Query 009542
Match_columns 532
No_of_seqs 323 out of 1221
Neff 4.6
Searched_HMMs 46136
Date Thu Mar 28 14:23:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009542.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009542hhsearch_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 4.3E-31 9.3E-36 252.7 19.2 176 255-479 3-180 (183)
2 cd06164 S2P-M50_SpoIVFB_CBS Sp 99.9 3.2E-25 6.8E-30 218.4 20.5 134 280-451 37-170 (227)
3 cd06161 S2P-M50_SpoIVFB SpoIVF 99.9 1.2E-23 2.5E-28 204.2 18.8 129 283-451 25-153 (208)
4 cd06163 S2P-M50_PDZ_RseP-like 99.9 6.6E-21 1.4E-25 182.5 15.0 113 290-448 3-145 (182)
5 cd05709 S2P-M50 Site-2 proteas 99.9 5.6E-21 1.2E-25 179.6 13.2 139 290-452 2-156 (180)
6 cd06159 S2P-M50_PDZ_Arch Uncha 99.8 3E-19 6.5E-24 179.9 18.3 119 285-450 107-228 (263)
7 PF02163 Peptidase_M50: Peptid 99.8 5.5E-19 1.2E-23 167.0 11.0 127 291-447 2-157 (192)
8 cd06162 S2P-M50_PDZ_SREBP Ster 99.8 6.4E-18 1.4E-22 171.3 15.6 113 291-451 130-249 (277)
9 cd06158 S2P-M50_like_1 Unchara 99.8 3.2E-18 7E-23 163.5 12.1 135 291-454 4-159 (181)
10 TIGR00054 RIP metalloprotease 99.5 1.1E-13 2.5E-18 147.3 16.4 80 291-370 9-119 (420)
11 PRK10779 zinc metallopeptidase 99.5 1.3E-13 2.7E-18 147.9 15.2 82 288-369 7-118 (449)
12 COG1994 SpoIVFB Zn-dependent p 99.3 1.8E-11 3.8E-16 121.0 14.3 128 285-452 41-176 (230)
13 COG0750 Predicted membrane-ass 98.9 2.1E-09 4.4E-14 111.4 5.6 242 168-451 82-338 (375)
14 PF13398 Peptidase_M50B: Pepti 97.4 0.00066 1.4E-08 66.3 8.2 65 297-369 23-88 (200)
15 COG0750 Predicted membrane-ass 96.0 0.021 4.6E-07 59.5 8.1 82 289-370 6-120 (375)
16 KOG2921 Intramembrane metallop 95.9 0.0064 1.4E-07 65.2 3.8 81 286-369 120-205 (484)
17 PF11667 DUF3267: Protein of u 77.2 1.8 4E-05 38.2 2.4 69 296-371 4-72 (111)
18 PF00413 Peptidase_M10: Matrix 60.7 5.1 0.00011 36.3 1.7 19 297-315 106-124 (154)
19 cd04279 ZnMc_MMP_like_1 Zinc-d 58.2 6.1 0.00013 36.5 1.8 22 296-317 104-125 (156)
20 PF07423 DUF1510: Protein of u 57.6 8.4 0.00018 38.9 2.7 55 174-232 159-214 (217)
21 PF13485 Peptidase_MA_2: Pepti 50.0 13 0.00029 31.6 2.4 18 298-315 27-44 (128)
22 cd04268 ZnMc_MMP_like Zinc-dep 48.3 12 0.00025 34.4 1.9 21 295-315 93-113 (165)
23 cd04278 ZnMc_MMP Zinc-dependen 48.1 8.1 0.00018 35.8 0.9 22 296-317 107-128 (157)
24 PF05572 Peptidase_M43: Pregna 47.7 9.2 0.0002 36.2 1.2 13 297-309 70-82 (154)
25 PF01435 Peptidase_M48: Peptid 43.4 16 0.00036 34.8 2.2 12 297-308 90-101 (226)
26 PF06114 DUF955: Domain of unk 41.6 16 0.00035 30.7 1.7 16 299-314 45-60 (122)
27 PF01434 Peptidase_M41: Peptid 41.3 20 0.00043 35.4 2.4 18 298-315 30-47 (213)
28 PF14247 DUF4344: Domain of un 40.5 28 0.00061 35.2 3.4 25 292-317 88-112 (220)
29 cd04277 ZnMc_serralysin_like Z 38.7 17 0.00037 34.6 1.5 22 297-318 114-135 (186)
30 KOG1832 HIV-1 Vpr-binding prot 38.6 29 0.00062 41.9 3.5 18 5-22 1354-1371(1516)
31 smart00235 ZnMc Zinc-dependent 38.3 16 0.00036 32.9 1.3 19 299-317 89-107 (140)
32 cd00203 ZnMc Zinc-dependent me 38.0 16 0.00036 33.3 1.2 21 295-315 95-115 (167)
33 PF13582 Reprolysin_3: Metallo 37.0 17 0.00038 31.8 1.2 13 298-310 109-121 (124)
34 PF13688 Reprolysin_5: Metallo 36.5 20 0.00042 34.1 1.5 21 296-316 142-162 (196)
35 PF14891 Peptidase_M91: Effect 35.7 24 0.00052 33.8 2.0 16 297-312 104-119 (174)
36 PF12315 DUF3633: Protein of u 35.3 27 0.00058 35.3 2.3 28 286-316 85-112 (212)
37 PTZ00429 beta-adaptin; Provisi 33.5 40 0.00087 39.8 3.7 36 73-108 606-641 (746)
38 PF02031 Peptidase_M7: Strepto 32.4 27 0.00059 32.9 1.7 10 299-308 80-89 (132)
39 PF13574 Reprolysin_2: Metallo 31.6 25 0.00054 33.6 1.3 21 296-316 111-131 (173)
40 cd04327 ZnMc_MMP_like_3 Zinc-d 30.6 32 0.0007 33.4 2.0 17 297-313 93-109 (198)
41 PRK03001 M48 family peptidase; 30.5 31 0.00068 35.4 2.0 12 297-308 125-136 (283)
42 PHA02456 zinc metallopeptidase 30.4 31 0.00066 32.0 1.6 19 300-318 83-101 (141)
43 PRK03982 heat shock protein Ht 29.9 33 0.00071 35.4 2.0 12 297-308 126-137 (288)
44 cd04269 ZnMc_adamalysin_II_lik 29.6 35 0.00077 32.5 2.1 20 296-315 131-150 (194)
45 cd04270 ZnMc_TACE_like Zinc-de 29.5 33 0.00072 34.6 1.9 18 295-312 166-183 (244)
46 COG2856 Predicted Zn peptidase 29.5 29 0.00063 34.9 1.5 16 299-314 75-90 (213)
47 PRK11037 hypothetical protein; 29.3 1.3E+02 0.0028 26.3 5.1 65 153-218 4-81 (83)
48 PF10263 SprT-like: SprT-like 28.9 40 0.00086 31.0 2.2 19 295-313 59-77 (157)
49 cd04267 ZnMc_ADAM_like Zinc-de 27.8 27 0.00059 33.2 0.9 20 296-315 133-152 (192)
50 PF09471 Peptidase_M64: IgA Pe 27.7 26 0.00056 36.2 0.8 14 297-310 217-230 (264)
51 PRK12462 phosphoserine aminotr 27.6 97 0.0021 33.5 5.1 67 150-224 8-76 (364)
52 COG0501 HtpX Zn-dependent prot 26.8 40 0.00087 33.9 2.0 11 298-308 159-169 (302)
53 smart00731 SprT SprT homologue 26.6 50 0.0011 30.7 2.4 16 297-312 60-75 (146)
54 PF13583 Reprolysin_4: Metallo 26.4 34 0.00074 33.7 1.3 17 299-315 140-156 (206)
55 PRK04897 heat shock protein Ht 26.0 42 0.00091 35.0 2.0 11 298-308 139-149 (298)
56 PF12388 Peptidase_M57: Dual-a 25.8 35 0.00076 34.5 1.3 27 291-317 128-154 (211)
57 COG5309 Exo-beta-1,3-glucanase 25.6 1.1E+02 0.0023 32.5 4.7 61 159-223 218-281 (305)
58 PLN02452 phosphoserine transam 25.0 1.2E+02 0.0026 32.5 5.3 67 150-224 11-79 (365)
59 COG0830 UreF Urease accessory 24.5 80 0.0017 32.3 3.6 31 418-448 158-188 (229)
60 PRK01345 heat shock protein Ht 24.3 47 0.001 35.1 2.0 12 297-308 125-136 (317)
61 PF13699 DUF4157: Domain of un 23.9 45 0.00099 28.3 1.5 12 298-309 63-74 (79)
62 PRK03072 heat shock protein Ht 23.9 48 0.001 34.4 2.0 11 297-307 128-138 (288)
63 COG3824 Predicted Zn-dependent 23.7 35 0.00077 31.9 0.8 14 295-308 108-121 (136)
64 PRK02391 heat shock protein Ht 23.6 50 0.0011 34.5 2.0 10 298-307 135-144 (296)
65 PF01447 Peptidase_M4: Thermol 23.4 51 0.0011 31.3 1.9 11 299-309 138-148 (150)
66 PRK05457 heat shock protein Ht 23.2 51 0.0011 34.2 2.0 10 298-307 136-145 (284)
67 KOG3320 40S ribosomal protein 23.0 1.1E+02 0.0025 30.3 4.1 27 198-224 74-100 (192)
68 KOG2719 Metalloprotease [Gener 22.1 50 0.0011 36.7 1.7 14 297-310 281-294 (428)
69 PF10692 DUF2498: Protein of u 21.7 1.5E+02 0.0032 25.9 4.1 64 154-218 4-80 (82)
70 cd04927 ACT_ACR-like_2 Second 21.5 1.1E+02 0.0024 25.2 3.3 35 170-215 40-74 (76)
71 PRK04860 hypothetical protein; 21.5 86 0.0019 30.2 3.0 21 294-314 61-81 (160)
72 PRK01265 heat shock protein Ht 21.4 58 0.0013 34.7 2.0 10 298-307 142-151 (324)
73 PF04298 Zn_peptidase_2: Putat 21.2 56 0.0012 33.3 1.7 12 298-309 91-102 (222)
74 TIGR01241 FtsH_fam ATP-depende 21.2 45 0.00097 36.9 1.1 18 298-315 313-330 (495)
75 PF01421 Reprolysin: Reprolysi 21.1 67 0.0014 30.8 2.2 21 295-315 130-150 (199)
76 PRK02870 heat shock protein Ht 21.1 59 0.0013 34.8 2.0 11 297-307 174-184 (336)
77 COG3091 SprT Zn-dependent meta 21.1 1.4E+02 0.0031 29.0 4.3 31 281-314 49-79 (156)
78 KOG0391 SNF2 family DNA-depend 21.0 1E+02 0.0022 38.7 4.0 21 176-196 599-619 (1958)
79 PF08525 OapA_N: Opacity-assoc 20.6 1.2E+02 0.0026 21.5 2.8 21 500-520 9-29 (30)
80 PF01990 ATP-synt_F: ATP synth 20.1 4.2E+02 0.0091 22.7 6.7 51 169-238 15-79 (95)
No 1
>cd06160 S2P-M50_like_2 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the S2P/M50 family of RIP proteases use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. In eukaryotic cells they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum stress responses. In prokaryotes they regulate such processes as sporulation, cell division, stress response, and cell differentiation. This group includes bacterial, eukaryotic, and Archaeal S2P/M50s homologs with additional putative N- and C-terminal transmembrane spanning regions, relative to the core protein, and no PDZ domains.
Probab=99.97 E-value=4.3e-31 Score=252.65 Aligned_cols=176 Identities=40% Similarity=0.706 Sum_probs=146.5
Q ss_pred HHHHHHHHHHHhcccccccchhccccchHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHcCCccCCccccccceeeccceE
Q 009542 255 FGLVTVFTLLLRNVPALQSNLLSTFDNLNLLTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAI 334 (532)
Q Consensus 255 l~l~T~~T~~~a~~~~L~~~~~~~~~~~~~l~~glp~al~Ll~iL~iHElGH~laAr~~Gvk~s~P~FIP~i~LgtFGAv 334 (532)
++++|+.+....+.-... + +..++++.+..+++++++++.++++||+||+++||++|+|++.++++|...+|++|++
T Consensus 3 ~~~~s~~~~~~~~~~~~~-~--~~~~~~~~~~~~~~~~l~l~~~l~iHElgH~~~A~~~G~~~~~~~l~P~~~~G~~G~~ 79 (183)
T cd06160 3 LLVLTLLTTLLVGAWLSG-N--DVPGNPLLLLQGLPFALALLAILGIHEMGHYLAARRHGVKASLPYFIPFPFIGTFGAF 79 (183)
T ss_pred HHHHHHHHHHHHHHHHhc-c--cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCccceeeeehHhcCcEEEE
Confidence 456677766655421111 1 2236778888999999999999999999999999999999999999998779999999
Q ss_pred EeeccccCCccceeeeeecchhhHHHHHHHHHHHHhhcCCCCCCcccccccchhhhhhhhhhHHhhhccccCCCCCccch
Q 009542 335 TRIRNIVSKREDLLKVAAAGPLAGFSLGFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVN 414 (532)
Q Consensus 335 i~~~s~~~~RkalfdIAlAGPLAg~llAlill~iGl~l~~s~~~~~~v~~~~f~~s~L~~~la~l~LG~~l~~~~~v~lh 414 (532)
+++++..++|+++++|++|||++|+++++++++++
T Consensus 80 ~~~~~~~~~~~~~~~IalAGPl~nl~lali~~~~~--------------------------------------------- 114 (183)
T cd06160 80 IRMRSPIPNRKALFDIALAGPLAGLLLALPVLIIG--------------------------------------------- 114 (183)
T ss_pred EEecCCCCChhHhehhhhhHHHHHHHHHHHHHHHH---------------------------------------------
Confidence 99998888999999999999999999987765443
Q ss_pred HHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHhhhhHHHHHHHHHHHHHHHHHHhhh--hhHHHHHH
Q 009542 415 PLVIWAWAGLLINAINSIPAGELDGGRIAFALWGRKASTRLTGVSIVLLGLSSLFSD--VTFYWVVL 479 (532)
Q Consensus 415 PL~~agwinLvLtafNLLPigpLDGGrIl~Allgrr~a~~i~~~~~ilLGl~~l~~~--~~l~W~il 479 (532)
+..++|+|+++++|||+|++|||||||+++++++|.+.++++++.+++|+.++.++ .+++|+.+
T Consensus 115 -~~~~~~~nl~l~~fNLLPi~PLDGGril~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~ 180 (183)
T cd06160 115 -LAVAGWVGLLVTALNLLPVGQLDGGHIVRALFGRRVAALIGIGLLVALGLLALYLSFSIWLLWALL 180 (183)
T ss_pred -HHHHHHHHHHHHHHHhCCCCCcChHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHH
Confidence 12368999999999999999999999999999999999999999899988888765 45555443
No 2
>cd06164 S2P-M50_SpoIVFB_CBS SpoIVFB Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50B), regulates intramembrane proteolysis (RIP), and is involved in the pro-sigmaK pathway of bacterial spore formation. In this subgroup, SpoIVFB (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain. SpoIVFB is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA (bypass-of-forespore A), and SpoIVB (sporulation protein, stage IV cell wall formation, B locus). SpoIVFB is negatively regulated by SpoIVFA and BofA and activated by SpoIVB. It is thought that SpoIVFB, SpoIVFA, and BofA are located in the mother-cell membrane that surrounds the forespore and that SpoIVB is secreted from the forespore into the space between the two where it activates SpoIVFB. It has been proposed tha
Probab=99.94 E-value=3.2e-25 Score=218.37 Aligned_cols=134 Identities=30% Similarity=0.390 Sum_probs=111.5
Q ss_pred cchHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHcCCccCCccccccceeeccceEEeeccccCCccceeeeeecchhhHH
Q 009542 280 DNLNLLTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAITRIRNIVSKREDLLKVAAAGPLAGF 359 (532)
Q Consensus 280 ~~~~~l~~glp~al~Ll~iL~iHElGH~laAr~~Gvk~s~P~FIP~i~LgtFGAvi~~~s~~~~RkalfdIAlAGPLAg~ 359 (532)
.+...+..++.++++++.++++||+||+++||++|+++. .+.+.+||+++++++...++++++.|++|||++|+
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 345667889999999999999999999999999999998 67788899999999888889999999999999999
Q ss_pred HHHHHHHHHHhhcCCCCCCcccccccchhhhhhhhhhHHhhhccccCCCCCccchHHHHHHHHHHHHHHHhhcCCCCCCh
Q 009542 360 SLGFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAINSIPAGELDG 439 (532)
Q Consensus 360 llAlill~iGl~l~~s~~~~~~v~~~~f~~s~L~~~la~l~LG~~l~~~~~v~lhPL~~agwinLvLtafNLLPigpLDG 439 (532)
+++++++++....+... .+. ....+.+.+|+|+++++|||+|++||||
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 0123456789999999999999999999
Q ss_pred HHHHHHHhhhhH
Q 009542 440 GRIAFALWGRKA 451 (532)
Q Consensus 440 GrIl~Allgrr~ 451 (532)
|||+++++.++.
T Consensus 159 gril~~ll~~~~ 170 (227)
T cd06164 159 GRVLRALLWRRT 170 (227)
T ss_pred HHHHHHHHHHhc
Confidence 999999987654
No 3
>cd06161 S2P-M50_SpoIVFB SpoIVFB Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50B), regulates intramembrane proteolysis (RIP), and is involved in the pro-sigmaK pathway of bacterial spore formation. SpoIVFB (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA (bypass-of-forespore A), and SpoIVB (sporulation protein, stage IV cell wall formation, B locus). SpoIVFB is negatively regulated by SpoIVFA and BofA and activated by SpoIVB. It is thought that SpoIVFB, SpoIVFA, and BofA are located in the mother-cell membrane that surrounds the forespore and that SpoIVB is secreted from the forespore into the space between the two where it activates SpoIVFB.
Probab=99.91 E-value=1.2e-23 Score=204.19 Aligned_cols=129 Identities=29% Similarity=0.433 Sum_probs=108.1
Q ss_pred HHHHhhHHHHHHHHHHHHHHHHHHHHHHHHcCCccCCccccccceeeccceEEeeccccCCccceeeeeecchhhHHHHH
Q 009542 283 NLLTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAITRIRNIVSKREDLLKVAAAGPLAGFSLG 362 (532)
Q Consensus 283 ~~l~~glp~al~Ll~iL~iHElGH~laAr~~Gvk~s~P~FIP~i~LgtFGAvi~~~s~~~~RkalfdIAlAGPLAg~llA 362 (532)
..+..++.+++.++.++++||+||+++||++|+++. .+.+.+||+++++++...+|++++.|++|||++|++++
T Consensus 25 ~~~~~~~~~~l~l~~~v~iHElgH~~~A~~~G~~v~------~i~l~p~Gg~~~~~~~~~~~~~~~lIalAGPl~n~~la 98 (208)
T cd06161 25 VAWLLGLLEALLLFLSVLLHELGHALVARRYGIRVR------SITLLPFGGVAELEEEPETPKEEFVIALAGPLVSLLLA 98 (208)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcc------ceEEEeeeeeeeeccCCCChhHheeeeeehHHHHHHHH
Confidence 456788899999999999999999999999999997 77888899999998777789999999999999999999
Q ss_pred HHHHHHHhhcCCCCCCcccccccchhhhhhhhhhHHhhhccccCCCCCccchHHHHHHHHHHHHHHHhhcCCCCCChHHH
Q 009542 363 FVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAINSIPAGELDGGRI 442 (532)
Q Consensus 363 lill~iGl~l~~s~~~~~~v~~~~f~~s~L~~~la~l~LG~~l~~~~~v~lhPL~~agwinLvLtafNLLPigpLDGGrI 442 (532)
+++.++....+.. + .....+.+.+++|+++++|||+|+.|||||||
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 00123556789999999999999999999999
Q ss_pred HHHHhhhhH
Q 009542 443 AFALWGRKA 451 (532)
Q Consensus 443 l~Allgrr~ 451 (532)
+++++.++.
T Consensus 145 l~~ll~~~~ 153 (208)
T cd06161 145 LRALLWRRT 153 (208)
T ss_pred HHHHHHHhc
Confidence 999987764
No 4
>cd06163 S2P-M50_PDZ_RseP-like RseP-like Site-2 proteases (S2P), zinc metalloproteases (MEROPS family M50A), cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. In Escherichia coli, the S2P homolog RseP is involved in the sigmaE pathway of extracytoplasmic stress responses. Also included in this group are such homologs as Bacillus subtilis YluC, Mycobacterium tuberculosis Rv2869c S2P, and Bordetella bronchiseptica HurP. Rv2869c S2P appears to have a role in the regulation of prokaryotic lipid biosynthesis and membrane composition and YluC of Bacillus has a role in transducing membrane stress. This group includes bacterial and eukaryotic S2P/M50s homologs with either one or two PDZ domains present. PDZ domains are believed to have a regulatory role. The RseP PDZ domain is required for the inhibitory reaction that prevents cleavage of its substrate, RseA.
Probab=99.86 E-value=6.6e-21 Score=182.46 Aligned_cols=113 Identities=34% Similarity=0.426 Sum_probs=88.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCccCCc--ccccc------------ceeeccceEEeeccccC-------------
Q 009542 290 PGALVTALVIGVHELGHILAAKSTGVELGVP--YFVPS------------WQIGSFGAITRIRNIVS------------- 342 (532)
Q Consensus 290 p~al~Ll~iL~iHElGH~laAr~~Gvk~s~P--~FIP~------------i~LgtFGAvi~~~s~~~------------- 342 (532)
.+.+++.+++++||+||+++||++|+++..- -|=|. +.+.++|+++++++..+
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 3556777789999999999999999998620 01121 33668999998864311
Q ss_pred ---CccceeeeeecchhhHHHHHHHHHHHHhhcCCCCCCcccccccchhhhhhhhhhHHhhhccccCCCCCccchHHHHH
Q 009542 343 ---KREDLLKVAAAGPLAGFSLGFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIW 419 (532)
Q Consensus 343 ---~RkalfdIAlAGPLAg~llAlill~iGl~l~~s~~~~~~v~~~~f~~s~L~~~la~l~LG~~l~~~~~v~lhPL~~a 419 (532)
++++++.|++|||++|+++|++++++. +.++
T Consensus 83 ~~~~~~~ri~V~lAGP~~NlilA~i~~~~~----------------------------------------------~~~~ 116 (182)
T cd06163 83 NSKPVWQRILIVFAGPLANFLLAIVLFAVL----------------------------------------------LSFL 116 (182)
T ss_pred ccCCcchhhhhhhhHHHHHHHHHHHHHHHH----------------------------------------------HHHH
Confidence 467899999999999999988664321 2246
Q ss_pred HHHHHHHHHHhhcCCCCCChHHHHHHHhh
Q 009542 420 AWAGLLINAINSIPAGELDGGRIAFALWG 448 (532)
Q Consensus 420 gwinLvLtafNLLPigpLDGGrIl~Allg 448 (532)
.++|+.+++|||+|++||||||++++++.
T Consensus 117 ~~~n~~l~~fNLlPippLDGg~il~~~~~ 145 (182)
T cd06163 117 ALLSINLGILNLLPIPALDGGHLLFLLIE 145 (182)
T ss_pred HHHHHHHHHHHcCCCCCCCHHHHHHHHHH
Confidence 78999999999999999999999999985
No 5
>cd05709 S2P-M50 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. The domain core structure appears to contain at least three transmembrane helices with a catalytic zinc atom coordinated by three conserved residues contained within the consensus sequence HExxH, together with a conserved aspartate residue. The S2P/M50 family of RIP proteases is widely distributed; in eukaryotic cells, they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum (ER) stress responses. In sterol-depleted mammalian cells, a two-step proteolytic process releases the N-terminal domains of sterol regulatory element-bindin
Probab=99.85 E-value=5.6e-21 Score=179.64 Aligned_cols=139 Identities=28% Similarity=0.322 Sum_probs=100.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCCccCC----cccccc-------ceeeccceEEeeccccC-----Cccceeeeeec
Q 009542 290 PGALVTALVIGVHELGHILAAKSTGVELGV----PYFVPS-------WQIGSFGAITRIRNIVS-----KREDLLKVAAA 353 (532)
Q Consensus 290 p~al~Ll~iL~iHElGH~laAr~~Gvk~s~----P~FIP~-------i~LgtFGAvi~~~s~~~-----~RkalfdIAlA 353 (532)
.+.+++++++.+||+||+++||++|+++.. ..+.|. +.+.++|+++++.+... +|++++.|++|
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 356678889999999999999999998752 122221 23445699998877554 48899999999
Q ss_pred chhhHHHHHHHHHHHHhhcCCCCCCcccccccchhhhhhhhhhHHhhhccccCCCCCccchHHHHHHHHHHHHHHHhhcC
Q 009542 354 GPLAGFSLGFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAINSIP 433 (532)
Q Consensus 354 GPLAg~llAlill~iGl~l~~s~~~~~~v~~~~f~~s~L~~~la~l~LG~~l~~~~~v~lhPL~~agwinLvLtafNLLP 433 (532)
||++|++++++++++....+..... .. ..+ ......+.+.+++|+|+.+++|||+|
T Consensus 82 GPl~nllla~i~~~~~~~~~~~~~~----~~---~~~-----------------~~~~~~~~l~~~~~~n~~l~~fNLlP 137 (180)
T cd05709 82 GPLANLLLALLLLLLLLLLGGLPPA----PV---GQA-----------------ASSGLANLLAFLALINLNLAVFNLLP 137 (180)
T ss_pred hHHHHHHHHHHHHHHHHHHccCCcc----ch---hhh-----------------HHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 9999999999987766543221000 00 000 00011245678899999999999999
Q ss_pred CCCCChHHHHHHHhhhhHH
Q 009542 434 AGELDGGRIAFALWGRKAS 452 (532)
Q Consensus 434 igpLDGGrIl~Allgrr~a 452 (532)
++|||||||+++++.++..
T Consensus 138 i~plDGg~il~~~l~~~~~ 156 (180)
T cd05709 138 IPPLDGGRILRALLEAIRG 156 (180)
T ss_pred CCCCChHHHHHHHHhHHHH
Confidence 9999999999999988764
No 6
>cd06159 S2P-M50_PDZ_Arch Uncharacterized Archaeal homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the S2P/M50 family of RIP proteases use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. In eukaryotic cells they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum stress responses. In prokaryotes they regulate such processes as sporulation, cell division, stress response, and cell differentiation. This group appears to be limited to Archaeal S2P/M50s homologs with additional putative N-terminal transmembrane spanning regions, relative to the core protein, and either one or two PDZ domains present.
Probab=99.82 E-value=3e-19 Score=179.88 Aligned_cols=119 Identities=26% Similarity=0.325 Sum_probs=93.7
Q ss_pred HHhhHHHHHHHHHHHHHHHHHHHHHHHHcCCccCCccccccceeeccceEEeecccc---CCccceeeeeecchhhHHHH
Q 009542 285 LTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAITRIRNIV---SKREDLLKVAAAGPLAGFSL 361 (532)
Q Consensus 285 l~~glp~al~Ll~iL~iHElGH~laAr~~Gvk~s~P~FIP~i~LgtFGAvi~~~s~~---~~RkalfdIAlAGPLAg~ll 361 (532)
+...+.+.++++.++.+||+||+++||++|+++..--+ .+.+.++||++++.+.. .++++++.|++|||++|+++
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 34556677788889999999999999999999983211 01223588999886544 46789999999999999999
Q ss_pred HHHHHHHHhhcCCCCCCcccccccchhhhhhhhhhHHhhhccccCCCCCccchHHHHHHHHHHHHHHHhhcCCCCCChHH
Q 009542 362 GFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAINSIPAGELDGGR 441 (532)
Q Consensus 362 Alill~iGl~l~~s~~~~~~v~~~~f~~s~L~~~la~l~LG~~l~~~~~v~lhPL~~agwinLvLtafNLLPigpLDGGr 441 (532)
|++++++.. +.+..|+|+.+++|||+|+.||||||
T Consensus 185 a~i~~~l~~---------------------------------------------l~~~~~~N~~l~lFNLlP~~PLDGg~ 219 (263)
T cd06159 185 ALIAFALFF---------------------------------------------LYWIFWINFLLGLFNCLPAIPLDGGH 219 (263)
T ss_pred HHHHHHHHH---------------------------------------------HHHHHHHHHHHHHHhCCCCCCCChHH
Confidence 987654321 22467899999999999999999999
Q ss_pred HHHHHhhhh
Q 009542 442 IAFALWGRK 450 (532)
Q Consensus 442 Il~Allgrr 450 (532)
++++++..+
T Consensus 220 il~~ll~~~ 228 (263)
T cd06159 220 VFRDLLEAL 228 (263)
T ss_pred HHHHHHHHH
Confidence 999997654
No 7
>PF02163 Peptidase_M50: Peptidase family M50; InterPro: IPR008915 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This entry contains metallopeptidases belonging to MEROPS peptidase family M50 (S2P protease family, clan MM). Members of the M50 metallopeptidase family include: mammalian sterol-regulatory element binding protein (SREBP) site 2 protease, Escherichia coli protease EcfE, stage IV sporulation protein FB and various hypothetical bacterial and eukaryotic homologues. A number of proteins are classified as non-peptidase homologues as they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity.; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 3B4R_A 3ID4_A 3ID2_A 2ZPL_B 3ID1_A 2ZPM_A 3ID3_B 2HGA_A.
Probab=99.78 E-value=5.5e-19 Score=167.03 Aligned_cols=127 Identities=29% Similarity=0.377 Sum_probs=79.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCccCCcc--c--ccc----------ceeeccceE---------------Eeecccc
Q 009542 291 GALVTALVIGVHELGHILAAKSTGVELGVPY--F--VPS----------WQIGSFGAI---------------TRIRNIV 341 (532)
Q Consensus 291 ~al~Ll~iL~iHElGH~laAr~~Gvk~s~P~--F--IP~----------i~LgtFGAv---------------i~~~s~~ 341 (532)
+.+++++++.+||+||+++|+++|+|+.... + .+. +.+.++|++ ...+...
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 3567778999999999999999999997542 1 111 011122332 2222234
Q ss_pred CCccceeeeeecchhhHHHHHHHHHHHHhhcCCCCCCcccccccchhhhhhhhhhHHhhhccccCCCCCccchHHHHHHH
Q 009542 342 SKREDLLKVAAAGPLAGFSLGFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAW 421 (532)
Q Consensus 342 ~~RkalfdIAlAGPLAg~llAlill~iGl~l~~s~~~~~~v~~~~f~~s~L~~~la~l~LG~~l~~~~~v~lhPL~~agw 421 (532)
.+|++.+.|++|||++|++++++++++......... ......+.+.+++|
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 567889999999999999999888766543211000 00112356778999
Q ss_pred HHHHHHHHhhcCCCCCChHHHHHHHh
Q 009542 422 AGLLINAINSIPAGELDGGRIAFALW 447 (532)
Q Consensus 422 inLvLtafNLLPigpLDGGrIl~All 447 (532)
+|+.++++||+|++||||||++++++
T Consensus 132 ~n~~l~~~NllPi~~lDG~~il~~l~ 157 (192)
T PF02163_consen 132 LNFILALFNLLPIPPLDGGRILRALL 157 (192)
T ss_dssp HHHHHHHHTTSSSSSSHHHHHHHHHH
T ss_pred HHHHHhhhhcccCCcCCHHHHHHHHH
Confidence 99999999999999999999999998
No 8
>cd06162 S2P-M50_PDZ_SREBP Sterol regulatory element-binding protein (SREBP) Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50A), regulates intramembrane proteolysis (RIP) of SREBP and is part of a signal transduction mechanism involved in sterol and lipid metabolism. In sterol-depleted mammalian cells, a two-step proteolytic process releases the N-terminal domains of SREBPs from membranes of the endoplasmic reticulum (ER). These domains translocate into the nucleus, where they activate genes of cholesterol and fatty acid biosynthesis. The first cleavage occurs at Site-1 within the ER lumen to generate an intermediate that is subsequently released from the membrane by cleavage at Site-2, which lies within the first transmembrane domain. It is the second proteolytic step that is carried out by the SREBP Site-2 protease (S2P) which is present in this CD family. This group appears to be limited to eumetazoan proteins and contains one PDZ domain.
Probab=99.77 E-value=6.4e-18 Score=171.25 Aligned_cols=113 Identities=25% Similarity=0.231 Sum_probs=89.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCccCCccccccceeecc----ceEEeeccc---cCCccceeeeeecchhhHHHHHH
Q 009542 291 GALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSF----GAITRIRNI---VSKREDLLKVAAAGPLAGFSLGF 363 (532)
Q Consensus 291 ~al~Ll~iL~iHElGH~laAr~~Gvk~s~P~FIP~i~LgtF----GAvi~~~s~---~~~RkalfdIAlAGPLAg~llAl 363 (532)
+.++++.++.+||+||+++|+++|+++. .+.+..| ||+++..+. ..++++++.|+.|||++|+++|+
T Consensus 130 ~l~al~isvvvHElgHal~A~~~gi~V~------~iGl~l~~~~pGa~ve~~~e~~~~~~~~~~l~Ia~AGp~~NlvLa~ 203 (277)
T cd06162 130 YFTALLISGVVHEMGHGVAAVREQVRVN------GFGIFFFIIYPGAYVDLFTDHLNLISPVQQLRIFCAGVWHNFVLGL 203 (277)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCeec------eEEEeeeeccCeeEEeecccccccCChhhhhheehhhHHHHHHHHH
Confidence 4466788999999999999999999998 4443334 889988433 23567789999999999999998
Q ss_pred HHHHHHhhcCCCCCCcccccccchhhhhhhhhhHHhhhccccCCCCCccchHHHHHHHHHHHHHHHhhcCCCCCChHHHH
Q 009542 364 VLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAINSIPAGELDGGRIA 443 (532)
Q Consensus 364 ill~iGl~l~~s~~~~~~v~~~~f~~s~L~~~la~l~LG~~l~~~~~v~lhPL~~agwinLvLtafNLLPigpLDGGrIl 443 (532)
+++++.+. ..+.+.+++|+.+++|||+|+.|||||||+
T Consensus 204 i~~~l~~~------------------------------------------~~l~~la~iNl~lavfNLlP~~pLDGg~il 241 (277)
T cd06162 204 VGYLLLIE------------------------------------------TFLKYLISLSGALAVINAVPCFALDGQWIL 241 (277)
T ss_pred HHHHHHHH------------------------------------------HHHHHHHHHHHHHHHhhcCCCCCCChHHHH
Confidence 77543210 013356789999999999999999999999
Q ss_pred HHHhhhhH
Q 009542 444 FALWGRKA 451 (532)
Q Consensus 444 ~Allgrr~ 451 (532)
++++.++.
T Consensus 242 ~~ll~~~~ 249 (277)
T cd06162 242 STFLEATL 249 (277)
T ss_pred HHHHHHHh
Confidence 99987654
No 9
>cd06158 S2P-M50_like_1 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the S2P/M50 family of RIP proteases use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. In eukaryotic cells they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum stress responses. In prokaryotes they regulate such processes as sporulation, cell division, stress response, and cell differentiation. This group includes bacterial, eukaryotic, and Archaeal S2P/M50s homologs with a minimal core protein and no PDZ domains.
Probab=99.76 E-value=3.2e-18 Score=163.47 Aligned_cols=135 Identities=25% Similarity=0.308 Sum_probs=92.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCccCC----cccccc--------ce--ee--ccceEEeec-----cccCCccceee
Q 009542 291 GALVTALVIGVHELGHILAAKSTGVELGV----PYFVPS--------WQ--IG--SFGAITRIR-----NIVSKREDLLK 349 (532)
Q Consensus 291 ~al~Ll~iL~iHElGH~laAr~~Gvk~s~----P~FIP~--------i~--Lg--tFGAvi~~~-----s~~~~Rkalfd 349 (532)
..++++.++..||+||+++|+++|+++.. -++.|. +. +. ..+++++.. ...++|++++.
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 44567779999999999999999999863 344552 00 11 023454432 12345688999
Q ss_pred eeecchhhHHHHHHHHHHHHhhcCCCCCCcccccccchhhhhhhhhhHHhhhccccCCCCCccchHHHHHHHHHHHHHHH
Q 009542 350 VAAAGPLAGFSLGFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAI 429 (532)
Q Consensus 350 IAlAGPLAg~llAlill~iGl~l~~s~~~~~~v~~~~f~~s~L~~~la~l~LG~~l~~~~~v~lhPL~~agwinLvLtaf 429 (532)
|++|||++|+++++++.++........+ ...+.+ ...+.+..++|+.+++|
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 9999999999999887655433211100 000111 12244567899999999
Q ss_pred hhcCCCCCChHHHHHHHhhhhHHHH
Q 009542 430 NSIPAGELDGGRIAFALWGRKASTR 454 (532)
Q Consensus 430 NLLPigpLDGGrIl~Allgrr~a~~ 454 (532)
||+|++|||||||+++++.++....
T Consensus 135 NLlPipPLDG~~il~~~l~~~~~~~ 159 (181)
T cd06158 135 NLLPIPPLDGSKILAALLPRRLAEA 159 (181)
T ss_pred HhCCCCCCChHHHHHHHcchhHHHH
Confidence 9999999999999999998886543
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=99.54 E-value=1.1e-13 Score=147.25 Aligned_cols=80 Identities=28% Similarity=0.431 Sum_probs=60.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCccCC-c-ccccc------------ceeeccceEEeeccc----------------
Q 009542 291 GALVTALVIGVHELGHILAAKSTGVELGV-P-YFVPS------------WQIGSFGAITRIRNI---------------- 340 (532)
Q Consensus 291 ~al~Ll~iL~iHElGH~laAr~~Gvk~s~-P-~FIP~------------i~LgtFGAvi~~~s~---------------- 340 (532)
+.+.+.+++++||+||+++||++|+++.. . -|=|. +.+.++|+++++...
T Consensus 9 ~~~~~~~~v~~HE~gH~~~a~~~g~~v~~FsiGfGp~l~~~~~~~tey~i~~~plGg~v~~~g~~~~~~~~~~~~~~~~f 88 (420)
T TIGR00054 9 SILALAVLIFVHELGHFLAARLCGIKVERFSIGFGPKILKFKKNGTEYAISLIPLGGYVKMKGLDKEMEVKPPETDGDLF 88 (420)
T ss_pred HHHHHHHHHHHHhHHHHHHHHHcCCEEEEEEEccCchheEEecCCeEEEEEEecCcceEeeccCCcccccCCcchhhhhh
Confidence 35566678899999999999999999862 1 11121 346789999998411
Q ss_pred -cCCccceeeeeecchhhHHHHHHHHHHHHh
Q 009542 341 -VSKREDLLKVAAAGPLAGFSLGFVLFLVGF 370 (532)
Q Consensus 341 -~~~RkalfdIAlAGPLAg~llAlill~iGl 370 (532)
..+.++++.|.+|||++|+++|++++++.+
T Consensus 89 ~~~~~~~r~~i~~aGp~~N~~~a~~~~~~~~ 119 (420)
T TIGR00054 89 NNKSVFQKAIIIFAGPLANFIFAIFVYIFIS 119 (420)
T ss_pred ccCCHHHHHHhhhcccHHHHHHHHHHHHHHH
Confidence 035578899999999999999998876443
No 11
>PRK10779 zinc metallopeptidase RseP; Provisional
Probab=99.52 E-value=1.3e-13 Score=147.90 Aligned_cols=82 Identities=21% Similarity=0.293 Sum_probs=61.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHcCCccCCc--ccccc-------------ceeeccceEEeeccc------------
Q 009542 288 GLPGALVTALVIGVHELGHILAAKSTGVELGVP--YFVPS-------------WQIGSFGAITRIRNI------------ 340 (532)
Q Consensus 288 glp~al~Ll~iL~iHElGH~laAr~~Gvk~s~P--~FIP~-------------i~LgtFGAvi~~~s~------------ 340 (532)
.+.+.+++.+++++||+||+++||++|+++..- -|=|. +-+.++|++.+|...
T Consensus 7 i~~fil~l~~li~vHElGHfl~Ar~~gv~V~~FsiGfGp~l~~~~~~~~Tey~i~~iPlGGyVk~~~e~~~~~~~~~~~~ 86 (449)
T PRK10779 7 LAAFIVALGVLITVHEFGHFWVARRCGVRVERFSIGFGKALWRRTDRQGTEYVIALIPLGGYVKMLDERVEPVAPELRHH 86 (449)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHcCCeeeEEEeecChhHeeEecCCCcEEEEEEEcCCCeeecCCCCCCcCChhhhhh
Confidence 344666677788999999999999999999731 11121 235688999987532
Q ss_pred ---cCCccceeeeeecchhhHHHHHHHHHHHH
Q 009542 341 ---VSKREDLLKVAAAGPLAGFSLGFVLFLVG 369 (532)
Q Consensus 341 ---~~~RkalfdIAlAGPLAg~llAlill~iG 369 (532)
.++.++++.|.+|||++|+++|++++++-
T Consensus 87 ~f~~k~~~~R~~i~~AGp~~N~ila~~~~~~~ 118 (449)
T PRK10779 87 AFNNKTVGQRAAIIAAGPIANFIFAIFAYWLV 118 (449)
T ss_pred hhccCCHHHhhhhhhhhHHHHHHHHHHHHHHH
Confidence 12357889999999999999999886543
No 12
>COG1994 SpoIVFB Zn-dependent proteases [General function prediction only]
Probab=99.33 E-value=1.8e-11 Score=121.00 Aligned_cols=128 Identities=26% Similarity=0.325 Sum_probs=84.0
Q ss_pred HHhhHHHHHHHHHHHHHHHHHHHHHHHHcCCccCCccccccceeeccceEEeeccccCCccceee-------eeec-chh
Q 009542 285 LTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAITRIRNIVSKREDLLK-------VAAA-GPL 356 (532)
Q Consensus 285 l~~glp~al~Ll~iL~iHElGH~laAr~~Gvk~s~P~FIP~i~LgtFGAvi~~~s~~~~Rkalfd-------IAlA-GPL 356 (532)
+.++....++++.-+..||+||...++++|.+.. .+.++.+|++...+..+.+.+..+. +++| ||+
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 4445555555777899999999999999999886 4444446677777665555544444 4444 555
Q ss_pred hHHHHHHHHHHHHhhcCCCCCCcccccccchhhhhhhhhhHHhhhccccCCCCCccchHHHHHHHHHHHHHHHhhcCCCC
Q 009542 357 AGFSLGFVLFLVGFIFPPSDGIGIVVDASVFHESFLAGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAINSIPAGE 436 (532)
Q Consensus 357 Ag~llAlill~iGl~l~~s~~~~~~v~~~~f~~s~L~~~la~l~LG~~l~~~~~v~lhPL~~agwinLvLtafNLLPigp 436 (532)
.|+.+++++ ... .+.. ...+ +....+...+.+|+++++|||+|++|
T Consensus 115 ~ni~la~~~-~~~--~~~~-----------~~~~--------------------~~~~~~~~la~~Nl~L~lFNLiPi~P 160 (230)
T COG1994 115 TNIALAVLG-LLA--LSLF-----------LYHS--------------------VLFAFLAALALVNLVLALFNLLPIPP 160 (230)
T ss_pred HHHHHHHHH-HHh--hccc-----------ccch--------------------hHHHHHHHHHHHHHHHHHHhCCCCCC
Confidence 555555443 000 0000 0000 00112335677999999999999999
Q ss_pred CChHHHHHHHhhhhHH
Q 009542 437 LDGGRIAFALWGRKAS 452 (532)
Q Consensus 437 LDGGrIl~Allgrr~a 452 (532)
|||||++|+++.++..
T Consensus 161 LDGg~vlr~~~~~~~~ 176 (230)
T COG1994 161 LDGGRVLRALLPRRYG 176 (230)
T ss_pred CChHHHHHHHccHHHH
Confidence 9999999999988765
No 13
>COG0750 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]
Probab=98.87 E-value=2.1e-09 Score=111.36 Aligned_cols=242 Identities=13% Similarity=0.041 Sum_probs=136.6
Q ss_pred cccccceeeeccccccCceEEEEeccCCchHHHHHHHHHHHHhhhCCceEEEEeecCCCCCcEEEEEcCCCCCCCCCChh
Q 009542 168 QVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFGDQYKLFLLVNPEDDKPVAVVVPRKTLQPETTAVP 247 (532)
Q Consensus 168 ~~Fg~dtF~~t~~~~~~~gvi~rGnLR~~~e~~y~~l~~~l~~~fGd~y~lfl~~~~~~~kPv~~v~P~~~~~p~~~~~~ 247 (532)
.+++.++|+.....+ ...+++.|.+.......+..+...+ ..|..+ ...|+.. + .. ..
T Consensus 82 ~~~~~~~f~~~~~~~-~~~~~~~Gp~~n~i~~~~~~~~~~~--~~G~~~---------~~~~~~~---~--v~---~~-- 139 (375)
T COG0750 82 PEPRPRAFNAKSVWQ-RIAIVFAGPLFNFILAIVLFVVLFF--VIGLVP---------VASPVVG---E--VA---PK-- 139 (375)
T ss_pred cCcchhhhhcccccc-hhheeechHHHHHHHHHHHHHhhhe--Eeeeee---------eccCeee---e--cC---CC--
Confidence 588899999999999 9999999999988766655544433 223111 1122221 0 00 00
Q ss_pred HHHHHHHHHHHHHHHHHHhcccccccchhccccchHHHHh------hHHHHHHHHHHHHHH--HHHHHHHHHHcCCccCC
Q 009542 248 EWFAAGAFGLVTVFTLLLRNVPALQSNLLSTFDNLNLLTN------GLPGALVTALVIGVH--ELGHILAAKSTGVELGV 319 (532)
Q Consensus 248 ~~~~~~ll~l~T~~T~~~a~~~~L~~~~~~~~~~~~~l~~------glp~al~Ll~iL~iH--ElGH~laAr~~Gvk~s~ 319 (532)
..+..+.+..|...+..+- +...+++.... +.++. .+.+.+.| +..|+.+++.++.....
T Consensus 140 ---------s~a~~a~l~~Gd~iv~~~~-~~i~~~~~~~~~~~~~~~~~~~--~~~i~~~~~~~~~~~~~~~~~~~~~~~ 207 (375)
T COG0750 140 ---------SAAALAGLRPGDRIVAVDG-EKVASWDDVRRLLVAAAGDVFN--LLTILVIRLDGEAHAVAAEIIKSLGLT 207 (375)
T ss_pred ---------CHHHHcCCCCCCEEEeECC-EEccCHHHHHHHHHhccCCccc--ceEEEEEeccceeeeccccceeeEeee
Confidence 0111223333333322221 11222322221 22222 34567788 99999999988888888
Q ss_pred ccccccceeeccceEEe--eccccCC-----ccceeeeeecchhhHHHHHHHHHHHHhhcCCCCCCcccccccchhhhhh
Q 009542 320 PYFVPSWQIGSFGAITR--IRNIVSK-----REDLLKVAAAGPLAGFSLGFVLFLVGFIFPPSDGIGIVVDASVFHESFL 392 (532)
Q Consensus 320 P~FIP~i~LgtFGAvi~--~~s~~~~-----RkalfdIAlAGPLAg~llAlill~iGl~l~~s~~~~~~v~~~~f~~s~L 392 (532)
|+++| ...+..++.++ ..+..++ ++...++..+++++.. +.-...++++.+... .......+..+.+
T Consensus 208 P~~~~-~~~~~~~~~i~~~~i~~~p~~~~~~~~~~~~~~~~~~i~~~-v~~~~~~~~~~~~~l----~~~~~~~~~~~~l 281 (375)
T COG0750 208 PVVIP-LKPGDKIVAVDVGAIGLSPNGEPDVGKVLVKYGPLEAVGLA-VEKTGRLVKLTLKML----KKLITGDLSLKNL 281 (375)
T ss_pred cceec-cCCCCEEEEeeeeeeeeccCCCCccceeeeccCHHHHHHHH-HHHHHHHHHHHHHHH----HHheecccccccc
Confidence 98877 44555555443 3334444 7889999999999943 333333333322100 0000001111112
Q ss_pred hhhhHHhhhccccCCCCCccchHHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHhhhhH
Q 009542 393 AGGFAKLLLGDVLKDGTPISVNPLVIWAWAGLLINAINSIPAGELDGGRIAFALWGRKA 451 (532)
Q Consensus 393 ~~~la~l~LG~~l~~~~~v~lhPL~~agwinLvLtafNLLPigpLDGGrIl~Allgrr~ 451 (532)
.+.+.....+... ......+++.+++|+|+.++++||+|+++|||||++++++.+..
T Consensus 282 ~Gpi~i~~~~~~~--~~~~~~~~l~~~~~lsi~lg~lNllP~p~LDGG~i~~~~~e~~~ 338 (375)
T COG0750 282 SGPIGIAKIAGAA--ASLGLINLLFFLALLSINLGILNLLPIPPLDGGHLLFYLLEALR 338 (375)
T ss_pred cCceehhhhhhHH--HhhHHHHHHHHHHHHHHHHHHHhccCCCccCccHHHHHHHHHHh
Confidence 2111111111100 01234689999999999999999999999999999999986654
No 14
>PF13398 Peptidase_M50B: Peptidase M50B-like
Probab=97.35 E-value=0.00066 Score=66.26 Aligned_cols=65 Identities=31% Similarity=0.274 Sum_probs=51.9
Q ss_pred HHHHHHHHHHHHHHHHcCCccCCccccccceeec-cceEEeeccccCCccceeeeeecchhhHHHHHHHHHHHH
Q 009542 297 LVIGVHELGHILAAKSTGVELGVPYFVPSWQIGS-FGAITRIRNIVSKREDLLKVAAAGPLAGFSLGFVLFLVG 369 (532)
Q Consensus 297 ~iL~iHElGH~laAr~~Gvk~s~P~FIP~i~Lgt-FGAvi~~~s~~~~RkalfdIAlAGPLAg~llAlill~iG 369 (532)
....+||+||+++|...|-++. .+.+.+ -++.+..+. +++...+.++.|||++..+++..++..+
T Consensus 23 l~t~~HE~gHal~a~l~G~~v~------~i~l~~~~~G~~~~~~--~~~~~~~~i~~aGyl~~~l~g~~~~~~~ 88 (200)
T PF13398_consen 23 LVTFVHELGHALAALLTGGRVK------GIVLFPDGSGVTVSSG--PSGIGRFLIALAGYLGPALFGLLLLWLL 88 (200)
T ss_pred HHHHHHHHHHHHHHHHhCCCcc------eEEEEeCCCceEEEec--CCCcchhHHhcccchHHHHHHHHHHHHH
Confidence 3578999999999999999998 555443 456777666 5666789999999999999887766555
No 15
>COG0750 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]
Probab=96.02 E-value=0.021 Score=59.45 Aligned_cols=82 Identities=28% Similarity=0.409 Sum_probs=53.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHcCCccCCcc--ccc-------c------ceeeccceEEeeccccC-----------
Q 009542 289 LPGALVTALVIGVHELGHILAAKSTGVELGVPY--FVP-------S------WQIGSFGAITRIRNIVS----------- 342 (532)
Q Consensus 289 lp~al~Ll~iL~iHElGH~laAr~~Gvk~s~P~--FIP-------~------i~LgtFGAvi~~~s~~~----------- 342 (532)
+.+.+.+...+.+||+||+|.||++|+++.... |-| . +...+.|++.++.....
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 334556666889999999999999999997421 112 0 12345666665532211
Q ss_pred -------CccceeeeeecchhhHHHHHHHHHHHHh
Q 009542 343 -------KREDLLKVAAAGPLAGFSLGFVLFLVGF 370 (532)
Q Consensus 343 -------~RkalfdIAlAGPLAg~llAlill~iGl 370 (532)
+-...+.+-+|||+.|++.++...+...
T Consensus 86 ~~~f~~~~~~~~~~~~~~Gp~~n~i~~~~~~~~~~ 120 (375)
T COG0750 86 PRAFNAKSVWQRIAIVFAGPLFNFILAIVLFVVLF 120 (375)
T ss_pred hhhhhcccccchhheeechHHHHHHHHHHHHHhhh
Confidence 1123678999999999998877765543
No 16
>KOG2921 consensus Intramembrane metalloprotease (sterol-regulatory element-binding protein (SREBP) protease) [Posttranslational modification, protein turnover, chaperones]
Probab=95.93 E-value=0.0064 Score=65.22 Aligned_cols=81 Identities=27% Similarity=0.295 Sum_probs=52.4
Q ss_pred HhhHHH-HHHHHHHHHHHHHHHHHHHHHcCCccCCccccccceeeccceEEeeccc----cCCccceeeeeecchhhHHH
Q 009542 286 TNGLPG-ALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAITRIRNI----VSKREDLLKVAAAGPLAGFS 360 (532)
Q Consensus 286 ~~glp~-al~Ll~iL~iHElGH~laAr~~Gvk~s~P~FIP~i~LgtFGAvi~~~s~----~~~RkalfdIAlAGPLAg~l 360 (532)
+.+++| ...++..+.+||+||+|||.+.|+++.. |--++..--=||++.+... .+. -....|.-||-.-||+
T Consensus 120 l~~I~yf~t~lvi~~vvHElGHalAA~segV~vng--fgIfi~aiyPgafvdl~~dhLqsl~~-fr~LrIfcAGIWHNfv 196 (484)
T KOG2921|consen 120 LSGIAYFLTSLVITVVVHELGHALAAASEGVQVNG--FGIFIAAIYPGAFVDLDNDHLQSLPS-FRALRIFCAGIWHNFV 196 (484)
T ss_pred cccchhhhhhHHHHHHHHHhhHHHHHHhcCceeee--eEEEEEEEcCchhhhhhhhHHhhcch-HHHHHHHhhhHHHHHH
Confidence 344554 4456678899999999999999999971 1001111112666655421 122 2345788999999999
Q ss_pred HHHHHHHHH
Q 009542 361 LGFVLFLVG 369 (532)
Q Consensus 361 lAlill~iG 369 (532)
+|+++.+.-
T Consensus 197 fallc~lal 205 (484)
T KOG2921|consen 197 FALLCVLAL 205 (484)
T ss_pred HHHHHHHHH
Confidence 998876543
No 17
>PF11667 DUF3267: Protein of unknown function (DUF3267); InterPro: IPR021683 This family of proteins has no known function.
Probab=77.24 E-value=1.8 Score=38.21 Aligned_cols=69 Identities=20% Similarity=0.186 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHHHHHHHcCCccCCccccccceeeccceEEeeccccCCccceeeeeecchhhHHHHHHHHHHHHhh
Q 009542 296 ALVIGVHELGHILAAKSTGVELGVPYFVPSWQIGSFGAITRIRNIVSKREDLLKVAAAGPLAGFSLGFVLFLVGFI 371 (532)
Q Consensus 296 l~iL~iHElGH~laAr~~Gvk~s~P~FIP~i~LgtFGAvi~~~s~~~~RkalfdIAlAGPLAg~llAlill~iGl~ 371 (532)
+..+.+||+-|.+..+.+|.+....+- +....+-.+.. .+ .+-.|..+.+...-|+ ++++++.++++..
T Consensus 4 ~~~~~~HEliH~l~~~~~~~~~~~~~g---~~~~~~~~~~~-~~-~~~sk~~~~i~~l~P~--ivl~~~~~~~~~~ 72 (111)
T PF11667_consen 4 IVLIPLHELIHGLFFKLFGKKPKVKFG---FKWKLGPFYAT-CN-EPISKWRFIIILLAPF--IVLTILPLILGFF 72 (111)
T ss_pred EeeHHHHHHHHHHHHHHhCCCCceEEE---EEeeeEEEEEe-cC-cEEeHHHHHHHHHHHH--HHHHHHHHHHHHH
Confidence 345689999999999999996631100 00000111222 22 2333455666666675 4455555444443
No 18
>PF00413 Peptidase_M10: Matrixin This Prosite motif covers only the active site.; InterPro: IPR001818 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M10 (clan MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA. Sequences having this domain are extracellular metalloproteases, such as collagenase and stromelysin, which degrade the extracellular matrix, are known as matrixins. They are zinc-dependent, calcium-activated proteases synthesised as inactive precursors (zymogens), which are proteolytically cleaved to yield the active enzyme [, ]. All matrixins and related proteins possess 2 domains: an N-terminal domain, and a zinc-binding active site domain. The N-terminal domain peptide, cleaved during the activation step, includes a conserved PRCGVPDV octapeptide, known as the cysteine switch, whose Cys residue chelates the active site zinc atom, rendering the enzyme inactive [, ]. The active enzyme degrades components of the extracellular matrix, playing a role in the initial steps of tissue remodelling during morphogenesis, wound healing, angiogenesis and tumour invasion [, ].; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis, 0031012 extracellular matrix; PDB: 1Q3A_C 3V96_B 1HV5_D 1CXV_A 1SRP_A 1FBL_A 1ZVX_A 1JH1_A 1I76_A 2OY4_A ....
Probab=60.71 E-value=5.1 Score=36.29 Aligned_cols=19 Identities=26% Similarity=0.543 Sum_probs=13.3
Q ss_pred HHHHHHHHHHHHHHHHcCC
Q 009542 297 LVIGVHELGHILAAKSTGV 315 (532)
Q Consensus 297 ~iL~iHElGH~laAr~~Gv 315 (532)
..+++||+||++=-..-..
T Consensus 106 ~~v~~HEiGHaLGL~H~~~ 124 (154)
T PF00413_consen 106 QSVAIHEIGHALGLDHSND 124 (154)
T ss_dssp HHHHHHHHHHHTTBESSSS
T ss_pred hhhhhhccccccCcCcCCC
Confidence 3578999999975544433
No 19
>cd04279 ZnMc_MMP_like_1 Zinc-dependent metalloprotease; MMP_like sub-family 1. A group of bacterial, archaeal, and fungal metalloproteinase domains similar to matrix metalloproteinases and astacin.
Probab=58.23 E-value=6.1 Score=36.55 Aligned_cols=22 Identities=32% Similarity=0.364 Sum_probs=18.0
Q ss_pred HHHHHHHHHHHHHHHHHcCCcc
Q 009542 296 ALVIGVHELGHILAAKSTGVEL 317 (532)
Q Consensus 296 l~iL~iHElGH~laAr~~Gvk~ 317 (532)
+..+++||+||.+=.+....+.
T Consensus 104 ~~~~~~HEiGHaLGL~H~~~~~ 125 (156)
T cd04279 104 LQAIALHELGHALGLWHHSDRP 125 (156)
T ss_pred HHHHHHHHhhhhhcCCCCCCCc
Confidence 4578999999999888777765
No 20
>PF07423 DUF1510: Protein of unknown function (DUF1510); InterPro: IPR009988 This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.
Probab=57.58 E-value=8.4 Score=38.88 Aligned_cols=55 Identities=27% Similarity=0.353 Sum_probs=38.9
Q ss_pred eeeeccccccCceEEEEeccCCchHHHHHHHHHHHHhhhCCceEEEEeec-CCCCCcEEE
Q 009542 174 TFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFGDQYKLFLLVN-PEDDKPVAV 232 (532)
Q Consensus 174 tF~~t~~~~~~~gvi~rGnLR~~~e~~y~~l~~~l~~~fGd~y~lfl~~~-~~~~kPv~~ 232 (532)
..|+|++..-.=-+.|.||= |.|.++|.+|+.+=. +++|+|++==- .++=||+-|
T Consensus 159 is~atgi~~~~mi~w~ign~-G~~~~a~gtVs~k~~---~~~YrV~i~WVd~eGWkP~kv 214 (217)
T PF07423_consen 159 ISYATGISEDNMIVWFIGNN-GSPQKAIGTVSDKDT---GKKYRVYIEWVDNEGWKPVKV 214 (217)
T ss_pred HHHhhCCChhheEEEhhhcC-CcccceeEEeccCCC---CceEEEEEEEecCCCccceee
Confidence 36899988877889999996 777999999886533 57899974221 122277643
No 21
>PF13485 Peptidase_MA_2: Peptidase MA superfamily
Probab=49.98 E-value=13 Score=31.57 Aligned_cols=18 Identities=28% Similarity=0.233 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHHHHcCC
Q 009542 298 VIGVHELGHILAAKSTGV 315 (532)
Q Consensus 298 iL~iHElGH~laAr~~Gv 315 (532)
-+++||++|.+.....+-
T Consensus 27 ~~l~HE~~H~~~~~~~~~ 44 (128)
T PF13485_consen 27 RVLAHELAHQWFGNYFGG 44 (128)
T ss_pred HHHHHHHHHHHHHHHcCC
Confidence 578999999999999763
No 22
>cd04268 ZnMc_MMP_like Zinc-dependent metalloprotease, MMP_like subfamily. This group contains matrix metalloproteinases (MMPs), serralysins, and the astacin_like family of proteases.
Probab=48.33 E-value=12 Score=34.43 Aligned_cols=21 Identities=29% Similarity=0.300 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHHHHHHHHcCC
Q 009542 295 TALVIGVHELGHILAAKSTGV 315 (532)
Q Consensus 295 Ll~iL~iHElGH~laAr~~Gv 315 (532)
-....++||+||++=-..-.-
T Consensus 93 ~~~~~~~HEiGHaLGL~H~~~ 113 (165)
T cd04268 93 RLRNTAEHELGHALGLRHNFA 113 (165)
T ss_pred HHHHHHHHHHHHHhcccccCc
Confidence 345788999999975554443
No 23
>cd04278 ZnMc_MMP Zinc-dependent metalloprotease, matrix metalloproteinase (MMP) sub-family. MMPs are responsible for a great deal of pericellular proteolysis of extracellular matrix and cell surface molecules, playing crucial roles in morphogenesis, cell fate specification, cell migration, tissue repair, tumorigenesis, gain or loss of tissue-specific functions, and apoptosis. In many instances, they are anchored to cell membranes via trans-membrane domains, and their activity is controlled via TIMPs (tissue inhibitors of metalloproteinases).
Probab=48.08 E-value=8.1 Score=35.81 Aligned_cols=22 Identities=23% Similarity=0.368 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHHHHcCCcc
Q 009542 296 ALVIGVHELGHILAAKSTGVEL 317 (532)
Q Consensus 296 l~iL~iHElGH~laAr~~Gvk~ 317 (532)
+..+++||+||++=-..-..+.
T Consensus 107 ~~~~~~HEiGHaLGL~H~~~~~ 128 (157)
T cd04278 107 LFSVAAHEIGHALGLGHSSDPD 128 (157)
T ss_pred HHHHHHHHhccccccCCCCCCc
Confidence 4467899999997665444433
No 24
>PF05572 Peptidase_M43: Pregnancy-associated plasma protein-A; InterPro: IPR008754 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase M43 (cytophagalysin family, clan MA(M)), subfamily M43. The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH. The type example of this family is the pregnancy-associated plasma protein A (PAPP-A), which cleaves insulin-like growth factor (IGF) binding protein-4 (IGFBP-4), causing a dramatic reduction in its affinity for IGF-I and -II. Through this mechanism, PAPP-A is a regulator of IGF bioactivity in several systems, including the Homo sapiens ovary and the cardiovascular system [, , , ].; PDB: 3LUN_A 3LUM_B 2J83_A 2CKI_A.
Probab=47.67 E-value=9.2 Score=36.22 Aligned_cols=13 Identities=38% Similarity=0.401 Sum_probs=10.4
Q ss_pred HHHHHHHHHHHHH
Q 009542 297 LVIGVHELGHILA 309 (532)
Q Consensus 297 ~iL~iHElGH~la 309 (532)
.-.++||+||++=
T Consensus 70 g~TltHEvGH~LG 82 (154)
T PF05572_consen 70 GKTLTHEVGHWLG 82 (154)
T ss_dssp SHHHHHHHHHHTT
T ss_pred ccchhhhhhhhhc
Confidence 3678999999863
No 25
>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=43.39 E-value=16 Score=34.83 Aligned_cols=12 Identities=50% Similarity=0.717 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHH
Q 009542 297 LVIGVHELGHIL 308 (532)
Q Consensus 297 ~iL~iHElGH~l 308 (532)
..++.||+||+.
T Consensus 90 ~aVlaHElgH~~ 101 (226)
T PF01435_consen 90 AAVLAHELGHIK 101 (226)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 367999999986
No 26
>PF06114 DUF955: Domain of unknown function (DUF955); InterPro: IPR010359 This is a family of bacterial and viral proteins with undetermined function. A conserved H-E-X-X-H motif is suggestive of a catalytic active site and shows similarity to IPR001915 from INTERPRO.; PDB: 3DTE_A 3DTK_A 3DTI_A.
Probab=41.61 E-value=16 Score=30.72 Aligned_cols=16 Identities=44% Similarity=0.574 Sum_probs=12.2
Q ss_pred HHHHHHHHHHHHHHcC
Q 009542 299 IGVHELGHILAAKSTG 314 (532)
Q Consensus 299 L~iHElGH~laAr~~G 314 (532)
.++||+||++.-....
T Consensus 45 ~laHELgH~~~~~~~~ 60 (122)
T PF06114_consen 45 TLAHELGHILLHHGDE 60 (122)
T ss_dssp HHHHHHHHHHHHH-HH
T ss_pred HHHHHHHHHHhhhccc
Confidence 5789999999766553
No 27
>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=41.29 E-value=20 Score=35.40 Aligned_cols=18 Identities=33% Similarity=0.316 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHHHHHcCC
Q 009542 298 VIGVHELGHILAAKSTGV 315 (532)
Q Consensus 298 iL~iHElGH~laAr~~Gv 315 (532)
.+.+||.||+++|..++-
T Consensus 30 ~~A~HEAGhAvva~~l~~ 47 (213)
T PF01434_consen 30 RIAYHEAGHAVVAYLLPP 47 (213)
T ss_dssp HHHHHHHHHHHHHHHSSS
T ss_pred HHHHHHHHHHHHHHHhcc
Confidence 578999999999999873
No 28
>PF14247 DUF4344: Domain of unknown function (DUF4344)
Probab=40.47 E-value=28 Score=35.19 Aligned_cols=25 Identities=32% Similarity=0.406 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcc
Q 009542 292 ALVTALVIGVHELGHILAAKSTGVEL 317 (532)
Q Consensus 292 al~Ll~iL~iHElGH~laAr~~Gvk~ 317 (532)
++..+..++.||+||++...+ ++++
T Consensus 88 ~~~~~~~~l~HE~GHAlI~~~-~lPv 112 (220)
T PF14247_consen 88 AIGNVLFTLYHELGHALIDDL-DLPV 112 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHHh-cCCc
Confidence 455666789999999998753 4444
No 29
>cd04277 ZnMc_serralysin_like Zinc-dependent metalloprotease, serralysin_like subfamily. Serralysins and related proteases are important virulence factors in pathogenic bacteria. They may be secreted into the medium via a mechanism found in gram-negative bacteria, that does not require n-terminal signal sequences which are cleaved after the transmembrane translocation. A calcium-binding domain c-terminal to the metalloprotease domain, which contains multiple tandem repeats of a nine-residue motif including the pattern GGxGxD, and which forms a parallel beta roll may be involved in the translocation mechanism and/or substrate binding. Serralysin family members may have a broad spectrum of substrates each, including host immunoglobulins, complement proteins, cell matrix and cytoskeletal proteins, as well as antimicrobial peptides.
Probab=38.72 E-value=17 Score=34.58 Aligned_cols=22 Identities=32% Similarity=0.451 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHHHHHcCCccC
Q 009542 297 LVIGVHELGHILAAKSTGVELG 318 (532)
Q Consensus 297 ~iL~iHElGH~laAr~~Gvk~s 318 (532)
...++||+||.+=-+.-+....
T Consensus 114 ~~t~~HEiGHaLGL~H~~~~~~ 135 (186)
T cd04277 114 YQTIIHEIGHALGLEHPGDYNG 135 (186)
T ss_pred HHHHHHHHHHHhcCCCCCcCCC
Confidence 4678999999987665554443
No 30
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=38.57 E-value=29 Score=41.88 Aligned_cols=18 Identities=28% Similarity=0.366 Sum_probs=8.7
Q ss_pred cccccccccCCCCccccc
Q 009542 5 TTFRGNLSLLPHCSSCCD 22 (532)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~ 22 (532)
+||-|.-..+--|++-.+
T Consensus 1354 aTi~v~R~~~Dlct~~~D 1371 (1516)
T KOG1832|consen 1354 ATIPVDRCLLDLCTEPTD 1371 (1516)
T ss_pred eeeecccchhhhhcCCcc
Confidence 444444444555555443
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=38.30 E-value=16 Score=32.85 Aligned_cols=19 Identities=32% Similarity=0.462 Sum_probs=13.4
Q ss_pred HHHHHHHHHHHHHHcCCcc
Q 009542 299 IGVHELGHILAAKSTGVEL 317 (532)
Q Consensus 299 L~iHElGH~laAr~~Gvk~ 317 (532)
+++||+||++=...-..+.
T Consensus 89 ~~~HEigHaLGl~H~~~~~ 107 (140)
T smart00235 89 VAAHELGHALGLYHEQSRS 107 (140)
T ss_pred cHHHHHHHHhcCCcCCCCC
Confidence 7899999998555444333
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=37.99 E-value=16 Score=33.34 Aligned_cols=21 Identities=29% Similarity=0.219 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHHHHHcCC
Q 009542 295 TALVIGVHELGHILAAKSTGV 315 (532)
Q Consensus 295 Ll~iL~iHElGH~laAr~~Gv 315 (532)
....+++||+||.+=.+.-..
T Consensus 95 ~~~~~~~HElGH~LGl~H~~~ 115 (167)
T cd00203 95 EGAQTIAHELGHALGFYHDHD 115 (167)
T ss_pred cchhhHHHHHHHHhCCCccCc
Confidence 345678999999986665443
No 33
>PF13582 Reprolysin_3: Metallo-peptidase family M12B Reprolysin-like; PDB: 3P24_C.
Probab=36.98 E-value=17 Score=31.79 Aligned_cols=13 Identities=38% Similarity=0.434 Sum_probs=10.1
Q ss_pred HHHHHHHHHHHHH
Q 009542 298 VIGVHELGHILAA 310 (532)
Q Consensus 298 iL~iHElGH~laA 310 (532)
..++||+||.+=+
T Consensus 109 ~~~~HEiGH~lGl 121 (124)
T PF13582_consen 109 DTFAHEIGHNLGL 121 (124)
T ss_dssp THHHHHHHHHTT-
T ss_pred eEeeehhhHhcCC
Confidence 6789999998644
No 34
>PF13688 Reprolysin_5: Metallo-peptidase family M12; PDB: 2FV5_B 3EWJ_A 3KME_A 3L0T_B 1BKC_E 3G42_D 2I47_D 2FV9_B 3LEA_A 1ZXC_B ....
Probab=36.46 E-value=20 Score=34.12 Aligned_cols=21 Identities=33% Similarity=0.414 Sum_probs=13.0
Q ss_pred HHHHHHHHHHHHHHHHHcCCc
Q 009542 296 ALVIGVHELGHILAAKSTGVE 316 (532)
Q Consensus 296 l~iL~iHElGH~laAr~~Gvk 316 (532)
-.+.++||+||-+=|..=+..
T Consensus 142 ~~~~~AHEiGH~lGa~HD~~~ 162 (196)
T PF13688_consen 142 GAITFAHEIGHNLGAPHDGDY 162 (196)
T ss_dssp HHHHHHHHHHHHTT-----SS
T ss_pred eehhhHHhHHHhcCCCCCCCC
Confidence 346789999999999876554
No 35
>PF14891 Peptidase_M91: Effector protein
Probab=35.75 E-value=24 Score=33.78 Aligned_cols=16 Identities=31% Similarity=0.299 Sum_probs=13.1
Q ss_pred HHHHHHHHHHHHHHHH
Q 009542 297 LVIGVHELGHILAAKS 312 (532)
Q Consensus 297 ~iL~iHElGH~laAr~ 312 (532)
++++.|||+|++-+..
T Consensus 104 ~v~L~HEL~HA~~~~~ 119 (174)
T PF14891_consen 104 FVVLYHELIHAYDYMN 119 (174)
T ss_pred HHHHHHHHHHHHHHHC
Confidence 4789999999987654
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=35.35 E-value=27 Score=35.32 Aligned_cols=28 Identities=32% Similarity=0.330 Sum_probs=19.3
Q ss_pred HhhHHHHHHHHHHHHHHHHHHHHHHHHcCCc
Q 009542 286 TNGLPGALVTALVIGVHELGHILAAKSTGVE 316 (532)
Q Consensus 286 ~~glp~al~Ll~iL~iHElGH~laAr~~Gvk 316 (532)
+.|+|-. ++.++++||++|+|. |..|.+
T Consensus 85 l~GLPrl--l~gsiLAHE~mHa~L-rl~g~~ 112 (212)
T PF12315_consen 85 LYGLPRL--LTGSILAHELMHAWL-RLNGFP 112 (212)
T ss_pred ECCCCHH--HHhhHHHHHHHHHHh-cccCCC
Confidence 4455543 446899999999998 455544
No 37
>PTZ00429 beta-adaptin; Provisional
Probab=33.52 E-value=40 Score=39.79 Aligned_cols=36 Identities=25% Similarity=0.226 Sum_probs=21.4
Q ss_pred CCChhhhcccCCCCCCCCCcCcccCCCCCCCccCCC
Q 009542 73 SNNDKEKEVHDGQENQPATASDQEDDKSQPDSQLDS 108 (532)
Q Consensus 73 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 108 (532)
++.||||+|+++.++.+++.++..++++..++++..
T Consensus 606 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 641 (746)
T PTZ00429 606 VELDEEDTEDDDAVELPSTPSMGTQDGSPAPSAAPA 641 (746)
T ss_pred cccccccccchhhccCCCCCCCCCCCCCCCcccccc
Confidence 344555666666667777777766666555455443
No 38
>PF02031 Peptidase_M7: Streptomyces extracellular neutral proteinase (M7) family; InterPro: IPR000013 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M7 (snapalysin family, clan MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA. With a molecular weight of around 16kDa, Streptomyces extracellular neutral protease is one of the smallest known proteases []; it is capable of hydrolysing milk proteins []. The enzyme is synthesised as a proenzyme with a signal peptide, a propeptide and an active domain that contains the conserved HEXXH motif characteristic of metalloproteases. Although family M7 shows active site sequence similarity to other members, it differs in one major respect: the third zinc ligand appears to be an aspartate residue rather than the usual histidine.; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis, 0005576 extracellular region; PDB: 1C7K_A 1KUH_A.
Probab=32.42 E-value=27 Score=32.85 Aligned_cols=10 Identities=80% Similarity=1.291 Sum_probs=8.8
Q ss_pred HHHHHHHHHH
Q 009542 299 IGVHELGHIL 308 (532)
Q Consensus 299 L~iHElGH~l 308 (532)
+.+||+||.+
T Consensus 80 IaaHE~GHiL 89 (132)
T PF02031_consen 80 IAAHELGHIL 89 (132)
T ss_dssp HHHHHHHHHH
T ss_pred eeeehhcccc
Confidence 6899999985
No 39
>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=31.58 E-value=25 Score=33.59 Aligned_cols=21 Identities=33% Similarity=0.286 Sum_probs=14.2
Q ss_pred HHHHHHHHHHHHHHHHHcCCc
Q 009542 296 ALVIGVHELGHILAAKSTGVE 316 (532)
Q Consensus 296 l~iL~iHElGH~laAr~~Gvk 316 (532)
-.-.++||+||.+=|..-+..
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 335689999999999887764
No 40
>cd04327 ZnMc_MMP_like_3 Zinc-dependent metalloprotease; MMP_like sub-family 3. A group of bacterial and fungal metalloproteinase domains similar to matrix metalloproteinases and astacin.
Probab=30.64 E-value=32 Score=33.38 Aligned_cols=17 Identities=29% Similarity=0.407 Sum_probs=12.2
Q ss_pred HHHHHHHHHHHHHHHHc
Q 009542 297 LVIGVHELGHILAAKST 313 (532)
Q Consensus 297 ~iL~iHElGH~laAr~~ 313 (532)
...++||+||++=...-
T Consensus 93 ~~~i~HElgHaLG~~HE 109 (198)
T cd04327 93 SRVVLHEFGHALGFIHE 109 (198)
T ss_pred HHHHHHHHHHHhcCccc
Confidence 35788999998755433
No 41
>PRK03001 M48 family peptidase; Provisional
Probab=30.52 E-value=31 Score=35.43 Aligned_cols=12 Identities=33% Similarity=0.426 Sum_probs=9.9
Q ss_pred HHHHHHHHHHHH
Q 009542 297 LVIGVHELGHIL 308 (532)
Q Consensus 297 ~iL~iHElGH~l 308 (532)
.++++||+||.-
T Consensus 125 ~aVlAHElgHi~ 136 (283)
T PRK03001 125 RGVMAHELAHVK 136 (283)
T ss_pred HHHHHHHHHHHh
Confidence 367999999974
No 42
>PHA02456 zinc metallopeptidase motif-containing protein
Probab=30.40 E-value=31 Score=32.00 Aligned_cols=19 Identities=26% Similarity=0.305 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHHcCCccC
Q 009542 300 GVHELGHILAAKSTGVELG 318 (532)
Q Consensus 300 ~iHElGH~laAr~~Gvk~s 318 (532)
+.||++|.|.-|.||.-..
T Consensus 83 L~HEL~H~WQ~RsYG~i~P 101 (141)
T PHA02456 83 LAHELNHAWQFRTYGLVQP 101 (141)
T ss_pred HHHHHHHHHhhhccceeee
Confidence 5799999999999997553
No 43
>PRK03982 heat shock protein HtpX; Provisional
Probab=29.91 E-value=33 Score=35.39 Aligned_cols=12 Identities=42% Similarity=0.362 Sum_probs=9.8
Q ss_pred HHHHHHHHHHHH
Q 009542 297 LVIGVHELGHIL 308 (532)
Q Consensus 297 ~iL~iHElGH~l 308 (532)
.+++.||+||.-
T Consensus 126 ~AVlAHElgHi~ 137 (288)
T PRK03982 126 EGVIAHELTHIK 137 (288)
T ss_pred HHHHHHHHHHHH
Confidence 367899999974
No 44
>cd04269 ZnMc_adamalysin_II_like Zinc-dependent metalloprotease; adamalysin_II_like subfamily. Adamalysin II is a snake venom zinc endopeptidase. This subfamily contains other snake venom metalloproteinases, as well as membrane-anchored metalloproteases belonging to the ADAM family. ADAMs (A Disintegrin And Metalloprotease) are glycoproteins, which play roles in cell signaling, cell fusion, and cell-cell interactions.
Probab=29.64 E-value=35 Score=32.50 Aligned_cols=20 Identities=35% Similarity=0.350 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHHHHcCC
Q 009542 296 ALVIGVHELGHILAAKSTGV 315 (532)
Q Consensus 296 l~iL~iHElGH~laAr~~Gv 315 (532)
.+.+++||+||-+=+..-+.
T Consensus 131 ~a~~~AHElGH~lG~~HD~~ 150 (194)
T cd04269 131 FAVTMAHELGHNLGMEHDDG 150 (194)
T ss_pred HHHHHHHHHHhhcCCCcCCC
Confidence 35788999999987765543
No 45
>cd04270 ZnMc_TACE_like Zinc-dependent metalloprotease; TACE_like subfamily. TACE, the tumor-necrosis factor-alpha converting enzyme, releases soluble TNF-alpha from transmembrane pro-TNF-alpha.
Probab=29.49 E-value=33 Score=34.61 Aligned_cols=18 Identities=28% Similarity=0.503 Sum_probs=14.0
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 009542 295 TALVIGVHELGHILAAKS 312 (532)
Q Consensus 295 Ll~iL~iHElGH~laAr~ 312 (532)
.+...++||+||-+=+..
T Consensus 166 ~~a~t~AHElGHnlGm~H 183 (244)
T cd04270 166 ESDLVTAHELGHNFGSPH 183 (244)
T ss_pred HHHHHHHHHHHHhcCCCC
Confidence 455789999999887653
No 46
>COG2856 Predicted Zn peptidase [Amino acid transport and metabolism]
Probab=29.48 E-value=29 Score=34.90 Aligned_cols=16 Identities=38% Similarity=0.463 Sum_probs=11.9
Q ss_pred HHHHHHHHHHHHHHcC
Q 009542 299 IGVHELGHILAAKSTG 314 (532)
Q Consensus 299 L~iHElGH~laAr~~G 314 (532)
.++||+||++.=+...
T Consensus 75 tlAHELGH~llH~~~~ 90 (213)
T COG2856 75 TLAHELGHALLHTDLN 90 (213)
T ss_pred HHHHHHhHHHhccccc
Confidence 4789999998755443
No 47
>PRK11037 hypothetical protein; Provisional
Probab=29.29 E-value=1.3e+02 Score=26.26 Aligned_cols=65 Identities=18% Similarity=0.366 Sum_probs=43.0
Q ss_pred ccCCCChhHH-----HHhhccccccceeeeccccccCceEEEEeccC-------C-chHHHHHHHHHHHHhhhCCceEE
Q 009542 153 EYIRIPKETI-----DILKDQVFGFDTFFVTNQEPYEGGVLFKGNLR-------G-QAAKTYEKISTRMKNKFGDQYKL 218 (532)
Q Consensus 153 ~~~~i~~edl-----~~ik~~~Fg~dtF~~t~~~~~~~gvi~rGnLR-------~-~~e~~y~~l~~~l~~~fGd~y~l 218 (532)
+..+|++++| +.||+.===+..-.+|++|-.++..+|||..= + +...||. +=+-|+-.+..+|+|
T Consensus 4 ~~~~I~~~~LL~~AN~iI~~Hedyi~GM~a~~Veqk~~VLVFkGeyFLD~~GlPT~KtTAvFN-MFK~LAh~LS~~y~L 81 (83)
T PRK11037 4 ETQPIDRETLLLEANKIIREHEDYLAGMRATDVEQKNGVLVFRGEYFLDEQGLPTAKTTAVFN-MFKHLAHVLSEKYHL 81 (83)
T ss_pred CCcccCHHHHHHHHHHHHHhhHHHhcccccceeeeeCCEEEEecceeecCCCCCCccchHHHH-HHHHHHHHhCcceec
Confidence 4557888888 46665333344568999999999999999832 2 2234443 334466666777876
No 48
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=28.93 E-value=40 Score=30.96 Aligned_cols=19 Identities=21% Similarity=0.123 Sum_probs=14.8
Q ss_pred HHHHHHHHHHHHHHHHHHc
Q 009542 295 TALVIGVHELGHILAAKST 313 (532)
Q Consensus 295 Ll~iL~iHElGH~laAr~~ 313 (532)
.+.-.++|||.|+++-...
T Consensus 59 ~~~~tL~HEm~H~~~~~~~ 77 (157)
T PF10263_consen 59 ELIDTLLHEMAHAAAYVFG 77 (157)
T ss_pred HHHHHHHHHHHHHHhhhcc
Confidence 4446789999999996663
No 49
>cd04267 ZnMc_ADAM_like Zinc-dependent metalloprotease, ADAM_like or reprolysin_like subgroup. The adamalysin_like or ADAM family of metalloproteases contains proteolytic domains from snake venoms, proteases from the mammalian reproductive tract, and the tumor necrosis factor alpha convertase, TACE. ADAMs (A Disintegrin And Metalloprotease) are glycoproteins, which play roles in cell signaling, cell fusion, and cell-cell interactions.
Probab=27.80 E-value=27 Score=33.18 Aligned_cols=20 Identities=40% Similarity=0.531 Sum_probs=15.6
Q ss_pred HHHHHHHHHHHHHHHHHcCC
Q 009542 296 ALVIGVHELGHILAAKSTGV 315 (532)
Q Consensus 296 l~iL~iHElGH~laAr~~Gv 315 (532)
.+.+++||+||.+=+..-+.
T Consensus 133 ~~~~~aHElGH~lG~~HD~~ 152 (192)
T cd04267 133 TALTMAHELGHNLGAEHDGG 152 (192)
T ss_pred ehhhhhhhHHhhcCCcCCCC
Confidence 34678999999988776654
No 50
>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=27.74 E-value=26 Score=36.23 Aligned_cols=14 Identities=36% Similarity=0.596 Sum_probs=10.6
Q ss_pred HHHHHHHHHHHHHH
Q 009542 297 LVIGVHELGHILAA 310 (532)
Q Consensus 297 ~iL~iHElGH~laA 310 (532)
.-+++||+||.+.-
T Consensus 217 ~~v~vHE~GHsf~~ 230 (264)
T PF09471_consen 217 KQVVVHEFGHSFGG 230 (264)
T ss_dssp HHHHHHHHHHHTT-
T ss_pred cceeeeeccccccc
Confidence 35789999998764
No 51
>PRK12462 phosphoserine aminotransferase; Provisional
Probab=27.63 E-value=97 Score=33.52 Aligned_cols=67 Identities=12% Similarity=0.160 Sum_probs=45.8
Q ss_pred CccccCCCChhHHHHhhccccccceeeeccccccCceEEEEeccCCchHHHHHHHHHHHHhhhC--CceEEEEeecC
Q 009542 150 QLDEYIRIPKETIDILKDQVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFG--DQYKLFLLVNP 224 (532)
Q Consensus 150 ~~~~~~~i~~edl~~ik~~~Fg~dtF~~t~~~~~~~gvi~rGnLR~~~e~~y~~l~~~l~~~fG--d~y~lfl~~~~ 224 (532)
....+..+|+|.++++++++.-|. .-+-+++=.+---.+=.+.|++.+++|+++|+ |.|.+++++-.
T Consensus 8 F~aGPa~lp~~Vl~~~~~~~~~~~--------~~g~si~eisHRs~~F~~i~~~~~~~Lr~Ll~~P~~y~Vlfl~Gg 76 (364)
T PRK12462 8 FSGGPGALPDTVLEQVRQAVVELP--------ETGLSVLGMSHRSSWFSSLLAQAEADLRDLLGIPDEYGVVFLQGG 76 (364)
T ss_pred ecCCCcCCCHHHHHHHHHHHhccc--------ccCccccccccccHHHHHHHHHHHHHHHHHhCCCCCCeEEEEecc
Confidence 445788999999999997543322 11123333333234568899999999999998 68988766654
No 52
>COG0501 HtpX Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]
Probab=26.75 E-value=40 Score=33.90 Aligned_cols=11 Identities=55% Similarity=0.818 Sum_probs=9.2
Q ss_pred HHHHHHHHHHH
Q 009542 298 VIGVHELGHIL 308 (532)
Q Consensus 298 iL~iHElGH~l 308 (532)
.++.||+||..
T Consensus 159 aVlaHElgHi~ 169 (302)
T COG0501 159 AVLAHELGHIK 169 (302)
T ss_pred HHHHHHHHHHh
Confidence 57899999963
No 53
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=26.62 E-value=50 Score=30.66 Aligned_cols=16 Identities=25% Similarity=0.003 Sum_probs=13.6
Q ss_pred HHHHHHHHHHHHHHHH
Q 009542 297 LVIGVHELGHILAAKS 312 (532)
Q Consensus 297 ~iL~iHElGH~laAr~ 312 (532)
.-++.|||+|+++-..
T Consensus 60 ~~~l~HEm~H~~~~~~ 75 (146)
T smart00731 60 RETLLHELCHAALYLF 75 (146)
T ss_pred HhhHHHHHHHHHHHHh
Confidence 4578999999999875
No 54
>PF13583 Reprolysin_4: Metallo-peptidase family M12B Reprolysin-like
Probab=26.44 E-value=34 Score=33.67 Aligned_cols=17 Identities=29% Similarity=0.280 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHHHHcCC
Q 009542 299 IGVHELGHILAAKSTGV 315 (532)
Q Consensus 299 L~iHElGH~laAr~~Gv 315 (532)
.++||+||.+=|+.-+-
T Consensus 140 ~~aHEiGH~lGl~H~~~ 156 (206)
T PF13583_consen 140 TFAHEIGHNLGLRHDFD 156 (206)
T ss_pred HHHHHHHHHhcCCCCcc
Confidence 48899999998887766
No 55
>PRK04897 heat shock protein HtpX; Provisional
Probab=25.98 E-value=42 Score=34.96 Aligned_cols=11 Identities=36% Similarity=0.383 Sum_probs=9.3
Q ss_pred HHHHHHHHHHH
Q 009542 298 VIGVHELGHIL 308 (532)
Q Consensus 298 iL~iHElGH~l 308 (532)
++++||+||.-
T Consensus 139 aVlAHElgHi~ 149 (298)
T PRK04897 139 GVIGHEISHIR 149 (298)
T ss_pred HHHHHHHHHHh
Confidence 67899999963
No 56
>PF12388 Peptidase_M57: Dual-action HEIGH metallo-peptidase; InterPro: IPR024653 This entry represents the metallopeptidases M10, M27 and M57. The catalytic triad for proteases in this entry is HE-H-H, which in many members is in the sequence motif HEIGH [].
Probab=25.85 E-value=35 Score=34.45 Aligned_cols=27 Identities=19% Similarity=0.146 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCcc
Q 009542 291 GALVTALVIGVHELGHILAAKSTGVEL 317 (532)
Q Consensus 291 ~al~Ll~iL~iHElGH~laAr~~Gvk~ 317 (532)
+..-+..-++.||+||.+=-|+-.+..
T Consensus 128 ~~~~~~~hvi~HEiGH~IGfRHTD~~~ 154 (211)
T PF12388_consen 128 YSVNVIEHVITHEIGHCIGFRHTDYFN 154 (211)
T ss_pred CchhHHHHHHHHHhhhhccccccCcCC
Confidence 344456678999999998877755443
No 57
>COG5309 Exo-beta-1,3-glucanase [Carbohydrate transport and metabolism]
Probab=25.63 E-value=1.1e+02 Score=32.54 Aligned_cols=61 Identities=16% Similarity=0.312 Sum_probs=42.8
Q ss_pred hhHHHHhhcccccc-ceeeeccccccCceEEEEeccCC--chHHHHHHHHHHHHhhhCCceEEEEeec
Q 009542 159 KETIDILKDQVFGF-DTFFVTNQEPYEGGVLFKGNLRG--QAAKTYEKISTRMKNKFGDQYKLFLLVN 223 (532)
Q Consensus 159 ~edl~~ik~~~Fg~-dtF~~t~~~~~~~gvi~rGnLR~--~~e~~y~~l~~~l~~~fGd~y~lfl~~~ 223 (532)
.|.++++|. .||= .+||+||+-.--.|--+-++.-. +..+.++++..+|++. | |.+|+++-
T Consensus 218 ~~q~e~vqs-a~g~~k~~~v~EtGWPS~G~~~G~a~pS~anq~~~~~~i~~~~~~~-G--~d~fvfeA 281 (305)
T COG5309 218 LEQLERVQS-ACGTKKTVWVTETGWPSDGRTYGSAVPSVANQKIAVQEILNALRSC-G--YDVFVFEA 281 (305)
T ss_pred HHHHHHHHH-hcCCCccEEEeeccCCCCCCccCCcCCChhHHHHHHHHHHhhhhcc-C--ccEEEeee
Confidence 677999998 7776 99999998755555555444443 3466778888888874 6 66665553
No 58
>PLN02452 phosphoserine transaminase
Probab=25.00 E-value=1.2e+02 Score=32.48 Aligned_cols=67 Identities=9% Similarity=0.186 Sum_probs=47.3
Q ss_pred CccccCCCChhHHHHhhccccccceeeeccccccCceEEEEeccCCchHHHHHHHHHHHHhhhC--CceEEEEeecC
Q 009542 150 QLDEYIRIPKETIDILKDQVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFG--DQYKLFLLVNP 224 (532)
Q Consensus 150 ~~~~~~~i~~edl~~ik~~~Fg~dtF~~t~~~~~~~gvi~rGnLR~~~e~~y~~l~~~l~~~fG--d~y~lfl~~~~ 224 (532)
....+..+|++.+++++.+.+-|. .-+-+++-.+---.+=.++++.++++|++.++ |.|.+++++-.
T Consensus 11 f~pGP~~lp~~Vl~~~~~~~~~~~--------~~g~s~~~~sHRs~~f~~i~~~~~~~L~~l~~~p~~y~v~~l~Gs 79 (365)
T PLN02452 11 FSAGPATLPANVLAKAQAELYNWE--------GSGMSVMEMSHRGKEFLSIIQKAEADLRELLDIPDNYEVLFLQGG 79 (365)
T ss_pred eeCCCCCCCHHHHHHHHHHHhccc--------ccCccccccCCCchHHHHHHHHHHHHHHHHhCCCCCceEEEEeCc
Confidence 445788999999999987554432 22334444444444567999999999999997 67988766544
No 59
>COG0830 UreF Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]
Probab=24.45 E-value=80 Score=32.28 Aligned_cols=31 Identities=32% Similarity=0.340 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHhhcCCCCCChHHHHHHHhh
Q 009542 418 IWAWAGLLINAINSIPAGELDGGRIAFALWG 448 (532)
Q Consensus 418 ~agwinLvLtafNLLPigpLDGGrIl~Allg 448 (532)
++.-.|++.++.=|+|.||+||=||+..+-.
T Consensus 158 ya~~~~lv~aavRlipLgQ~~gq~il~~l~~ 188 (229)
T COG0830 158 YAWASNLVSAAVRLIPLGQLDGQKILAQLEP 188 (229)
T ss_pred HHHHHHHHHHHHHhcccCcHHHHHHHHHhhH
Confidence 4445799999999999999999999998843
No 60
>PRK01345 heat shock protein HtpX; Provisional
Probab=24.29 E-value=47 Score=35.05 Aligned_cols=12 Identities=33% Similarity=0.454 Sum_probs=10.0
Q ss_pred HHHHHHHHHHHH
Q 009542 297 LVIGVHELGHIL 308 (532)
Q Consensus 297 ~iL~iHElGH~l 308 (532)
..++.||+||.-
T Consensus 125 ~aVlAHElgHi~ 136 (317)
T PRK01345 125 AGVMAHELAHVK 136 (317)
T ss_pred HHHHHHHHHHHH
Confidence 367899999975
No 61
>PF13699 DUF4157: Domain of unknown function (DUF4157)
Probab=23.93 E-value=45 Score=28.29 Aligned_cols=12 Identities=33% Similarity=0.650 Sum_probs=10.1
Q ss_pred HHHHHHHHHHHH
Q 009542 298 VIGVHELGHILA 309 (532)
Q Consensus 298 iL~iHElGH~la 309 (532)
.++.||++|.+-
T Consensus 63 ~llaHEl~Hv~Q 74 (79)
T PF13699_consen 63 ALLAHELAHVVQ 74 (79)
T ss_pred hhHhHHHHHHHh
Confidence 478999999874
No 62
>PRK03072 heat shock protein HtpX; Provisional
Probab=23.91 E-value=48 Score=34.37 Aligned_cols=11 Identities=36% Similarity=0.395 Sum_probs=9.1
Q ss_pred HHHHHHHHHHH
Q 009542 297 LVIGVHELGHI 307 (532)
Q Consensus 297 ~iL~iHElGH~ 307 (532)
..++.||+||.
T Consensus 128 ~aVlAHElgHi 138 (288)
T PRK03072 128 RGVLGHELSHV 138 (288)
T ss_pred HHHHHHHHHHH
Confidence 36789999995
No 63
>COG3824 Predicted Zn-dependent protease [General function prediction only]
Probab=23.67 E-value=35 Score=31.93 Aligned_cols=14 Identities=29% Similarity=0.558 Sum_probs=11.7
Q ss_pred HHHHHHHHHHHHHH
Q 009542 295 TALVIGVHELGHIL 308 (532)
Q Consensus 295 Ll~iL~iHElGH~l 308 (532)
.+..+++||+||.+
T Consensus 108 ~vthvliHEIgHhF 121 (136)
T COG3824 108 QVTHVLIHEIGHHF 121 (136)
T ss_pred Hhhhhhhhhhhhhc
Confidence 55688999999975
No 64
>PRK02391 heat shock protein HtpX; Provisional
Probab=23.56 E-value=50 Score=34.54 Aligned_cols=10 Identities=40% Similarity=0.733 Sum_probs=8.7
Q ss_pred HHHHHHHHHH
Q 009542 298 VIGVHELGHI 307 (532)
Q Consensus 298 iL~iHElGH~ 307 (532)
.++.||+||.
T Consensus 135 aVlaHElgHi 144 (296)
T PRK02391 135 AVLAHELSHV 144 (296)
T ss_pred HHHHHHHHHH
Confidence 5789999995
No 65
>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=23.39 E-value=51 Score=31.28 Aligned_cols=11 Identities=36% Similarity=0.495 Sum_probs=9.7
Q ss_pred HHHHHHHHHHH
Q 009542 299 IGVHELGHILA 309 (532)
Q Consensus 299 L~iHElGH~la 309 (532)
++.|||+|.++
T Consensus 138 VvaHEltHGVt 148 (150)
T PF01447_consen 138 VVAHELTHGVT 148 (150)
T ss_dssp HHHHHHHHHHH
T ss_pred eeeeccccccc
Confidence 68999999986
No 66
>PRK05457 heat shock protein HtpX; Provisional
Probab=23.16 E-value=51 Score=34.19 Aligned_cols=10 Identities=40% Similarity=0.723 Sum_probs=8.8
Q ss_pred HHHHHHHHHH
Q 009542 298 VIGVHELGHI 307 (532)
Q Consensus 298 iL~iHElGH~ 307 (532)
.++.||+||.
T Consensus 136 aVlAHElgHi 145 (284)
T PRK05457 136 AVLAHEISHI 145 (284)
T ss_pred HHHHHHHHHH
Confidence 6789999996
No 67
>KOG3320 consensus 40S ribosomal protein S7 [Translation, ribosomal structure and biogenesis]
Probab=23.03 E-value=1.1e+02 Score=30.32 Aligned_cols=27 Identities=15% Similarity=0.321 Sum_probs=20.9
Q ss_pred HHHHHHHHHHHHhhhCCceEEEEeecC
Q 009542 198 AKTYEKISTRMKNKFGDQYKLFLLVNP 224 (532)
Q Consensus 198 e~~y~~l~~~l~~~fGd~y~lfl~~~~ 224 (532)
.+.|.+|...||.+|+|+|.+|+.+..
T Consensus 74 qki~~~LvreleKKF~gk~Vifia~Rr 100 (192)
T KOG3320|consen 74 QKIQVRLVRELEKKFSGKHVIFIAQRR 100 (192)
T ss_pred HHHHHHHHHHHHHhcCCceEEEEEeee
Confidence 455556666999999999999876654
No 68
>KOG2719 consensus Metalloprotease [General function prediction only]
Probab=22.13 E-value=50 Score=36.66 Aligned_cols=14 Identities=36% Similarity=0.513 Sum_probs=11.1
Q ss_pred HHHHHHHHHHHHHH
Q 009542 297 LVIGVHELGHILAA 310 (532)
Q Consensus 297 ~iL~iHElGH~laA 310 (532)
.++++||+||+---
T Consensus 281 ~AVl~HELGHW~~~ 294 (428)
T KOG2719|consen 281 VAVLAHELGHWKLN 294 (428)
T ss_pred HHHHHHHhhHHHHh
Confidence 47899999998543
No 69
>PF10692 DUF2498: Protein of unknown function (DUF2498); InterPro: IPR019633 This entry represents proteins found in gammaproteobacteria, including YciN from Escherichia coli. Their function is not known. ; PDB: 3M92_A.
Probab=21.67 E-value=1.5e+02 Score=25.85 Aligned_cols=64 Identities=16% Similarity=0.309 Sum_probs=36.4
Q ss_pred cCCCChhHH-----HHhhccccccceeeeccccccCceEEEEeccC----Cch----HHHHHHHHHHHHhhhCCceEE
Q 009542 154 YIRIPKETI-----DILKDQVFGFDTFFVTNQEPYEGGVLFKGNLR----GQA----AKTYEKISTRMKNKFGDQYKL 218 (532)
Q Consensus 154 ~~~i~~edl-----~~ik~~~Fg~dtF~~t~~~~~~~gvi~rGnLR----~~~----e~~y~~l~~~l~~~fGd~y~l 218 (532)
.-+|++++| +.||+.===+..-.+|++|-.++..+|||+.= |-| ..||. +=+-|+-.+.++|.|
T Consensus 4 ~~~I~~~~LL~~AN~iI~~Hddyi~GM~a~~Veqk~~VLVFkGeyFLD~~GlPT~KtTAvFN-mFK~LAh~LS~~y~L 80 (82)
T PF10692_consen 4 KQPISRQALLEIANQIIREHDDYIHGMRATSVEQKGDVLVFKGEYFLDEQGLPTAKTTAVFN-MFKHLAHVLSEKYHL 80 (82)
T ss_dssp SEEE-HHHHHHHHHHHHHHHHHHHTT--EEEEEECTTEEEEEE-----TTS---HHHHHHHH-HHHHHHHHHCCCEEE
T ss_pred CcccCHHHHHHHHHHHHHhhHhhhccccccceeeECCEEEEecceeecCCCCCCcchHHHHH-HHHHHHHHcCcceEe
Confidence 346777777 34554222223367899999999999999932 222 33443 345567777888976
No 70
>cd04927 ACT_ACR-like_2 Second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=21.54 E-value=1.1e+02 Score=25.22 Aligned_cols=35 Identities=23% Similarity=0.314 Sum_probs=25.0
Q ss_pred cccceeeeccccccCceEEEEeccCCchHHHHHHHHHHHHhhhCCc
Q 009542 170 FGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFGDQ 215 (532)
Q Consensus 170 Fg~dtF~~t~~~~~~~gvi~rGnLR~~~e~~y~~l~~~l~~~fGd~ 215 (532)
.-+||||+++.. |+ ...++..++|++.|++.+|+-
T Consensus 40 ~v~D~F~V~d~~---------~~--~~~~~~~~~l~~~L~~~L~~~ 74 (76)
T cd04927 40 RVLDLFFITDAR---------EL--LHTKKRREETYDYLRAVLGDS 74 (76)
T ss_pred EEEEEEEEeCCC---------CC--CCCHHHHHHHHHHHHHHHchh
Confidence 467999997531 11 244567788999999999863
No 71
>PRK04860 hypothetical protein; Provisional
Probab=21.52 E-value=86 Score=30.21 Aligned_cols=21 Identities=29% Similarity=0.284 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHHHHHHcC
Q 009542 294 VTALVIGVHELGHILAAKSTG 314 (532)
Q Consensus 294 ~Ll~iL~iHElGH~laAr~~G 314 (532)
..+.-++.||++|+++=..+|
T Consensus 61 ~~l~~~v~HEl~H~~~~~~~g 81 (160)
T PRK04860 61 AFIDEVVPHELAHLLVYQLFG 81 (160)
T ss_pred HHHHhHHHHHHHHHHHHHHcC
Confidence 445567899999999999988
No 72
>PRK01265 heat shock protein HtpX; Provisional
Probab=21.40 E-value=58 Score=34.73 Aligned_cols=10 Identities=50% Similarity=0.979 Sum_probs=8.8
Q ss_pred HHHHHHHHHH
Q 009542 298 VIGVHELGHI 307 (532)
Q Consensus 298 iL~iHElGH~ 307 (532)
.++.||+||+
T Consensus 142 aVlAHElgHi 151 (324)
T PRK01265 142 AVAGHELGHL 151 (324)
T ss_pred HHHHHHHHHH
Confidence 5789999996
No 73
>PF04298 Zn_peptidase_2: Putative neutral zinc metallopeptidase; InterPro: IPR007395 Members of this family of bacterial proteins are described as hypothetical proteins or zinc-dependent proteases. The majority have a HExxH zinc-binding motif characteristic of neutral zinc metallopeptidases, however there is no evidence to support their function as metallopeptidases.
Probab=21.20 E-value=56 Score=33.27 Aligned_cols=12 Identities=33% Similarity=0.822 Sum_probs=10.3
Q ss_pred HHHHHHHHHHHH
Q 009542 298 VIGVHELGHILA 309 (532)
Q Consensus 298 iL~iHElGH~la 309 (532)
.+.+||.||++.
T Consensus 91 aVAAHEvGHAiQ 102 (222)
T PF04298_consen 91 AVAAHEVGHAIQ 102 (222)
T ss_pred HHHHHHHhHHHh
Confidence 578999999875
No 74
>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH. HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.
Probab=21.18 E-value=45 Score=36.89 Aligned_cols=18 Identities=28% Similarity=0.364 Sum_probs=15.4
Q ss_pred HHHHHHHHHHHHHHHcCC
Q 009542 298 VIGVHELGHILAAKSTGV 315 (532)
Q Consensus 298 iL~iHElGH~laAr~~Gv 315 (532)
.+..||.||++++..++.
T Consensus 313 ~~A~hEaGhAlv~~~l~~ 330 (495)
T TIGR01241 313 LVAYHEAGHALVGLLLKD 330 (495)
T ss_pred HHHHHHHhHHHHHHhcCC
Confidence 578999999999998753
No 75
>PF01421 Reprolysin: Reprolysin (M12B) family zinc metalloprotease This Prosite motif covers only the active site.; InterPro: IPR001590 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M12, subfamily M12B (adamalysin family, clan (MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA and the predicted active site residues for members of this family and thermolysin occur in the motif HEXXH []. The adamalysins are zinc dependent endopeptidases found in snake venom. There are some mammalian proteins such as P78325 from SWISSPROT, and fertilin Q28472 from SWISSPROT. Fertilin and closely related proteins appear to not have some active site residues and may not be active enzymes. CD156 (also called ADAM8 (3.4.24 from EC) or MS2 human) has been implicated in extravasation of leukocytes. CD molecules are leucocyte antigens on cell surfaces. CD antigens nomenclature is updated at Protein Reviews On The Web (http://prow.nci.nih.gov/). ; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 2E3X_A 2W15_A 2W14_A 2W13_A 2W12_A 1ND1_A 3K7L_A 2DW2_A 2DW0_B 2DW1_A ....
Probab=21.15 E-value=67 Score=30.80 Aligned_cols=21 Identities=43% Similarity=0.494 Sum_probs=14.1
Q ss_pred HHHHHHHHHHHHHHHHHHcCC
Q 009542 295 TALVIGVHELGHILAAKSTGV 315 (532)
Q Consensus 295 Ll~iL~iHElGH~laAr~~Gv 315 (532)
.++.+++||+||.+=+..-+.
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 445678999999887776666
No 76
>PRK02870 heat shock protein HtpX; Provisional
Probab=21.10 E-value=59 Score=34.81 Aligned_cols=11 Identities=45% Similarity=0.673 Sum_probs=9.4
Q ss_pred HHHHHHHHHHH
Q 009542 297 LVIGVHELGHI 307 (532)
Q Consensus 297 ~iL~iHElGH~ 307 (532)
..++.||+||.
T Consensus 174 ~aVlAHELgHi 184 (336)
T PRK02870 174 QAVMAHELSHI 184 (336)
T ss_pred HHHHHHHHHHH
Confidence 36789999998
No 77
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=21.10 E-value=1.4e+02 Score=28.96 Aligned_cols=31 Identities=26% Similarity=0.224 Sum_probs=21.9
Q ss_pred chHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHcC
Q 009542 281 NLNLLTNGLPGALVTALVIGVHELGHILAAKSTG 314 (532)
Q Consensus 281 ~~~~l~~glp~al~Ll~iL~iHElGH~laAr~~G 314 (532)
||.++.+ ....++.-++-||++|+.+=..+|
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 5655443 233455567899999999988877
No 78
>KOG0391 consensus SNF2 family DNA-dependent ATPase [General function prediction only]
Probab=21.04 E-value=1e+02 Score=38.70 Aligned_cols=21 Identities=33% Similarity=0.358 Sum_probs=15.1
Q ss_pred eeccccccCceEEEEeccCCc
Q 009542 176 FVTNQEPYEGGVLFKGNLRGQ 196 (532)
Q Consensus 176 ~~t~~~~~~~gvi~rGnLR~~ 196 (532)
-+|.+-..+---+.|||||.-
T Consensus 599 l~tTqVktpvPsLLrGqLReY 619 (1958)
T KOG0391|consen 599 LVTTQVKTPVPSLLRGQLREY 619 (1958)
T ss_pred eeeeeeccCchHHHHHHHHHH
Confidence 345555667777999999963
No 79
>PF08525 OapA_N: Opacity-associated protein A N-terminal motif; InterPro: IPR013731 This domain is found in the Haemophilus influenzae opacity-associated protein (OapA). It is required for efficient nasopharyngeal mucosal colonisation, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [, ]. This motif occurs at the N terminus of these proteins. It contains a conserved histidine followed by a run of hydrophobic residues. Many of the proteins in this entry are unassigned peptidases belonging to MEROPS peptidase family M23B.
Probab=20.58 E-value=1.2e+02 Score=21.48 Aligned_cols=21 Identities=24% Similarity=0.078 Sum_probs=15.5
Q ss_pred hhHHHHHHHHHHHHHHhhccc
Q 009542 500 DKYIALGVLVLFLGLLVCLPY 520 (532)
Q Consensus 500 ~~r~~lg~l~l~l~ll~llP~ 520 (532)
.-|++++.++.++.++++.|.
T Consensus 9 ~Hr~~l~~l~~v~l~ll~~Ps 29 (30)
T PF08525_consen 9 LHRRALIALSAVVLVLLLWPS 29 (30)
T ss_pred HHHHHHHHHHHHHHHHHhccC
Confidence 346777777777777888775
No 80
>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=20.09 E-value=4.2e+02 Score=22.67 Aligned_cols=51 Identities=18% Similarity=0.428 Sum_probs=33.1
Q ss_pred ccccceeeeccccccCceEEEEeccCCchHHHHHHHHHHHHhhhCCceEEEEeecC--------------CCCCcEEEEE
Q 009542 169 VFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFGDQYKLFLLVNP--------------EDDKPVAVVV 234 (532)
Q Consensus 169 ~Fg~dtF~~t~~~~~~~gvi~rGnLR~~~e~~y~~l~~~l~~~fGd~y~lfl~~~~--------------~~~kPv~~v~ 234 (532)
..|++++++. .+++++.+.+++-+++ +.|-+.++.+. +..+|+++.+
T Consensus 15 LaGv~~~~~~----------------~~~ee~~~~l~~l~~~---~~~gIIii~e~~~~~~~~~l~~~~~~~~~P~iv~I 75 (95)
T PF01990_consen 15 LAGVEGVYVN----------------TDPEEAEEALKELLKD---EDVGIIIITEDLAEKIRDELDEYREESSLPLIVEI 75 (95)
T ss_dssp HTTSEEEEES----------------HSHHHHHHHHHHHHHH---TTEEEEEEEHHHHTTHHHHHHHHHHTSSSSEEEEE
T ss_pred HcCCCCccCC----------------CCHHHHHHHHHHHhcC---CCccEEEeeHHHHHHHHHHHHHHHhccCCceEEEc
Confidence 5677777775 4566666666665533 24666555544 2467999999
Q ss_pred cCCC
Q 009542 235 PRKT 238 (532)
Q Consensus 235 P~~~ 238 (532)
|...
T Consensus 76 P~~~ 79 (95)
T PF01990_consen 76 PSKE 79 (95)
T ss_dssp STTC
T ss_pred CCCC
Confidence 9975
Done!