKVAAAGPLAGFSLGFVLFLVGFIFPPSDGIGIVVDASVFHESFLAG 275 (413)
Q Consensus 203 fiP~~~Lg~fGavi~--~~~~~~~-----r~~lf~IaiAGPlag~lval~~l~~g~~l~~~~~~~~~~~~~~f~~s~L~g 275 (413)
++| ...+..+..++ ..+..++ ++...++..+++++ ..+.-...+.++.++... ......++.+.+.|
T Consensus 210 ~~~-~~~~~~~~~i~~~~i~~~p~~~~~~~~~~~~~~~~~~i~-~~v~~~~~~~~~~~~~l~----~~~~~~~~~~~l~G 283 (375)
T COG0750 210 VIP-LKPGDKIVAVDVGAIGLSPNGEPDVGKVLVKYGPLEAVG-LAVEKTGRLVKLTLKMLK----KLITGDLSLKNLSG 283 (375)
T ss_pred eec-cCCCCEEEEeeeeeeeeccCCCCccceeeeccCHHHHHH-HHHHHHHHHHHHHHHHHH----HheecccccccccC
Confidence 876 45566665553 3344444 78899999999998 344444444443322000 00011122222222
Q ss_pred HHHHHhhccccCCCCCccchHHHHHHHHHHHHHHHhhcCCCCCchHHHHHHhhhhHH
Q 015105 276 GFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAINSIPAGELDGGRIAFALWGRKA 332 (413)
Q Consensus 276 ~la~l~LG~~l~~~~~v~~~pl~~ag~~gl~ltafNLLPigpLDGGrIl~allg~r~ 332 (413)
.+.....++... +....|++.+++|+|+.++++||+|+++|||||++++++.++.
T Consensus 284 pi~i~~~~~~~~--~~~~~~~l~~~~~lsi~lg~lNllP~p~LDGG~i~~~~~e~~~ 338 (375)
T COG0750 284 PIGIAKIAGAAA--SLGLINLLFFLALLSINLGILNLLPIPPLDGGHLLFYLLEALR 338 (375)
T ss_pred ceehhhhhhHHH--hhHHHHHHHHHHHHHHHHHHHhccCCCccCccHHHHHHHHHHh
Confidence 222111111100 1235689999999999999999999999999999999976654
No 14
>PF13398 Peptidase_M50B: Peptidase M50B-like
Probab=97.26 E-value=0.00036 Score=65.90 Aligned_cols=65 Identities=31% Similarity=0.274 Sum_probs=51.9
Q ss_pred HHHHHHHHHHHHHHHHcCCcccCccccccceeee-eeeEEEccccccCccceeEEEecchhHHHHHHHHHHHHh
Q 015105 178 LVIGVHELGHILAAKSTGVELGVPYFVPSWQIGS-FGAITRIRNIVSKREDLLKVAAAGPLAGFSLGFVLFLVG 250 (413)
Q Consensus 178 ~iL~iHElGH~laAr~~Gv~~~~P~fiP~~~Lg~-fGavi~~~~~~~~r~~lf~IaiAGPlag~lval~~l~~g 250 (413)
....+||+||.++|...|-|+. .+.+.+ -++.+..+. +++...+.++.|||++..+++..++..+
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 4588999999999999999997 444433 477777766 5666788999999999999887776655
No 15
>KOG2921 consensus Intramembrane metalloprotease (sterol-regulatory element-binding protein (SREBP) protease) [Posttranslational modification, protein turnover, chaperones]
Probab=96.11 E-value=0.0045 Score=63.86 Aligned_cols=83 Identities=29% Similarity=0.304 Sum_probs=54.7
Q ss_pred HhHHHHHH-HHHHHHHHHHHHHHHHHHHcCCcccCccccccceeeeeeeEEEcccccc---CccceeEEEecchhHHHHH
Q 015105 167 TNGLPGAL-VTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAITRIRNIVS---KREDLLKVAAAGPLAGFSL 242 (413)
Q Consensus 167 ~~gl~~al-~l~~iL~iHElGH~laAr~~Gv~~~~P~fiP~~~Lg~fGavi~~~~~~~---~r~~lf~IaiAGPlag~lv 242 (413)
+++++|.+ .++....+||+||+|+|.+.|+++.- |-=.+..--=||++.++..-- +.-+...|.-||--=||++
T Consensus 120 l~~I~yf~t~lvi~~vvHElGHalAA~segV~vng--fgIfi~aiyPgafvdl~~dhLqsl~~fr~LrIfcAGIWHNfvf 197 (484)
T KOG2921|consen 120 LSGIAYFLTSLVITVVVHELGHALAAASEGVQVNG--FGIFIAAIYPGAFVDLDNDHLQSLPSFRALRIFCAGIWHNFVF 197 (484)
T ss_pred cccchhhhhhHHHHHHHHHhhHHHHHHhcCceeee--eEEEEEEEcCchhhhhhhhHHhhcchHHHHHHHhhhHHHHHHH
Confidence 44555544 46678899999999999999999861 100011111277777654321 1123458889999999999
Q ss_pred HHHHHHHhh
Q 015105 243 GFVLFLVGF 251 (413)
Q Consensus 243 al~~l~~g~ 251 (413)
|+++.+.-.
T Consensus 198 allc~lal~ 206 (484)
T KOG2921|consen 198 ALLCVLALF 206 (484)
T ss_pred HHHHHHHHH
Confidence 988766544
No 16
>COG0750 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]
Probab=95.89 E-value=0.025 Score=57.42 Aligned_cols=82 Identities=28% Similarity=0.409 Sum_probs=54.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHcCCcccCcc--ccc-------c------ceeeeeeeEEEcccccc-----------
Q 015105 170 LPGALVTALVIGVHELGHILAAKSTGVELGVPY--FVP-------S------WQIGSFGAITRIRNIVS----------- 223 (413)
Q Consensus 170 l~~al~l~~iL~iHElGH~laAr~~Gv~~~~P~--fiP-------~------~~Lg~fGavi~~~~~~~----------- 223 (413)
+.+.+.+...+..||+||++.||++|+++.... |-| . +..-+.|+++++.....
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 445566777889999999999999999986421 112 1 12345677765533211
Q ss_pred -------CccceeEEEecchhHHHHHHHHHHHHhh
Q 015105 224 -------KREDLLKVAAAGPLAGFSLGFVLFLVGF 251 (413)
Q Consensus 224 -------~r~~lf~IaiAGPlag~lval~~l~~g~ 251 (413)
+-+..+.+..+||++|++.++.......
T Consensus 86 ~~~f~~~~~~~~~~~~~~Gp~~n~i~~~~~~~~~~ 120 (375)
T COG0750 86 PRAFNAKSVWQRIAIVFAGPLFNFILAIVLFVVLF 120 (375)
T ss_pred hhhhhcccccchhheeechHHHHHHHHHHHHHhhh
Confidence 1122577889999999987777666554
No 17
>PF00413 Peptidase_M10: Matrixin This Prosite motif covers only the active site.; InterPro: IPR001818 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M10 (clan MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA. Sequences having this domain are extracellular metalloproteases, such as collagenase and stromelysin, which degrade the extracellular matrix, are known as matrixins. They are zinc-dependent, calcium-activated proteases synthesised as inactive precursors (zymogens), which are proteolytically cleaved to yield the active enzyme [, ]. All matrixins and related proteins possess 2 domains: an N-terminal domain, and a zinc-binding active site domain. The N-terminal domain peptide, cleaved during the activation step, includes a conserved PRCGVPDV octapeptide, known as the cysteine switch, whose Cys residue chelates the active site zinc atom, rendering the enzyme inactive [, ]. The active enzyme degrades components of the extracellular matrix, playing a role in the initial steps of tissue remodelling during morphogenesis, wound healing, angiogenesis and tumour invasion [, ].; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis, 0031012 extracellular matrix; PDB: 1Q3A_C 3V96_B 1HV5_D 1CXV_A 1SRP_A 1FBL_A 1ZVX_A 1JH1_A 1I76_A 2OY4_A ....
Probab=60.99 E-value=4.9 Score=35.19 Aligned_cols=21 Identities=24% Similarity=0.436 Sum_probs=14.8
Q ss_pred HHHHHHHHHHHHHHHHcCCcc
Q 015105 178 LVIGVHELGHILAAKSTGVEL 198 (413)
Q Consensus 178 ~iL~iHElGH~laAr~~Gv~~ 198 (413)
..+++||+||.+=-.+...+-
T Consensus 106 ~~v~~HEiGHaLGL~H~~~~~ 126 (154)
T PF00413_consen 106 QSVAIHEIGHALGLDHSNDPN 126 (154)
T ss_dssp HHHHHHHHHHHTTBESSSSTT
T ss_pred hhhhhhccccccCcCcCCCcc
Confidence 468899999998665544433
No 18
>cd04279 ZnMc_MMP_like_1 Zinc-dependent metalloprotease; MMP_like sub-family 1. A group of bacterial, archaeal, and fungal metalloproteinase domains similar to matrix metalloproteinases and astacin.
Probab=59.03 E-value=5.7 Score=35.43 Aligned_cols=22 Identities=32% Similarity=0.364 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHHHHHHcCCcc
Q 015105 177 ALVIGVHELGHILAAKSTGVEL 198 (413)
Q Consensus 177 ~~iL~iHElGH~laAr~~Gv~~ 198 (413)
+..+++||+||.+=.++...+-
T Consensus 104 ~~~~~~HEiGHaLGL~H~~~~~ 125 (156)
T cd04279 104 LQAIALHELGHALGLWHHSDRP 125 (156)
T ss_pred HHHHHHHHhhhhhcCCCCCCCc
Confidence 4578899999999888887765
No 19
>PF11667 DUF3267: Protein of unknown function (DUF3267); InterPro: IPR021683 This family of proteins has no known function.
Probab=58.31 E-value=3.8 Score=34.85 Aligned_cols=68 Identities=22% Similarity=0.258 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHHHHHHcCCcccCcccccccee-eeeeeEEEccccccCccceeEEEecchhHHHHHHHHHHHHhhh
Q 015105 177 ALVIGVHELGHILAAKSTGVELGVPYFVPSWQI-GSFGAITRIRNIVSKREDLLKVAAAGPLAGFSLGFVLFLVGFI 252 (413)
Q Consensus 177 ~~iL~iHElGH~laAr~~Gv~~~~P~fiP~~~L-g~fGavi~~~~~~~~r~~lf~IaiAGPlag~lval~~l~~g~~ 252 (413)
+..+.+||+-|.+..+.+|.+... .+.. ...+......+..-+ |..+.+...-|. ++++++.++.+..
T Consensus 4 ~~~~~~HEliH~l~~~~~~~~~~~-----~~g~~~~~~~~~~~~~~~~s-k~~~~i~~l~P~--ivl~~~~~~~~~~ 72 (111)
T PF11667_consen 4 IVLIPLHELIHGLFFKLFGKKPKV-----KFGFKWKLGPFYATCNEPIS-KWRFIIILLAPF--IVLTILPLILGFF 72 (111)
T ss_pred EeeHHHHHHHHHHHHHHhCCCCce-----EEEEEeeeEEEEEecCcEEe-HHHHHHHHHHHH--HHHHHHHHHHHHH
Confidence 345689999999999999996521 1111 112222222333333 445566666674 4555555555443
No 20
>PF05572 Peptidase_M43: Pregnancy-associated plasma protein-A; InterPro: IPR008754 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase M43 (cytophagalysin family, clan MA(M)), subfamily M43. The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH. The type example of this family is the pregnancy-associated plasma protein A (PAPP-A), which cleaves insulin-like growth factor (IGF) binding protein-4 (IGFBP-4), causing a dramatic reduction in its affinity for IGF-I and -II. Through this mechanism, PAPP-A is a regulator of IGF bioactivity in several systems, including the Homo sapiens ovary and the cardiovascular system [, , , ].; PDB: 3LUN_A 3LUM_B 2J83_A 2CKI_A.
Probab=52.03 E-value=7.1 Score=35.56 Aligned_cols=15 Identities=33% Similarity=0.275 Sum_probs=10.9
Q ss_pred HHHHHHHHHHHHHHH
Q 015105 178 LVIGVHELGHILAAK 192 (413)
Q Consensus 178 ~iL~iHElGH~laAr 192 (413)
.-.++||+||++=-+
T Consensus 70 g~TltHEvGH~LGL~ 84 (154)
T PF05572_consen 70 GKTLTHEVGHWLGLY 84 (154)
T ss_dssp SHHHHHHHHHHTT--
T ss_pred ccchhhhhhhhhccc
Confidence 467899999997543
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=50.18 E-value=15 Score=32.62 Aligned_cols=24 Identities=25% Similarity=0.235 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHHHHHHHHHcCCcc
Q 015105 175 VTALVIGVHELGHILAAKSTGVEL 198 (413)
Q Consensus 175 ~l~~iL~iHElGH~laAr~~Gv~~ 198 (413)
.-....++||+||.+=-++-.-+.
T Consensus 92 ~~~~~~~~HEiGHaLGL~H~~~~~ 115 (165)
T cd04268 92 ARLRNTAEHELGHALGLRHNFAAS 115 (165)
T ss_pred HHHHHHHHHHHHHHhcccccCcCC
Confidence 355678999999998776666543
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=47.99 E-value=8.1 Score=34.56 Aligned_cols=23 Identities=22% Similarity=0.352 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHHHHHHcCCcc
Q 015105 176 TALVIGVHELGHILAAKSTGVEL 198 (413)
Q Consensus 176 l~~iL~iHElGH~laAr~~Gv~~ 198 (413)
-+..++.||+||.+=-.+...+.
T Consensus 106 ~~~~~~~HEiGHaLGL~H~~~~~ 128 (157)
T cd04278 106 DLFSVAAHEIGHALGLGHSSDPD 128 (157)
T ss_pred hHHHHHHHHhccccccCCCCCCc
Confidence 35568899999998775544443
No 23
>PF13485 Peptidase_MA_2: Peptidase MA superfamily
Probab=47.97 E-value=15 Score=30.27 Aligned_cols=18 Identities=28% Similarity=0.233 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHHHHcCC
Q 015105 179 VIGVHELGHILAAKSTGV 196 (413)
Q Consensus 179 iL~iHElGH~laAr~~Gv 196 (413)
-+++||++|.+.....+-
T Consensus 27 ~~l~HE~~H~~~~~~~~~ 44 (128)
T PF13485_consen 27 RVLAHELAHQWFGNYFGG 44 (128)
T ss_pred HHHHHHHHHHHHHHHcCC
Confidence 688999999999998763
No 24
>KOG3320 consensus 40S ribosomal protein S7 [Translation, ribosomal structure and biogenesis]
Probab=47.19 E-value=33 Score=32.39 Aligned_cols=26 Identities=15% Similarity=0.336 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHhhhCCceEEEEeecC
Q 015105 80 KTYEKISTRMKNKFGDQYKLFLLVNP 105 (413)
Q Consensus 80 ~~~~~l~~~l~~~~gd~y~lf~~~~~ 105 (413)
+.|.+|-+.||.+|+|+|.+|+.+..
T Consensus 75 ki~~~LvreleKKF~gk~Vifia~Rr 100 (192)
T KOG3320|consen 75 KIQVRLVRELEKKFSGKHVIFIAQRR 100 (192)
T ss_pred HHHHHHHHHHHHhcCCceEEEEEeee
Confidence 44555556899999999999866554
No 25
>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=43.77 E-value=14 Score=30.09 Aligned_cols=17 Identities=41% Similarity=0.542 Sum_probs=12.5
Q ss_pred HHHHHHHHHHHHHHHcC
Q 015105 179 VIGVHELGHILAAKSTG 195 (413)
Q Consensus 179 iL~iHElGH~laAr~~G 195 (413)
..++||+||++.-....
T Consensus 44 f~laHELgH~~~~~~~~ 60 (122)
T PF06114_consen 44 FTLAHELGHILLHHGDE 60 (122)
T ss_dssp HHHHHHHHHHHHHH-HH
T ss_pred HHHHHHHHHHHhhhccc
Confidence 36799999999865543
No 26
>PF01435 Peptidase_M48: Peptidase family M48 This is family M48 in the peptidase classification. ; InterPro: IPR001915 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M48 (Ste24 endopeptidase family, clan M-); members of both subfamily are represented. The members of this set of proteins are mostly described as probable protease htpX homologue (3.4.24 from EC) or CAAX prenyl protease 1, which proteolytically removes the C-terminal three residues of farnesylated proteins. They are integral membrane proteins associated with the endoplasmic reticulum and Golgi, binding one zinc ion per subunit. In Saccharomyces cerevisiae (Baker's yeast) Ste24p is required for the first NH2-terminal proteolytic processing event within the a-factor precursor, which takes place after COOH-terminal CAAX modification is complete. The Ste24p contains multiple predicted membrane spans, a zinc metalloprotease motif (HEXXH), and a COOH-terminal ER retrieval signal (KKXX). The HEXXH protease motif is critical for Ste24p activity, since Ste24p fails to function when conserved residues within this motif are mutated. The Ste24p homologues occur in a diverse group of organisms, including Escherichia coli, Schizosaccharomyces pombe (Fission yeast), Haemophilus influenzae, and Homo sapiens (Human), which indicates that the gene is highly conserved throughout evolution. Ste24p and the proteins related to it define a subfamily of proteins that are likely to function as intracellular, membrane-associated zinc metalloproteases []. HtpX is a zinc-dependent endoprotease member of the membrane-localized proteolytic system in E. coli, which participates in the proteolytic quality control of membrane proteins in conjunction with FtsH, a membrane-bound and ATP-dependent protease. Biochemical characterisation revealed that HtpX undergoes self-degradation upon cell disruption or membrane solubilization. It can also degraded casein and cleaves solubilized membrane proteins, for example, SecY []. Expression of HtpX in the plasma membrane is under the control of CpxR, with the metalloproteinase active site of HtpX located on the cytosolic side of the membrane. This suggests a potential role for HtpX in the response to mis-folded proteins [].; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis, 0016020 membrane; PDB: 3CQB_A 3C37_B.
Probab=43.52 E-value=15 Score=33.96 Aligned_cols=12 Identities=50% Similarity=0.717 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHH
Q 015105 178 LVIGVHELGHIL 189 (413)
Q Consensus 178 ~iL~iHElGH~l 189 (413)
..+++||+||..
T Consensus 90 ~aVlaHElgH~~ 101 (226)
T PF01435_consen 90 AAVLAHELGHIK 101 (226)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 368899999986
No 27
>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=42.44 E-value=14 Score=34.01 Aligned_cols=23 Identities=30% Similarity=0.439 Sum_probs=17.1
Q ss_pred HHHHHHHHHHHHHHHHHcCCccc
Q 015105 177 ALVIGVHELGHILAAKSTGVELG 199 (413)
Q Consensus 177 ~~iL~iHElGH~laAr~~Gv~~~ 199 (413)
..-.++||+||.+=-++-+....
T Consensus 113 ~~~t~~HEiGHaLGL~H~~~~~~ 135 (186)
T cd04277 113 GYQTIIHEIGHALGLEHPGDYNG 135 (186)
T ss_pred hHHHHHHHHHHHhcCCCCCcCCC
Confidence 44678999999998766665543
No 28
>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=41.91 E-value=31 Score=27.35 Aligned_cols=35 Identities=23% Similarity=0.314 Sum_probs=25.6
Q ss_pred cccceeeeccccccCCeEEEEeccCCchHHHHHHHHHHHHhhhCCc
Q 015105 51 FGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFGDQ 96 (413)
Q Consensus 51 f~~~tf~~t~~~~~~~gvi~rGnLr~~~~~~~~~l~~~l~~~~gd~ 96 (413)
.-.|+||+++.. |+ ..+++..+++++.|++.+|+.
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 567999998642 12 245567788999999999864
No 29
>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=41.32 E-value=14 Score=34.01 Aligned_cols=21 Identities=33% Similarity=0.286 Sum_probs=14.2
Q ss_pred HHHHHHHHHHHHHHHHHcCCc
Q 015105 177 ALVIGVHELGHILAAKSTGVE 197 (413)
Q Consensus 177 ~~iL~iHElGH~laAr~~Gv~ 197 (413)
-.-.++||+||.+=|.+-+-.
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 334589999999999887764
No 30
>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=40.89 E-value=13 Score=34.09 Aligned_cols=22 Identities=32% Similarity=0.403 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHHHHHHHHcCCc
Q 015105 176 TALVIGVHELGHILAAKSTGVE 197 (413)
Q Consensus 176 l~~iL~iHElGH~laAr~~Gv~ 197 (413)
.-...++||+||-+=|.+=+..
T Consensus 141 ~~~~~~AHEiGH~lGa~HD~~~ 162 (196)
T PF13688_consen 141 NGAITFAHEIGHNLGAPHDGDY 162 (196)
T ss_dssp HHHHHHHHHHHHHTT-----SS
T ss_pred ceehhhHHhHHHhcCCCCCCCC
Confidence 4457899999999999886654
No 31
>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=40.86 E-value=14 Score=32.12 Aligned_cols=20 Identities=30% Similarity=0.441 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHHHcCCccc
Q 015105 180 IGVHELGHILAAKSTGVELG 199 (413)
Q Consensus 180 L~iHElGH~laAr~~Gv~~~ 199 (413)
.++||+||.+-..+-..+-.
T Consensus 89 ~~~HEigHaLGl~H~~~~~d 108 (140)
T smart00235 89 VAAHELGHALGLYHEQSRSD 108 (140)
T ss_pred cHHHHHHHHhcCCcCCCCCc
Confidence 79999999997776665554
No 32
>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=39.85 E-value=15 Score=32.50 Aligned_cols=22 Identities=27% Similarity=0.215 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHHHHHHHHcCCc
Q 015105 176 TALVIGVHELGHILAAKSTGVE 197 (413)
Q Consensus 176 l~~iL~iHElGH~laAr~~Gv~ 197 (413)
....+++||+||.+=.++...+
T Consensus 95 ~~~~~~~HElGH~LGl~H~~~~ 116 (167)
T cd00203 95 EGAQTIAHELGHALGFYHDHDR 116 (167)
T ss_pred cchhhHHHHHHHHhCCCccCcC
Confidence 4456789999999987766543
No 33
>PF01434 Peptidase_M41: Peptidase family M41 This is family M41 in the peptidase classification. ; InterPro: IPR000642 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M41 (FtsH endopeptidase family, clan MA(E)). The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH. The peptidase M41 family belong to a larger family of zinc metalloproteases. This family includes the cell division protein FtsH, and the yeast mitochondrial respiratory chain complexes assembly protein, which is a putative ATP-dependent protease required for assembly of the mitochondrial respiratory chain and ATPase complexes. FtsH is an integral membrane protein, which seems to act as an ATP-dependent zinc metallopeptidase that binds one zinc ion.; GO: 0004222 metalloendopeptidase activity, 0005524 ATP binding, 0006508 proteolysis; PDB: 4EIW_C 2DHR_E 1IY1_A 1IY2_A 1IY0_A 1IXZ_A 2CE7_F 2CEA_F 3KDS_E 2QZ4_A ....
Probab=39.80 E-value=23 Score=33.68 Aligned_cols=18 Identities=33% Similarity=0.316 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHHHHHcCC
Q 015105 179 VIGVHELGHILAAKSTGV 196 (413)
Q Consensus 179 iL~iHElGH~laAr~~Gv 196 (413)
.+.+||.||+++|...+-
T Consensus 30 ~~A~HEAGhAvva~~l~~ 47 (213)
T PF01434_consen 30 RIAYHEAGHAVVAYLLPP 47 (213)
T ss_dssp HHHHHHHHHHHHHHHSSS
T ss_pred HHHHHHHHHHHHHHHhcc
Confidence 578999999999998873
No 34
>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=36.78 E-value=21 Score=32.04 Aligned_cols=11 Identities=73% Similarity=1.189 Sum_probs=9.3
Q ss_pred HHHHHHHHHHH
Q 015105 180 IGVHELGHILA 190 (413)
Q Consensus 180 L~iHElGH~la 190 (413)
+.+||+||.+-
T Consensus 80 IaaHE~GHiLG 90 (132)
T PF02031_consen 80 IAAHELGHILG 90 (132)
T ss_dssp HHHHHHHHHHT
T ss_pred eeeehhccccC
Confidence 77999999873
No 35
>PF13582 Reprolysin_3: Metallo-peptidase family M12B Reprolysin-like; PDB: 3P24_C.
Probab=35.51 E-value=16 Score=30.81 Aligned_cols=14 Identities=36% Similarity=0.423 Sum_probs=10.3
Q ss_pred HHHHHHHHHHHHHH
Q 015105 179 VIGVHELGHILAAK 192 (413)
Q Consensus 179 iL~iHElGH~laAr 192 (413)
..++||+||-+=++
T Consensus 109 ~~~~HEiGH~lGl~ 122 (124)
T PF13582_consen 109 DTFAHEIGHNLGLN 122 (124)
T ss_dssp THHHHHHHHHTT--
T ss_pred eEeeehhhHhcCCC
Confidence 67899999987543
No 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=35.08 E-value=26 Score=33.90 Aligned_cols=21 Identities=29% Similarity=0.265 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHHHHHHHHHcCC
Q 015105 175 VTALVIGVHELGHILAAKSTGV 196 (413)
Q Consensus 175 ~l~~iL~iHElGH~laAr~~Gv 196 (413)
.+.+++++||++|+|. |..|.
T Consensus 91 ll~gsiLAHE~mHa~L-rl~g~ 111 (212)
T PF12315_consen 91 LLTGSILAHELMHAWL-RLNGF 111 (212)
T ss_pred HHHhhHHHHHHHHHHh-cccCC
Confidence 3567899999999998 44453
No 37
>PF14247 DUF4344: Domain of unknown function (DUF4344)
Probab=34.42 E-value=41 Score=32.69 Aligned_cols=20 Identities=40% Similarity=0.489 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 015105 173 ALVTALVIGVHELGHILAAK 192 (413)
Q Consensus 173 al~l~~iL~iHElGH~laAr 192 (413)
++.-+...+.||+||++...
T Consensus 88 ~~~~~~~~l~HE~GHAlI~~ 107 (220)
T PF14247_consen 88 AIGNVLFTLYHELGHALIDD 107 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 55566778899999999865
No 38
>COG2856 Predicted Zn peptidase [Amino acid transport and metabolism]
Probab=34.24 E-value=22 Score=34.37 Aligned_cols=14 Identities=43% Similarity=0.551 Sum_probs=11.0
Q ss_pred HHHHHHHHHHHHHH
Q 015105 180 IGVHELGHILAAKS 193 (413)
Q Consensus 180 L~iHElGH~laAr~ 193 (413)
.++||+||++.=+.
T Consensus 75 tlAHELGH~llH~~ 88 (213)
T COG2856 75 TLAHELGHALLHTD 88 (213)
T ss_pred HHHHHHhHHHhccc
Confidence 57899999997443
No 39
>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=33.74 E-value=23 Score=33.16 Aligned_cols=21 Identities=24% Similarity=0.251 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHHHcCCcc
Q 015105 178 LVIGVHELGHILAAKSTGVEL 198 (413)
Q Consensus 178 ~iL~iHElGH~laAr~~Gv~~ 198 (413)
...++||+||++=-.+-.-+.
T Consensus 93 ~~~i~HElgHaLG~~HEh~rp 113 (198)
T cd04327 93 SRVVLHEFGHALGFIHEHQSP 113 (198)
T ss_pred HHHHHHHHHHHhcCcccccCC
Confidence 357789999998765544443
No 40
>cd04270 ZnMc_TACE_like Zinc-dependent metalloprotease; TACE_like subfamily. TACE, the tumor-necrosis factor-alpha converting enzyme, releases soluble TNF-alpha from transmembrane pro-TNF-alpha.
Probab=31.98 E-value=28 Score=33.82 Aligned_cols=18 Identities=28% Similarity=0.503 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 015105 176 TALVIGVHELGHILAAKS 193 (413)
Q Consensus 176 l~~iL~iHElGH~laAr~ 193 (413)
.....++||+||-+=+.+
T Consensus 166 ~~a~t~AHElGHnlGm~H 183 (244)
T cd04270 166 ESDLVTAHELGHNFGSPH 183 (244)
T ss_pred HHHHHHHHHHHHhcCCCC
Confidence 456789999999987664
No 41
>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=31.61 E-value=27 Score=32.13 Aligned_cols=20 Identities=35% Similarity=0.350 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHHHHHHcCC
Q 015105 177 ALVIGVHELGHILAAKSTGV 196 (413)
Q Consensus 177 ~~iL~iHElGH~laAr~~Gv 196 (413)
...+++||+||-+=+.+-+.
T Consensus 131 ~a~~~AHElGH~lG~~HD~~ 150 (194)
T cd04269 131 FAVTMAHELGHNLGMEHDDG 150 (194)
T ss_pred HHHHHHHHHHhhcCCCcCCC
Confidence 35788999999998775554
No 42
>PF05265 DUF723: Protein of unknown function (DUF723); InterPro: IPR007929 This family contains several uncharacterised proteins from Neisseria meningitidis. These proteins may have a role in DNA binding.
Probab=31.27 E-value=87 Score=24.53 Aligned_cols=36 Identities=28% Similarity=0.540 Sum_probs=28.3
Q ss_pred HHHHHHHHHHhhhCCceEEEEeecCCCCCcEEEEecCCC
Q 015105 81 TYEKISTRMKNKFGDQYKLFLLVNPEDDKPVAVVVPRKT 119 (413)
Q Consensus 81 ~~~~l~~~l~~~~gd~y~lf~~~~~~~~kpv~~~~P~~~ 119 (413)
.++..+.+.+++||| |.+ ++=.....|+.+.-|..-
T Consensus 4 t~~~~~~r~~e~Fp~-~sl--vef~g~~~PvtI~CP~HG 39 (60)
T PF05265_consen 4 TFESAASRFEEKFPH-YSL--VEFSGVATPVTIRCPKHG 39 (60)
T ss_pred eHHHHHHHHHHHCCC-ceE--EEEeCCCCceEEECCCCC
Confidence 467778999999999 765 555556899999999863
No 43
>PRK03001 M48 family peptidase; Provisional
Probab=30.95 E-value=30 Score=34.27 Aligned_cols=12 Identities=33% Similarity=0.426 Sum_probs=10.0
Q ss_pred HHHHHHHHHHHH
Q 015105 178 LVIGVHELGHIL 189 (413)
Q Consensus 178 ~iL~iHElGH~l 189 (413)
..+++||+||.-
T Consensus 125 ~aVlAHElgHi~ 136 (283)
T PRK03001 125 RGVMAHELAHVK 136 (283)
T ss_pred HHHHHHHHHHHh
Confidence 368899999975
No 44
>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=30.39 E-value=22 Score=35.40 Aligned_cols=15 Identities=33% Similarity=0.505 Sum_probs=11.5
Q ss_pred HHHHHHHHHHHHHHH
Q 015105 177 ALVIGVHELGHILAA 191 (413)
Q Consensus 177 ~~iL~iHElGH~laA 191 (413)
+.-+++||+||.+.-
T Consensus 216 ~~~v~vHE~GHsf~~ 230 (264)
T PF09471_consen 216 FKQVVVHEFGHSFGG 230 (264)
T ss_dssp HHHHHHHHHHHHTT-
T ss_pred ccceeeeeccccccc
Confidence 456889999998763
No 45
>PRK03982 heat shock protein HtpX; Provisional
Probab=30.24 E-value=32 Score=34.21 Aligned_cols=11 Identities=45% Similarity=0.480 Sum_probs=9.4
Q ss_pred HHHHHHHHHHH
Q 015105 179 VIGVHELGHIL 189 (413)
Q Consensus 179 iL~iHElGH~l 189 (413)
.+++||+||.-
T Consensus 127 AVlAHElgHi~ 137 (288)
T PRK03982 127 GVIAHELTHIK 137 (288)
T ss_pred HHHHHHHHHHH
Confidence 68899999974
No 46
>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=30.08 E-value=23 Score=32.47 Aligned_cols=20 Identities=40% Similarity=0.531 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHHHHHHHcCC
Q 015105 177 ALVIGVHELGHILAAKSTGV 196 (413)
Q Consensus 177 ~~iL~iHElGH~laAr~~Gv 196 (413)
....++||+||.+=+.+-+.
T Consensus 133 ~~~~~aHElGH~lG~~HD~~ 152 (192)
T cd04267 133 TALTMAHELGHNLGAEHDGG 152 (192)
T ss_pred ehhhhhhhHHhhcCCcCCCC
Confidence 35688999999998877654
No 47
>PHA02456 zinc metallopeptidase motif-containing protein
Probab=30.07 E-value=31 Score=30.36 Aligned_cols=18 Identities=28% Similarity=0.351 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHcCCcc
Q 015105 181 GVHELGHILAAKSTGVEL 198 (413)
Q Consensus 181 ~iHElGH~laAr~~Gv~~ 198 (413)
+.||+.|.|.-|.||.-.
T Consensus 83 L~HEL~H~WQ~RsYG~i~ 100 (141)
T PHA02456 83 LAHELNHAWQFRTYGLVQ 100 (141)
T ss_pred HHHHHHHHHhhhccceee
Confidence 579999999999999754
No 48
>PF14891 Peptidase_M91: Effector protein
Probab=29.66 E-value=34 Score=31.45 Aligned_cols=18 Identities=28% Similarity=0.252 Sum_probs=14.0
Q ss_pred HHHHHHHHHHHHHHHHHc
Q 015105 177 ALVIGVHELGHILAAKST 194 (413)
Q Consensus 177 ~~iL~iHElGH~laAr~~ 194 (413)
-++.+.|||+|++-...=
T Consensus 103 p~v~L~HEL~HA~~~~~G 120 (174)
T PF14891_consen 103 PFVVLYHELIHAYDYMNG 120 (174)
T ss_pred HHHHHHHHHHHHHHHHCC
Confidence 357899999999876543
No 49
>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=29.05 E-value=27 Score=33.71 Aligned_cols=24 Identities=21% Similarity=0.315 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHcCC
Q 015105 173 ALVTALVIGVHELGHILAAKSTGV 196 (413)
Q Consensus 173 al~l~~iL~iHElGH~laAr~~Gv 196 (413)
..-...-+++||+||.+=-|+-..
T Consensus 129 ~~~~~~hvi~HEiGH~IGfRHTD~ 152 (211)
T PF12388_consen 129 SVNVIEHVITHEIGHCIGFRHTDY 152 (211)
T ss_pred chhHHHHHHHHHhhhhccccccCc
Confidence 334566689999999987776543
No 50
>COG5495 Uncharacterized conserved protein [Function unknown]
Probab=29.05 E-value=38 Score=33.66 Aligned_cols=37 Identities=24% Similarity=0.379 Sum_probs=24.2
Q ss_pred ChhHHHHhhccccccceeeeccccccCCeEEEEeccCCchHHHHHHHHHHHHhhhCCce
Q 015105 39 PKETIDILKDQVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFGDQY 97 (413)
Q Consensus 39 ~~~~~~~~k~~~f~~~tf~~t~~~~~~~gvi~rGnLr~~~~~~~~~l~~~l~~~~gd~y 97 (413)
.+||++++|++||++ |+.+ ++.-.+-++|..+.|.+|
T Consensus 129 l~edl~rl~d~~~~i-----~eaD-----------------~~g~ai~q~la~emgg~~ 165 (289)
T COG5495 129 LDEDLSRLKDTIFGI-----TEAD-----------------DVGYAIVQSLALEMGGEP 165 (289)
T ss_pred CHHHHHhCcccEEEe-----eccc-----------------ccccHHHHHHHHHhCCCc
Confidence 689999999977654 4443 223334566666667666
No 51
>PF13583 Reprolysin_4: Metallo-peptidase family M12B Reprolysin-like
Probab=28.78 E-value=19 Score=34.07 Aligned_cols=18 Identities=28% Similarity=0.215 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHcCCc
Q 015105 180 IGVHELGHILAAKSTGVE 197 (413)
Q Consensus 180 L~iHElGH~laAr~~Gv~ 197 (413)
.++||+||.+=|++-+-.
T Consensus 140 ~~aHEiGH~lGl~H~~~~ 157 (206)
T PF13583_consen 140 TFAHEIGHNLGLRHDFDY 157 (206)
T ss_pred HHHHHHHHHhcCCCCccc
Confidence 488999999999887763
No 52
>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=28.46 E-value=36 Score=30.96 Aligned_cols=11 Identities=36% Similarity=0.495 Sum_probs=9.8
Q ss_pred HHHHHHHHHHH
Q 015105 180 IGVHELGHILA 190 (413)
Q Consensus 180 L~iHElGH~la 190 (413)
+++||++|.++
T Consensus 138 VvaHEltHGVt 148 (150)
T PF01447_consen 138 VVAHELTHGVT 148 (150)
T ss_dssp HHHHHHHHHHH
T ss_pred eeeeccccccc
Confidence 68999999986
No 53
>PRK04897 heat shock protein HtpX; Provisional
Probab=27.10 E-value=39 Score=33.93 Aligned_cols=11 Identities=36% Similarity=0.383 Sum_probs=9.3
Q ss_pred HHHHHHHHHHH
Q 015105 179 VIGVHELGHIL 189 (413)
Q Consensus 179 iL~iHElGH~l 189 (413)
.+++||+||.-
T Consensus 139 aVlAHElgHi~ 149 (298)
T PRK04897 139 GVIGHEISHIR 149 (298)
T ss_pred HHHHHHHHHHh
Confidence 68899999964
No 54
>PLN02452 phosphoserine transaminase
Probab=27.09 E-value=1.1e+02 Score=31.60 Aligned_cols=64 Identities=9% Similarity=0.221 Sum_probs=44.8
Q ss_pred cccCCChhHHHHhhccccccceeeeccccccCCeEEEEeccCCchHHHHHHHHHHHHhhhC--CceEEEEeecC
Q 015105 34 EYIRIPKETIDILKDQVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFG--DQYKLFLLVNP 105 (413)
Q Consensus 34 ~~~~i~~~~~~~~k~~~f~~~tf~~t~~~~~~~gvi~rGnLr~~~~~~~~~l~~~l~~~~g--d~y~lf~~~~~ 105 (413)
.|..+|++.+++++.+++-|+ .-+-++.-.+---.+=.+++++++++|++.++ |.|.+.+++-+
T Consensus 14 GP~~lp~~Vl~~~~~~~~~~~--------~~g~s~~~~sHRs~~f~~i~~~~~~~L~~l~~~p~~y~v~~l~Gs 79 (365)
T PLN02452 14 GPATLPANVLAKAQAELYNWE--------GSGMSVMEMSHRGKEFLSIIQKAEADLRELLDIPDNYEVLFLQGG 79 (365)
T ss_pred CCCCCCHHHHHHHHHHHhccc--------ccCccccccCCCchHHHHHHHHHHHHHHHHhCCCCCceEEEEeCc
Confidence 466899999999998655443 22334444444344556999999999999987 67888666544
No 55
>PRK12462 phosphoserine aminotransferase; Provisional
Probab=26.72 E-value=1.1e+02 Score=31.94 Aligned_cols=64 Identities=13% Similarity=0.194 Sum_probs=43.5
Q ss_pred cccCCChhHHHHhhccccccceeeeccccccCCeEEEEeccCCchHHHHHHHHHHHHhhhC--CceEEEEeecC
Q 015105 34 EYIRIPKETIDILKDQVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFG--DQYKLFLLVNP 105 (413)
Q Consensus 34 ~~~~i~~~~~~~~k~~~f~~~tf~~t~~~~~~~gvi~rGnLr~~~~~~~~~l~~~l~~~~g--d~y~lf~~~~~ 105 (413)
.|..+|+|.++++++++.-|.. -+-+++=.+---.+=.+.|++.+++|++.|+ |+|.+++++-+
T Consensus 11 GPa~lp~~Vl~~~~~~~~~~~~--------~g~si~eisHRs~~F~~i~~~~~~~Lr~Ll~~P~~y~Vlfl~Gg 76 (364)
T PRK12462 11 GPGALPDTVLEQVRQAVVELPE--------TGLSVLGMSHRSSWFSSLLAQAEADLRDLLGIPDEYGVVFLQGG 76 (364)
T ss_pred CCcCCCHHHHHHHHHHHhcccc--------cCccccccccccHHHHHHHHHHHHHHHHHhCCCCCCeEEEEecc
Confidence 4568999999999986544321 1123332332224566899999999999998 68988766654
No 56
>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=26.70 E-value=38 Score=33.03 Aligned_cols=13 Identities=31% Similarity=0.805 Sum_probs=11.0
Q ss_pred HHHHHHHHHHHHH
Q 015105 178 LVIGVHELGHILA 190 (413)
Q Consensus 178 ~iL~iHElGH~la 190 (413)
..+.+||.||++.
T Consensus 90 vaVAAHEvGHAiQ 102 (222)
T PF04298_consen 90 VAVAAHEVGHAIQ 102 (222)
T ss_pred HHHHHHHHhHHHh
Confidence 4678999999986
No 57
>COG5309 Exo-beta-1,3-glucanase [Carbohydrate transport and metabolism]
Probab=26.70 E-value=98 Score=31.32 Aligned_cols=62 Identities=16% Similarity=0.287 Sum_probs=40.3
Q ss_pred hhHHHHhhcccccc-ceeeeccccccCCeEEEEeccCC--chHHHHHHHHHHHHhhhCCceEEEEeecC
Q 015105 40 KETIDILKDQVFGF-DTFFVTNQEPYEGGVLFKGNLRG--QAAKTYEKISTRMKNKFGDQYKLFLLVNP 105 (413)
Q Consensus 40 ~~~~~~~k~~~f~~-~tf~~t~~~~~~~gvi~rGnLr~--~~~~~~~~l~~~l~~~~gd~y~lf~~~~~ 105 (413)
.|.++++|. .||= .+||+||+-.--.|--+-++.-. +..+.++++..+|+++ | |.+|+++-=
T Consensus 218 ~~q~e~vqs-a~g~~k~~~v~EtGWPS~G~~~G~a~pS~anq~~~~~~i~~~~~~~-G--~d~fvfeAF 282 (305)
T COG5309 218 LEQLERVQS-ACGTKKTVWVTETGWPSDGRTYGSAVPSVANQKIAVQEILNALRSC-G--YDVFVFEAF 282 (305)
T ss_pred HHHHHHHHH-hcCCCccEEEeeccCCCCCCccCCcCCChhHHHHHHHHHHhhhhcc-C--ccEEEeeec
Confidence 688999999 5555 99999998644344333333322 2456777888888774 6 555655543
No 58
>PF01990 ATP-synt_F: ATP synthase (F/14-kDa) subunit; InterPro: IPR008218 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The V-ATPases (or V1V0-ATPase) and A-ATPases (or A1A0-ATPase) are each composed of two linked complexes: the V1 or A1 complex contains the catalytic core that hydrolyses/synthesizes ATP, and the V0 or A0 complex that forms the membrane-spanning pore. The V- and A-ATPases both contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, , ]. The V- and A-ATPases more closely resemble one another in subunit structure than they do the F-ATPases, although the function of A-ATPases is closer to that of F-ATPases. This entry represents subunit F found in the V1 complex of V-ATPases (both eukaryotic and bacterial), as well as in the A1 complex of A-ATPases. Subunit F is a 16 kDa protein that is required for the assembly and activity of V-ATPase, and has a potential role in the differential targeting and regulation of the enzyme for specific organelles. This subunit is not necessary for the rotation of the ATPase V1 rotor, but it does promote catalysis []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0046933 hydrogen ion transporting ATP synthase activity, rotational mechanism, 0046961 proton-transporting ATPase activity, rotational mechanism, 0015991 ATP hydrolysis coupled proton transport, 0033178 proton-transporting two-sector ATPase complex, catalytic domain; PDB: 2D00_E 3A5C_P 3J0J_H 3A5D_H 2OV6_A 2QAI_B 3AON_B 2I4R_A.
Probab=26.38 E-value=2.5e+02 Score=22.93 Aligned_cols=59 Identities=17% Similarity=0.402 Sum_probs=36.1
Q ss_pred hhHHHHhhccccccceeeeccccccCCeEEEEeccCCchHHHHHHHHHHHHhhhCCceEEEEeecC--------------
Q 015105 40 KETIDILKDQVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFGDQYKLFLLVNP-------------- 105 (413)
Q Consensus 40 ~~~~~~~k~~~f~~~tf~~t~~~~~~~gvi~rGnLr~~~~~~~~~l~~~l~~~~gd~y~lf~~~~~-------------- 105 (413)
+|.+.-+| ..|++++++. .+++++.+.+++-+++. .|.+.++.+.
T Consensus 7 ~~~v~gFr--LaGv~~~~~~----------------~~~ee~~~~l~~l~~~~---~~gIIii~e~~~~~~~~~l~~~~~ 65 (95)
T PF01990_consen 7 RDTVLGFR--LAGVEGVYVN----------------TDPEEAEEALKELLKDE---DVGIIIITEDLAEKIRDELDEYRE 65 (95)
T ss_dssp HHHHHHHH--HTTSEEEEES----------------HSHHHHHHHHHHHHHHT---TEEEEEEEHHHHTTHHHHHHHHHH
T ss_pred HHHHHHHH--HcCCCCccCC----------------CCHHHHHHHHHHHhcCC---CccEEEeeHHHHHHHHHHHHHHHh
Confidence 34444455 4777877776 45566666665555332 4555555443
Q ss_pred CCCCcEEEEecCCC
Q 015105 106 EDDKPVAVVVPRKT 119 (413)
Q Consensus 106 ~~~kpv~~~~P~~~ 119 (413)
+..+|+++.+|...
T Consensus 66 ~~~~P~iv~IP~~~ 79 (95)
T PF01990_consen 66 ESSLPLIVEIPSKE 79 (95)
T ss_dssp TSSSSEEEEESTTC
T ss_pred ccCCceEEEcCCCC
Confidence 24679999999874
No 59
>PF13699 DUF4157: Domain of unknown function (DUF4157)
Probab=25.52 E-value=41 Score=27.29 Aligned_cols=12 Identities=33% Similarity=0.650 Sum_probs=10.1
Q ss_pred HHHHHHHHHHHH
Q 015105 179 VIGVHELGHILA 190 (413)
Q Consensus 179 iL~iHElGH~la 190 (413)
.++.||++|.+.
T Consensus 63 ~llaHEl~Hv~Q 74 (79)
T PF13699_consen 63 ALLAHELAHVVQ 74 (79)
T ss_pred hhHhHHHHHHHh
Confidence 478999999875
No 60
>PF11711 Tim54: Inner membrane protein import complex subunit Tim54; InterPro: IPR021056 Mitochondrial function depends on the import of hundreds of different proteins synthesised in the cytosol. Protein import is a multi-step pathway which includes the binding of precursor proteins to surface receptors, translocation of the precursor across one or both mitochondrial membranes, and folding and assembly of the imported protein inside the mitochondrion. Most precursor proteins carry amino-terminal targeting signals, called pre-sequences, and are imported into mitochondria via import complexes located in both the outer and the inner membrane (IM). The IM complex, TIM, is made up of at least two proteins which mediate translocation of proteins into the matrix by removing their signal peptide and another pair of proteins, Tim54 and Tim22, that insert the polytopic proteins, that carry internal targeting information, into the inner membrane [].
Probab=24.94 E-value=1e+02 Score=32.47 Aligned_cols=65 Identities=17% Similarity=0.206 Sum_probs=40.8
Q ss_pred cchhhhhHHHHHHhhhhCC-CCCCCcCcccccCCChhHHHHhhccccccceeeeccccccCCeEEEEec
Q 015105 6 LIQKVASSRMMAMEKLLVD-PRCQPQQLDEYIRIPKETIDILKDQVFGFDTFFVTNQEPYEGGVLFKGN 73 (413)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~i~~~~~~~~k~~~f~~~tf~~t~~~~~~~gvi~rGn 73 (413)
+||+.-++|+...+..... +..+ +..++ ..-..+++...|+ ++|+-.-+-.....-.+|+||.|+
T Consensus 114 dIr~~vAerIR~~Rr~~~~~~~~~-~~~e~-~~~~~~~~~~~r~-~~gv~~~~~~~~~~~~gG~i~IGR 179 (382)
T PF11711_consen 114 DIRAKVAERIRKLRREALEEPSSE-PPIEE-EPEKEKILFDPRD-VLGVYYPNPPLDPEGAGGVICIGR 179 (382)
T ss_pred HHHHHHHHHHHHHHHHHhcccccC-Ccccc-ccchhhhhhhhhh-hccccccccccccCCCCceEEEcc
Confidence 5788888888888777653 3221 11222 3444566777776 666654444445555689999996
No 61
>PRK01345 heat shock protein HtpX; Provisional
Probab=24.90 E-value=45 Score=33.90 Aligned_cols=12 Identities=33% Similarity=0.454 Sum_probs=10.0
Q ss_pred HHHHHHHHHHHH
Q 015105 178 LVIGVHELGHIL 189 (413)
Q Consensus 178 ~iL~iHElGH~l 189 (413)
..+++||+||.-
T Consensus 125 ~aVlAHElgHi~ 136 (317)
T PRK01345 125 AGVMAHELAHVK 136 (317)
T ss_pred HHHHHHHHHHHH
Confidence 368899999985
No 62
>COG0501 HtpX Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]
Probab=24.81 E-value=46 Score=32.43 Aligned_cols=11 Identities=55% Similarity=0.818 Sum_probs=9.2
Q ss_pred HHHHHHHHHHH
Q 015105 179 VIGVHELGHIL 189 (413)
Q Consensus 179 iL~iHElGH~l 189 (413)
.++.||+||..
T Consensus 159 aVlaHElgHi~ 169 (302)
T COG0501 159 AVLAHELGHIK 169 (302)
T ss_pred HHHHHHHHHHh
Confidence 57899999974
No 63
>COG3824 Predicted Zn-dependent protease [General function prediction only]
Probab=24.73 E-value=33 Score=30.58 Aligned_cols=14 Identities=29% Similarity=0.558 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHHHH
Q 015105 176 TALVIGVHELGHIL 189 (413)
Q Consensus 176 l~~iL~iHElGH~l 189 (413)
.+...++||+||.+
T Consensus 108 ~vthvliHEIgHhF 121 (136)
T COG3824 108 QVTHVLIHEIGHHF 121 (136)
T ss_pred Hhhhhhhhhhhhhc
Confidence 56788999999975
No 64
>PRK03072 heat shock protein HtpX; Provisional
Probab=24.55 E-value=46 Score=33.25 Aligned_cols=10 Identities=40% Similarity=0.508 Sum_probs=8.8
Q ss_pred HHHHHHHHHH
Q 015105 179 VIGVHELGHI 188 (413)
Q Consensus 179 iL~iHElGH~ 188 (413)
.+++||+||.
T Consensus 129 aVlAHElgHi 138 (288)
T PRK03072 129 GVLGHELSHV 138 (288)
T ss_pred HHHHHHHHHH
Confidence 5889999995
No 65
>TIGR02500 type_III_yscD type III secretion apparatus protein, YscD/HrpQ family. This family represents a conserved protein of bacterial type III secretion systems. Gene symbols are variable from species to species. Members are designated YscD in Yersinia, HrpQ in Pseudomonas syringae, and EscD in enteropathogenic Escherichia coli. In the Chlamydiae, this model describes the C-terminal 400 residues of a longer protein.
Probab=24.54 E-value=2.1e+02 Score=29.94 Aligned_cols=38 Identities=11% Similarity=0.172 Sum_probs=33.7
Q ss_pred ccCCeEEEEeccCCchHHHHHHHHHHHHhhhCCceEEE
Q 015105 63 PYEGGVLFKGNLRGQAAKTYEKISTRMKNKFGDQYKLF 100 (413)
Q Consensus 63 ~~~~gvi~rGnLr~~~~~~~~~l~~~l~~~~gd~y~lf 100 (413)
.-++.+...|+|..+..+.|+++.+++++++|..|.+.
T Consensus 302 ~~~~~i~lsG~l~~~~~~~~~~~l~~f~~~~~~~~~~~ 339 (410)
T TIGR02500 302 ESGREIALSGQLDSEKRSRLQELLAAFKQRDGVIPDVV 339 (410)
T ss_pred ecCCEEEEEecCCHHHHHHHHHHHHHHHHhCCCCceEE
Confidence 34579999999999999999999999999999878663
No 66
>PRK02391 heat shock protein HtpX; Provisional
Probab=24.37 E-value=47 Score=33.43 Aligned_cols=10 Identities=40% Similarity=0.733 Sum_probs=8.7
Q ss_pred HHHHHHHHHH
Q 015105 179 VIGVHELGHI 188 (413)
Q Consensus 179 iL~iHElGH~ 188 (413)
.+++||+||.
T Consensus 135 aVlaHElgHi 144 (296)
T PRK02391 135 AVLAHELSHV 144 (296)
T ss_pred HHHHHHHHHH
Confidence 5889999995
No 67
>PRK05457 heat shock protein HtpX; Provisional
Probab=24.16 E-value=48 Score=33.14 Aligned_cols=10 Identities=40% Similarity=0.723 Sum_probs=8.8
Q ss_pred HHHHHHHHHH
Q 015105 179 VIGVHELGHI 188 (413)
Q Consensus 179 iL~iHElGH~ 188 (413)
.+++||+||.
T Consensus 136 aVlAHElgHi 145 (284)
T PRK05457 136 AVLAHEISHI 145 (284)
T ss_pred HHHHHHHHHH
Confidence 5889999995
No 68
>COG0830 UreF Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]
Probab=23.86 E-value=89 Score=30.60 Aligned_cols=32 Identities=31% Similarity=0.348 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHHhhcCCCCCchHHHHHHhhh
Q 015105 298 VIWAWAGLLINAINSIPAGELDGGRIAFALWG 329 (413)
Q Consensus 298 ~~ag~~gl~ltafNLLPigpLDGGrIl~allg 329 (413)
.+..-.|++.++.=|+|.||.||=+|+..+-.
T Consensus 157 lya~~~~lv~aavRlipLgQ~~gq~il~~l~~ 188 (229)
T COG0830 157 LYAWASNLVSAAVRLIPLGQLDGQKILAQLEP 188 (229)
T ss_pred HHHHHHHHHHHHHHhcccCcHHHHHHHHHhhH
Confidence 34445699999999999999999999998743
No 69
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=23.77 E-value=48 Score=29.57 Aligned_cols=17 Identities=24% Similarity=-0.021 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHHHHHHH
Q 015105 177 ALVIGVHELGHILAAKS 193 (413)
Q Consensus 177 ~~iL~iHElGH~laAr~ 193 (413)
+.-++.||+.|+++-..
T Consensus 59 l~~~l~HEm~H~~~~~~ 75 (146)
T smart00731 59 LRETLLHELCHAALYLF 75 (146)
T ss_pred HHhhHHHHHHHHHHHHh
Confidence 34578999999999864
No 70
>PRK01265 heat shock protein HtpX; Provisional
Probab=22.85 E-value=52 Score=33.73 Aligned_cols=10 Identities=50% Similarity=0.979 Sum_probs=8.8
Q ss_pred HHHHHHHHHH
Q 015105 179 VIGVHELGHI 188 (413)
Q Consensus 179 iL~iHElGH~ 188 (413)
.+++||+||.
T Consensus 142 aVlAHElgHi 151 (324)
T PRK01265 142 AVAGHELGHL 151 (324)
T ss_pred HHHHHHHHHH
Confidence 5789999996
No 71
>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=22.70 E-value=61 Score=28.66 Aligned_cols=19 Identities=21% Similarity=0.123 Sum_probs=14.5
Q ss_pred HHHHHHHHHHHHHHHHHHc
Q 015105 176 TALVIGVHELGHILAAKST 194 (413)
Q Consensus 176 l~~iL~iHElGH~laAr~~ 194 (413)
-+.-.+.|||.|+++-...
T Consensus 59 ~~~~tL~HEm~H~~~~~~~ 77 (157)
T PF10263_consen 59 ELIDTLLHEMAHAAAYVFG 77 (157)
T ss_pred HHHHHHHHHHHHHHhhhcc
Confidence 4445889999999996553
No 72
>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=22.16 E-value=61 Score=29.93 Aligned_cols=21 Identities=43% Similarity=0.494 Sum_probs=14.2
Q ss_pred HHHHHHHHHHHHHHHHHHcCC
Q 015105 176 TALVIGVHELGHILAAKSTGV 196 (413)
Q Consensus 176 l~~iL~iHElGH~laAr~~Gv 196 (413)
..+.+++||+||.+=+.+-+.
T Consensus 130 ~~a~~~AHelGH~lGm~HD~~ 150 (199)
T PF01421_consen 130 SFAVIIAHELGHNLGMPHDGD 150 (199)
T ss_dssp HHHHHHHHHHHHHTT---TTT
T ss_pred HHHHHHHHHHHHhcCCCCCCC
Confidence 445678999999987777766
No 73
>PRK02870 heat shock protein HtpX; Provisional
Probab=22.12 E-value=55 Score=33.73 Aligned_cols=10 Identities=50% Similarity=0.793 Sum_probs=9.0
Q ss_pred HHHHHHHHHH
Q 015105 179 VIGVHELGHI 188 (413)
Q Consensus 179 iL~iHElGH~ 188 (413)
.+++||+||.
T Consensus 175 aVlAHELgHi 184 (336)
T PRK02870 175 AVMAHELSHI 184 (336)
T ss_pred HHHHHHHHHH
Confidence 6889999998
No 74
>cd04272 ZnMc_salivary_gland_MPs Zinc-dependent metalloprotease, salivary_gland_MPs. Metalloproteases secreted by the salivary glands of arthropods.
Probab=21.92 E-value=54 Score=31.02 Aligned_cols=20 Identities=35% Similarity=0.512 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHHHHHcCCc
Q 015105 178 LVIGVHELGHILAAKSTGVE 197 (413)
Q Consensus 178 ~iL~iHElGH~laAr~~Gv~ 197 (413)
+..++||+||-+=+.+-+..
T Consensus 146 ~~~~AHElGH~lG~~HD~~~ 165 (220)
T cd04272 146 VYTMTHELAHLLGAPHDGSP 165 (220)
T ss_pred HHHHHHHHHHHhCCCCCCCC
Confidence 37889999999988876554
No 75
>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=21.71 E-value=6.9e+02 Score=23.59 Aligned_cols=82 Identities=23% Similarity=0.406 Sum_probs=45.6
Q ss_pred HHHHHHHHHHHHhhcCCCCCchHHHHHHhh-hhHHHHHHH-HHHHHHHHHHHHh---------h---h----h--H-HHH
Q 015105 299 IWAWAGLLINAINSIPAGELDGGRIAFALW-GRKASTRLT-GVSIVLLGLSSLF---------S---D----V--T-FYW 357 (413)
Q Consensus 299 ~ag~~gl~ltafNLLPigpLDGGrIl~all-g~r~~~~~~-~~~~~llgl~~l~---------~---~----~--~-l~W 357 (413)
+++.++.+.-.||.-+++| +-+++-.. |.......+ .+..+++|+.++. . + . . .+|
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 4566677777899999999 77888764 333222222 2222233322211 0 1 1 1 233
Q ss_pred HHHHHHHHhCCCCCCCCCCCCCChhHHH
Q 015105 358 VVLVFFLQRGPIAPLSEEITDPDDKYIA 385 (413)
Q Consensus 358 ~ili~~~~r~~~~P~~~evt~~~~~r~~ 385 (413)
+++ |..-+|..|..+.+.+++.....
T Consensus 110 ~iv--F~~lnP~fp~~~~~~~l~~nTii 135 (173)
T PF11085_consen 110 AIV--FFVLNPIFPMIKPVTELDWNTII 135 (173)
T ss_pred HHH--HHHhcccccCChhhhhCchhHHH
Confidence 332 33357888888888888766544
No 76
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=21.22 E-value=1.4e+02 Score=27.64 Aligned_cols=31 Identities=26% Similarity=0.224 Sum_probs=21.7
Q ss_pred chHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHcC
Q 015105 162 NLNLLTNGLPGALVTALVIGVHELGHILAAKSTG 195 (413)
Q Consensus 162 ~~~~~~~gl~~al~l~~iL~iHElGH~laAr~~G 195 (413)
||..+.. ....++.-++-||++|+.+-..+|
T Consensus 49 NP~ll~e---n~~~f~~~vV~HELaHl~ly~~~g 79 (156)
T COG3091 49 NPKLLEE---NGEDFIEQVVPHELAHLHLYQEFG 79 (156)
T ss_pred CHHHHHH---ccHHHHHHHHHHHHHHHHHHHHcC
Confidence 5554432 233455667899999999998887
No 77
>PF04228 Zn_peptidase: Putative neutral zinc metallopeptidase; InterPro: IPR007343 Members of this family of bacterial proteins are described as hypothetical proteins or zinc metallopeptidases. The majority have a HExxH zinc-binding motif characteristic of neutral zinc metallopeptidases, however there is no evidence to support their function as metallopeptidases.
Probab=21.14 E-value=62 Score=32.73 Aligned_cols=15 Identities=27% Similarity=0.330 Sum_probs=11.7
Q ss_pred HHHHHHHHHHHHHHH
Q 015105 179 VIGVHELGHILAAKS 193 (413)
Q Consensus 179 iL~iHElGH~laAr~ 193 (413)
-+++||+||.+....
T Consensus 172 yVlAHEyGHHVQ~l~ 186 (292)
T PF04228_consen 172 YVLAHEYGHHVQNLL 186 (292)
T ss_pred HHHHHHHHHHHHHHh
Confidence 367999999987543
No 78
>KOG2719 consensus Metalloprotease [General function prediction only]
Probab=20.74 E-value=55 Score=34.87 Aligned_cols=14 Identities=36% Similarity=0.491 Sum_probs=11.1
Q ss_pred HHHHHHHHHHHHHH
Q 015105 177 ALVIGVHELGHILA 190 (413)
Q Consensus 177 ~~iL~iHElGH~la 190 (413)
+.++++||+||+--
T Consensus 280 l~AVl~HELGHW~~ 293 (428)
T KOG2719|consen 280 LVAVLAHELGHWKL 293 (428)
T ss_pred HHHHHHHHhhHHHH
Confidence 35788999999854
No 79
>cd06459 M3B_Oligoendopeptidase_F Peptidase family M3B Oligopeptidase F (PepF; Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and includes oligoendopeptidase F from Lactococcus lactis. This enzyme hydrolyzes peptides containing between 7 and 17 amino acids with fairly broad specificity. The PepF gene is duplicated in L. lactis on the plasmid that bears it, while a shortened second copy is found in Bacillus subtilis. Most bacterial PepFs are cytoplasmic endopeptidases; however, the PepF Bacillus amyloliquefaciens oligopeptidase is a secreted protein and may facilitate the process of sporulation. Specifically, the yjbG gene encoding the homolog of the PepF1 and PepF2 oligoendopeptidases of Lactococcus lactis has been identified in Bacillus subtilis as an inhibitor of sporulation initiation when over expressed from a multicopy plasmid.
Probab=20.71 E-value=55 Score=33.56 Aligned_cols=16 Identities=31% Similarity=0.422 Sum_probs=11.7
Q ss_pred HHHHHHHHHHHHHHHc
Q 015105 179 VIGVHELGHILAAKST 194 (413)
Q Consensus 179 iL~iHElGH~laAr~~ 194 (413)
..++||+||++-....
T Consensus 224 ~tl~HE~GHa~h~~~~ 239 (427)
T cd06459 224 FTLAHELGHAFHSYLS 239 (427)
T ss_pred HHHHHHhhHHHHHHHH
Confidence 4679999998755443
No 80
>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=20.49 E-value=62 Score=33.97 Aligned_cols=21 Identities=19% Similarity=0.303 Sum_probs=16.9
Q ss_pred HHHHHHHHHHHHHHHHcCCcc
Q 015105 178 LVIGVHELGHILAAKSTGVEL 198 (413)
Q Consensus 178 ~iL~iHElGH~laAr~~Gv~~ 198 (413)
+..++||+||.+-...-+.+.
T Consensus 243 v~tLfHE~GHa~H~~ls~~~~ 263 (458)
T PF01432_consen 243 VETLFHEFGHAMHSLLSRTKY 263 (458)
T ss_dssp HHHHHHHHHHHHHHHHCCCSS
T ss_pred HHHHHHHHhHHHHHHHhcccc
Confidence 357899999999988777664
No 81
>cd04280 ZnMc_astacin_like Zinc-dependent metalloprotease, astacin_like subfamily or peptidase family M12A, a group of zinc-dependent proteolytic enzymes with a HExxH zinc-binding site/active site. Members of this family may have an amino terminal propeptide, which is cleaved to yield the active protease domain, which is consequently always found at the N-terminus in multi-domain architectures. This family includes: astacin, a digestive enzyme from Crayfish; meprin, a multiple domain membrane component that is constructed from a homologous alpha and beta chain, proteins involved in (bone) morphogenesis, tolloid from drosophila, and the sea urchin SPAN protein, which may also play a role in development.
Probab=20.20 E-value=53 Score=30.38 Aligned_cols=22 Identities=27% Similarity=0.067 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHHHHcCCcccC
Q 015105 179 VIGVHELGHILAAKSTGVELGV 200 (413)
Q Consensus 179 iL~iHElGH~laAr~~Gv~~~~ 200 (413)
..++||+||++-..+-.-|..+
T Consensus 76 g~v~HE~~HalG~~HEh~R~DR 97 (180)
T cd04280 76 GTIVHELMHALGFYHEQSRPDR 97 (180)
T ss_pred chhHHHHHHHhcCcchhccccc
Confidence 5789999999876666666543
No 82
>PF05683 Fumerase_C: Fumarase C-terminus; InterPro: IPR004647 This entry represents various Fe-S type hydro-lyases, including the beta subunit from both L-tartrate dehydratase (TtdB; EC:4.2.1.32) and class 2 fumarate hydratase (FumC; (4.2.1.2 from EC) []. A number of Fe-S cluster-containing hydro-lyases share a conserved motif, including argininosuccinate lyase, adenylosuccinate lyase, aspartase, class I fumarate hydratase (fumarase), and tartrate dehydratase (see IPR000362 from INTERPRO). Proteins in this group represent a subset of closely related proteins or modules, including the Escherichia coli tartrate dehydratase beta chain and the C-terminal region of the class I fumarase (where the N-terminal region is homologous to the tartrate dehydratase alpha chain). The activity of the archaeal proteins in this group is unknown.; GO: 0016836 hydro-lyase activity; PDB: 2ISB_A.
Probab=20.18 E-value=1.2e+02 Score=29.29 Aligned_cols=44 Identities=16% Similarity=0.225 Sum_probs=30.2
Q ss_pred cccccCCChhHHHHhhccccccceeeeccccccCCeEEEEeccCCchHHHHHHHHHHHHh
Q 015105 32 LDEYIRIPKETIDILKDQVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKN 91 (413)
Q Consensus 32 ~~~~~~i~~~~~~~~k~~~f~~~tf~~t~~~~~~~gvi~rGnLr~~~~~~~~~l~~~l~~ 91 (413)
..-..|+++||++.+|- ++-|...|.+-.-++.+|+|+.+.+++
T Consensus 29 ~~L~tPlt~e~i~~L~v----------------GD~V~LsG~i~taRDaaH~ri~e~l~~ 72 (205)
T PF05683_consen 29 IELTTPLTEEDIRKLKV----------------GDTVYLSGTIYTARDAAHKRIVELLER 72 (205)
T ss_dssp EEEESS--HHHHHH--T----------------T-EEEEEEEEEE--HHHHHHHHHHHHH
T ss_pred EEcCCCCCHHHHhhCCC----------------CCEEEEeeEEEEEhHHHHHHHHHHHHc
Confidence 34466899999999984 456777788888899999999999997
Done!