Query 008143
Match_columns 576
No_of_seqs 262 out of 602
Neff 4.3
Searched_HMMs 46136
Date Thu Mar 28 20:01:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008143.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008143hhsearch_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 7.9E-32 1.7E-36 259.3 19.9 178 275-520 2-181 (183)
2 cd06164 S2P-M50_SpoIVFB_CBS Sp 99.9 3.1E-22 6.8E-27 198.3 19.2 129 322-491 42-170 (227)
3 cd06161 S2P-M50_SpoIVFB SpoIVF 99.9 1.5E-20 3.3E-25 183.5 18.0 126 323-491 28-153 (208)
4 cd05709 S2P-M50 Site-2 proteas 99.8 5E-19 1.1E-23 167.2 13.6 132 327-491 2-155 (180)
5 cd06163 S2P-M50_PDZ_RseP-like 99.8 1.8E-17 3.8E-22 160.0 15.4 106 328-488 4-145 (182)
6 PF02163 Peptidase_M50: Peptid 99.7 1.1E-16 2.3E-21 152.1 12.5 127 328-487 2-157 (192)
7 cd06159 S2P-M50_PDZ_Arch Uncha 99.7 6.1E-16 1.3E-20 157.1 15.9 117 324-490 109-228 (263)
8 cd06162 S2P-M50_PDZ_SREBP Ster 99.6 2E-14 4.3E-19 147.0 17.3 117 328-491 130-249 (277)
9 cd06158 S2P-M50_like_1 Unchara 99.5 2.8E-13 6.1E-18 130.4 13.0 132 329-492 5-157 (181)
10 COG0750 Predicted membrane-ass 99.2 2.4E-12 5.2E-17 133.5 1.2 149 332-491 181-338 (375)
11 TIGR00054 RIP metalloprotease 99.1 1.2E-09 2.5E-14 117.4 17.5 73 327-405 8-117 (420)
12 COG1994 SpoIVFB Zn-dependent p 99.1 1.3E-09 2.8E-14 108.4 13.2 135 323-492 42-176 (230)
13 PRK10779 zinc metallopeptidase 98.5 2.1E-07 4.6E-12 100.8 8.4 80 325-405 7-117 (449)
14 PF13398 Peptidase_M50B: Pepti 96.7 0.0032 6.8E-08 62.0 6.1 66 334-406 23-88 (200)
15 PRK10779 zinc metallopeptidase 96.6 0.0042 9.2E-08 67.8 6.9 34 454-487 377-410 (449)
16 COG0750 Predicted membrane-ass 94.5 0.14 3.1E-06 53.6 8.6 79 326-407 6-120 (375)
17 KOG2921 Intramembrane metallop 93.8 0.079 1.7E-06 57.8 4.9 147 324-483 121-281 (484)
18 PF05572 Peptidase_M43: Pregna 57.3 4.9 0.00011 38.4 1.0 15 334-348 70-84 (154)
19 PF00413 Peptidase_M10: Matrix 50.5 8.9 0.00019 35.0 1.5 23 335-357 107-129 (154)
20 PRK12821 aspartyl/glutamyl-tRN 48.9 80 0.0017 35.8 8.7 87 389-484 108-209 (477)
21 PF06114 DUF955: Domain of unk 46.9 11 0.00023 32.1 1.4 17 335-351 44-60 (122)
22 PRK12462 phosphoserine aminotr 46.2 36 0.00079 37.1 5.5 65 162-237 10-76 (364)
23 PF01435 Peptidase_M48: Peptid 45.7 13 0.00028 35.8 1.9 19 334-354 90-108 (226)
24 cd04279 ZnMc_MMP_like_1 Zinc-d 42.2 16 0.00035 34.1 1.9 25 334-358 105-130 (156)
25 PF13688 Reprolysin_5: Metallo 41.9 13 0.00028 35.6 1.2 21 332-352 141-161 (196)
26 PF13485 Peptidase_MA_2: Pepti 41.3 19 0.00041 30.8 2.1 17 335-351 27-43 (128)
27 cd04268 ZnMc_MMP_like Zinc-dep 39.6 25 0.00055 32.4 2.8 22 331-352 92-113 (165)
28 PF11667 DUF3267: Protein of u 39.0 32 0.0007 30.6 3.2 69 333-408 4-72 (111)
29 PLN02452 phosphoserine transam 38.0 60 0.0013 35.1 5.6 65 162-237 13-79 (365)
30 PF13574 Reprolysin_2: Metallo 37.6 17 0.00038 35.0 1.4 19 334-352 112-130 (173)
31 COG2856 Predicted Zn peptidase 36.5 17 0.00037 36.9 1.2 16 336-351 75-90 (213)
32 PF14181 YqfQ: YqfQ-like prote 35.9 40 0.00087 33.1 3.5 22 96-117 115-136 (161)
33 cd00203 ZnMc Zinc-dependent me 34.9 19 0.00041 33.2 1.1 20 333-352 96-115 (167)
34 cd04269 ZnMc_adamalysin_II_lik 34.6 25 0.00054 33.8 1.9 20 333-352 131-150 (194)
35 cd04278 ZnMc_MMP Zinc-dependen 33.4 18 0.00039 33.8 0.7 21 334-354 108-128 (157)
36 cd04270 ZnMc_TACE_like Zinc-de 33.0 25 0.00055 35.8 1.8 21 331-351 165-185 (244)
37 cd04277 ZnMc_serralysin_like Z 32.1 24 0.00052 33.9 1.3 18 334-351 114-131 (186)
38 PF13582 Reprolysin_3: Metallo 31.3 22 0.00047 31.5 0.8 14 335-348 109-122 (124)
39 smart00235 ZnMc Zinc-dependent 31.1 24 0.00053 32.0 1.2 19 336-354 89-107 (140)
40 cd04267 ZnMc_ADAM_like Zinc-de 30.6 19 0.00041 34.5 0.4 20 333-352 133-152 (192)
41 PF13699 DUF4157: Domain of un 28.5 33 0.00072 29.5 1.5 14 335-348 63-76 (79)
42 PRK03001 M48 family peptidase; 27.9 35 0.00076 35.4 1.8 12 334-345 125-136 (283)
43 COG3824 Predicted Zn-dependent 27.4 27 0.00059 33.1 0.8 16 331-346 107-122 (136)
44 PF02031 Peptidase_M7: Strepto 27.3 35 0.00076 32.6 1.5 12 336-347 80-91 (132)
45 PF13583 Reprolysin_4: Metallo 26.8 27 0.00059 34.7 0.7 16 337-352 141-156 (206)
46 PF14891 Peptidase_M91: Effect 25.8 42 0.00092 32.4 1.8 16 334-349 104-119 (174)
47 PRK03982 heat shock protein Ht 25.7 41 0.00088 35.0 1.8 12 334-345 126-137 (288)
48 PF12315 DUF3633: Protein of u 24.7 47 0.001 34.0 2.0 27 322-351 84-110 (212)
49 PF01421 Reprolysin: Reprolysi 24.0 51 0.0011 31.9 2.0 21 332-352 130-150 (199)
50 PRK04897 heat shock protein Ht 23.9 46 0.00099 35.0 1.8 12 334-345 138-149 (298)
51 PRK02870 heat shock protein Ht 23.8 40 0.00087 36.4 1.4 18 334-354 174-191 (336)
52 PF14247 DUF4344: Domain of un 23.5 72 0.0016 32.7 3.0 21 329-349 88-108 (220)
53 cd04327 ZnMc_MMP_like_3 Zinc-d 23.4 43 0.00092 32.8 1.4 17 336-352 95-111 (198)
54 cd04275 ZnMc_pappalysin_like Z 22.4 16 0.00036 37.1 -1.8 16 334-349 138-153 (225)
55 PHA02456 zinc metallopeptidase 22.3 51 0.0011 31.0 1.6 18 337-354 83-100 (141)
56 PRK10733 hflB ATP-dependent me 21.8 1E+02 0.0022 35.9 4.2 29 334-362 409-439 (644)
57 cd04272 ZnMc_salivary_gland_MP 21.8 48 0.001 32.8 1.4 20 334-353 146-165 (220)
58 PF01434 Peptidase_M41: Peptid 21.4 85 0.0018 31.2 3.1 50 334-386 29-84 (213)
59 COG0830 UreF Urease accessory 21.4 1.1E+02 0.0023 31.7 3.8 32 458-489 158-189 (229)
60 PRK01345 heat shock protein Ht 20.9 57 0.0012 34.7 1.8 12 334-345 125-136 (317)
61 COG0501 HtpX Zn-dependent prot 20.6 60 0.0013 32.9 1.8 17 335-353 159-175 (302)
62 PRK02391 heat shock protein Ht 20.6 59 0.0013 34.3 1.8 11 334-344 134-144 (296)
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=100.00 E-value=7.9e-32 Score=259.28 Aligned_cols=178 Identities=40% Similarity=0.715 Sum_probs=148.9
Q ss_pred HHHHHHHHHHHHHHHHhhhcCCCccccccccCCCCCCCCcccchhHHHHhhHHHHHHHHHHHhhhHHHHHHHHhhCCccc
Q 008143 275 LLFLLTIGSSVELGIASQINRLPPEIVKYFTDPNAIDPPNVELLYPFVESALPLAYGVLGVLLFHDVGHFLAAFPKKVKL 354 (576)
Q Consensus 275 ~LfllTl~TTl~aGa~~~~~~l~~e~~~~~~~p~~~~p~~~~~l~~~l~~glPfal~ll~IL~vHElGHylaArr~gVk~ 354 (576)
+++++|++|..++|+..+.++++ + ++ ..+..+++++++++.++.+||+||+++||++|+|+
T Consensus 2 ~~~~~s~~~~~~~~~~~~~~~~~----------~-----~~----~~~~~~~~~~l~l~~~l~iHElgH~~~A~~~G~~~ 62 (183)
T cd06160 2 LLLVLTLLTTLLVGAWLSGNDVP----------G-----NP----LLLLQGLPFALALLAILGIHEMGHYLAARRHGVKA 62 (183)
T ss_pred HHHHHHHHHHHHHHHHHhccccc----------c-----cH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCc
Confidence 57899999999999876544332 1 11 22568999999999999999999999999999999
Q ss_pred ccceeecccccccceeEeeCCCCCCChhhhhhheehhhHHHHHHHHHHHHHHHhhcCCCCCCCCcccCCccccchhhHHH
Q 008143 355 SIPFFIPNITLGSFGAITQFKSILPDRSTKVDISLAGPIAGAALSFSMFVVGLLLSSNPDAAGDLVQVPSTLFQGSLLLG 434 (576)
Q Consensus 355 slPyFIP~~~lGTfGAvir~ks~~p~RkaLFDIaiAGPLAG~vval~llivGl~ls~~~~~~~~l~~~p~~~f~~s~Llg 434 (576)
+.|+++|++.+|++|+++++++..++|+++++|++|||++|+++++++++++
T Consensus 63 ~~~~l~P~~~~G~~G~~~~~~~~~~~~~~~~~IalAGPl~nl~lali~~~~~---------------------------- 114 (183)
T cd06160 63 SLPYFIPFPFIGTFGAFIRMRSPIPNRKALFDIALAGPLAGLLLALPVLIIG---------------------------- 114 (183)
T ss_pred cceeeeehHhcCcEEEEEEecCCCCChhHhehhhhhHHHHHHHHHHHHHHHH----------------------------
Confidence 9999999988999999999999999999999999999999999998775542
Q ss_pred HHHHHhhccccccccccchhHHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHhhhhHHHHHHHHHHHHHHHHHhhhh--h
Q 008143 435 LISRATLGYTAMHASTVTIHPLVIAGWCGLTTTAFNMLPVGCLDGGRAVQGAFGRNALIGFGLTTYTMLGLGVLGGP--L 512 (576)
Q Consensus 435 ~la~l~LG~~~~~~~~v~lhPla~aGWlGL~vTaLNLLPvGqLDGGrIl~Al~Grr~~~~~g~~t~lll~Lg~l~~~--l 512 (576)
+..++|+|++++++||+|++|||||||+|+++++|.+..+++.+...+++..+.++ .
T Consensus 115 ---------------------~~~~~~~nl~l~~fNLLPi~PLDGGril~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~ 173 (183)
T cd06160 115 ---------------------LAVAGWVGLLVTALNLLPVGQLDGGHIVRALFGRRVAALIGIGLLVALGLLALYLSFSI 173 (183)
T ss_pred ---------------------HHHHHHHHHHHHHHHhCCCCCcChHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHhhHHH
Confidence 12468999999999999999999999999999999888888877655555544444 5
Q ss_pred HHHHHHHH
Q 008143 513 SLPWGLYV 520 (576)
Q Consensus 513 ~l~W~l~v 520 (576)
|++|..++
T Consensus 174 ~l~~~~~~ 181 (183)
T cd06160 174 WLLWALLL 181 (183)
T ss_pred HHHHHHHH
Confidence 56665543
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=99.89 E-value=3.1e-22 Score=198.29 Aligned_cols=129 Identities=22% Similarity=0.305 Sum_probs=107.5
Q ss_pred HHhhHHHHHHHHHHHhhhHHHHHHHHhhCCcccccceeecccccccceeEeeCCCCCCChhhhhhheehhhHHHHHHHHH
Q 008143 322 VESALPLAYGVLGVLLFHDVGHFLAAFPKKVKLSIPFFIPNITLGSFGAITQFKSILPDRSTKVDISLAGPIAGAALSFS 401 (576)
Q Consensus 322 l~~glPfal~ll~IL~vHElGHylaArr~gVk~slPyFIP~~~lGTfGAvir~ks~~p~RkaLFDIaiAGPLAG~vval~ 401 (576)
+..|+.++++++.++++||+||+++||++|+|+....+.|+ |+++++++.++++++++.|++|||+++++++++
T Consensus 42 ~~~g~~~~~~l~~~v~iHElgH~~~A~~~G~~v~~i~l~p~------Gg~~~~~~~~~~~~~~~~IalAGPl~Nllla~i 115 (227)
T cd06164 42 WLLGLAAALLLFASVLLHELGHSLVARRYGIPVRSITLFLF------GGVARLEREPETPGQEFVIAIAGPLVSLVLALL 115 (227)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCeECeEEEEee------eEEEEecCCCCCHHHHhhhhhhHHHHHHHHHHH
Confidence 45789999999999999999999999999999998888775 999999999999999999999999999999988
Q ss_pred HHHHHHhhcCCCCCCCCcccCCccccchhhHHHHHHHHhhccccccccccchhHHHHHHHHHHHHHHHhhcCCCCCChHH
Q 008143 402 MFVVGLLLSSNPDAAGDLVQVPSTLFQGSLLLGLISRATLGYTAMHASTVTIHPLVIAGWCGLTTTAFNMLPVGCLDGGR 481 (576)
Q Consensus 402 llivGl~ls~~~~~~~~l~~~p~~~f~~s~Llg~la~l~LG~~~~~~~~v~lhPla~aGWlGL~vTaLNLLPvGqLDGGr 481 (576)
++++....... + .+.+ ..-+.+.+|+|++++++||+|+.||||||
T Consensus 116 ~~~l~~~~~~~----------~-----~~~~--------------------~~~~~~~~~~Nl~l~~fNLlP~~PLDGgr 160 (227)
T cd06164 116 FLLLSLALPGS----------G-----AGPL--------------------GVLLGYLALINLLLAVFNLLPAFPLDGGR 160 (227)
T ss_pred HHHHHHHhccc----------c-----chHH--------------------HHHHHHHHHHHHHHHHHhCcCCCCCChHH
Confidence 87665433210 0 0110 01234678999999999999999999999
Q ss_pred HHHHHhhhhH
Q 008143 482 AVQGAFGRNA 491 (576)
Q Consensus 482 Il~Al~Grr~ 491 (576)
|+++++.++.
T Consensus 161 il~~ll~~~~ 170 (227)
T cd06164 161 VLRALLWRRT 170 (227)
T ss_pred HHHHHHHHhc
Confidence 9999997654
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=99.86 E-value=1.5e-20 Score=183.47 Aligned_cols=126 Identities=25% Similarity=0.330 Sum_probs=105.2
Q ss_pred HhhHHHHHHHHHHHhhhHHHHHHHHhhCCcccccceeecccccccceeEeeCCCCCCChhhhhhheehhhHHHHHHHHHH
Q 008143 323 ESALPLAYGVLGVLLFHDVGHFLAAFPKKVKLSIPFFIPNITLGSFGAITQFKSILPDRSTKVDISLAGPIAGAALSFSM 402 (576)
Q Consensus 323 ~~glPfal~ll~IL~vHElGHylaArr~gVk~slPyFIP~~~lGTfGAvir~ks~~p~RkaLFDIaiAGPLAG~vval~l 402 (576)
..++.+++.++.++++||+||+++||++|+++....+.|+ |+++++++...+|++.+.|++|||++++++++.+
T Consensus 28 ~~~~~~~l~l~~~v~iHElgH~~~A~~~G~~v~~i~l~p~------Gg~~~~~~~~~~~~~~~lIalAGPl~n~~la~~~ 101 (208)
T cd06161 28 LLGLLEALLLFLSVLLHELGHALVARRYGIRVRSITLLPF------GGVAELEEEPETPKEEFVIALAGPLVSLLLAGLF 101 (208)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccceEEEee------eeeeeeccCCCChhHheeeeeehHHHHHHHHHHH
Confidence 4678899999999999999999999999999988877775 9999999888899999999999999999999887
Q ss_pred HHHHHhhcCCCCCCCCcccCCccccchhhHHHHHHHHhhccccccccccchhHHHHHHHHHHHHHHHhhcCCCCCChHHH
Q 008143 403 FVVGLLLSSNPDAAGDLVQVPSTLFQGSLLLGLISRATLGYTAMHASTVTIHPLVIAGWCGLTTTAFNMLPVGCLDGGRA 482 (576)
Q Consensus 403 livGl~ls~~~~~~~~l~~~p~~~f~~s~Llg~la~l~LG~~~~~~~~v~lhPla~aGWlGL~vTaLNLLPvGqLDGGrI 482 (576)
.++....+.. + .....+...+|+|++++++||+|+.|||||||
T Consensus 102 ~~l~~~~~~~-----------------~--------------------~~~~~~~~~~~~N~~l~lfNLlPi~pLDGg~i 144 (208)
T cd06161 102 YLLYLLLPGG-----------------G--------------------PLSSLLEFLAQVNLILGLFNLLPALPLDGGRV 144 (208)
T ss_pred HHHHHHcccc-----------------h--------------------HHHHHHHHHHHHHHHHHHHHccCCCCCChHHH
Confidence 6654322110 0 01123456789999999999999999999999
Q ss_pred HHHHhhhhH
Q 008143 483 VQGAFGRNA 491 (576)
Q Consensus 483 l~Al~Grr~ 491 (576)
+++++.++.
T Consensus 145 l~~ll~~~~ 153 (208)
T cd06161 145 LRALLWRRT 153 (208)
T ss_pred HHHHHHHhc
Confidence 999998763
No 4
>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=99.80 E-value=5e-19 Score=167.16 Aligned_cols=132 Identities=28% Similarity=0.372 Sum_probs=100.7
Q ss_pred HHHHHHHHHHhhhHHHHHHHHhhCCccc-----------------ccceeecccccccceeEeeCCCCCCC-----hhhh
Q 008143 327 PLAYGVLGVLLFHDVGHFLAAFPKKVKL-----------------SIPFFIPNITLGSFGAITQFKSILPD-----RSTK 384 (576)
Q Consensus 327 Pfal~ll~IL~vHElGHylaArr~gVk~-----------------slPyFIP~~~lGTfGAvir~ks~~p~-----RkaL 384 (576)
.+.++++.++.+||+||+++||++|+++ ...+++|+ |+++++.+..++ |++.
T Consensus 2 ~~~~~~~i~i~iHE~gH~~~A~~~G~~~~~~~~~~~~~~~~~~~~~~~~~ip~------gG~~~~~~~~~~~~~~~~~~~ 75 (180)
T cd05709 2 AFILALLISVTVHELGHALVARRLGVKVARFSGGFTLNPLKHGDPYGIILIPL------GGYAKPVGENPRAFKKPRWQR 75 (180)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHcCCCchheeeeEEECCcCCCCEehHHHHhc------cCeeccCCCChhhhccchhhh
Confidence 3567788899999999999999999954 45556665 889888887664 8999
Q ss_pred hhheehhhHHHHHHHHHHHHHHHhhcCCCCCCCCcccCCccccchhhHHHHHHHHhhccccccccccchhHHHHHHHHHH
Q 008143 385 VDISLAGPIAGAALSFSMFVVGLLLSSNPDAAGDLVQVPSTLFQGSLLLGLISRATLGYTAMHASTVTIHPLVIAGWCGL 464 (576)
Q Consensus 385 FDIaiAGPLAG~vval~llivGl~ls~~~~~~~~l~~~p~~~f~~s~Llg~la~l~LG~~~~~~~~v~lhPla~aGWlGL 464 (576)
+.|++|||+++++++++++++............ .. .......+.+.+.+|+++
T Consensus 76 ~~i~laGPl~nllla~i~~~~~~~~~~~~~~~~----------~~-----------------~~~~~~~~~l~~~~~~n~ 128 (180)
T cd05709 76 LLVALAGPLANLLLALLLLLLLLLLGGLPPAPV----------GQ-----------------AASSGLANLLAFLALINL 128 (180)
T ss_pred hhhhhhhHHHHHHHHHHHHHHHHHHccCCccch----------hh-----------------hHHHHHHHHHHHHHHHHH
Confidence 999999999999999988766544432110000 00 001122345678899999
Q ss_pred HHHHHhhcCCCCCChHHHHHHHhhhhH
Q 008143 465 TTTAFNMLPVGCLDGGRAVQGAFGRNA 491 (576)
Q Consensus 465 ~vTaLNLLPvGqLDGGrIl~Al~Grr~ 491 (576)
.+.++||+|+.||||||++++++.++.
T Consensus 129 ~l~~fNLlPi~plDGg~il~~~l~~~~ 155 (180)
T cd05709 129 NLAVFNLLPIPPLDGGRILRALLEAIR 155 (180)
T ss_pred HHHHHHhCCCCCCChHHHHHHHHhHHH
Confidence 999999999999999999999998764
No 5
>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=99.75 E-value=1.8e-17 Score=159.98 Aligned_cols=106 Identities=26% Similarity=0.369 Sum_probs=86.3
Q ss_pred HHHHHHHHHhhhHHHHHHHHhhCCccccc--------------------ceeecccccccceeEeeCCCCCC--------
Q 008143 328 LAYGVLGVLLFHDVGHFLAAFPKKVKLSI--------------------PFFIPNITLGSFGAITQFKSILP-------- 379 (576)
Q Consensus 328 fal~ll~IL~vHElGHylaArr~gVk~sl--------------------PyFIP~~~lGTfGAvir~ks~~p-------- 379 (576)
+.+++..++.+||+||+++||++|+|+.- --.+| +|++.++++..+
T Consensus 4 ~~i~l~~~v~iHElGH~~~Ar~~Gv~v~~f~iGfGp~l~~~~~~~t~~~i~~iP------lGGyv~~~~~~~~~~~~~~~ 77 (182)
T cd06163 4 FILVLGILIFVHELGHFLVAKLFGVKVEEFSIGFGPKLFSFKKGETEYSISAIP------LGGYVKMLGEDPEEEADPED 77 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCeeeEeeeecCceeeeeecCCeEEEEEEEE------eccEEEecCCCccccccccc
Confidence 56677888999999999999999999874 12345 499999875432
Q ss_pred --------ChhhhhhheehhhHHHHHHHHHHHHHHHhhcCCCCCCCCcccCCccccchhhHHHHHHHHhhcccccccccc
Q 008143 380 --------DRSTKVDISLAGPIAGAALSFSMFVVGLLLSSNPDAAGDLVQVPSTLFQGSLLLGLISRATLGYTAMHASTV 451 (576)
Q Consensus 380 --------~RkaLFDIaiAGPLAG~vval~llivGl~ls~~~~~~~~l~~~p~~~f~~s~Llg~la~l~LG~~~~~~~~v 451 (576)
++++.+-|++|||+++++++++++++-
T Consensus 78 ~~~~f~~~~~~~ri~V~lAGP~~NlilA~i~~~~~--------------------------------------------- 112 (182)
T cd06163 78 DPRSFNSKPVWQRILIVFAGPLANFLLAIVLFAVL--------------------------------------------- 112 (182)
T ss_pred chHHHccCCcchhhhhhhhHHHHHHHHHHHHHHHH---------------------------------------------
Confidence 467788899999999999998664320
Q ss_pred chhHHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHhh
Q 008143 452 TIHPLVIAGWCGLTTTAFNMLPVGCLDGGRAVQGAFG 488 (576)
Q Consensus 452 ~lhPla~aGWlGL~vTaLNLLPvGqLDGGrIl~Al~G 488 (576)
+.+..++|+.+..+||+|+.||||||++++++.
T Consensus 113 ----~~~~~~~n~~l~~fNLlPippLDGg~il~~~~~ 145 (182)
T cd06163 113 ----LSFLALLSINLGILNLLPIPALDGGHLLFLLIE 145 (182)
T ss_pred ----HHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHHH
Confidence 235678999999999999999999999999995
No 6
>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=99.70 E-value=1.1e-16 Score=152.08 Aligned_cols=127 Identities=29% Similarity=0.326 Sum_probs=80.3
Q ss_pred HHHHHHHHHhhhHHHHHHHHhhCCcccccceeec--ccc---------------c-------cc-----ceeEeeCCCCC
Q 008143 328 LAYGVLGVLLFHDVGHFLAAFPKKVKLSIPFFIP--NIT---------------L-------GS-----FGAITQFKSIL 378 (576)
Q Consensus 328 fal~ll~IL~vHElGHylaArr~gVk~slPyFIP--~~~---------------l-------GT-----fGAvir~ks~~ 378 (576)
+.++++.++.+||+||+++||++|+|+.....-+ .+. + |. .++....+...
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 4567888999999999999999999998763221 110 1 11 34455555667
Q ss_pred CChhhhhhheehhhHHHHHHHHHHHHHHHhhcCCCCCCCCcccCCccccchhhHHHHHHHHhhccccccccccchhHHHH
Q 008143 379 PDRSTKVDISLAGPIAGAALSFSMFVVGLLLSSNPDAAGDLVQVPSTLFQGSLLLGLISRATLGYTAMHASTVTIHPLVI 458 (576)
Q Consensus 379 p~RkaLFDIaiAGPLAG~vval~llivGl~ls~~~~~~~~l~~~p~~~f~~s~Llg~la~l~LG~~~~~~~~v~lhPla~ 458 (576)
.+|++.+.|++|||+++++++++.+.+........ .......+.+.+
T Consensus 82 ~~~~~~~~i~laGp~~nllla~i~~~l~~~~~~~~---------------------------------~~~~~~~~~~~~ 128 (192)
T PF02163_consen 82 RSRWKRILIALAGPLANLLLAIIALLLLYLLSGSV---------------------------------GWSSFFAEFLFF 128 (192)
T ss_dssp --TTCHHHHHHHHHHHHHHHHHHHHHHTTS----------------------------------------EETTEEHHHH
T ss_pred CCccceEEEEEEcHHHHHHHHHHHHHHHHHHhccc---------------------------------cccHHHHHHHHH
Confidence 78899999999999999999988765532221100 011223356778
Q ss_pred HHHHHHHHHHHhhcCCCCCChHHHHHHHh
Q 008143 459 AGWCGLTTTAFNMLPVGCLDGGRAVQGAF 487 (576)
Q Consensus 459 aGWlGL~vTaLNLLPvGqLDGGrIl~Al~ 487 (576)
++|+++.+.++||+|+.+|||||++++++
T Consensus 129 ~~~~n~~l~~~NllPi~~lDG~~il~~l~ 157 (192)
T PF02163_consen 129 FAWLNFILALFNLLPIPPLDGGRILRALL 157 (192)
T ss_dssp HHHHHHHHHHHTTSSSSSSHHHHHHHHHH
T ss_pred HHHHHHHHhhhhcccCCcCCHHHHHHHHH
Confidence 99999999999999999999999999998
No 7
>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=99.68 E-value=6.1e-16 Score=157.06 Aligned_cols=117 Identities=20% Similarity=0.194 Sum_probs=92.5
Q ss_pred hhHHHHHHHHHHHhhhHHHHHHHHhhCCcccccceeecccccccceeEeeCCCCC---CChhhhhhheehhhHHHHHHHH
Q 008143 324 SALPLAYGVLGVLLFHDVGHFLAAFPKKVKLSIPFFIPNITLGSFGAITQFKSIL---PDRSTKVDISLAGPIAGAALSF 400 (576)
Q Consensus 324 ~glPfal~ll~IL~vHElGHylaArr~gVk~slPyFIP~~~lGTfGAvir~ks~~---p~RkaLFDIaiAGPLAG~vval 400 (576)
..+.+.++++.++.+||+||+++||++|+++...-+.= .+-.+||+++..+.. .+|++.+-|+.|||++++++++
T Consensus 109 ~~~~~~iaL~isv~iHElgHa~~Ar~~G~~V~~iGl~l--~~ip~Gg~v~~~~~~~~~~~~~~~~~Ia~AGP~~Nlvla~ 186 (263)
T cd06159 109 PLPYGIIALVVGVVVHELSHGILARVEGIKVKSGGLLL--LIIPPGAFVEPDEEELNKADRRIRLRIFAAGVTANFVVAL 186 (263)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcCCEECchhHHH--HhhhcEEEEEecchhhccCChhheeeeeeehHHHHHHHHH
Confidence 55667788999999999999999999999988632210 011258998887654 5688899999999999999998
Q ss_pred HHHHHHHhhcCCCCCCCCcccCCccccchhhHHHHHHHHhhccccccccccchhHHHHHHHHHHHHHHHhhcCCCCCChH
Q 008143 401 SMFVVGLLLSSNPDAAGDLVQVPSTLFQGSLLLGLISRATLGYTAMHASTVTIHPLVIAGWCGLTTTAFNMLPVGCLDGG 480 (576)
Q Consensus 401 ~llivGl~ls~~~~~~~~l~~~p~~~f~~s~Llg~la~l~LG~~~~~~~~v~lhPla~aGWlGL~vTaLNLLPvGqLDGG 480 (576)
+++++-. +....|+|+.+.++||+|+.|||||
T Consensus 187 i~~~l~~------------------------------------------------l~~~~~~N~~l~lFNLlP~~PLDGg 218 (263)
T cd06159 187 IAFALFF------------------------------------------------LYWIFWINFLLGLFNCLPAIPLDGG 218 (263)
T ss_pred HHHHHHH------------------------------------------------HHHHHHHHHHHHHHhCCCCCCCChH
Confidence 7654310 2245789999999999999999999
Q ss_pred HHHHHHhhhh
Q 008143 481 RAVQGAFGRN 490 (576)
Q Consensus 481 rIl~Al~Grr 490 (576)
|++++++..+
T Consensus 219 ~il~~ll~~~ 228 (263)
T cd06159 219 HVFRDLLEAL 228 (263)
T ss_pred HHHHHHHHHH
Confidence 9999999643
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=99.61 E-value=2e-14 Score=147.05 Aligned_cols=117 Identities=18% Similarity=0.121 Sum_probs=89.9
Q ss_pred HHHHHHHHHhhhHHHHHHHHhhCCcccccceeecccccccceeEeeCCCC---CCChhhhhhheehhhHHHHHHHHHHHH
Q 008143 328 LAYGVLGVLLFHDVGHFLAAFPKKVKLSIPFFIPNITLGSFGAITQFKSI---LPDRSTKVDISLAGPIAGAALSFSMFV 404 (576)
Q Consensus 328 fal~ll~IL~vHElGHylaArr~gVk~slPyFIP~~~lGTfGAvir~ks~---~p~RkaLFDIaiAGPLAG~vval~lli 404 (576)
+.++++.++.+||+||.++||++|+++..--+.++..++ ||+++..+. ..++++.+-|+.|||+++++++++.++
T Consensus 130 ~l~al~isvvvHElgHal~A~~~gi~V~~iGl~l~~~~p--Ga~ve~~~e~~~~~~~~~~l~Ia~AGp~~NlvLa~i~~~ 207 (277)
T cd06162 130 YFTALLISGVVHEMGHGVAAVREQVRVNGFGIFFFIIYP--GAYVDLFTDHLNLISPVQQLRIFCAGVWHNFVLGLVGYL 207 (277)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCeeceEEEeeeeccC--eeEEeecccccccCChhhhhheehhhHHHHHHHHHHHHH
Confidence 456788999999999999999999999875555543233 899887432 345667889999999999999987654
Q ss_pred HHHhhcCCCCCCCCcccCCccccchhhHHHHHHHHhhccccccccccchhHHHHHHHHHHHHHHHhhcCCCCCChHHHHH
Q 008143 405 VGLLLSSNPDAAGDLVQVPSTLFQGSLLLGLISRATLGYTAMHASTVTIHPLVIAGWCGLTTTAFNMLPVGCLDGGRAVQ 484 (576)
Q Consensus 405 vGl~ls~~~~~~~~l~~~p~~~f~~s~Llg~la~l~LG~~~~~~~~v~lhPla~aGWlGL~vTaLNLLPvGqLDGGrIl~ 484 (576)
.- . ++ + +....++++.+.++||+|+-|||||||++
T Consensus 208 l~--~-------------------~~-~-----------------------l~~la~iNl~lavfNLlP~~pLDGg~il~ 242 (277)
T cd06162 208 LL--I-------------------ET-F-----------------------LKYLISLSGALAVINAVPCFALDGQWILS 242 (277)
T ss_pred HH--H-------------------HH-H-----------------------HHHHHHHHHHHHHhhcCCCCCCChHHHHH
Confidence 21 0 00 0 22456788888899999999999999999
Q ss_pred HHhhhhH
Q 008143 485 GAFGRNA 491 (576)
Q Consensus 485 Al~Grr~ 491 (576)
+++.++.
T Consensus 243 ~ll~~~~ 249 (277)
T cd06162 243 TFLEATL 249 (277)
T ss_pred HHHHHHh
Confidence 9997553
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=99.49 E-value=2.8e-13 Score=130.43 Aligned_cols=132 Identities=21% Similarity=0.271 Sum_probs=85.5
Q ss_pred HHHHHHHHhhhHHHHHHHHhhCCccccc----ceeeccc---cccc---------ceeEee-----CCCCCCChhhhhhh
Q 008143 329 AYGVLGVLLFHDVGHFLAAFPKKVKLSI----PFFIPNI---TLGS---------FGAITQ-----FKSILPDRSTKVDI 387 (576)
Q Consensus 329 al~ll~IL~vHElGHylaArr~gVk~sl----PyFIP~~---~lGT---------fGAvir-----~ks~~p~RkaLFDI 387 (576)
.++++..+..||+||.++|+++|.++.. -.+-|.- .+|+ .++..+ .+....+|++.+-|
T Consensus 5 ~~~~~~~i~~HE~aHa~~A~~~Gd~t~~~~Grltlnp~~hid~~g~l~~~~~~~~~~G~a~p~~~~~~~~~~~r~~~~~v 84 (181)
T cd06158 5 IIAVLLAITLHEFAHAYVAYRLGDPTARRAGRLTLNPLAHIDPIGTIILPLLLPFLFGWAKPVPVNPRNFKNPRRGMLLV 84 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcHHHHcCceecCcHHhcCcchHHHHHHHHHhCeEEecccccChHhhcccHhhHhhh
Confidence 4557778899999999999999998752 2222310 0111 123322 11223467889999
Q ss_pred eehhhHHHHHHHHHHHHHHHhhcCCCCCCCCcccCCccccchhhHHHHHHHHhhccccccccccchhHHHHHHHHHHHHH
Q 008143 388 SLAGPIAGAALSFSMFVVGLLLSSNPDAAGDLVQVPSTLFQGSLLLGLISRATLGYTAMHASTVTIHPLVIAGWCGLTTT 467 (576)
Q Consensus 388 aiAGPLAG~vval~llivGl~ls~~~~~~~~l~~~p~~~f~~s~Llg~la~l~LG~~~~~~~~v~lhPla~aGWlGL~vT 467 (576)
++|||+++++++++..+.- .+.... . .. ..+.+. .-+....++|+...
T Consensus 85 alAGP~~n~~la~i~~~~~-~~~~~~---~------~~--~~~~l~--------------------~~~~~~~~~Ni~l~ 132 (181)
T cd06158 85 SLAGPLSNLLLALLFALLL-RLLPAF---G------GV--VASFLF--------------------LMLAYGVLINLVLA 132 (181)
T ss_pred hhhhHHHHHHHHHHHHHHH-HHhccc---c------ch--hhHHHH--------------------HHHHHHHHHHHHHH
Confidence 9999999999998765432 221110 0 00 011111 11234568899999
Q ss_pred HHhhcCCCCCChHHHHHHHhhhhHH
Q 008143 468 AFNMLPVGCLDGGRAVQGAFGRNAL 492 (576)
Q Consensus 468 aLNLLPvGqLDGGrIl~Al~Grr~~ 492 (576)
.|||+|+.|||||||+++++.++..
T Consensus 133 lfNLlPipPLDG~~il~~~l~~~~~ 157 (181)
T cd06158 133 VFNLLPIPPLDGSKILAALLPRRLA 157 (181)
T ss_pred HHHhCCCCCCChHHHHHHHcchhHH
Confidence 9999999999999999999988764
No 10
>COG0750 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]
Probab=99.22 E-value=2.4e-12 Score=133.47 Aligned_cols=149 Identities=21% Similarity=0.161 Sum_probs=106.1
Q ss_pred HHHHHhhh--HHHHHHHHhhCCcccccceeecccccccceeEee--CCCCCCC-----hhhhhhheehhhHHHHHHHHHH
Q 008143 332 VLGVLLFH--DVGHFLAAFPKKVKLSIPFFIPNITLGSFGAITQ--FKSILPD-----RSTKVDISLAGPIAGAALSFSM 402 (576)
Q Consensus 332 ll~IL~vH--ElGHylaArr~gVk~slPyFIP~~~lGTfGAvir--~ks~~p~-----RkaLFDIaiAGPLAG~vval~l 402 (576)
.+.+++.| +..|+.+++.++.....|+++| ...|+.++.++ ..+..|+ ++.+++++.+++++ ..+.-..
T Consensus 181 ~~~i~~~~~~~~~~~~~~~~~~~~~~~P~~~~-~~~~~~~~~i~~~~i~~~p~~~~~~~~~~~~~~~~~~i~-~~v~~~~ 258 (375)
T COG0750 181 LLTILVIRLDGEAHAVAAEIIKSLGLTPVVIP-LKPGDKIVAVDVGAIGLSPNGEPDVGKVLVKYGPLEAVG-LAVEKTG 258 (375)
T ss_pred ceEEEEEeccceeeeccccceeeEeeecceec-cCCCCEEEEeeeeeeeeccCCCCccceeeeccCHHHHHH-HHHHHHH
Confidence 46788999 9999999999999999999998 66888888886 7777777 99999999999988 5555566
Q ss_pred HHHHHhhcCCCCCCCCcccCCccccchhhHHHHHHHHhhccccccccccchhHHHHHHHHHHHHHHHhhcCCCCCChHHH
Q 008143 403 FVVGLLLSSNPDAAGDLVQVPSTLFQGSLLLGLISRATLGYTAMHASTVTIHPLVIAGWCGLTTTAFNMLPVGCLDGGRA 482 (576)
Q Consensus 403 livGl~ls~~~~~~~~l~~~p~~~f~~s~Llg~la~l~LG~~~~~~~~v~lhPla~aGWlGL~vTaLNLLPvGqLDGGrI 482 (576)
.++++.++.. .+.+...+..+.+.+-+.-...+.. ..+....|++.+++|+++.++++||+|+.||||||+
T Consensus 259 ~~~~~~~~~l-------~~~~~~~~~~~~l~Gpi~i~~~~~~--~~~~~~~~~l~~~~~lsi~lg~lNllP~p~LDGG~i 329 (375)
T COG0750 259 RLVKLTLKML-------KKLITGDLSLKNLSGPIGIAKIAGA--AASLGLINLLFFLALLSINLGILNLLPIPPLDGGHL 329 (375)
T ss_pred HHHHHHHHHH-------HHheecccccccccCceehhhhhhH--HHhhHHHHHHHHHHHHHHHHHHHhccCCCccCccHH
Confidence 6666655410 0011111111111111111111110 111345699999999999999999999999999999
Q ss_pred HHHHhhhhH
Q 008143 483 VQGAFGRNA 491 (576)
Q Consensus 483 l~Al~Grr~ 491 (576)
+++++.+..
T Consensus 330 ~~~~~e~~~ 338 (375)
T COG0750 330 LFYLLEALR 338 (375)
T ss_pred HHHHHHHHh
Confidence 999997654
No 11
>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=99.15 E-value=1.2e-09 Score=117.39 Aligned_cols=73 Identities=25% Similarity=0.390 Sum_probs=56.8
Q ss_pred HHHHHHHHHHhhhHHHHHHHHhhCCccccc--------------------ceeecccccccceeEeeCCCC--------C
Q 008143 327 PLAYGVLGVLLFHDVGHFLAAFPKKVKLSI--------------------PFFIPNITLGSFGAITQFKSI--------L 378 (576)
Q Consensus 327 Pfal~ll~IL~vHElGHylaArr~gVk~sl--------------------PyFIP~~~lGTfGAvir~ks~--------~ 378 (576)
.+.+.+..+.++||+|||++||++||++.. -=.||+ |++.+|... +
T Consensus 8 ~~~~~~~~~v~~HE~gH~~~a~~~g~~v~~FsiGfGp~l~~~~~~~tey~i~~~pl------Gg~v~~~g~~~~~~~~~~ 81 (420)
T TIGR00054 8 ASILALAVLIFVHELGHFLAARLCGIKVERFSIGFGPKILKFKKNGTEYAISLIPL------GGYVKMKGLDKEMEVKPP 81 (420)
T ss_pred HHHHHHHHHHHHHhHHHHHHHHHcCCEEEEEEEccCchheEEecCCeEEEEEEecC------cceEeeccCCcccccCCc
Confidence 346677788999999999999999999862 123554 999998411 0
Q ss_pred ---------CChhhhhhheehhhHHHHHHHHHHHHH
Q 008143 379 ---------PDRSTKVDISLAGPIAGAALSFSMFVV 405 (576)
Q Consensus 379 ---------p~RkaLFDIaiAGPLAG~vval~lliv 405 (576)
.++++.+-|.+|||++++++|++++++
T Consensus 82 ~~~~~~f~~~~~~~r~~i~~aGp~~N~~~a~~~~~~ 117 (420)
T TIGR00054 82 ETDGDLFNNKSVFQKAIIIFAGPLANFIFAIFVYIF 117 (420)
T ss_pred chhhhhhccCCHHHHHHhhhcccHHHHHHHHHHHHH
Confidence 356677889999999999999988664
No 12
>COG1994 SpoIVFB Zn-dependent proteases [General function prediction only]
Probab=99.08 E-value=1.3e-09 Score=108.40 Aligned_cols=135 Identities=26% Similarity=0.327 Sum_probs=91.7
Q ss_pred HhhHHHHHHHHHHHhhhHHHHHHHHhhCCcccccceeecccccccceeEeeCCCCCCChhhhhhheehhhHHHHHHHHHH
Q 008143 323 ESALPLAYGVLGVLLFHDVGHFLAAFPKKVKLSIPFFIPNITLGSFGAITQFKSILPDRSTKVDISLAGPIAGAALSFSM 402 (576)
Q Consensus 323 ~~glPfal~ll~IL~vHElGHylaArr~gVk~slPyFIP~~~lGTfGAvir~ks~~p~RkaLFDIaiAGPLAG~vval~l 402 (576)
..+....++++.-+..||+||+..++++++++....+. .+|++..++..+.+++..+.+..+||+++..+ .++
T Consensus 42 ~~~~~~~~~l~~rl~l~~~gh~~~~~~~~~~l~~~~i~------~~~g~~~~~~~~v~~~~~~~~~~~g~lvs~al-gpl 114 (230)
T COG1994 42 GDGTAAFVGLAHRLVLHPLGHSDEAGRLGLKLLLALLF------GFGGFGFLKPVPVNPRGEFLIRLAGPLVSLAL-GPL 114 (230)
T ss_pred hhhHHHHHHHhHHHhhhHhhHHHHHHHHHHHHHHHHHH------hccceeeecCcCcCHHHHhhhhccchhHHHHH-HHH
Confidence 34556666688899999999999999999887654433 26889999999999999999998888887764 222
Q ss_pred HHHHHhhcCCCCCCCCcccCCccccchhhHHHHHHHHhhccccccccccchhHHHHHHHHHHHHHHHhhcCCCCCChHHH
Q 008143 403 FVVGLLLSSNPDAAGDLVQVPSTLFQGSLLLGLISRATLGYTAMHASTVTIHPLVIAGWCGLTTTAFNMLPVGCLDGGRA 482 (576)
Q Consensus 403 livGl~ls~~~~~~~~l~~~p~~~f~~s~Llg~la~l~LG~~~~~~~~v~lhPla~aGWlGL~vTaLNLLPvGqLDGGrI 482 (576)
.-+.+...... ... .... .+.+. --+...+-+|+++..|||+|+.||||||+
T Consensus 115 ~ni~la~~~~~-~~~-~~~~------~~~~~--------------------~~~~~la~~Nl~L~lFNLiPi~PLDGg~v 166 (230)
T COG1994 115 TNIALAVLGLL-ALS-LFLY------HSVLF--------------------AFLAALALVNLVLALFNLLPIPPLDGGRV 166 (230)
T ss_pred HHHHHHHHHHH-hhc-cccc------chhHH--------------------HHHHHHHHHHHHHHHHhCCCCCCCChHHH
Confidence 11111100000 000 0000 00000 01224567899999999999999999999
Q ss_pred HHHHhhhhHH
Q 008143 483 VQGAFGRNAL 492 (576)
Q Consensus 483 l~Al~Grr~~ 492 (576)
+|+..-++..
T Consensus 167 lr~~~~~~~~ 176 (230)
T COG1994 167 LRALLPRRYG 176 (230)
T ss_pred HHHHccHHHH
Confidence 9999988764
No 13
>PRK10779 zinc metallopeptidase RseP; Provisional
Probab=98.52 E-value=2.1e-07 Score=100.77 Aligned_cols=80 Identities=20% Similarity=0.284 Sum_probs=56.4
Q ss_pred hHHHHHHHHHHHhhhHHHHHHHHhhCCcccccceeecc---c---c--------cc--cceeEeeCCCCC----------
Q 008143 325 ALPLAYGVLGVLLFHDVGHFLAAFPKKVKLSIPFFIPN---I---T--------LG--SFGAITQFKSIL---------- 378 (576)
Q Consensus 325 glPfal~ll~IL~vHElGHylaArr~gVk~slPyFIP~---~---~--------lG--TfGAvir~ks~~---------- 378 (576)
-+.|.+++..++++||+|||++||+.||++.- |.|=+ + . ++ =+|++.+|...-
T Consensus 7 i~~fil~l~~li~vHElGHfl~Ar~~gv~V~~-FsiGfGp~l~~~~~~~~Tey~i~~iPlGGyVk~~~e~~~~~~~~~~~ 85 (449)
T PRK10779 7 LAAFIVALGVLITVHEFGHFWVARRCGVRVER-FSIGFGKALWRRTDRQGTEYVIALIPLGGYVKMLDERVEPVAPELRH 85 (449)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHcCCeeeE-EEeecChhHeeEecCCCcEEEEEEEcCCCeeecCCCCCCcCChhhhh
Confidence 34467777788899999999999999999974 11110 0 0 00 138888876431
Q ss_pred -----CChhhhhhheehhhHHHHHHHHHHHHH
Q 008143 379 -----PDRSTKVDISLAGPIAGAALSFSMFVV 405 (576)
Q Consensus 379 -----p~RkaLFDIaiAGPLAG~vval~lliv 405 (576)
.+.++-+-|.+|||++++++|++++..
T Consensus 86 ~~f~~k~~~~R~~i~~AGp~~N~ila~~~~~~ 117 (449)
T PRK10779 86 HAFNNKTVGQRAAIIAAGPIANFIFAIFAYWL 117 (449)
T ss_pred hhhccCCHHHhhhhhhhhHHHHHHHHHHHHHH
Confidence 234566779999999999999887544
No 14
>PF13398 Peptidase_M50B: Peptidase M50B-like
Probab=96.69 E-value=0.0032 Score=62.00 Aligned_cols=66 Identities=23% Similarity=0.282 Sum_probs=54.3
Q ss_pred HHHhhhHHHHHHHHhhCCcccccceeecccccccceeEeeCCCCCCChhhhhhheehhhHHHHHHHHHHHHHH
Q 008143 334 GVLLFHDVGHFLAAFPKKVKLSIPFFIPNITLGSFGAITQFKSILPDRSTKVDISLAGPIAGAALSFSMFVVG 406 (576)
Q Consensus 334 ~IL~vHElGHylaArr~gVk~slPyFIP~~~lGTfGAvir~ks~~p~RkaLFDIaiAGPLAG~vval~llivG 406 (576)
....+||+||.++|.-.|-++......|. -++.+..+. +++-..+-++.|||++..+.+..++..+
T Consensus 23 l~t~~HE~gHal~a~l~G~~v~~i~l~~~-----~~G~~~~~~--~~~~~~~~i~~aGyl~~~l~g~~~~~~~ 88 (200)
T PF13398_consen 23 LVTFVHELGHALAALLTGGRVKGIVLFPD-----GSGVTVSSG--PSGIGRFLIALAGYLGPALFGLLLLWLL 88 (200)
T ss_pred HHHHHHHHHHHHHHHHhCCCcceEEEEeC-----CCceEEEec--CCCcchhHHhcccchHHHHHHHHHHHHH
Confidence 34789999999999999999998888886 467777766 6666778899999999999887776654
No 15
>PRK10779 zinc metallopeptidase RseP; Provisional
Probab=96.59 E-value=0.0042 Score=67.79 Aligned_cols=34 Identities=24% Similarity=0.346 Sum_probs=30.6
Q ss_pred hHHHHHHHHHHHHHHHhhcCCCCCChHHHHHHHh
Q 008143 454 HPLVIAGWCGLTTTAFNMLPVGCLDGGRAVQGAF 487 (576)
Q Consensus 454 hPla~aGWlGL~vTaLNLLPvGqLDGGrIl~Al~ 487 (576)
.-+.+.+.+.+-+..+||||+-.|||||++..++
T Consensus 377 ~~l~~~a~iSi~Lgi~NLlPiP~LDGG~l~f~~~ 410 (449)
T PRK10779 377 YYLMFLALISVNLGIINLFPLPVLDGGHLLFLAI 410 (449)
T ss_pred HHHHHHHHHHHHHHHHHcCCCCccCchHHHHHHH
Confidence 4566788899999999999999999999999887
No 16
>COG0750 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]
Probab=94.55 E-value=0.14 Score=53.59 Aligned_cols=79 Identities=24% Similarity=0.421 Sum_probs=50.5
Q ss_pred HHHHHHHHHHHhhhHHHHHHHHhhCCcccccc------------------eeecccccccceeEeeCCCCCCC-------
Q 008143 326 LPLAYGVLGVLLFHDVGHFLAAFPKKVKLSIP------------------FFIPNITLGSFGAITQFKSILPD------- 380 (576)
Q Consensus 326 lPfal~ll~IL~vHElGHylaArr~gVk~slP------------------yFIP~~~lGTfGAvir~ks~~p~------- 380 (576)
+.+.+.+......||+||+|.||+.++++... |.+..+.+ |++.++......
T Consensus 6 i~~i~~~~~lv~~he~gh~~~a~~~~~~v~~f~ig~g~~l~~~~~~~~~~~~i~~~pl---ggyv~~~~~~~~~~~~~~~ 82 (375)
T COG0750 6 IAFIIALGVLVFVHELGHFWVARRCGVKVERFSIGFGPKLFSRKDKGGTEYVLSAIPL---GGYVKMLGEDAEEVVLKGP 82 (375)
T ss_pred HHHHHHHHHHHHHHHHhhHHHHHhcCceeEEEEeccCcceEEEEcCCceEEEEeecCc---cceEEEecCcccccccccc
Confidence 44666777888999999999999999988642 22211222 444333322221
Q ss_pred --hhh---------hhhheehhhHHHHHHHHHHHHHHH
Q 008143 381 --RST---------KVDISLAGPIAGAALSFSMFVVGL 407 (576)
Q Consensus 381 --Rka---------LFDIaiAGPLAG~vval~llivGl 407 (576)
+.+ -+-+-.|||+++++.++.+.+...
T Consensus 83 ~~~~~~f~~~~~~~~~~~~~~Gp~~n~i~~~~~~~~~~ 120 (375)
T COG0750 83 EPRPRAFNAKSVWQRIAIVFAGPLFNFILAIVLFVVLF 120 (375)
T ss_pred CcchhhhhcccccchhheeechHHHHHHHHHHHHHhhh
Confidence 111 245789999999998777665543
No 17
>KOG2921 consensus Intramembrane metalloprotease (sterol-regulatory element-binding protein (SREBP) protease) [Posttranslational modification, protein turnover, chaperones]
Probab=93.79 E-value=0.079 Score=57.77 Aligned_cols=147 Identities=21% Similarity=0.305 Sum_probs=86.4
Q ss_pred hhHHHHH-HHHHHHhhhHHHHHHHHhhCCccccc-ceeecccccccceeEeeC-----CCCCCChhhhhhheehhhHHHH
Q 008143 324 SALPLAY-GVLGVLLFHDVGHFLAAFPKKVKLSI-PFFIPNITLGSFGAITQF-----KSILPDRSTKVDISLAGPIAGA 396 (576)
Q Consensus 324 ~glPfal-~ll~IL~vHElGHylaArr~gVk~sl-PyFIP~~~lGTfGAvir~-----ks~~p~RkaLFDIaiAGPLAG~ 396 (576)
.+++|.+ +++..+.+||+||.|||.+.||++.. -.||-++.- ||++.+ ++.++ =++ ..|--||-.=+|
T Consensus 121 ~~I~yf~t~lvi~~vvHElGHalAA~segV~vngfgIfi~aiyP---gafvdl~~dhLqsl~~-fr~-LrIfcAGIWHNf 195 (484)
T KOG2921|consen 121 SGIAYFLTSLVITVVVHELGHALAAASEGVQVNGFGIFIAAIYP---GAFVDLDNDHLQSLPS-FRA-LRIFCAGIWHNF 195 (484)
T ss_pred ccchhhhhhHHHHHHHHHhhHHHHHHhcCceeeeeEEEEEEEcC---chhhhhhhhHHhhcch-HHH-HHHHhhhHHHHH
Confidence 4555544 56677889999999999999999873 122222112 566543 44433 333 478899999999
Q ss_pred HHHHHHHHH----HHhhcCCCCCCCC---cccCCccccchhhHHHHHHHHhhccccccccccchhHHHHHHHHHHHHHHH
Q 008143 397 ALSFSMFVV----GLLLSSNPDAAGD---LVQVPSTLFQGSLLLGLISRATLGYTAMHASTVTIHPLVIAGWCGLTTTAF 469 (576)
Q Consensus 397 vval~lliv----Gl~ls~~~~~~~~---l~~~p~~~f~~s~Llg~la~l~LG~~~~~~~~v~lhPla~aGWlGL~vTaL 469 (576)
+.|+.+.+. +..+|+.= +.+. ...+| ..|+|.+=. .+..|+...+..+..+|- ..-|.=++-|++
T Consensus 196 vfallc~lal~~lpViLsPfy-a~g~gV~Vtev~----~~Spl~gpr-GL~vgdvitsldgcpV~~--v~dW~ecl~tsl 267 (484)
T KOG2921|consen 196 VFALLCVLALFLLPVILSPFY-AHGEGVTVTEVP----SVSPLFGPR-GLSVGDVITSLDGCPVHK--VSDWLECLATSL 267 (484)
T ss_pred HHHHHHHHHHHhhhHhhchhh-hcCceEEEEecc----ccCCCcCcc-cCCccceEEecCCcccCC--HHHHHHHHHhhc
Confidence 988876443 33333310 0011 01111 123332211 123454444445555665 367999999999
Q ss_pred hhcCCCCCChHHHH
Q 008143 470 NMLPVGCLDGGRAV 483 (576)
Q Consensus 470 NLLPvGqLDGGrIl 483 (576)
|+=|--.-|+--+-
T Consensus 268 ~~~ngycvsas~vq 281 (484)
T KOG2921|consen 268 DKENGYCVSASLVQ 281 (484)
T ss_pred ccCCCeeecHHHHh
Confidence 99998887765443
No 18
>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=57.29 E-value=4.9 Score=38.41 Aligned_cols=15 Identities=47% Similarity=0.935 Sum_probs=11.1
Q ss_pred HHHhhhHHHHHHHHh
Q 008143 334 GVLLFHDVGHFLAAF 348 (576)
Q Consensus 334 ~IL~vHElGHylaAr 348 (576)
+-.++||+|||+--+
T Consensus 70 g~TltHEvGH~LGL~ 84 (154)
T PF05572_consen 70 GKTLTHEVGHWLGLY 84 (154)
T ss_dssp SHHHHHHHHHHTT--
T ss_pred ccchhhhhhhhhccc
Confidence 467899999997544
No 19
>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=50.52 E-value=8.9 Score=34.96 Aligned_cols=23 Identities=22% Similarity=0.258 Sum_probs=16.9
Q ss_pred HHhhhHHHHHHHHhhCCcccccc
Q 008143 335 VLLFHDVGHFLAAFPKKVKLSIP 357 (576)
Q Consensus 335 IL~vHElGHylaArr~gVk~slP 357 (576)
-.+.||+||.+=-..-.-+-+..
T Consensus 107 ~v~~HEiGHaLGL~H~~~~~svM 129 (154)
T PF00413_consen 107 SVAIHEIGHALGLDHSNDPNSVM 129 (154)
T ss_dssp HHHHHHHHHHTTBESSSSTTSTT
T ss_pred hhhhhccccccCcCcCCCcccce
Confidence 56899999999886665554443
No 20
>PRK12821 aspartyl/glutamyl-tRNA amidotransferase subunit C-like protein; Provisional
Probab=48.94 E-value=80 Score=35.82 Aligned_cols=87 Identities=22% Similarity=0.327 Sum_probs=45.6
Q ss_pred ehhhHHHHHHHHHHHHHHHhhcCCCCCCCCcccCCccccchhhH---HHHHHHHhhccc-cccccccchhHHHHHHHHHH
Q 008143 389 LAGPIAGAALSFSMFVVGLLLSSNPDAAGDLVQVPSTLFQGSLL---LGLISRATLGYT-AMHASTVTIHPLVIAGWCGL 464 (576)
Q Consensus 389 iAGPLAG~vval~llivGl~ls~~~~~~~~l~~~p~~~f~~s~L---lg~la~l~LG~~-~~~~~~v~lhPla~aGWlGL 464 (576)
+-||+.|.+++++.=++|+..++ + .-.|+..+. ..+ ..++.|.++-.. ..+....+..+.++.. +|+
T Consensus 108 LFGP~~G~l~g~lsDlLg~if~~-----G--~fFpGFTLs-A~L~GlIyGl~r~~l~~~~~~~~~~~~~~~y~~~s-~~~ 178 (477)
T PRK12821 108 LFGPIIGIFSAATIDFLTVIFSG-----G--VFNYGYVLG-AILTGMIAGILREVLISTKYLKNRNLSDFAYLVLS-VGM 178 (477)
T ss_pred HhhhHHHHHHHHHHHHHHhhcCC-----C--CccHHHHHH-HHHHHHHHHHHHHHHHHHHHhcccchhhhHHHHHH-HHH
Confidence 45999999999988888844432 1 112221111 111 222334333321 1223344444555543 444
Q ss_pred HHH-----HH------hhcCCCCCChHHHHH
Q 008143 465 TTT-----AF------NMLPVGCLDGGRAVQ 484 (576)
Q Consensus 465 ~vT-----aL------NLLPvGqLDGGrIl~ 484 (576)
++. -+ |-||.-+-|||--++
T Consensus 179 ~~a~fl~~~~~~~~~~~~~~~~~~~~~f~~~ 209 (477)
T PRK12821 179 VIASFLLTQFFVISVTTNLPEIRINGGFDLS 209 (477)
T ss_pred HHHHHHHHHHhhhcccccccccccCCCeEEE
Confidence 433 33 889999999996554
No 21
>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=46.89 E-value=11 Score=32.09 Aligned_cols=17 Identities=29% Similarity=0.522 Sum_probs=12.9
Q ss_pred HHhhhHHHHHHHHhhCC
Q 008143 335 VLLFHDVGHFLAAFPKK 351 (576)
Q Consensus 335 IL~vHElGHylaArr~g 351 (576)
..++||+||++.-....
T Consensus 44 f~laHELgH~~~~~~~~ 60 (122)
T PF06114_consen 44 FTLAHELGHILLHHGDE 60 (122)
T ss_dssp HHHHHHHHHHHHHH-HH
T ss_pred HHHHHHHHHHHhhhccc
Confidence 35899999999876654
No 22
>PRK12462 phosphoserine aminotransferase; Provisional
Probab=46.19 E-value=36 Score=37.07 Aligned_cols=65 Identities=14% Similarity=0.298 Sum_probs=46.6
Q ss_pred hCCCCCCHHhHHHHhccccccceeeeecccccCCCCCeEEEEeccCCcHHHHHHHHHHHHHHHhC--CceeEEEEecC
Q 008143 162 LGPEKVDPADVKLIKENLFGYSTFWVTKEEPFGDLGEGILFLGNLRGKREDVYAKLQSRLVEITG--DKYNFFMVEEP 237 (576)
Q Consensus 162 ~~~~~i~~~d~~~lk~~~Fg~dtF~~T~~~~~~~~~~gvif~GnLR~~~e~v~~~L~~~l~~~fG--d~y~lfLveep 237 (576)
-||..+|++.++++++++. .|+..+-+++=.+-=-.+=.++|++.+++|+++++ |.|.+++++..
T Consensus 10 aGPa~lp~~Vl~~~~~~~~-----------~~~~~g~si~eisHRs~~F~~i~~~~~~~Lr~Ll~~P~~y~Vlfl~Gg 76 (364)
T PRK12462 10 GGPGALPDTVLEQVRQAVV-----------ELPETGLSVLGMSHRSSWFSSLLAQAEADLRDLLGIPDEYGVVFLQGG 76 (364)
T ss_pred CCCcCCCHHHHHHHHHHHh-----------cccccCccccccccccHHHHHHHHHHHHHHHHHhCCCCCCeEEEEecc
Confidence 4999999999999997433 33322233333332234568899999999999998 68999888765
No 23
>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=45.72 E-value=13 Score=35.80 Aligned_cols=19 Identities=26% Similarity=0.466 Sum_probs=13.4
Q ss_pred HHHhhhHHHHHHHHhhCCccc
Q 008143 334 GVLLFHDVGHFLAAFPKKVKL 354 (576)
Q Consensus 334 ~IL~vHElGHylaArr~gVk~ 354 (576)
..+++||+||+. .+|..+.
T Consensus 90 ~aVlaHElgH~~--~~h~~~~ 108 (226)
T PF01435_consen 90 AAVLAHELGHIK--HRHILKS 108 (226)
T ss_dssp HHHHHHHHHHHH--TTHCCCC
T ss_pred HHHHHHHHHHHH--cCCcchH
Confidence 467999999986 4444443
No 24
>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=42.20 E-value=16 Score=34.05 Aligned_cols=25 Identities=16% Similarity=0.400 Sum_probs=19.9
Q ss_pred HHHhhhHHHHHHHHhhCCccc-ccce
Q 008143 334 GVLLFHDVGHFLAAFPKKVKL-SIPF 358 (576)
Q Consensus 334 ~IL~vHElGHylaArr~gVk~-slPy 358 (576)
.-.++||+||.+=.+...-+- +..|
T Consensus 105 ~~~~~HEiGHaLGL~H~~~~~~siM~ 130 (156)
T cd04279 105 QAIALHELGHALGLWHHSDRPEDAMY 130 (156)
T ss_pred HHHHHHHhhhhhcCCCCCCCccceee
Confidence 456899999999999988876 5444
No 25
>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=41.85 E-value=13 Score=35.64 Aligned_cols=21 Identities=24% Similarity=0.243 Sum_probs=13.2
Q ss_pred HHHHHhhhHHHHHHHHhhCCc
Q 008143 332 VLGVLLFHDVGHFLAAFPKKV 352 (576)
Q Consensus 332 ll~IL~vHElGHylaArr~gV 352 (576)
.-.+.++||+||-+=|..=+-
T Consensus 141 ~~~~~~AHEiGH~lGa~HD~~ 161 (196)
T PF13688_consen 141 NGAITFAHEIGHNLGAPHDGD 161 (196)
T ss_dssp HHHHHHHHHHHHHTT-----S
T ss_pred ceehhhHHhHHHhcCCCCCCC
Confidence 346789999999999886443
No 26
>PF13485 Peptidase_MA_2: Peptidase MA superfamily
Probab=41.31 E-value=19 Score=30.82 Aligned_cols=17 Identities=18% Similarity=0.057 Sum_probs=14.7
Q ss_pred HHhhhHHHHHHHHhhCC
Q 008143 335 VLLFHDVGHFLAAFPKK 351 (576)
Q Consensus 335 IL~vHElGHylaArr~g 351 (576)
-+++||++|.+.....+
T Consensus 27 ~~l~HE~~H~~~~~~~~ 43 (128)
T PF13485_consen 27 RVLAHELAHQWFGNYFG 43 (128)
T ss_pred HHHHHHHHHHHHHHHcC
Confidence 67899999999988854
No 27
>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=39.62 E-value=25 Score=32.43 Aligned_cols=22 Identities=23% Similarity=0.158 Sum_probs=16.3
Q ss_pred HHHHHHhhhHHHHHHHHhhCCc
Q 008143 331 GVLGVLLFHDVGHFLAAFPKKV 352 (576)
Q Consensus 331 ~ll~IL~vHElGHylaArr~gV 352 (576)
.-+.-..+||+||.+=.+.-.-
T Consensus 92 ~~~~~~~~HEiGHaLGL~H~~~ 113 (165)
T cd04268 92 ARLRNTAEHELGHALGLRHNFA 113 (165)
T ss_pred HHHHHHHHHHHHHHhcccccCc
Confidence 3456778999999987766554
No 28
>PF11667 DUF3267: Protein of unknown function (DUF3267); InterPro: IPR021683 This family of proteins has no known function.
Probab=38.96 E-value=32 Score=30.63 Aligned_cols=69 Identities=14% Similarity=0.055 Sum_probs=37.9
Q ss_pred HHHHhhhHHHHHHHHhhCCcccccceeecccccccceeEeeCCCCCCChhhhhhheehhhHHHHHHHHHHHHHHHh
Q 008143 333 LGVLLFHDVGHFLAAFPKKVKLSIPFFIPNITLGSFGAITQFKSILPDRSTKVDISLAGPIAGAALSFSMFVVGLL 408 (576)
Q Consensus 333 l~IL~vHElGHylaArr~gVk~slPyFIP~~~lGTfGAvir~ks~~p~RkaLFDIaiAGPLAG~vval~llivGl~ 408 (576)
+..+.+||+=|.+..+.++-+....+=+ ....+-+... .+.+-+|++ +-+...-|. ++++++.++.++.
T Consensus 4 ~~~~~~HEliH~l~~~~~~~~~~~~~g~---~~~~~~~~~~-~~~~~sk~~-~~i~~l~P~--ivl~~~~~~~~~~ 72 (111)
T PF11667_consen 4 IVLIPLHELIHGLFFKLFGKKPKVKFGF---KWKLGPFYAT-CNEPISKWR-FIIILLAPF--IVLTILPLILGFF 72 (111)
T ss_pred EeeHHHHHHHHHHHHHHhCCCCceEEEE---EeeeEEEEEe-cCcEEeHHH-HHHHHHHHH--HHHHHHHHHHHHH
Confidence 4556899999999999998855321111 0111222223 333444544 555555564 4555555555444
No 29
>PLN02452 phosphoserine transaminase
Probab=37.95 E-value=60 Score=35.12 Aligned_cols=65 Identities=14% Similarity=0.293 Sum_probs=47.8
Q ss_pred hCCCCCCHHhHHHHhccccccceeeeecccccCCCCCeEEEEeccCCcHHHHHHHHHHHHHHHhC--CceeEEEEecC
Q 008143 162 LGPEKVDPADVKLIKENLFGYSTFWVTKEEPFGDLGEGILFLGNLRGKREDVYAKLQSRLVEITG--DKYNFFMVEEP 237 (576)
Q Consensus 162 ~~~~~i~~~d~~~lk~~~Fg~dtF~~T~~~~~~~~~~gvif~GnLR~~~e~v~~~L~~~l~~~fG--d~y~lfLveep 237 (576)
.||..++++.+++++..++ .|++.+-+++-.+---.+=.+++++++++|+++++ |.|.+++++-.
T Consensus 13 pGP~~lp~~Vl~~~~~~~~-----------~~~~~g~s~~~~sHRs~~f~~i~~~~~~~L~~l~~~p~~y~v~~l~Gs 79 (365)
T PLN02452 13 AGPATLPANVLAKAQAELY-----------NWEGSGMSVMEMSHRGKEFLSIIQKAEADLRELLDIPDNYEVLFLQGG 79 (365)
T ss_pred CCCCCCCHHHHHHHHHHHh-----------cccccCccccccCCCchHHHHHHHHHHHHHHHHhCCCCCceEEEEeCc
Confidence 4999999999999987333 34443445554443344557999999999999997 68998888665
No 30
>PF13574 Reprolysin_2: Metallo-peptidase family M12B Reprolysin-like; PDB: 1KAP_P 1JIW_P 1AKL_A 1OM7_A 1OM8_A 1O0T_A 1OM6_A 1H71_P 1O0Q_A 1OMJ_A ....
Probab=37.63 E-value=17 Score=34.96 Aligned_cols=19 Identities=26% Similarity=0.139 Sum_probs=12.4
Q ss_pred HHHhhhHHHHHHHHhhCCc
Q 008143 334 GVLLFHDVGHFLAAFPKKV 352 (576)
Q Consensus 334 ~IL~vHElGHylaArr~gV 352 (576)
...++||+||-+-|..-+=
T Consensus 112 ~~~~aHElGH~lGa~Hd~~ 130 (173)
T PF13574_consen 112 IDTFAHELGHQLGAPHDFD 130 (173)
T ss_dssp HHHHHHHHHHHHT---SSS
T ss_pred eeeehhhhHhhcCCCCCCC
Confidence 3459999999999877543
No 31
>COG2856 Predicted Zn peptidase [Amino acid transport and metabolism]
Probab=36.55 E-value=17 Score=36.89 Aligned_cols=16 Identities=31% Similarity=0.397 Sum_probs=12.6
Q ss_pred HhhhHHHHHHHHhhCC
Q 008143 336 LLFHDVGHFLAAFPKK 351 (576)
Q Consensus 336 L~vHElGHylaArr~g 351 (576)
.++||+||++.=++-.
T Consensus 75 tlAHELGH~llH~~~~ 90 (213)
T COG2856 75 TLAHELGHALLHTDLN 90 (213)
T ss_pred HHHHHHhHHHhccccc
Confidence 4789999999866554
No 32
>PF14181 YqfQ: YqfQ-like protein
Probab=35.90 E-value=40 Score=33.10 Aligned_cols=22 Identities=14% Similarity=0.155 Sum_probs=10.1
Q ss_pred ccccCCcCccccccccCCCccC
Q 008143 96 VATTSSALDETEEKSSSSSSSS 117 (576)
Q Consensus 96 ~~~~~~~~~~~~~~~~~~~~~~ 117 (576)
+.++...+++.+++++..+...
T Consensus 115 ~~~~~~~~~~~~~~~k~~~~~~ 136 (161)
T PF14181_consen 115 VEDEPEEKTEKKRKRKREVPKP 136 (161)
T ss_pred cccCCCCcccccccccccCCCc
Confidence 4444444445554454444333
No 33
>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=34.89 E-value=19 Score=33.20 Aligned_cols=20 Identities=20% Similarity=0.318 Sum_probs=15.5
Q ss_pred HHHHhhhHHHHHHHHhhCCc
Q 008143 333 LGVLLFHDVGHFLAAFPKKV 352 (576)
Q Consensus 333 l~IL~vHElGHylaArr~gV 352 (576)
....++||+||.+=.+...-
T Consensus 96 ~~~~~~HElGH~LGl~H~~~ 115 (167)
T cd00203 96 GAQTIAHELGHALGFYHDHD 115 (167)
T ss_pred chhhHHHHHHHHhCCCccCc
Confidence 45778999999998776543
No 34
>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=34.58 E-value=25 Score=33.83 Aligned_cols=20 Identities=25% Similarity=0.361 Sum_probs=16.2
Q ss_pred HHHHhhhHHHHHHHHhhCCc
Q 008143 333 LGVLLFHDVGHFLAAFPKKV 352 (576)
Q Consensus 333 l~IL~vHElGHylaArr~gV 352 (576)
.++.++||+||-+=+.+-+-
T Consensus 131 ~a~~~AHElGH~lG~~HD~~ 150 (194)
T cd04269 131 FAVTMAHELGHNLGMEHDDG 150 (194)
T ss_pred HHHHHHHHHHhhcCCCcCCC
Confidence 46789999999998876554
No 35
>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=33.36 E-value=18 Score=33.79 Aligned_cols=21 Identities=19% Similarity=0.064 Sum_probs=14.9
Q ss_pred HHHhhhHHHHHHHHhhCCccc
Q 008143 334 GVLLFHDVGHFLAAFPKKVKL 354 (576)
Q Consensus 334 ~IL~vHElGHylaArr~gVk~ 354 (576)
.-.+.||+||.+=...-.-+-
T Consensus 108 ~~~~~HEiGHaLGL~H~~~~~ 128 (157)
T cd04278 108 FSVAAHEIGHALGLGHSSDPD 128 (157)
T ss_pred HHHHHHHhccccccCCCCCCc
Confidence 355899999998886544433
No 36
>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=32.99 E-value=25 Score=35.77 Aligned_cols=21 Identities=14% Similarity=0.218 Sum_probs=16.7
Q ss_pred HHHHHHhhhHHHHHHHHhhCC
Q 008143 331 GVLGVLLFHDVGHFLAAFPKK 351 (576)
Q Consensus 331 ~ll~IL~vHElGHylaArr~g 351 (576)
.+.++.++||+||-+=+..-.
T Consensus 165 ~~~a~t~AHElGHnlGm~HD~ 185 (244)
T cd04270 165 KESDLVTAHELGHNFGSPHDP 185 (244)
T ss_pred hHHHHHHHHHHHHhcCCCCCC
Confidence 346788999999999887544
No 37
>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=32.12 E-value=24 Score=33.86 Aligned_cols=18 Identities=22% Similarity=0.292 Sum_probs=14.0
Q ss_pred HHHhhhHHHHHHHHhhCC
Q 008143 334 GVLLFHDVGHFLAAFPKK 351 (576)
Q Consensus 334 ~IL~vHElGHylaArr~g 351 (576)
.-.++||+||.+=-++-+
T Consensus 114 ~~t~~HEiGHaLGL~H~~ 131 (186)
T cd04277 114 YQTIIHEIGHALGLEHPG 131 (186)
T ss_pred HHHHHHHHHHHhcCCCCC
Confidence 456899999999876643
No 38
>PF13582 Reprolysin_3: Metallo-peptidase family M12B Reprolysin-like; PDB: 3P24_C.
Probab=31.35 E-value=22 Score=31.46 Aligned_cols=14 Identities=29% Similarity=0.406 Sum_probs=10.2
Q ss_pred HHhhhHHHHHHHHh
Q 008143 335 VLLFHDVGHFLAAF 348 (576)
Q Consensus 335 IL~vHElGHylaAr 348 (576)
..++||+||-+=++
T Consensus 109 ~~~~HEiGH~lGl~ 122 (124)
T PF13582_consen 109 DTFAHEIGHNLGLN 122 (124)
T ss_dssp THHHHHHHHHTT--
T ss_pred eEeeehhhHhcCCC
Confidence 66899999987554
No 39
>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=31.11 E-value=24 Score=32.01 Aligned_cols=19 Identities=21% Similarity=0.504 Sum_probs=14.1
Q ss_pred HhhhHHHHHHHHhhCCccc
Q 008143 336 LLFHDVGHFLAAFPKKVKL 354 (576)
Q Consensus 336 L~vHElGHylaArr~gVk~ 354 (576)
.++||+||.+-.+.-+-+-
T Consensus 89 ~~~HEigHaLGl~H~~~~~ 107 (140)
T smart00235 89 VAAHELGHALGLYHEQSRS 107 (140)
T ss_pred cHHHHHHHHhcCCcCCCCC
Confidence 6899999999766544443
No 40
>cd04267 ZnMc_ADAM_like Zinc-dependent metalloprotease, ADAM_like or reprolysin_like subgroup. The adamalysin_like or ADAM family of metalloproteases contains proteolytic domains from snake venoms, proteases from the mammalian reproductive tract, and the tumor necrosis factor alpha convertase, TACE. ADAMs (A Disintegrin And Metalloprotease) are glycoproteins, which play roles in cell signaling, cell fusion, and cell-cell interactions.
Probab=30.61 E-value=19 Score=34.50 Aligned_cols=20 Identities=25% Similarity=0.305 Sum_probs=16.5
Q ss_pred HHHHhhhHHHHHHHHhhCCc
Q 008143 333 LGVLLFHDVGHFLAAFPKKV 352 (576)
Q Consensus 333 l~IL~vHElGHylaArr~gV 352 (576)
.+..++||+||.+-+.+-+-
T Consensus 133 ~~~~~aHElGH~lG~~HD~~ 152 (192)
T cd04267 133 TALTMAHELGHNLGAEHDGG 152 (192)
T ss_pred ehhhhhhhHHhhcCCcCCCC
Confidence 46789999999998887654
No 41
>PF13699 DUF4157: Domain of unknown function (DUF4157)
Probab=28.47 E-value=33 Score=29.48 Aligned_cols=14 Identities=29% Similarity=0.503 Sum_probs=11.0
Q ss_pred HHhhhHHHHHHHHh
Q 008143 335 VLLFHDVGHFLAAF 348 (576)
Q Consensus 335 IL~vHElGHylaAr 348 (576)
-+++||+.|.+.=+
T Consensus 63 ~llaHEl~Hv~Qq~ 76 (79)
T PF13699_consen 63 ALLAHELAHVVQQR 76 (79)
T ss_pred hhHhHHHHHHHhhc
Confidence 46899999998643
No 42
>PRK03001 M48 family peptidase; Provisional
Probab=27.90 E-value=35 Score=35.38 Aligned_cols=12 Identities=17% Similarity=0.362 Sum_probs=9.9
Q ss_pred HHHhhhHHHHHH
Q 008143 334 GVLLFHDVGHFL 345 (576)
Q Consensus 334 ~IL~vHElGHyl 345 (576)
..+++||+||+-
T Consensus 125 ~aVlAHElgHi~ 136 (283)
T PRK03001 125 RGVMAHELAHVK 136 (283)
T ss_pred HHHHHHHHHHHh
Confidence 456899999985
No 43
>COG3824 Predicted Zn-dependent protease [General function prediction only]
Probab=27.36 E-value=27 Score=33.14 Aligned_cols=16 Identities=25% Similarity=0.644 Sum_probs=13.1
Q ss_pred HHHHHHhhhHHHHHHH
Q 008143 331 GVLGVLLFHDVGHFLA 346 (576)
Q Consensus 331 ~ll~IL~vHElGHyla 346 (576)
-++...++||+||++-
T Consensus 107 d~vthvliHEIgHhFG 122 (136)
T COG3824 107 DQVTHVLIHEIGHHFG 122 (136)
T ss_pred hHhhhhhhhhhhhhcC
Confidence 3568899999999873
No 44
>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=27.34 E-value=35 Score=32.56 Aligned_cols=12 Identities=33% Similarity=0.742 Sum_probs=9.3
Q ss_pred HhhhHHHHHHHH
Q 008143 336 LLFHDVGHFLAA 347 (576)
Q Consensus 336 L~vHElGHylaA 347 (576)
+.+||+||.+--
T Consensus 80 IaaHE~GHiLGL 91 (132)
T PF02031_consen 80 IAAHELGHILGL 91 (132)
T ss_dssp HHHHHHHHHHT-
T ss_pred eeeehhccccCC
Confidence 579999998743
No 45
>PF13583 Reprolysin_4: Metallo-peptidase family M12B Reprolysin-like
Probab=26.76 E-value=27 Score=34.68 Aligned_cols=16 Identities=25% Similarity=0.299 Sum_probs=13.5
Q ss_pred hhhHHHHHHHHhhCCc
Q 008143 337 LFHDVGHFLAAFPKKV 352 (576)
Q Consensus 337 ~vHElGHylaArr~gV 352 (576)
++||+||.+=|++-+=
T Consensus 141 ~aHEiGH~lGl~H~~~ 156 (206)
T PF13583_consen 141 FAHEIGHNLGLRHDFD 156 (206)
T ss_pred HHHHHHHHhcCCCCcc
Confidence 8899999999887554
No 46
>PF14891 Peptidase_M91: Effector protein
Probab=25.76 E-value=42 Score=32.40 Aligned_cols=16 Identities=25% Similarity=0.355 Sum_probs=13.4
Q ss_pred HHHhhhHHHHHHHHhh
Q 008143 334 GVLLFHDVGHFLAAFP 349 (576)
Q Consensus 334 ~IL~vHElGHylaArr 349 (576)
++.+.|||+|.+-...
T Consensus 104 ~v~L~HEL~HA~~~~~ 119 (174)
T PF14891_consen 104 FVVLYHELIHAYDYMN 119 (174)
T ss_pred HHHHHHHHHHHHHHHC
Confidence 5789999999987754
No 47
>PRK03982 heat shock protein HtpX; Provisional
Probab=25.73 E-value=41 Score=35.00 Aligned_cols=12 Identities=17% Similarity=0.349 Sum_probs=9.5
Q ss_pred HHHhhhHHHHHH
Q 008143 334 GVLLFHDVGHFL 345 (576)
Q Consensus 334 ~IL~vHElGHyl 345 (576)
..+++||+||+-
T Consensus 126 ~AVlAHElgHi~ 137 (288)
T PRK03982 126 EGVIAHELTHIK 137 (288)
T ss_pred HHHHHHHHHHHH
Confidence 356899999973
No 48
>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=24.73 E-value=47 Score=34.02 Aligned_cols=27 Identities=26% Similarity=0.261 Sum_probs=20.0
Q ss_pred HHhhHHHHHHHHHHHhhhHHHHHHHHhhCC
Q 008143 322 VESALPLAYGVLGVLLFHDVGHFLAAFPKK 351 (576)
Q Consensus 322 l~~glPfal~ll~IL~vHElGHylaArr~g 351 (576)
++.|||-. +.+.+++||++|.|. |-.|
T Consensus 84 vl~GLPrl--l~gsiLAHE~mHa~L-rl~g 110 (212)
T PF12315_consen 84 VLYGLPRL--LTGSILAHELMHAWL-RLNG 110 (212)
T ss_pred EECCCCHH--HHhhHHHHHHHHHHh-cccC
Confidence 35677754 568889999999998 3344
No 49
>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=23.99 E-value=51 Score=31.87 Aligned_cols=21 Identities=24% Similarity=0.376 Sum_probs=14.5
Q ss_pred HHHHHhhhHHHHHHHHhhCCc
Q 008143 332 VLGVLLFHDVGHFLAAFPKKV 352 (576)
Q Consensus 332 ll~IL~vHElGHylaArr~gV 352 (576)
.++..++||+||-+=+..-+-
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 456788999999988877665
No 50
>PRK04897 heat shock protein HtpX; Provisional
Probab=23.89 E-value=46 Score=34.98 Aligned_cols=12 Identities=17% Similarity=0.343 Sum_probs=9.5
Q ss_pred HHHhhhHHHHHH
Q 008143 334 GVLLFHDVGHFL 345 (576)
Q Consensus 334 ~IL~vHElGHyl 345 (576)
..+++||+||+-
T Consensus 138 ~aVlAHElgHi~ 149 (298)
T PRK04897 138 EGVIGHEISHIR 149 (298)
T ss_pred HHHHHHHHHHHh
Confidence 356899999964
No 51
>PRK02870 heat shock protein HtpX; Provisional
Probab=23.77 E-value=40 Score=36.42 Aligned_cols=18 Identities=17% Similarity=0.449 Sum_probs=12.9
Q ss_pred HHHhhhHHHHHHHHhhCCccc
Q 008143 334 GVLLFHDVGHFLAAFPKKVKL 354 (576)
Q Consensus 334 ~IL~vHElGHylaArr~gVk~ 354 (576)
..+++||+||+ |.++++.
T Consensus 174 ~aVlAHELgHi---k~~di~~ 191 (336)
T PRK02870 174 QAVMAHELSHI---RHGDIRL 191 (336)
T ss_pred HHHHHHHHHHH---HcccHHH
Confidence 45689999998 5555543
No 52
>PF14247 DUF4344: Domain of unknown function (DUF4344)
Probab=23.50 E-value=72 Score=32.68 Aligned_cols=21 Identities=33% Similarity=0.450 Sum_probs=17.2
Q ss_pred HHHHHHHHhhhHHHHHHHHhh
Q 008143 329 AYGVLGVLLFHDVGHFLAAFP 349 (576)
Q Consensus 329 al~ll~IL~vHElGHylaArr 349 (576)
+++-+.-.+.||+||.+...+
T Consensus 88 ~~~~~~~~l~HE~GHAlI~~~ 108 (220)
T PF14247_consen 88 AIGNVLFTLYHELGHALIDDL 108 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHHh
Confidence 566677778999999998864
No 53
>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=23.44 E-value=43 Score=32.83 Aligned_cols=17 Identities=24% Similarity=0.532 Sum_probs=12.3
Q ss_pred HhhhHHHHHHHHhhCCc
Q 008143 336 LLFHDVGHFLAAFPKKV 352 (576)
Q Consensus 336 L~vHElGHylaArr~gV 352 (576)
..+||+||.+=...-.-
T Consensus 95 ~i~HElgHaLG~~HEh~ 111 (198)
T cd04327 95 VVLHEFGHALGFIHEHQ 111 (198)
T ss_pred HHHHHHHHHhcCccccc
Confidence 57799999986654433
No 54
>cd04275 ZnMc_pappalysin_like Zinc-dependent metalloprotease, pappalysin_like subfamily. The pregnancy-associated plasma protein A (PAPP-A or pappalysin-1) cleaves insulin-like growth factor-binding proteins 4 and 5, thereby promoting cell growth by releasing bound growth factor. This model includes pappalysins and related metalloprotease domains from all three kingdoms of life. The three-dimensional structure of an archaeal representative, ulilysin, has been solved.
Probab=22.37 E-value=16 Score=37.08 Aligned_cols=16 Identities=38% Similarity=0.721 Sum_probs=12.5
Q ss_pred HHHhhhHHHHHHHHhh
Q 008143 334 GVLLFHDVGHFLAAFP 349 (576)
Q Consensus 334 ~IL~vHElGHylaArr 349 (576)
+-.++||+||++-.+.
T Consensus 138 g~t~~HEvGH~lGL~H 153 (225)
T cd04275 138 GDTATHEVGHWLGLYH 153 (225)
T ss_pred cceeEEeccceeeeee
Confidence 4678999999986543
No 55
>PHA02456 zinc metallopeptidase motif-containing protein
Probab=22.35 E-value=51 Score=31.02 Aligned_cols=18 Identities=17% Similarity=0.100 Sum_probs=15.8
Q ss_pred hhhHHHHHHHHhhCCccc
Q 008143 337 LFHDVGHFLAAFPKKVKL 354 (576)
Q Consensus 337 ~vHElGHylaArr~gVk~ 354 (576)
+.||+.|.|.-|.||.-.
T Consensus 83 L~HEL~H~WQ~RsYG~i~ 100 (141)
T PHA02456 83 LAHELNHAWQFRTYGLVQ 100 (141)
T ss_pred HHHHHHHHHhhhccceee
Confidence 689999999999999643
No 56
>PRK10733 hflB ATP-dependent metalloprotease; Reviewed
Probab=21.81 E-value=1e+02 Score=35.90 Aligned_cols=29 Identities=17% Similarity=0.240 Sum_probs=21.2
Q ss_pred HHHhhhHHHHHHHHhhC--Ccccccceeecc
Q 008143 334 GVLLFHDVGHFLAAFPK--KVKLSIPFFIPN 362 (576)
Q Consensus 334 ~IL~vHElGHylaArr~--gVk~slPyFIP~ 362 (576)
-....||.||++++..+ ..++.....+|-
T Consensus 409 ~~~a~he~gha~~~~~~~~~~~~~~v~i~pr 439 (644)
T PRK10733 409 ESTAYHEAGHAIIGRLVPEHDPVHKVTIIPR 439 (644)
T ss_pred HHHHHHHHHHHHHHHHccCCCceeEEEEecc
Confidence 46788999999999765 355555566775
No 57
>cd04272 ZnMc_salivary_gland_MPs Zinc-dependent metalloprotease, salivary_gland_MPs. Metalloproteases secreted by the salivary glands of arthropods.
Probab=21.80 E-value=48 Score=32.82 Aligned_cols=20 Identities=20% Similarity=0.230 Sum_probs=16.5
Q ss_pred HHHhhhHHHHHHHHhhCCcc
Q 008143 334 GVLLFHDVGHFLAAFPKKVK 353 (576)
Q Consensus 334 ~IL~vHElGHylaArr~gVk 353 (576)
+..++||+||-+-+.+-+-.
T Consensus 146 ~~~~AHElGH~lG~~HD~~~ 165 (220)
T cd04272 146 VYTMTHELAHLLGAPHDGSP 165 (220)
T ss_pred HHHHHHHHHHHhCCCCCCCC
Confidence 47899999999998876544
No 58
>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=21.44 E-value=85 Score=31.25 Aligned_cols=50 Identities=28% Similarity=0.377 Sum_probs=27.0
Q ss_pred HHHhhhHHHHHHHHhhCC--cccccceeecccccccceeEeeCC---C-CCCChhhhhh
Q 008143 334 GVLLFHDVGHFLAAFPKK--VKLSIPFFIPNITLGSFGAITQFK---S-ILPDRSTKVD 386 (576)
Q Consensus 334 ~IL~vHElGHylaArr~g--Vk~slPyFIP~~~lGTfGAvir~k---s-~~p~RkaLFD 386 (576)
-.+.+||.||.++|-..+ .++..-..+|- |.-++++.+. . ...+|..+.+
T Consensus 29 ~~~A~HEAGhAvva~~l~~~~~v~~vsi~pr---g~~~G~~~~~~~~~~~~~t~~~l~~ 84 (213)
T PF01434_consen 29 RRIAYHEAGHAVVAYLLPPADPVSKVSIVPR---GSALGFTQFTPDEDRYIRTRSYLED 84 (213)
T ss_dssp HHHHHHHHHHHHHHHHSSS---EEEEESSTT---CCCCHCCEECHHTT-SS-BHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhcccccEEEEEEecC---CCcceeEEeccchhcccccHHHHHh
Confidence 467899999999998764 23333333453 3333444432 1 2356665543
No 59
>COG0830 UreF Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]
Probab=21.39 E-value=1.1e+02 Score=31.74 Aligned_cols=32 Identities=25% Similarity=0.320 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHhhcCCCCCChHHHHHHHhhh
Q 008143 458 IAGWCGLTTTAFNMLPVGCLDGGRAVQGAFGR 489 (576)
Q Consensus 458 ~aGWlGL~vTaLNLLPvGqLDGGrIl~Al~Gr 489 (576)
.+.-.|++.++.=|+|.||+||=+|+..+-..
T Consensus 158 ya~~~~lv~aavRlipLgQ~~gq~il~~l~~~ 189 (229)
T COG0830 158 YAWASNLVSAAVRLIPLGQLDGQKILAQLEPL 189 (229)
T ss_pred HHHHHHHHHHHHHhcccCcHHHHHHHHHhhHH
Confidence 34445899999999999999999999877644
No 60
>PRK01345 heat shock protein HtpX; Provisional
Probab=20.87 E-value=57 Score=34.73 Aligned_cols=12 Identities=17% Similarity=0.404 Sum_probs=9.9
Q ss_pred HHHhhhHHHHHH
Q 008143 334 GVLLFHDVGHFL 345 (576)
Q Consensus 334 ~IL~vHElGHyl 345 (576)
..+++||+||.-
T Consensus 125 ~aVlAHElgHi~ 136 (317)
T PRK01345 125 AGVMAHELAHVK 136 (317)
T ss_pred HHHHHHHHHHHH
Confidence 456899999986
No 61
>COG0501 HtpX Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]
Probab=20.62 E-value=60 Score=32.92 Aligned_cols=17 Identities=24% Similarity=0.440 Sum_probs=11.7
Q ss_pred HHhhhHHHHHHHHhhCCcc
Q 008143 335 VLLFHDVGHFLAAFPKKVK 353 (576)
Q Consensus 335 IL~vHElGHylaArr~gVk 353 (576)
-+++||+||.. .+|-+.
T Consensus 159 aVlaHElgHi~--~rd~~~ 175 (302)
T COG0501 159 AVLAHELGHIK--NRHTLV 175 (302)
T ss_pred HHHHHHHHHHh--cccHHH
Confidence 45899999963 455444
No 62
>PRK02391 heat shock protein HtpX; Provisional
Probab=20.56 E-value=59 Score=34.31 Aligned_cols=11 Identities=27% Similarity=0.600 Sum_probs=8.9
Q ss_pred HHHhhhHHHHH
Q 008143 334 GVLLFHDVGHF 344 (576)
Q Consensus 334 ~IL~vHElGHy 344 (576)
..+++||+||+
T Consensus 134 ~aVlaHElgHi 144 (296)
T PRK02391 134 EAVLAHELSHV 144 (296)
T ss_pred HHHHHHHHHHH
Confidence 35689999995
Done!