Query 020057
Match_columns 331
No_of_seqs 180 out of 285
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 06:40:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020057.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020057hhsearch_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 99.1 1.4E-10 3E-15 104.4 5.6 75 253-330 2-76 (183)
2 cd06164 S2P-M50_SpoIVFB_CBS Sp 97.7 9.5E-05 2.1E-09 68.6 6.9 46 279-324 37-82 (227)
3 cd06161 S2P-M50_SpoIVFB SpoIVF 97.3 0.00031 6.8E-09 64.0 4.4 43 282-324 25-67 (208)
4 cd06159 S2P-M50_PDZ_Arch Uncha 97.1 0.0014 2.9E-08 62.7 6.9 34 285-318 108-141 (263)
5 cd06162 S2P-M50_PDZ_SREBP Ster 95.3 0.018 4E-07 55.8 3.9 28 291-318 131-158 (277)
6 KOG2921 Intramembrane metallop 90.6 0.21 4.6E-06 51.3 3.1 41 285-325 120-162 (484)
7 PF05572 Peptidase_M43: Pregna 76.0 1.2 2.6E-05 39.4 0.9 12 297-308 71-82 (154)
8 PF06114 DUF955: Domain of unk 64.7 4.1 8.9E-05 31.6 1.6 14 299-312 46-59 (122)
9 PF07423 DUF1510: Protein of u 58.6 5.7 0.00012 37.6 1.6 63 159-230 150-213 (217)
10 PF13485 Peptidase_MA_2: Pepti 56.7 8.9 0.00019 30.0 2.2 17 297-313 27-43 (128)
11 PF13688 Reprolysin_5: Metallo 55.2 6.7 0.00014 34.5 1.4 16 296-311 143-158 (196)
12 PRK03982 heat shock protein Ht 52.8 8.7 0.00019 36.7 1.9 12 295-307 126-137 (288)
13 PRK03001 M48 family peptidase; 52.8 8.7 0.00019 36.6 1.9 11 296-307 126-136 (283)
14 PF01435 Peptidase_M48: Peptid 52.0 10 0.00022 33.3 2.1 17 298-316 92-108 (226)
15 COG0501 HtpX Zn-dependent prot 51.7 9.4 0.0002 35.4 1.9 13 294-307 157-169 (302)
16 PF13582 Reprolysin_3: Metallo 50.4 7.5 0.00016 31.5 0.9 13 297-309 109-121 (124)
17 cd04267 ZnMc_ADAM_like Zinc-de 49.9 7.4 0.00016 34.2 0.8 18 296-313 134-151 (192)
18 COG5309 Exo-beta-1,3-glucanase 49.8 31 0.00068 34.4 5.2 61 158-222 218-281 (305)
19 COG1994 SpoIVFB Zn-dependent p 49.8 14 0.0003 34.4 2.6 41 283-323 40-80 (230)
20 PF00413 Peptidase_M10: Matrix 48.9 11 0.00023 31.6 1.6 13 298-310 108-120 (154)
21 cd04279 ZnMc_MMP_like_1 Zinc-d 48.8 11 0.00024 32.3 1.7 20 297-316 106-125 (156)
22 PF13574 Reprolysin_2: Metallo 48.6 7.6 0.00016 34.5 0.7 17 296-312 112-128 (173)
23 PRK04897 heat shock protein Ht 47.9 11 0.00025 36.3 1.9 11 296-307 139-149 (298)
24 PRK02870 heat shock protein Ht 47.8 10 0.00022 37.8 1.5 10 296-306 175-184 (336)
25 cd04269 ZnMc_adamalysin_II_lik 47.1 13 0.00028 32.8 2.0 17 295-311 131-147 (194)
26 PRK11037 hypothetical protein; 46.9 65 0.0014 26.7 5.7 65 152-217 4-81 (83)
27 PRK01345 heat shock protein Ht 45.6 13 0.00028 36.5 1.9 13 294-307 124-136 (317)
28 PRK12462 phosphoserine aminotr 45.5 42 0.00092 33.8 5.5 66 150-223 9-76 (364)
29 PF02031 Peptidase_M7: Strepto 45.1 13 0.00028 33.1 1.6 11 298-308 80-90 (132)
30 PRK03072 heat shock protein Ht 44.5 14 0.0003 35.7 1.9 11 296-307 129-139 (288)
31 cd04275 ZnMc_pappalysin_like Z 43.0 4 8.7E-05 38.4 -2.0 12 297-308 139-150 (225)
32 PRK05457 heat shock protein Ht 42.8 15 0.00034 35.4 1.9 10 296-306 136-145 (284)
33 KOG2719 Metalloprotease [Gener 42.4 14 0.00031 38.4 1.6 12 296-308 282-293 (428)
34 COG2856 Predicted Zn peptidase 42.3 13 0.00029 34.9 1.4 14 299-312 76-89 (213)
35 PRK02391 heat shock protein Ht 42.1 16 0.00035 35.5 1.9 10 296-306 135-144 (296)
36 PLN02452 phosphoserine transam 41.6 58 0.0012 32.5 5.7 67 149-223 11-79 (365)
37 PF10692 DUF2498: Protein of u 41.5 83 0.0018 26.0 5.6 64 153-217 4-80 (82)
38 PRK01265 heat shock protein Ht 41.0 17 0.00037 36.2 1.9 10 296-306 142-151 (324)
39 cd00203 ZnMc Zinc-dependent me 40.6 14 0.00031 31.1 1.2 17 295-311 96-112 (167)
40 COG3824 Predicted Zn-dependent 39.6 13 0.00029 33.0 0.8 18 196-213 21-38 (136)
41 PF04315 DUF462: Protein of un 39.3 16 0.00035 33.5 1.4 11 299-309 45-55 (164)
42 PF01434 Peptidase_M41: Peptid 36.1 25 0.00054 32.2 2.1 18 296-313 29-46 (213)
43 PF13699 DUF4157: Domain of un 35.7 22 0.00049 28.2 1.5 12 298-309 64-75 (79)
44 PF01421 Reprolysin: Reprolysi 35.6 26 0.00057 31.1 2.1 21 293-313 129-149 (199)
45 PF12046 DUF3529: Protein of u 34.9 1.9E+02 0.0042 26.8 7.5 20 194-216 40-59 (173)
46 smart00235 ZnMc Zinc-dependent 34.6 21 0.00045 29.8 1.2 13 298-310 89-101 (140)
47 cd04270 ZnMc_TACE_like Zinc-de 33.5 26 0.00057 32.9 1.8 17 295-311 167-183 (244)
48 cd04268 ZnMc_MMP_like Zinc-dep 33.3 39 0.00084 28.6 2.7 15 296-310 95-109 (165)
49 PF13583 Reprolysin_4: Metallo 32.1 23 0.00049 32.5 1.1 15 299-313 141-155 (206)
50 KOG1832 HIV-1 Vpr-binding prot 32.0 48 0.001 38.2 3.7 15 5-19 1354-1368(1516)
51 cd04277 ZnMc_serralysin_like Z 31.2 25 0.00055 30.9 1.2 14 297-310 115-128 (186)
52 PF04228 Zn_peptidase: Putativ 31.1 41 0.0009 33.1 2.8 12 299-310 174-185 (292)
53 cd04278 ZnMc_MMP Zinc-dependen 31.0 22 0.00049 30.5 0.9 13 298-310 110-122 (157)
54 PF15281 Consortin_C: Consorti 30.2 1.1E+02 0.0023 26.8 4.8 12 297-308 101-112 (113)
55 PF10263 SprT-like: SprT-like 29.3 31 0.00067 29.3 1.4 11 299-309 64-74 (157)
56 cd04272 ZnMc_salivary_gland_MP 28.7 34 0.00075 31.1 1.7 18 296-313 146-163 (220)
57 PF01990 ATP-synt_F: ATP synth 27.6 2.8E+02 0.0061 22.1 6.6 51 168-237 15-79 (95)
58 PF08002 DUF1697: Protein of u 26.9 1.3E+02 0.0028 26.1 4.9 57 154-218 17-75 (137)
59 PF08800 VirE_N: VirE N-termin 26.7 2E+02 0.0044 24.8 6.0 59 154-212 39-112 (136)
60 TIGR02500 type_III_yscD type I 26.2 1.6E+02 0.0034 29.9 6.0 39 181-219 302-340 (410)
61 PF14891 Peptidase_M91: Effect 25.7 46 0.00099 29.6 1.9 16 296-311 104-119 (174)
62 PTZ00429 beta-adaptin; Provisi 25.4 88 0.0019 34.7 4.3 32 75-106 608-639 (746)
63 PHA02456 zinc metallopeptidase 24.2 46 0.001 29.5 1.6 23 299-321 83-107 (141)
64 cd04927 ACT_ACR-like_2 Second 23.9 99 0.0021 23.8 3.2 34 169-213 40-73 (76)
65 PF05683 Fumerase_C: Fumarase 23.7 1.1E+02 0.0023 29.2 3.9 43 152-210 31-73 (205)
66 PF01431 Peptidase_M13: Peptid 23.5 58 0.0012 29.0 2.1 19 290-308 31-49 (206)
67 KOG0391 SNF2 family DNA-depend 23.2 1.3E+02 0.0027 36.1 5.0 18 297-314 813-830 (1958)
68 PF13492 GAF_3: GAF domain; PD 23.1 1.7E+02 0.0037 22.4 4.4 28 195-222 1-29 (129)
69 PF11667 DUF3267: Protein of u 23.0 27 0.00058 28.7 -0.1 21 295-315 4-24 (111)
70 PF05265 DUF723: Protein of un 23.0 1.6E+02 0.0034 23.1 4.1 36 199-237 4-39 (60)
71 PF12388 Peptidase_M57: Dual-a 22.5 50 0.0011 31.4 1.6 22 289-310 127-148 (211)
72 PF04155 Ground-like: Ground-l 22.4 58 0.0013 25.3 1.7 26 194-219 22-47 (76)
73 PF01454 MAGE: MAGE family; I 22.3 3.7E+02 0.008 23.9 7.0 26 193-220 29-54 (195)
74 PRK13267 archaemetzincin-like 22.1 45 0.00097 30.5 1.2 11 298-308 128-138 (179)
75 PF09471 Peptidase_M64: IgA Pe 22.1 45 0.00098 32.2 1.2 12 297-308 218-229 (264)
76 KOG2236 Uncharacterized conser 22.0 1.2E+02 0.0025 32.3 4.2 22 140-161 179-200 (483)
77 PF08219 TOM13: Outer membrane 21.6 73 0.0016 26.1 2.1 20 297-318 54-73 (77)
78 PRK06842 fumarate hydratase; P 21.4 95 0.002 29.0 3.1 61 154-237 7-67 (185)
79 PLN03199 delta6-acyl-lipid des 21.3 2E+02 0.0044 29.9 5.9 17 195-212 109-125 (485)
80 PF07998 Peptidase_M54: Peptid 21.1 44 0.00095 31.2 0.9 31 185-216 5-37 (194)
81 smart00731 SprT SprT homologue 21.0 57 0.0012 28.1 1.5 11 300-310 64-74 (146)
82 PF12315 DUF3633: Protein of u 20.7 58 0.0013 31.1 1.6 27 284-313 84-110 (212)
83 KOG2987 Fatty acid desaturase 20.5 2.7E+02 0.0058 28.0 6.1 13 296-308 84-96 (324)
84 TIGR01364 serC_1 phosphoserine 20.5 1.4E+02 0.0031 29.2 4.4 60 155-222 2-63 (349)
85 KOG3320 40S ribosomal protein 20.2 1.5E+02 0.0033 27.9 4.2 27 196-222 73-99 (192)
86 COG4783 Putative Zn-dependent 20.2 62 0.0013 34.3 1.8 7 300-306 135-141 (484)
No 1
>cd06160 S2P-M50_like_2 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the S2P/M50 family of RIP proteases use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. In eukaryotic cells they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum stress responses. In prokaryotes they regulate such processes as sporulation, cell division, stress response, and cell differentiation. This group includes bacterial, eukaryotic, and Archaeal S2P/M50s homologs with additional putative N- and C-terminal transmembrane spanning regions, relative to the core protein, and no PDZ domains.
Probab=99.08 E-value=1.4e-10 Score=104.42 Aligned_cols=75 Identities=35% Similarity=0.461 Sum_probs=61.9
Q ss_pred HHHHHHHHHHHhhccccccccchhhccchhHhhhchhhHHHHHHHHHHHHHHHHHHHHHcCCccccceeccccccccc
Q 020057 253 AFGLVTVFTLLLRNVPALQSNLLSTFDNLNLLTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQALLV 330 (331)
Q Consensus 253 LLfl~Tl~TTl~aGa~~L~~~~L~~f~~p~~l~~gLP~al~ll~ILgvHE~GHylaArr~gVklSlPyFIP~~QLGsv 330 (331)
+++++|++|....+...... .+.++++.+..+++++++++.++.+||+||+++||++|+|+..|+|+|++++|++
T Consensus 2 ~~~~~s~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~l~l~~~l~iHElgH~~~A~~~G~~~~~~~l~P~~~~G~~ 76 (183)
T cd06160 2 LLLVLTLLTTLLVGAWLSGN---DVPGNPLLLLQGLPFALALLAILGIHEMGHYLAARRHGVKASLPYFIPFPFIGTF 76 (183)
T ss_pred HHHHHHHHHHHHHHHHHhcc---cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCccceeeeehHhcCcE
Confidence 45688998888877531111 2336788899999999999999999999999999999999999999998777754
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=97.69 E-value=9.5e-05 Score=68.62 Aligned_cols=46 Identities=26% Similarity=0.249 Sum_probs=39.7
Q ss_pred cchhHhhhchhhHHHHHHHHHHHHHHHHHHHHHcCCccccceeccc
Q 020057 279 DNLNLLTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVPS 324 (331)
Q Consensus 279 ~~p~~l~~gLP~al~ll~ILgvHE~GHylaArr~gVklSlPyFIP~ 324 (331)
.++..+.-|+.++++++.++.+||+||+++||++|+|+.--.+.|+
T Consensus 37 ~~~~~~~~g~~~~~~l~~~v~iHElgH~~~A~~~G~~v~~i~l~p~ 82 (227)
T cd06164 37 LGAVAWLLGLAAALLLFASVLLHELGHSLVARRYGIPVRSITLFLF 82 (227)
T ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCeECeEEEEee
Confidence 3455677899999999999999999999999999999987677764
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=97.25 E-value=0.00031 Score=63.96 Aligned_cols=43 Identities=33% Similarity=0.417 Sum_probs=37.0
Q ss_pred hHhhhchhhHHHHHHHHHHHHHHHHHHHHHcCCccccceeccc
Q 020057 282 NLLTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVPS 324 (331)
Q Consensus 282 ~~l~~gLP~al~ll~ILgvHE~GHylaArr~gVklSlPyFIP~ 324 (331)
..+..++.+++.++.++.+||+||+++||++|+++.--.+.|+
T Consensus 25 ~~~~~~~~~~l~l~~~v~iHElgH~~~A~~~G~~v~~i~l~p~ 67 (208)
T cd06161 25 VAWLLGLLEALLLFLSVLLHELGHALVARRYGIRVRSITLLPF 67 (208)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccceEEEee
Confidence 3566788999999999999999999999999999876666664
No 4
>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=97.08 E-value=0.0014 Score=62.69 Aligned_cols=34 Identities=24% Similarity=0.292 Sum_probs=28.0
Q ss_pred hhchhhHHHHHHHHHHHHHHHHHHHHHcCCcccc
Q 020057 285 TNGLPGALVTALVIGVHELGHILAAKSTGVELGV 318 (331)
Q Consensus 285 ~~gLP~al~ll~ILgvHE~GHylaArr~gVklSl 318 (331)
...+.+.++++..+.+||+||.++||++|+++..
T Consensus 108 i~~~~~~iaL~isv~iHElgHa~~Ar~~G~~V~~ 141 (263)
T cd06159 108 IPLPYGIIALVVGVVVHELSHGILARVEGIKVKS 141 (263)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHcCCEECc
Confidence 3455566677778889999999999999999875
No 5
>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=95.27 E-value=0.018 Score=55.76 Aligned_cols=28 Identities=29% Similarity=0.218 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcccc
Q 020057 291 ALVTALVIGVHELGHILAAKSTGVELGV 318 (331)
Q Consensus 291 al~ll~ILgvHE~GHylaArr~gVklSl 318 (331)
.++++....+||+||.++|+++|+++.-
T Consensus 131 l~al~isvvvHElgHal~A~~~gi~V~~ 158 (277)
T cd06162 131 FTALLISGVVHEMGHGVAAVREQVRVNG 158 (277)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCeece
Confidence 3455566778999999999999999875
No 6
>KOG2921 consensus Intramembrane metalloprotease (sterol-regulatory element-binding protein (SREBP) protease) [Posttranslational modification, protein turnover, chaperones]
Probab=90.57 E-value=0.21 Score=51.29 Aligned_cols=41 Identities=37% Similarity=0.592 Sum_probs=29.1
Q ss_pred hhchhhHHHHHHH-HHHHHHHHHHHHHHcCCccc-cceecccc
Q 020057 285 TNGLPGALVTALV-IGVHELGHILAAKSTGVELG-VPYFVPSW 325 (331)
Q Consensus 285 ~~gLP~al~ll~I-LgvHE~GHylaArr~gVklS-lPyFIP~~ 325 (331)
+++++|-+..+.| +-+|||||-|||.+.||++. .=.||=++
T Consensus 120 l~~I~yf~t~lvi~~vvHElGHalAA~segV~vngfgIfi~ai 162 (484)
T KOG2921|consen 120 LSGIAYFLTSLVITVVVHELGHALAAASEGVQVNGFGIFIAAI 162 (484)
T ss_pred cccchhhhhhHHHHHHHHHhhHHHHHHhcCceeeeeEEEEEEE
Confidence 5677776655544 44799999999999999975 33344333
No 7
>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=76.04 E-value=1.2 Score=39.38 Aligned_cols=12 Identities=42% Similarity=0.556 Sum_probs=9.7
Q ss_pred HHHHHHHHHHHH
Q 020057 297 VIGVHELGHILA 308 (331)
Q Consensus 297 ILgvHE~GHyla 308 (331)
-.++||+|||+=
T Consensus 71 ~TltHEvGH~LG 82 (154)
T PF05572_consen 71 KTLTHEVGHWLG 82 (154)
T ss_dssp HHHHHHHHHHTT
T ss_pred cchhhhhhhhhc
Confidence 556999999973
No 8
>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=64.72 E-value=4.1 Score=31.65 Aligned_cols=14 Identities=50% Similarity=0.688 Sum_probs=10.7
Q ss_pred HHHHHHHHHHHHHc
Q 020057 299 GVHELGHILAAKST 312 (331)
Q Consensus 299 gvHE~GHylaArr~ 312 (331)
.+||+||++.-...
T Consensus 46 laHELgH~~~~~~~ 59 (122)
T PF06114_consen 46 LAHELGHILLHHGD 59 (122)
T ss_dssp HHHHHHHHHHHH-H
T ss_pred HHHHHHHHHhhhcc
Confidence 48999999986654
No 9
>PF07423 DUF1510: Protein of unknown function (DUF1510); InterPro: IPR009988 This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.
Probab=58.56 E-value=5.7 Score=37.62 Aligned_cols=63 Identities=21% Similarity=0.302 Sum_probs=43.4
Q ss_pred hHHHHHhhcccccceEEEEeeeeeCCeEEEEcccCChHHHHHHHHHHHHHHhcCCceEEEEEecCCCC-CceE
Q 020057 159 ETIDILKDQVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFGDQYKLFLLVNPEDD-KPVA 230 (331)
Q Consensus 159 EdLk~IK~~~FG~dTFfvT~~e~~~qGVIfRGNLRg~pEevy~kL~~kLee~fGDrY~LfLvee~edg-KPV~ 230 (331)
-|++-|+.. ..|+|++..-+=-+.|.||= |.|.+++..|+.+= . |.+|+++|-=-.+.| ||+-
T Consensus 150 ~DW~Em~~A-----is~atgi~~~~mi~w~ign~-G~~~~a~gtVs~k~--~-~~~YrV~i~WVd~eGWkP~k 213 (217)
T PF07423_consen 150 VDWNEMLKA-----ISYATGISEDNMIVWFIGNN-GSPQKAIGTVSDKD--T-GKKYRVYIEWVDNEGWKPVK 213 (217)
T ss_pred cCHHHHHHH-----HHHhhCCChhheEEEhhhcC-CcccceeEEeccCC--C-CceEEEEEEEecCCCcccee
Confidence 455544443 67899998888889999994 77799999988753 3 678997752111223 7764
No 10
>PF13485 Peptidase_MA_2: Peptidase MA superfamily
Probab=56.73 E-value=8.9 Score=30.00 Aligned_cols=17 Identities=29% Similarity=0.311 Sum_probs=14.0
Q ss_pred HHHHHHHHHHHHHHHcC
Q 020057 297 VIGVHELGHILAAKSTG 313 (331)
Q Consensus 297 ILgvHE~GHylaArr~g 313 (331)
-+.+||++|.|.....+
T Consensus 27 ~~l~HE~~H~~~~~~~~ 43 (128)
T PF13485_consen 27 RVLAHELAHQWFGNYFG 43 (128)
T ss_pred HHHHHHHHHHHHHHHcC
Confidence 45699999999988754
No 11
>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=55.17 E-value=6.7 Score=34.47 Aligned_cols=16 Identities=38% Similarity=0.511 Sum_probs=11.2
Q ss_pred HHHHHHHHHHHHHHHH
Q 020057 296 LVIGVHELGHILAAKS 311 (331)
Q Consensus 296 ~ILgvHE~GHylaArr 311 (331)
.+..+||+||-|=|..
T Consensus 143 ~~~~AHEiGH~lGa~H 158 (196)
T PF13688_consen 143 AITFAHEIGHNLGAPH 158 (196)
T ss_dssp HHHHHHHHHHHTT---
T ss_pred ehhhHHhHHHhcCCCC
Confidence 4677999999998874
No 12
>PRK03982 heat shock protein HtpX; Provisional
Probab=52.80 E-value=8.7 Score=36.73 Aligned_cols=12 Identities=58% Similarity=0.653 Sum_probs=8.9
Q ss_pred HHHHHHHHHHHHH
Q 020057 295 ALVIGVHELGHIL 307 (331)
Q Consensus 295 l~ILgvHE~GHyl 307 (331)
.+|+ +||+||+-
T Consensus 126 ~AVl-AHElgHi~ 137 (288)
T PRK03982 126 EGVI-AHELTHIK 137 (288)
T ss_pred HHHH-HHHHHHHH
Confidence 3444 89999984
No 13
>PRK03001 M48 family peptidase; Provisional
Probab=52.77 E-value=8.7 Score=36.64 Aligned_cols=11 Identities=45% Similarity=0.688 Sum_probs=8.4
Q ss_pred HHHHHHHHHHHH
Q 020057 296 LVIGVHELGHIL 307 (331)
Q Consensus 296 ~ILgvHE~GHyl 307 (331)
+|| +||+||+-
T Consensus 126 aVl-AHElgHi~ 136 (283)
T PRK03001 126 GVM-AHELAHVK 136 (283)
T ss_pred HHH-HHHHHHHh
Confidence 444 89999984
No 14
>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=52.02 E-value=10 Score=33.35 Aligned_cols=17 Identities=35% Similarity=0.460 Sum_probs=11.6
Q ss_pred HHHHHHHHHHHHHHcCCcc
Q 020057 298 IGVHELGHILAAKSTGVEL 316 (331)
Q Consensus 298 LgvHE~GHylaArr~gVkl 316 (331)
+.+||+||+. .+|..+.
T Consensus 92 VlaHElgH~~--~~h~~~~ 108 (226)
T PF01435_consen 92 VLAHELGHIK--HRHILKS 108 (226)
T ss_dssp HHHHHHHHHH--TTHCCCC
T ss_pred HHHHHHHHHH--cCCcchH
Confidence 3489999986 4554444
No 15
>COG0501 HtpX Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]
Probab=51.74 E-value=9.4 Score=35.40 Aligned_cols=13 Identities=54% Similarity=0.818 Sum_probs=9.3
Q ss_pred HHHHHHHHHHHHHH
Q 020057 294 TALVIGVHELGHIL 307 (331)
Q Consensus 294 ll~ILgvHE~GHyl 307 (331)
+.+|| +||+||+.
T Consensus 157 l~aVl-aHElgHi~ 169 (302)
T COG0501 157 LEAVL-AHELGHIK 169 (302)
T ss_pred HHHHH-HHHHHHHh
Confidence 34455 89999973
No 16
>PF13582 Reprolysin_3: Metallo-peptidase family M12B Reprolysin-like; PDB: 3P24_C.
Probab=50.40 E-value=7.5 Score=31.55 Aligned_cols=13 Identities=38% Similarity=0.434 Sum_probs=9.4
Q ss_pred HHHHHHHHHHHHH
Q 020057 297 VIGVHELGHILAA 309 (331)
Q Consensus 297 ILgvHE~GHylaA 309 (331)
...+||+||-+=+
T Consensus 109 ~~~~HEiGH~lGl 121 (124)
T PF13582_consen 109 DTFAHEIGHNLGL 121 (124)
T ss_dssp THHHHHHHHHTT-
T ss_pred eEeeehhhHhcCC
Confidence 4558999998744
No 17
>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=49.88 E-value=7.4 Score=34.24 Aligned_cols=18 Identities=44% Similarity=0.639 Sum_probs=13.8
Q ss_pred HHHHHHHHHHHHHHHHcC
Q 020057 296 LVIGVHELGHILAAKSTG 313 (331)
Q Consensus 296 ~ILgvHE~GHylaArr~g 313 (331)
+...+||+||.+=+..-+
T Consensus 134 ~~~~aHElGH~lG~~HD~ 151 (192)
T cd04267 134 ALTMAHELGHNLGAEHDG 151 (192)
T ss_pred hhhhhhhHHhhcCCcCCC
Confidence 456799999999776544
No 18
>COG5309 Exo-beta-1,3-glucanase [Carbohydrate transport and metabolism]
Probab=49.84 E-value=31 Score=34.36 Aligned_cols=61 Identities=16% Similarity=0.312 Sum_probs=46.1
Q ss_pred HhHHHHHhhccccc-ceEEEEeeeeeCCeEEEEcccCC--hHHHHHHHHHHHHHHhcCCceEEEEEec
Q 020057 158 KETIDILKDQVFGF-DTFFVTNQEPYEGGVLFKGNLRG--QAAKTYEKISTRMKNKFGDQYKLFLLVN 222 (331)
Q Consensus 158 ~EdLk~IK~~~FG~-dTFfvT~~e~~~qGVIfRGNLRg--~pEevy~kL~~kLee~fGDrY~LfLvee 222 (331)
.|.|++||. .||= .+|||||+-.--.|.-+-++.-. +..+.++++...|+.. | |..|+++-
T Consensus 218 ~~q~e~vqs-a~g~~k~~~v~EtGWPS~G~~~G~a~pS~anq~~~~~~i~~~~~~~-G--~d~fvfeA 281 (305)
T COG5309 218 LEQLERVQS-ACGTKKTVWVTETGWPSDGRTYGSAVPSVANQKIAVQEILNALRSC-G--YDVFVFEA 281 (305)
T ss_pred HHHHHHHHH-hcCCCccEEEeeccCCCCCCccCCcCCChhHHHHHHHHHHhhhhcc-C--ccEEEeee
Confidence 677999998 7776 99999999655555555555433 4678889999999888 9 77787764
No 19
>COG1994 SpoIVFB Zn-dependent proteases [General function prediction only]
Probab=49.75 E-value=14 Score=34.40 Aligned_cols=41 Identities=24% Similarity=0.259 Sum_probs=30.9
Q ss_pred HhhhchhhHHHHHHHHHHHHHHHHHHHHHcCCccccceecc
Q 020057 283 LLTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVP 323 (331)
Q Consensus 283 ~l~~gLP~al~ll~ILgvHE~GHylaArr~gVklSlPyFIP 323 (331)
.+.++....++++.-+..||+||+..++++++++-.-.+.+
T Consensus 40 ~~~~~~~~~~~l~~rl~l~~~gh~~~~~~~~~~l~~~~i~~ 80 (230)
T COG1994 40 SLGDGTAAFVGLAHRLVLHPLGHSDEAGRLGLKLLLALLFG 80 (230)
T ss_pred HHhhhHHHHHHHhHHHhhhHhhHHHHHHHHHHHHHHHHHHh
Confidence 34555665555555777999999999999999887766653
No 20
>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=48.85 E-value=11 Score=31.59 Aligned_cols=13 Identities=38% Similarity=0.889 Sum_probs=9.6
Q ss_pred HHHHHHHHHHHHH
Q 020057 298 IGVHELGHILAAK 310 (331)
Q Consensus 298 LgvHE~GHylaAr 310 (331)
.++|||||-+=-.
T Consensus 108 v~~HEiGHaLGL~ 120 (154)
T PF00413_consen 108 VAIHEIGHALGLD 120 (154)
T ss_dssp HHHHHHHHHTTBE
T ss_pred hhhhccccccCcC
Confidence 3489999987543
No 21
>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=48.79 E-value=11 Score=32.30 Aligned_cols=20 Identities=35% Similarity=0.446 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHHcCCcc
Q 020057 297 VIGVHELGHILAAKSTGVEL 316 (331)
Q Consensus 297 ILgvHE~GHylaArr~gVkl 316 (331)
-..+|||||-+=.+...-+-
T Consensus 106 ~~~~HEiGHaLGL~H~~~~~ 125 (156)
T cd04279 106 AIALHELGHALGLWHHSDRP 125 (156)
T ss_pred HHHHHHhhhhhcCCCCCCCc
Confidence 34589999999887766653
No 22
>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=48.56 E-value=7.6 Score=34.48 Aligned_cols=17 Identities=41% Similarity=0.483 Sum_probs=11.2
Q ss_pred HHHHHHHHHHHHHHHHc
Q 020057 296 LVIGVHELGHILAAKST 312 (331)
Q Consensus 296 ~ILgvHE~GHylaArr~ 312 (331)
....+|||||-|=|..-
T Consensus 112 ~~~~aHElGH~lGa~Hd 128 (173)
T PF13574_consen 112 IDTFAHELGHQLGAPHD 128 (173)
T ss_dssp HHHHHHHHHHHHT---S
T ss_pred eeeehhhhHhhcCCCCC
Confidence 34579999999988653
No 23
>PRK04897 heat shock protein HtpX; Provisional
Probab=47.90 E-value=11 Score=36.34 Aligned_cols=11 Identities=55% Similarity=0.616 Sum_probs=8.4
Q ss_pred HHHHHHHHHHHH
Q 020057 296 LVIGVHELGHIL 307 (331)
Q Consensus 296 ~ILgvHE~GHyl 307 (331)
+|+ +||+||+-
T Consensus 139 aVl-AHElgHi~ 149 (298)
T PRK04897 139 GVI-GHEISHIR 149 (298)
T ss_pred HHH-HHHHHHHh
Confidence 344 89999974
No 24
>PRK02870 heat shock protein HtpX; Provisional
Probab=47.77 E-value=10 Score=37.85 Aligned_cols=10 Identities=60% Similarity=0.959 Sum_probs=7.9
Q ss_pred HHHHHHHHHHH
Q 020057 296 LVIGVHELGHI 306 (331)
Q Consensus 296 ~ILgvHE~GHy 306 (331)
+|+ +||+||+
T Consensus 175 aVl-AHELgHi 184 (336)
T PRK02870 175 AVM-AHELSHI 184 (336)
T ss_pred HHH-HHHHHHH
Confidence 344 8999998
No 25
>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=47.12 E-value=13 Score=32.82 Aligned_cols=17 Identities=41% Similarity=0.473 Sum_probs=13.1
Q ss_pred HHHHHHHHHHHHHHHHH
Q 020057 295 ALVIGVHELGHILAAKS 311 (331)
Q Consensus 295 l~ILgvHE~GHylaArr 311 (331)
.++..+||+||-+=+..
T Consensus 131 ~a~~~AHElGH~lG~~H 147 (194)
T cd04269 131 FAVTMAHELGHNLGMEH 147 (194)
T ss_pred HHHHHHHHHHhhcCCCc
Confidence 35778999999886653
No 26
>PRK11037 hypothetical protein; Provisional
Probab=46.94 E-value=65 Score=26.66 Aligned_cols=65 Identities=18% Similarity=0.383 Sum_probs=43.8
Q ss_pred cccCCCHhHH-----HHHhhcccccceEEEEeeeeeCCeEEEEccc--CC------hHHHHHHHHHHHHHHhcCCceEE
Q 020057 152 EYIRIPKETI-----DILKDQVFGFDTFFVTNQEPYEGGVLFKGNL--RG------QAAKTYEKISTRMKNKFGDQYKL 217 (331)
Q Consensus 152 ~~~~ip~EdL-----k~IK~~~FG~dTFfvT~~e~~~qGVIfRGNL--Rg------~pEevy~kL~~kLee~fGDrY~L 217 (331)
+..+|++++| ++||+.===+...++|+++..++..+|||.. .. +...||+ +-+.|+-.+..+|.|
T Consensus 4 ~~~~I~~~~LL~~AN~iI~~Hedyi~GM~a~~Veqk~~VLVFkGeyFLD~~GlPT~KtTAvFN-MFK~LAh~LS~~y~L 81 (83)
T PRK11037 4 ETQPIDRETLLLEANKIIREHEDYLAGMRATDVEQKNGVLVFRGEYFLDEQGLPTAKTTAVFN-MFKHLAHVLSEKYHL 81 (83)
T ss_pred CCcccCHHHHHHHHHHHHHhhHHHhcccccceeeeeCCEEEEecceeecCCCCCCccchHHHH-HHHHHHHHhCcceec
Confidence 4557888887 3555432234457899999999999999983 21 2345554 556677777888884
No 27
>PRK01345 heat shock protein HtpX; Provisional
Probab=45.60 E-value=13 Score=36.48 Aligned_cols=13 Identities=46% Similarity=0.644 Sum_probs=9.4
Q ss_pred HHHHHHHHHHHHHH
Q 020057 294 TALVIGVHELGHIL 307 (331)
Q Consensus 294 ll~ILgvHE~GHyl 307 (331)
+.+|+ +||+||+-
T Consensus 124 L~aVl-AHElgHi~ 136 (317)
T PRK01345 124 VAGVM-AHELAHVK 136 (317)
T ss_pred HHHHH-HHHHHHHH
Confidence 33454 89999985
No 28
>PRK12462 phosphoserine aminotransferase; Provisional
Probab=45.50 E-value=42 Score=33.82 Aligned_cols=66 Identities=12% Similarity=0.178 Sum_probs=48.3
Q ss_pred cccccCCCHhHHHHHhhcccccceEEEEeeeeeCCeEEEEcccCChHHHHHHHHHHHHHHhcC--CceEEEEEecC
Q 020057 150 LDEYIRIPKETIDILKDQVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFG--DQYKLFLLVNP 223 (331)
Q Consensus 150 ~~~~~~ip~EdLk~IK~~~FG~dTFfvT~~e~~~qGVIfRGNLRg~pEevy~kL~~kLee~fG--DrY~LfLvee~ 223 (331)
...+..+|+|.|++++.++.-|.. -+-+|+=.+---.+-.++|+++.++|++.|+ +.|.+++++.+
T Consensus 9 ~aGPa~lp~~Vl~~~~~~~~~~~~--------~g~si~eisHRs~~F~~i~~~~~~~Lr~Ll~~P~~y~Vlfl~Gg 76 (364)
T PRK12462 9 SGGPGALPDTVLEQVRQAVVELPE--------TGLSVLGMSHRSSWFSSLLAQAEADLRDLLGIPDEYGVVFLQGG 76 (364)
T ss_pred cCCCcCCCHHHHHHHHHHHhcccc--------cCccccccccccHHHHHHHHHHHHHHHHHhCCCCCCeEEEEecc
Confidence 456789999999999987544432 1223443333334779999999999999999 68999888864
No 29
>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=45.10 E-value=13 Score=33.09 Aligned_cols=11 Identities=73% Similarity=1.189 Sum_probs=8.7
Q ss_pred HHHHHHHHHHH
Q 020057 298 IGVHELGHILA 308 (331)
Q Consensus 298 LgvHE~GHyla 308 (331)
..+||+||.+-
T Consensus 80 IaaHE~GHiLG 90 (132)
T PF02031_consen 80 IAAHELGHILG 90 (132)
T ss_dssp HHHHHHHHHHT
T ss_pred eeeehhccccC
Confidence 45899999863
No 30
>PRK03072 heat shock protein HtpX; Provisional
Probab=44.54 E-value=14 Score=35.65 Aligned_cols=11 Identities=45% Similarity=0.655 Sum_probs=8.2
Q ss_pred HHHHHHHHHHHH
Q 020057 296 LVIGVHELGHIL 307 (331)
Q Consensus 296 ~ILgvHE~GHyl 307 (331)
+|+ +||+||+-
T Consensus 129 aVl-AHElgHi~ 139 (288)
T PRK03072 129 GVL-GHELSHVY 139 (288)
T ss_pred HHH-HHHHHHHh
Confidence 344 89999973
No 31
>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=43.05 E-value=4 Score=38.35 Aligned_cols=12 Identities=42% Similarity=0.659 Sum_probs=9.8
Q ss_pred HHHHHHHHHHHH
Q 020057 297 VIGVHELGHILA 308 (331)
Q Consensus 297 ILgvHE~GHyla 308 (331)
..++||+|||+-
T Consensus 139 ~t~~HEvGH~lG 150 (225)
T cd04275 139 DTATHEVGHWLG 150 (225)
T ss_pred ceeEEeccceee
Confidence 456999999974
No 32
>PRK05457 heat shock protein HtpX; Provisional
Probab=42.79 E-value=15 Score=35.38 Aligned_cols=10 Identities=50% Similarity=0.929 Sum_probs=7.8
Q ss_pred HHHHHHHHHHH
Q 020057 296 LVIGVHELGHI 306 (331)
Q Consensus 296 ~ILgvHE~GHy 306 (331)
+|+ +||+||+
T Consensus 136 aVl-AHElgHi 145 (284)
T PRK05457 136 AVL-AHEISHI 145 (284)
T ss_pred HHH-HHHHHHH
Confidence 344 8999997
No 33
>KOG2719 consensus Metalloprotease [General function prediction only]
Probab=42.44 E-value=14 Score=38.37 Aligned_cols=12 Identities=50% Similarity=0.728 Sum_probs=8.8
Q ss_pred HHHHHHHHHHHHH
Q 020057 296 LVIGVHELGHILA 308 (331)
Q Consensus 296 ~ILgvHE~GHyla 308 (331)
+|| +||+|||-.
T Consensus 282 AVl-~HELGHW~~ 293 (428)
T KOG2719|consen 282 AVL-AHELGHWKL 293 (428)
T ss_pred HHH-HHHhhHHHH
Confidence 344 899999853
No 34
>COG2856 Predicted Zn peptidase [Amino acid transport and metabolism]
Probab=42.34 E-value=13 Score=34.88 Aligned_cols=14 Identities=43% Similarity=0.534 Sum_probs=10.8
Q ss_pred HHHHHHHHHHHHHc
Q 020057 299 GVHELGHILAAKST 312 (331)
Q Consensus 299 gvHE~GHylaArr~ 312 (331)
.+||+||+|.=++-
T Consensus 76 lAHELGH~llH~~~ 89 (213)
T COG2856 76 LAHELGHALLHTDL 89 (213)
T ss_pred HHHHHhHHHhcccc
Confidence 38999999975543
No 35
>PRK02391 heat shock protein HtpX; Provisional
Probab=42.12 E-value=16 Score=35.53 Aligned_cols=10 Identities=50% Similarity=0.939 Sum_probs=7.8
Q ss_pred HHHHHHHHHHH
Q 020057 296 LVIGVHELGHI 306 (331)
Q Consensus 296 ~ILgvHE~GHy 306 (331)
+|+ +||+||+
T Consensus 135 aVl-aHElgHi 144 (296)
T PRK02391 135 AVL-AHELSHV 144 (296)
T ss_pred HHH-HHHHHHH
Confidence 344 8999996
No 36
>PLN02452 phosphoserine transaminase
Probab=41.61 E-value=58 Score=32.48 Aligned_cols=67 Identities=9% Similarity=0.186 Sum_probs=50.6
Q ss_pred CcccccCCCHhHHHHHhhcccccceEEEEeeeeeCCeEEEEcccCChHHHHHHHHHHHHHHhcC--CceEEEEEecC
Q 020057 149 QLDEYIRIPKETIDILKDQVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFG--DQYKLFLLVNP 223 (331)
Q Consensus 149 ~~~~~~~ip~EdLk~IK~~~FG~dTFfvT~~e~~~qGVIfRGNLRg~pEevy~kL~~kLee~fG--DrY~LfLvee~ 223 (331)
....+..+|++.+++++.+++.|. -.+-+++-.+---.+=.++++.++++|++.++ +.|.+++++.+
T Consensus 11 f~pGP~~lp~~Vl~~~~~~~~~~~--------~~g~s~~~~sHRs~~f~~i~~~~~~~L~~l~~~p~~y~v~~l~Gs 79 (365)
T PLN02452 11 FSAGPATLPANVLAKAQAELYNWE--------GSGMSVMEMSHRGKEFLSIIQKAEADLRELLDIPDNYEVLFLQGG 79 (365)
T ss_pred eeCCCCCCCHHHHHHHHHHHhccc--------ccCccccccCCCchHHHHHHHHHHHHHHHHhCCCCCceEEEEeCc
Confidence 355688999999999998755443 22445655555445678999999999999998 67998888765
No 37
>PF10692 DUF2498: Protein of unknown function (DUF2498); InterPro: IPR019633 This entry represents proteins found in gammaproteobacteria, including YciN from Escherichia coli. Their function is not known. ; PDB: 3M92_A.
Probab=41.45 E-value=83 Score=26.01 Aligned_cols=64 Identities=14% Similarity=0.304 Sum_probs=38.2
Q ss_pred ccCCCHhHH-----HHHhhcccccceEEEEeeeeeCCeEEEEccc--CC------hHHHHHHHHHHHHHHhcCCceEE
Q 020057 153 YIRIPKETI-----DILKDQVFGFDTFFVTNQEPYEGGVLFKGNL--RG------QAAKTYEKISTRMKNKFGDQYKL 217 (331)
Q Consensus 153 ~~~ip~EdL-----k~IK~~~FG~dTFfvT~~e~~~qGVIfRGNL--Rg------~pEevy~kL~~kLee~fGDrY~L 217 (331)
..+|++++| ++||+.===+....+|+++..++..+|||+. .. +...||+ +-+.|+-.+..||.|
T Consensus 4 ~~~I~~~~LL~~AN~iI~~Hddyi~GM~a~~Veqk~~VLVFkGeyFLD~~GlPT~KtTAvFN-mFK~LAh~LS~~y~L 80 (82)
T PF10692_consen 4 KQPISRQALLEIANQIIREHDDYIHGMRATSVEQKGDVLVFKGEYFLDEQGLPTAKTTAVFN-MFKHLAHVLSEKYHL 80 (82)
T ss_dssp SEEE-HHHHHHHHHHHHHHHHHHHTT--EEEEEECTTEEEEEE-----TTS---HHHHHHHH-HHHHHHHHHCCCEEE
T ss_pred CcccCHHHHHHHHHHHHHhhHhhhccccccceeeECCEEEEecceeecCCCCCCcchHHHHH-HHHHHHHHcCcceEe
Confidence 345666665 3444321123346799999999999999983 22 2344554 567777788889984
No 38
>PRK01265 heat shock protein HtpX; Provisional
Probab=40.99 E-value=17 Score=36.16 Aligned_cols=10 Identities=60% Similarity=0.903 Sum_probs=7.8
Q ss_pred HHHHHHHHHHH
Q 020057 296 LVIGVHELGHI 306 (331)
Q Consensus 296 ~ILgvHE~GHy 306 (331)
+|+ +||+||+
T Consensus 142 aVl-AHElgHi 151 (324)
T PRK01265 142 AVA-GHELGHL 151 (324)
T ss_pred HHH-HHHHHHH
Confidence 344 8999996
No 39
>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=40.57 E-value=14 Score=31.12 Aligned_cols=17 Identities=35% Similarity=0.356 Sum_probs=12.4
Q ss_pred HHHHHHHHHHHHHHHHH
Q 020057 295 ALVIGVHELGHILAAKS 311 (331)
Q Consensus 295 l~ILgvHE~GHylaArr 311 (331)
.....+||+||-+=.+.
T Consensus 96 ~~~~~~HElGH~LGl~H 112 (167)
T cd00203 96 GAQTIAHELGHALGFYH 112 (167)
T ss_pred chhhHHHHHHHHhCCCc
Confidence 34566899999986553
No 40
>COG3824 Predicted Zn-dependent protease [General function prediction only]
Probab=39.61 E-value=13 Score=32.99 Aligned_cols=18 Identities=11% Similarity=0.488 Sum_probs=13.6
Q ss_pred HHHHHHHHHHHHHHhcCC
Q 020057 196 AAKTYEKISTRMKNKFGD 213 (331)
Q Consensus 196 pEevy~kL~~kLee~fGD 213 (331)
..++|..|-+.++.+.|+
T Consensus 21 a~~A~d~lP~efr~l~~~ 38 (136)
T COG3824 21 ASDALDHLPQEFRDLMGN 38 (136)
T ss_pred HHHHHHhCcHHHHHHhcC
Confidence 356788888888888774
No 41
>PF04315 DUF462: Protein of unknown function, DUF462; InterPro: IPR007411 This family consists of bacterial proteins of uncharacterised function.
Probab=39.35 E-value=16 Score=33.52 Aligned_cols=11 Identities=36% Similarity=0.591 Sum_probs=9.8
Q ss_pred HHHHHHHHHHH
Q 020057 299 GVHELGHILAA 309 (331)
Q Consensus 299 gvHE~GHylaA 309 (331)
+.||++||-.|
T Consensus 45 ALHEIaHWciA 55 (164)
T PF04315_consen 45 ALHEIAHWCIA 55 (164)
T ss_pred HHHHHHHHHhc
Confidence 36999999998
No 42
>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=36.12 E-value=25 Score=32.23 Aligned_cols=18 Identities=33% Similarity=0.309 Sum_probs=15.2
Q ss_pred HHHHHHHHHHHHHHHHcC
Q 020057 296 LVIGVHELGHILAAKSTG 313 (331)
Q Consensus 296 ~ILgvHE~GHylaArr~g 313 (331)
-++++||.||-++|-...
T Consensus 29 ~~~A~HEAGhAvva~~l~ 46 (213)
T PF01434_consen 29 RRIAYHEAGHAVVAYLLP 46 (213)
T ss_dssp HHHHHHHHHHHHHHHHSS
T ss_pred HHHHHHHHHHHHHHHHhc
Confidence 478899999999998654
No 43
>PF13699 DUF4157: Domain of unknown function (DUF4157)
Probab=35.74 E-value=22 Score=28.25 Aligned_cols=12 Identities=33% Similarity=0.642 Sum_probs=9.8
Q ss_pred HHHHHHHHHHHH
Q 020057 298 IGVHELGHILAA 309 (331)
Q Consensus 298 LgvHE~GHylaA 309 (331)
|.+||+.|.+.=
T Consensus 64 llaHEl~Hv~Qq 75 (79)
T PF13699_consen 64 LLAHELAHVVQQ 75 (79)
T ss_pred hHhHHHHHHHhh
Confidence 559999999864
No 44
>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=35.56 E-value=26 Score=31.07 Aligned_cols=21 Identities=43% Similarity=0.569 Sum_probs=12.5
Q ss_pred HHHHHHHHHHHHHHHHHHHcC
Q 020057 293 VTALVIGVHELGHILAAKSTG 313 (331)
Q Consensus 293 ~ll~ILgvHE~GHylaArr~g 313 (331)
...+...+||+||-+=...-+
T Consensus 129 ~~~a~~~AHelGH~lGm~HD~ 149 (199)
T PF01421_consen 129 LSFAVIIAHELGHNLGMPHDG 149 (199)
T ss_dssp HHHHHHHHHHHHHHTT---TT
T ss_pred HHHHHHHHHHHHHhcCCCCCC
Confidence 334566699999987554433
No 45
>PF12046 DUF3529: Protein of unknown function (DUF3529); InterPro: IPR021919 This family of proteins is functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 176 to 190 amino acids in length.
Probab=34.91 E-value=1.9e+02 Score=26.85 Aligned_cols=20 Identities=10% Similarity=0.400 Sum_probs=18.3
Q ss_pred ChHHHHHHHHHHHHHHhcCCceE
Q 020057 194 GQAAKTYEKISTRMKNKFGDQYK 216 (331)
Q Consensus 194 g~pEevy~kL~~kLee~fGDrY~ 216 (331)
++++++-+.|++.++++ | |+
T Consensus 40 ~p~~~~~~~l~~yf~~r-~--y~ 59 (173)
T PF12046_consen 40 QPPDEVLEQLKAYFEQR-N--YR 59 (173)
T ss_pred CCHHHHHHHHHHHHHhc-C--ce
Confidence 46999999999999999 8 88
No 46
>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=34.57 E-value=21 Score=29.77 Aligned_cols=13 Identities=46% Similarity=0.777 Sum_probs=10.0
Q ss_pred HHHHHHHHHHHHH
Q 020057 298 IGVHELGHILAAK 310 (331)
Q Consensus 298 LgvHE~GHylaAr 310 (331)
..+|||||-+=..
T Consensus 89 ~~~HEigHaLGl~ 101 (140)
T smart00235 89 VAAHELGHALGLY 101 (140)
T ss_pred cHHHHHHHHhcCC
Confidence 3589999988544
No 47
>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=33.51 E-value=26 Score=32.86 Aligned_cols=17 Identities=29% Similarity=0.534 Sum_probs=13.1
Q ss_pred HHHHHHHHHHHHHHHHH
Q 020057 295 ALVIGVHELGHILAAKS 311 (331)
Q Consensus 295 l~ILgvHE~GHylaArr 311 (331)
.++..+|||||-|=+..
T Consensus 167 ~a~t~AHElGHnlGm~H 183 (244)
T cd04270 167 SDLVTAHELGHNFGSPH 183 (244)
T ss_pred HHHHHHHHHHHhcCCCC
Confidence 45667999999887653
No 48
>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=33.33 E-value=39 Score=28.59 Aligned_cols=15 Identities=40% Similarity=0.556 Sum_probs=10.5
Q ss_pred HHHHHHHHHHHHHHH
Q 020057 296 LVIGVHELGHILAAK 310 (331)
Q Consensus 296 ~ILgvHE~GHylaAr 310 (331)
.-..+|||||-+=-.
T Consensus 95 ~~~~~HEiGHaLGL~ 109 (165)
T cd04268 95 RNTAEHELGHALGLR 109 (165)
T ss_pred HHHHHHHHHHHhccc
Confidence 344589999987443
No 49
>PF13583 Reprolysin_4: Metallo-peptidase family M12B Reprolysin-like
Probab=32.09 E-value=23 Score=32.46 Aligned_cols=15 Identities=33% Similarity=0.394 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHHHcC
Q 020057 299 GVHELGHILAAKSTG 313 (331)
Q Consensus 299 gvHE~GHylaArr~g 313 (331)
.+||+||-+=|+.-+
T Consensus 141 ~aHEiGH~lGl~H~~ 155 (206)
T PF13583_consen 141 FAHEIGHNLGLRHDF 155 (206)
T ss_pred HHHHHHHHhcCCCCc
Confidence 689999999876443
No 50
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=31.98 E-value=48 Score=38.19 Aligned_cols=15 Identities=27% Similarity=0.414 Sum_probs=6.5
Q ss_pred cccccccccCCCCcc
Q 020057 5 TTFRGNLSLLPHCSS 19 (331)
Q Consensus 5 ~~~~~~~~~~~~~~~ 19 (331)
+||-|.-..+--|++
T Consensus 1354 aTi~v~R~~~Dlct~ 1368 (1516)
T KOG1832|consen 1354 ATIPVDRCLLDLCTE 1368 (1516)
T ss_pred eeeecccchhhhhcC
Confidence 344444344444544
No 51
>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=31.19 E-value=25 Score=30.94 Aligned_cols=14 Identities=36% Similarity=0.601 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHHHH
Q 020057 297 VIGVHELGHILAAK 310 (331)
Q Consensus 297 ILgvHE~GHylaAr 310 (331)
-..+||+||-+=-+
T Consensus 115 ~t~~HEiGHaLGL~ 128 (186)
T cd04277 115 QTIIHEIGHALGLE 128 (186)
T ss_pred HHHHHHHHHHhcCC
Confidence 44579999987543
No 52
>PF04228 Zn_peptidase: Putative neutral zinc metallopeptidase; InterPro: IPR007343 Members of this family of bacterial proteins are described as hypothetical proteins or zinc metallopeptidases. The majority have a HExxH zinc-binding motif characteristic of neutral zinc metallopeptidases, however there is no evidence to support their function as metallopeptidases.
Probab=31.14 E-value=41 Score=33.08 Aligned_cols=12 Identities=33% Similarity=0.415 Sum_probs=9.9
Q ss_pred HHHHHHHHHHHH
Q 020057 299 GVHELGHILAAK 310 (331)
Q Consensus 299 gvHE~GHylaAr 310 (331)
.+||.||.+...
T Consensus 174 lAHEyGHHVQ~l 185 (292)
T PF04228_consen 174 LAHEYGHHVQNL 185 (292)
T ss_pred HHHHHHHHHHHH
Confidence 499999998754
No 53
>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=30.97 E-value=22 Score=30.48 Aligned_cols=13 Identities=38% Similarity=0.772 Sum_probs=10.0
Q ss_pred HHHHHHHHHHHHH
Q 020057 298 IGVHELGHILAAK 310 (331)
Q Consensus 298 LgvHE~GHylaAr 310 (331)
.+.|||||-+=-.
T Consensus 110 ~~~HEiGHaLGL~ 122 (157)
T cd04278 110 VAAHEIGHALGLG 122 (157)
T ss_pred HHHHHhccccccC
Confidence 3489999987654
No 54
>PF15281 Consortin_C: Consortin C-terminus
Probab=30.19 E-value=1.1e+02 Score=26.76 Aligned_cols=12 Identities=42% Similarity=0.537 Sum_probs=9.6
Q ss_pred HHHHHHHHHHHH
Q 020057 297 VIGVHELGHILA 308 (331)
Q Consensus 297 ILgvHE~GHyla 308 (331)
-.++||+-||+.
T Consensus 101 ~q~~~~l~hW~~ 112 (113)
T PF15281_consen 101 KQGLAELKHWLT 112 (113)
T ss_pred HHHHHHhhhhhc
Confidence 456899999985
No 55
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=29.30 E-value=31 Score=29.31 Aligned_cols=11 Identities=36% Similarity=0.440 Sum_probs=9.4
Q ss_pred HHHHHHHHHHH
Q 020057 299 GVHELGHILAA 309 (331)
Q Consensus 299 gvHE~GHylaA 309 (331)
..|||.|+++-
T Consensus 64 L~HEm~H~~~~ 74 (157)
T PF10263_consen 64 LLHEMAHAAAY 74 (157)
T ss_pred HHHHHHHHHhh
Confidence 38999999984
No 56
>cd04272 ZnMc_salivary_gland_MPs Zinc-dependent metalloprotease, salivary_gland_MPs. Metalloproteases secreted by the salivary glands of arthropods.
Probab=28.73 E-value=34 Score=31.11 Aligned_cols=18 Identities=39% Similarity=0.597 Sum_probs=13.4
Q ss_pred HHHHHHHHHHHHHHHHcC
Q 020057 296 LVIGVHELGHILAAKSTG 313 (331)
Q Consensus 296 ~ILgvHE~GHylaArr~g 313 (331)
+...+||+||-+=+..-+
T Consensus 146 ~~~~AHElGH~lG~~HD~ 163 (220)
T cd04272 146 VYTMTHELAHLLGAPHDG 163 (220)
T ss_pred HHHHHHHHHHHhCCCCCC
Confidence 366799999998666443
No 57
>PF01990 ATP-synt_F: ATP synthase (F/14-kDa) subunit; InterPro: IPR008218 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The V-ATPases (or V1V0-ATPase) and A-ATPases (or A1A0-ATPase) are each composed of two linked complexes: the V1 or A1 complex contains the catalytic core that hydrolyses/synthesizes ATP, and the V0 or A0 complex that forms the membrane-spanning pore. The V- and A-ATPases both contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, , ]. The V- and A-ATPases more closely resemble one another in subunit structure than they do the F-ATPases, although the function of A-ATPases is closer to that of F-ATPases. This entry represents subunit F found in the V1 complex of V-ATPases (both eukaryotic and bacterial), as well as in the A1 complex of A-ATPases. Subunit F is a 16 kDa protein that is required for the assembly and activity of V-ATPase, and has a potential role in the differential targeting and regulation of the enzyme for specific organelles. This subunit is not necessary for the rotation of the ATPase V1 rotor, but it does promote catalysis []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0046933 hydrogen ion transporting ATP synthase activity, rotational mechanism, 0046961 proton-transporting ATPase activity, rotational mechanism, 0015991 ATP hydrolysis coupled proton transport, 0033178 proton-transporting two-sector ATPase complex, catalytic domain; PDB: 2D00_E 3A5C_P 3J0J_H 3A5D_H 2OV6_A 2QAI_B 3AON_B 2I4R_A.
Probab=27.61 E-value=2.8e+02 Score=22.08 Aligned_cols=51 Identities=18% Similarity=0.413 Sum_probs=35.5
Q ss_pred ccccceEEEEeeeeeCCeEEEEcccCChHHHHHHHHHHHHHHhcCCceEEEEEecC--------------CCCCceEEEe
Q 020057 168 VFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFGDQYKLFLLVNP--------------EDDKPVAVVV 233 (331)
Q Consensus 168 ~FG~dTFfvT~~e~~~qGVIfRGNLRg~pEevy~kL~~kLee~fGDrY~LfLvee~--------------edgKPV~vVl 233 (331)
..|++++++. .+++++.+.+++-+++. . |-+.++.+. ....|+++.+
T Consensus 15 LaGv~~~~~~----------------~~~ee~~~~l~~l~~~~-~--~gIIii~e~~~~~~~~~l~~~~~~~~~P~iv~I 75 (95)
T PF01990_consen 15 LAGVEGVYVN----------------TDPEEAEEALKELLKDE-D--VGIIIITEDLAEKIRDELDEYREESSLPLIVEI 75 (95)
T ss_dssp HTTSEEEEES----------------HSHHHHHHHHHHHHHHT-T--EEEEEEEHHHHTTHHHHHHHHHHTSSSSEEEEE
T ss_pred HcCCCCccCC----------------CCHHHHHHHHHHHhcCC-C--ccEEEeeHHHHHHHHHHHHHHHhccCCceEEEc
Confidence 5677777664 57778887777777544 3 666666653 1357999999
Q ss_pred cCCC
Q 020057 234 PRKT 237 (331)
Q Consensus 234 P~~~ 237 (331)
|...
T Consensus 76 P~~~ 79 (95)
T PF01990_consen 76 PSKE 79 (95)
T ss_dssp STTC
T ss_pred CCCC
Confidence 9986
No 58
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=26.86 E-value=1.3e+02 Score=26.06 Aligned_cols=57 Identities=23% Similarity=0.405 Sum_probs=35.9
Q ss_pred cCCCHhHHHHHhhcccccceEEEEeeeee-CCe-EEEEcccCChHHHHHHHHHHHHHHhcCCceEEE
Q 020057 154 IRIPKETIDILKDQVFGFDTFFVTNQEPY-EGG-VLFKGNLRGQAAKTYEKISTRMKNKFGDQYKLF 218 (331)
Q Consensus 154 ~~ip~EdLk~IK~~~FG~dTFfvT~~e~~-~qG-VIfRGNLRg~pEevy~kL~~kLee~fGDrY~Lf 218 (331)
-+|+-+||+.+=.++ | .+++.-| +-| |+|. -..+++++=.+|.+.|+++||-.-.++
T Consensus 17 nki~MaeLr~~l~~~-G-----f~~V~Tyi~SGNvvf~--~~~~~~~l~~~ie~~l~~~fG~~v~v~ 75 (137)
T PF08002_consen 17 NKIKMAELREALEDL-G-----FTNVRTYIQSGNVVFE--SDRDPAELAAKIEKALEERFGFDVPVI 75 (137)
T ss_dssp S---HHHHHHHHHHC-T------EEEEEETTTTEEEEE--ESS-HHHHHHHHHHHHHHH-TT---EE
T ss_pred CcccHHHHHHHHHHc-C-----CCCceEEEeeCCEEEe--cCCChHHHHHHHHHHHHHhcCCCeEEE
Confidence 467888887655432 3 3788755 444 9999 667899999999999999999544433
No 59
>PF08800 VirE_N: VirE N-terminal domain; InterPro: IPR014907 This domain is associated with the N terminus of Virulence E proteins. The function of the domain is unknown.
Probab=26.67 E-value=2e+02 Score=24.78 Aligned_cols=59 Identities=15% Similarity=0.201 Sum_probs=42.2
Q ss_pred cCCCHhHHHHHhhcccccceEEEEeeeeeCCe--EEEEcccCChH-------------HHHHHHHHHHHHHhcC
Q 020057 154 IRIPKETIDILKDQVFGFDTFFVTNQEPYEGG--VLFKGNLRGQA-------------AKTYEKISTRMKNKFG 212 (331)
Q Consensus 154 ~~ip~EdLk~IK~~~FG~dTFfvT~~e~~~qG--VIfRGNLRg~p-------------Eevy~kL~~kLee~fG 212 (331)
-.+++|+++.+|..++.-.-.++.=+-+.+.| ++++-...... ..+|+.+.+..++.+|
T Consensus 39 D~l~~ee~~~~r~~l~~~p~t~~~f~SpSG~GvKi~v~~~~~~~~~lp~~~~~~~~~h~~~y~~~~~~y~~~~~ 112 (136)
T PF08800_consen 39 DHLDPEEAEELRQLLFEDPYTLAAFVSPSGRGVKIIVPFDYPDGSRLPQDEEEAELFHAHAYEAAVEYYQRLLG 112 (136)
T ss_pred CCCCHHHHHHHHHHHhcCCcEEEEEEcCCCCeEEEEEEecCCCCccccchhHHHHHHHHHHHHHHHHHHhhhcC
Confidence 34558899999987776665567777777777 56665544433 5788888888888877
No 60
>TIGR02500 type_III_yscD type III secretion apparatus protein, YscD/HrpQ family. This family represents a conserved protein of bacterial type III secretion systems. Gene symbols are variable from species to species. Members are designated YscD in Yersinia, HrpQ in Pseudomonas syringae, and EscD in enteropathogenic Escherichia coli. In the Chlamydiae, this model describes the C-terminal 400 residues of a longer protein.
Probab=26.17 E-value=1.6e+02 Score=29.90 Aligned_cols=39 Identities=13% Similarity=0.202 Sum_probs=34.6
Q ss_pred eeCCeEEEEcccCChHHHHHHHHHHHHHHhcCCceEEEE
Q 020057 181 PYEGGVLFKGNLRGQAAKTYEKISTRMKNKFGDQYKLFL 219 (331)
Q Consensus 181 ~~~qGVIfRGNLRg~pEevy~kL~~kLee~fGDrY~LfL 219 (331)
..++.+...|.|..+..+.|+++.+.++++||..|.+.+
T Consensus 302 ~~~~~i~lsG~l~~~~~~~~~~~l~~f~~~~~~~~~~~~ 340 (410)
T TIGR02500 302 ESGREIALSGQLDSEKRSRLQELLAAFKQRDGVIPDVVL 340 (410)
T ss_pred ecCCEEEEEecCCHHHHHHHHHHHHHHHHhCCCCceEEE
Confidence 446789999999999999999999999999998787664
No 61
>PF14891 Peptidase_M91: Effector protein
Probab=25.65 E-value=46 Score=29.64 Aligned_cols=16 Identities=31% Similarity=0.299 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHHHHHH
Q 020057 296 LVIGVHELGHILAAKS 311 (331)
Q Consensus 296 ~ILgvHE~GHylaArr 311 (331)
++.+.|||+|-|-...
T Consensus 104 ~v~L~HEL~HA~~~~~ 119 (174)
T PF14891_consen 104 FVVLYHELIHAYDYMN 119 (174)
T ss_pred HHHHHHHHHHHHHHHC
Confidence 4667999999887653
No 62
>PTZ00429 beta-adaptin; Provisional
Probab=25.43 E-value=88 Score=34.66 Aligned_cols=32 Identities=28% Similarity=0.251 Sum_probs=14.8
Q ss_pred ChhhhhhccCCCCCCCCcccccCCCCCCCCcC
Q 020057 75 NDKEKEVHDGQENQPATASDQEDDKSQPDSQL 106 (331)
Q Consensus 75 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 106 (331)
.|||++|+++.++.+++.++...+++..+|++
T Consensus 608 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 639 (746)
T PTZ00429 608 LDEEDTEDDDAVELPSTPSMGTQDGSPAPSAA 639 (746)
T ss_pred cccccccchhhccCCCCCCCCCCCCCCCcccc
Confidence 33444444444455555555444444333443
No 63
>PHA02456 zinc metallopeptidase motif-containing protein
Probab=24.22 E-value=46 Score=29.45 Aligned_cols=23 Identities=22% Similarity=0.345 Sum_probs=17.7
Q ss_pred HHHHHHHHHHHHHcCCc--ccccee
Q 020057 299 GVHELGHILAAKSTGVE--LGVPYF 321 (331)
Q Consensus 299 gvHE~GHylaArr~gVk--lSlPyF 321 (331)
..||+.|.|.-|.||.- ++.||.
T Consensus 83 L~HEL~H~WQ~RsYG~i~PITY~F~ 107 (141)
T PHA02456 83 LAHELNHAWQFRTYGLVQPITYAFS 107 (141)
T ss_pred HHHHHHHHHhhhccceeeeeehhhh
Confidence 37999999999999964 344443
No 64
>cd04927 ACT_ACR-like_2 Second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=23.89 E-value=99 Score=23.82 Aligned_cols=34 Identities=24% Similarity=0.307 Sum_probs=23.3
Q ss_pred cccceEEEEeeeeeCCeEEEEcccCChHHHHHHHHHHHHHHhcCC
Q 020057 169 FGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFGD 213 (331)
Q Consensus 169 FG~dTFfvT~~e~~~qGVIfRGNLRg~pEevy~kL~~kLee~fGD 213 (331)
.-+|+|||++- ++ . ...++..++|++.|.+.+|+
T Consensus 40 ~v~D~F~V~d~----~~-----~--~~~~~~~~~l~~~L~~~L~~ 73 (76)
T cd04927 40 RVLDLFFITDA----RE-----L--LHTKKRREETYDYLRAVLGD 73 (76)
T ss_pred EEEEEEEEeCC----CC-----C--CCCHHHHHHHHHHHHHHHch
Confidence 35688998642 11 1 13456778899999999885
No 65
>PF05683 Fumerase_C: Fumarase C-terminus; InterPro: IPR004647 This entry represents various Fe-S type hydro-lyases, including the beta subunit from both L-tartrate dehydratase (TtdB; EC:4.2.1.32) and class 2 fumarate hydratase (FumC; (4.2.1.2 from EC) []. A number of Fe-S cluster-containing hydro-lyases share a conserved motif, including argininosuccinate lyase, adenylosuccinate lyase, aspartase, class I fumarate hydratase (fumarase), and tartrate dehydratase (see IPR000362 from INTERPRO). Proteins in this group represent a subset of closely related proteins or modules, including the Escherichia coli tartrate dehydratase beta chain and the C-terminal region of the class I fumarase (where the N-terminal region is homologous to the tartrate dehydratase alpha chain). The activity of the archaeal proteins in this group is unknown.; GO: 0016836 hydro-lyase activity; PDB: 2ISB_A.
Probab=23.70 E-value=1.1e+02 Score=29.15 Aligned_cols=43 Identities=16% Similarity=0.179 Sum_probs=30.2
Q ss_pred cccCCCHhHHHHHhhcccccceEEEEeeeeeCCeEEEEcccCChHHHHHHHHHHHHHHh
Q 020057 152 EYIRIPKETIDILKDQVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNK 210 (331)
Q Consensus 152 ~~~~ip~EdLk~IK~~~FG~dTFfvT~~e~~~qGVIfRGNLRg~pEevy~kL~~kLee~ 210 (331)
=..|+.+|+++.||- ++-|...|.+-.-++.+|++|.+.|++-
T Consensus 31 L~tPlt~e~i~~L~v----------------GD~V~LsG~i~taRDaaH~ri~e~l~~g 73 (205)
T PF05683_consen 31 LTTPLTEEDIRKLKV----------------GDTVYLSGTIYTARDAAHKRIVELLERG 73 (205)
T ss_dssp EESS--HHHHHH--T----------------T-EEEEEEEEEE--HHHHHHHHHHHHHT
T ss_pred cCCCCCHHHHhhCCC----------------CCEEEEeeEEEEEhHHHHHHHHHHHHcC
Confidence 356899999999995 6777888888888899999999999865
No 66
>PF01431 Peptidase_M13: Peptidase family M13 This is family M13 in the peptidase classification. ; InterPro: IPR018497 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 M13 (neprilysin family, clan MA(E)). 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 []. M13 peptidases are well-studied proteases found in a wide range of organisms including mammals and bacteria. In mammals they participate in processes such as cardiovascular development, blood-pressure regulation, nervous control of respiration, and regulation of the function of neuropeptides in the central nervous system. In bacteria they may be used for digestion of milk [, ]. The family includes eukaryotic and prokaryotic oligopeptidases, as well as some of the proteins responsible for the molecular basis of the blood group antigens e.g. Kell []. Neprilysin (3.4.24.11 from EC), is another member of this group, it is variously known as common acute lymphoblastic leukemia antigen (CALLA), enkephalinase (gp100) and neutral endopeptidase metalloendopeptidase (NEP). It is a plasma membrane-bound mammalian enzyme that is able to digest biologically-active peptides, including enkephalins []. The zinc ligands of neprilysin are known and are analogous to those in thermolysin, a related peptidase [, ]. Neprilysins, like thermolysin, are inhibited by phosphoramidon, which appears to selectively inhibit this family in mammals. The enzymes are all oligopeptidases, digesting oligo- and polypeptides, but not proteins []. Neprilysin consists of a short cytoplasmic domain, a membrane-spanning region and a large extracellular domain. The cytoplasmic domain contains a conformationally-restrained octapeptide, which is thought to act as a stop transfer sequence that prevents proteolysis and secretion [, ].; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 2QPJ_A 1R1I_A 1R1J_A 1Y8J_A 1R1H_A 1DMT_A 2YB9_A 3DWB_A 3ZUK_A.
Probab=23.48 E-value=58 Score=28.95 Aligned_cols=19 Identities=26% Similarity=0.039 Sum_probs=13.8
Q ss_pred hHHHHHHHHHHHHHHHHHH
Q 020057 290 GALVTALVIGVHELGHILA 308 (331)
Q Consensus 290 ~al~ll~ILgvHE~GHyla 308 (331)
+-+|.++.+.+|||+|-+-
T Consensus 31 ~~yg~lG~ilahel~hafd 49 (206)
T PF01431_consen 31 LNYGGLGFILAHELMHAFD 49 (206)
T ss_dssp HHHHTHHHHHHHHHHHCTS
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3346677777899999663
No 67
>KOG0391 consensus SNF2 family DNA-dependent ATPase [General function prediction only]
Probab=23.16 E-value=1.3e+02 Score=36.14 Aligned_cols=18 Identities=28% Similarity=0.390 Sum_probs=14.8
Q ss_pred HHHHHHHHHHHHHHHcCC
Q 020057 297 VIGVHELGHILAAKSTGV 314 (331)
Q Consensus 297 ILgvHE~GHylaArr~gV 314 (331)
|=|..|++|-+++|-|+|
T Consensus 813 iEgsqeyn~klV~RLHkV 830 (1958)
T KOG0391|consen 813 IEGSQEYNHKLVIRLHKV 830 (1958)
T ss_pred cccchhhchHHHHHHHHH
Confidence 556788999999999876
No 68
>PF13492 GAF_3: GAF domain; PDB: 3EEA_A 4DMZ_A 4DN0_A 1VHM_A.
Probab=23.07 E-value=1.7e+02 Score=22.40 Aligned_cols=28 Identities=29% Similarity=0.462 Sum_probs=22.5
Q ss_pred hHHHHHHHHHHHHHHhcC-CceEEEEEec
Q 020057 195 QAAKTYEKISTRMKNKFG-DQYKLFLLVN 222 (331)
Q Consensus 195 ~pEevy~kL~~kLee~fG-DrY~LfLvee 222 (331)
+++++++++.+.+.+.+| ++.-++++++
T Consensus 1 dl~~l~~~i~~~l~~~~~~~~~~l~~~d~ 29 (129)
T PF13492_consen 1 DLDELLERILELLRELLGADRAALFLLDE 29 (129)
T ss_dssp -HHHHHHHHHHHHHHHST-SEEEEEEEET
T ss_pred CHHHHHHHHHHHHHHHhCCCEEEEEEEEC
Confidence 578999999999999999 5666676654
No 69
>PF11667 DUF3267: Protein of unknown function (DUF3267); InterPro: IPR021683 This family of proteins has no known function.
Probab=23.01 E-value=27 Score=28.68 Aligned_cols=21 Identities=38% Similarity=0.350 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHHHHHHHcCCc
Q 020057 295 ALVIGVHELGHILAAKSTGVE 315 (331)
Q Consensus 295 l~ILgvHE~GHylaArr~gVk 315 (331)
+.++.+||+-|.+..+.++-+
T Consensus 4 ~~~~~~HEliH~l~~~~~~~~ 24 (111)
T PF11667_consen 4 IVLIPLHELIHGLFFKLFGKK 24 (111)
T ss_pred EeeHHHHHHHHHHHHHHhCCC
Confidence 345579999999999988773
No 70
>PF05265 DUF723: Protein of unknown function (DUF723); InterPro: IPR007929 This family contains several uncharacterised proteins from Neisseria meningitidis. These proteins may have a role in DNA binding.
Probab=22.99 E-value=1.6e+02 Score=23.13 Aligned_cols=36 Identities=28% Similarity=0.524 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHhcCCceEEEEEecCCCCCceEEEecCCC
Q 020057 199 TYEKISTRMKNKFGDQYKLFLLVNPEDDKPVAVVVPRKT 237 (331)
Q Consensus 199 vy~kL~~kLee~fGDrY~LfLvee~edgKPV~vVlP~~~ 237 (331)
.++....+++++||+ |.|+ +-.....|+.|.-|.--
T Consensus 4 t~~~~~~r~~e~Fp~-~slv--ef~g~~~PvtI~CP~HG 39 (60)
T PF05265_consen 4 TFESAASRFEEKFPH-YSLV--EFSGVATPVTIRCPKHG 39 (60)
T ss_pred eHHHHHHHHHHHCCC-ceEE--EEeCCCCceEEECCCCC
Confidence 366778899999999 7744 43345789999988774
No 71
>PF12388 Peptidase_M57: Dual-action HEIGH metallo-peptidase; InterPro: IPR024653 This entry represents the metallopeptidases M10, M27 and M57. The catalytic triad for proteases in this entry is HE-H-H, which in many members is in the sequence motif HEIGH [].
Probab=22.49 E-value=50 Score=31.35 Aligned_cols=22 Identities=18% Similarity=0.250 Sum_probs=15.1
Q ss_pred hhHHHHHHHHHHHHHHHHHHHH
Q 020057 289 PGALVTALVIGVHELGHILAAK 310 (331)
Q Consensus 289 P~al~ll~ILgvHE~GHylaAr 310 (331)
+++.-...-..+|||||-+==|
T Consensus 127 ~~~~~~~~hvi~HEiGH~IGfR 148 (211)
T PF12388_consen 127 NYSVNVIEHVITHEIGHCIGFR 148 (211)
T ss_pred CCchhHHHHHHHHHhhhhcccc
Confidence 3455555556699999987544
No 72
>PF04155 Ground-like: Ground-like domain; InterPro: IPR007284 This group of proteins contain one or more copies of the ground-like domain, which are specific to Caenorhabditis elegans and Caenorhabditis briggsae. It has been proposed that the ground-like domain containing proteins may bind and modulate the activity of Patched-like membrane molecules, reminiscent of the modulating activities of neuropeptides [].
Probab=22.45 E-value=58 Score=25.30 Aligned_cols=26 Identities=12% Similarity=0.323 Sum_probs=23.5
Q ss_pred ChHHHHHHHHHHHHHHhcCCceEEEE
Q 020057 194 GQAAKTYEKISTRMKNKFGDQYKLFL 219 (331)
Q Consensus 194 g~pEevy~kL~~kLee~fGDrY~LfL 219 (331)
.++..+-+.|++.++++||.+|.++.
T Consensus 22 ~~~~~s~~~Iq~~~e~~f~~~f~vIc 47 (76)
T PF04155_consen 22 CNLSISKRAIQKAAEKRFGGSFEVIC 47 (76)
T ss_pred CCHHHHHHHHHHHHHHHhCCCEEEEE
Confidence 78899999999999999999999654
No 73
>PF01454 MAGE: MAGE family; InterPro: IPR002190 The first mammalian members of the MAGE (melanoma-associated antigen) gene family were originally described as completely silent in normal adult tissues, with the exception of male germ cells and, for some of them, placenta. By contrast, these genes were expressed in various kinds of tumors. However, other members of the family were recently found to be expressed in normal cells, indicating that the family is larger and more disparate than initially expected. MAGE-like genes have also been identified in non-mammalian species, including Drosophila melanogaster (Fruit fly) and Danio rerio (Zebrafish). Although no MAGE homologous sequences have been identified in Caenorhabditis elegans, Saccharomyces cerevisiae (Baker's yeast) or Schizosaccharomyces pombe (Fission yeast), MAGE sequences have been found in several vegetal species, including Arabidopsis thaliana (Mouse-ear cress) []. The only region of homology shared by all of the members of the family is a stretch of about 200 amino acids which has been named the MAGE conserved domain. The MAGE conserved domain is usually located close to the C-terminal, although it can also be found in a more central position in some proteins. The MAGE conserved domain is generally present as a single copy but it is duplicated in some proteins. It has been proposed that the MAGE conserved domain of MAGE-D proteins might interact with p75 neurotrophin or related receptors [].; PDB: 3NW0_B 2WA0_A 1I4F_C.
Probab=22.28 E-value=3.7e+02 Score=23.87 Aligned_cols=26 Identities=19% Similarity=0.525 Sum_probs=21.0
Q ss_pred CChHHHHHHHHHHHHHHhcCCceEEEEE
Q 020057 193 RGQAAKTYEKISTRMKNKFGDQYKLFLL 220 (331)
Q Consensus 193 Rg~pEevy~kL~~kLee~fGDrY~LfLv 220 (331)
+..-.++|++.++.|++.|| |.|.-+
T Consensus 29 ~~~f~~v~~~a~~~L~~vFG--~eL~ev 54 (195)
T PF01454_consen 29 RRKFPEVFERANEILEDVFG--FELVEV 54 (195)
T ss_dssp GGGHHHHHHHHHHHHHHHH---EEEEES
T ss_pred HHHhHHHHHHHHHHHHHHhc--eEEEEe
Confidence 55679999999999999999 985543
No 74
>PRK13267 archaemetzincin-like protein; Reviewed
Probab=22.15 E-value=45 Score=30.48 Aligned_cols=11 Identities=55% Similarity=0.730 Sum_probs=8.8
Q ss_pred HHHHHHHHHHH
Q 020057 298 IGVHELGHILA 308 (331)
Q Consensus 298 LgvHE~GHyla 308 (331)
.++||+||-+-
T Consensus 128 ~~~HElGH~lG 138 (179)
T PRK13267 128 EVTHELGHTLG 138 (179)
T ss_pred HHHHHHHHHcC
Confidence 36999999863
No 75
>PF09471 Peptidase_M64: IgA Peptidase M64; InterPro: IPR019026 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This is a family of highly selective metallo-endopeptidases belonging to the MEROPS peptidase family M64 (IgA peptidase, clan MA). The primary structure of the Clostridium ramosum IgA peptidase shows no significant overall similarity to any other known metallo-endopeptidase []. ; PDB: 3P1V_A 4DF9_D.
Probab=22.07 E-value=45 Score=32.24 Aligned_cols=12 Identities=42% Similarity=0.739 Sum_probs=9.2
Q ss_pred HHHHHHHHHHHH
Q 020057 297 VIGVHELGHILA 308 (331)
Q Consensus 297 ILgvHE~GHyla 308 (331)
-+.+||+||-++
T Consensus 218 ~v~vHE~GHsf~ 229 (264)
T PF09471_consen 218 QVVVHEFGHSFG 229 (264)
T ss_dssp HHHHHHHHHHTT
T ss_pred ceeeeecccccc
Confidence 456999999654
No 76
>KOG2236 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.99 E-value=1.2e+02 Score=32.31 Aligned_cols=22 Identities=27% Similarity=0.314 Sum_probs=14.5
Q ss_pred CCCCCCCCCCcccccCCCHhHH
Q 020057 140 SPLPGVKPQQLDEYIRIPKETI 161 (331)
Q Consensus 140 ~p~~g~~~~~~~~~~~ip~EdL 161 (331)
.|++.-....+++-.++++++|
T Consensus 179 ~p~ktr~e~ll~elPpv~~~~i 200 (483)
T KOG2236|consen 179 KPQKTRNEHLLDELPPVEPEEI 200 (483)
T ss_pred cCCCCCCchhhhcCCCCCccce
Confidence 5666666666677777777764
No 77
>PF08219 TOM13: Outer membrane protein TOM13; InterPro: IPR013262 The TOM13 family of proteins are mitochondrial outer membrane proteins that mediate the assembly of beta-barrel proteins [].; GO: 0005741 mitochondrial outer membrane
Probab=21.58 E-value=73 Score=26.11 Aligned_cols=20 Identities=20% Similarity=0.183 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHHHHHcCCcccc
Q 020057 297 VIGVHELGHILAAKSTGVELGV 318 (331)
Q Consensus 297 ILgvHE~GHylaArr~gVklSl 318 (331)
=|.+||++++| ...|-|+-+
T Consensus 54 El~AhE~~fr~--gW~g~ki~P 73 (77)
T PF08219_consen 54 ELFAHEIAFRL--GWSGTKIFP 73 (77)
T ss_pred HHHHHHHHHHh--ccCcceecC
Confidence 56699999988 446666544
No 78
>PRK06842 fumarate hydratase; Provisional
Probab=21.42 E-value=95 Score=29.02 Aligned_cols=61 Identities=16% Similarity=0.287 Sum_probs=45.4
Q ss_pred cCCCHhHHHHHhhcccccceEEEEeeeeeCCeEEEEcccCChHHHHHHHHHHHHHHhcCCceEEEEEecCCCCCceEEEe
Q 020057 154 IRIPKETIDILKDQVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFGDQYKLFLLVNPEDDKPVAVVV 233 (331)
Q Consensus 154 ~~ip~EdLk~IK~~~FG~dTFfvT~~e~~~qGVIfRGNLRg~pEevy~kL~~kLee~fGDrY~LfLvee~edgKPV~vVl 233 (331)
.|+.+||++.||- ++-|...|.+-.-++.+|++|.+.+++ |...- | + ..++.++..-
T Consensus 7 tPl~~e~i~~L~v----------------GD~V~LsG~i~taRDaAHkrl~e~l~~--G~~lP-~---d-l~g~~Iy~~G 63 (185)
T PRK06842 7 TPLTEEKVKDLKA----------------GDSVLISGYIYTARDAAHKRLIELLDK--GEELP-I---D-IKDQIIYYVG 63 (185)
T ss_pred CCCCHHHHhhCCC----------------CCEEEEeEEEEEEeHHHHHHHHHHHhc--CCCCC-c---C-cCCCEEEEec
Confidence 5789999999885 777888888888889999999999877 43322 2 1 2466777777
Q ss_pred cCCC
Q 020057 234 PRKT 237 (331)
Q Consensus 234 P~~~ 237 (331)
|...
T Consensus 64 P~~~ 67 (185)
T PRK06842 64 PSPA 67 (185)
T ss_pred CCCC
Confidence 7664
No 79
>PLN03199 delta6-acyl-lipid desaturase-like protein; Provisional
Probab=21.34 E-value=2e+02 Score=29.88 Aligned_cols=17 Identities=18% Similarity=0.352 Sum_probs=13.7
Q ss_pred hHHHHHHHHHHHHHHhcC
Q 020057 195 QAAKTYEKISTRMKNKFG 212 (331)
Q Consensus 195 ~pEevy~kL~~kLee~fG 212 (331)
+..+-|.+|++++++. |
T Consensus 109 ~~~~~y~~L~~~v~~~-g 125 (485)
T PLN03199 109 AFEKGYRDLRAKLIMM-G 125 (485)
T ss_pred HHHHHHHHHHHHHHHc-C
Confidence 3467899999999986 7
No 80
>PF07998 Peptidase_M54: Peptidase family M54; InterPro: IPR012962 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 represents zinc-dependent peptidases belonging to the MEROPS peptidase family M54, more commonly known as the archaemetzincins. The family has a wide taxonomic distribution, being found in archaea, bacteria and eukaryotes. Two human homologues have been characterised []. ; GO: 0008237 metallopeptidase activity, 0008270 zinc ion binding; PDB: 3LMC_A 2XHQ_A 2X7M_A.
Probab=21.09 E-value=44 Score=31.19 Aligned_cols=31 Identities=16% Similarity=0.267 Sum_probs=17.3
Q ss_pred eEEEEcccC--ChHHHHHHHHHHHHHHhcCCceE
Q 020057 185 GVLFKGNLR--GQAAKTYEKISTRMKNKFGDQYK 216 (331)
Q Consensus 185 GVIfRGNLR--g~pEevy~kL~~kLee~fGDrY~ 216 (331)
++.+.||-. ---.++|+++.+.+++. |-...
T Consensus 5 ~~~~~g~~~~~~~~~~v~d~v~~~~~~~-~l~v~ 37 (194)
T PF07998_consen 5 AFVYIGNTEFEWLFFEVYDRVNRFLSEF-GLPVK 37 (194)
T ss_dssp EEESSS--T---THHHHHHHHHHHHHHH-H-S-E
T ss_pred EEEEECCchhHHHHHHHHHHHHHHHHHc-CCceE
Confidence 345566633 23467888888888886 54454
No 81
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=20.99 E-value=57 Score=28.12 Aligned_cols=11 Identities=36% Similarity=0.362 Sum_probs=9.8
Q ss_pred HHHHHHHHHHH
Q 020057 300 VHELGHILAAK 310 (331)
Q Consensus 300 vHE~GHylaAr 310 (331)
.|||.|+++-.
T Consensus 64 ~HEm~H~~~~~ 74 (146)
T smart00731 64 LHELCHAALYL 74 (146)
T ss_pred HHHHHHHHHHH
Confidence 79999999874
No 82
>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=20.70 E-value=58 Score=31.10 Aligned_cols=27 Identities=33% Similarity=0.551 Sum_probs=17.2
Q ss_pred hhhchhhHHHHHHHHHHHHHHHHHHHHHcC
Q 020057 284 LTNGLPGALVTALVIGVHELGHILAAKSTG 313 (331)
Q Consensus 284 l~~gLP~al~ll~ILgvHE~GHylaArr~g 313 (331)
++.|||--+. .+|| +||++|-|. |-.|
T Consensus 84 vl~GLPrll~-gsiL-AHE~mHa~L-rl~g 110 (212)
T PF12315_consen 84 VLYGLPRLLT-GSIL-AHELMHAWL-RLNG 110 (212)
T ss_pred EECCCCHHHH-hhHH-HHHHHHHHh-cccC
Confidence 4567774332 2344 999999998 3344
No 83
>KOG2987 consensus Fatty acid desaturase [Lipid transport and metabolism]
Probab=20.54 E-value=2.7e+02 Score=28.02 Aligned_cols=13 Identities=46% Similarity=0.841 Sum_probs=10.5
Q ss_pred HHHHHHHHHHHHH
Q 020057 296 LVIGVHELGHILA 308 (331)
Q Consensus 296 ~ILgvHE~GHyla 308 (331)
..|++||+.|-.+
T Consensus 84 l~LAIHeiSHN~a 96 (324)
T KOG2987|consen 84 LTLAIHEISHNLA 96 (324)
T ss_pred HHHHHHHhhhhhh
Confidence 4788999999665
No 84
>TIGR01364 serC_1 phosphoserine aminotransferase. This model represents the common form of the phosphoserine aminotransferase SerC. The phosphoserine aminotransferase of the archaeon Methanosarcina barkeri and putative phosphoserine aminotransferase of Mycobacterium tuberculosis are represented by separate models. All are members of the class V aminotransferases (pfam00266).
Probab=20.53 E-value=1.4e+02 Score=29.16 Aligned_cols=60 Identities=10% Similarity=0.208 Sum_probs=41.6
Q ss_pred CCCHhHHHHHhhcccccceEEEEeeeeeCCeEEEEcccCChHHHHHHHHHHHHHHhcC--CceEEEEEec
Q 020057 155 RIPKETIDILKDQVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFG--DQYKLFLLVN 222 (331)
Q Consensus 155 ~ip~EdLk~IK~~~FG~dTFfvT~~e~~~qGVIfRGNLRg~pEevy~kL~~kLee~fG--DrY~LfLvee 222 (331)
.+|.+.++++++ ||.+.- .-.-|+.-.+.--.+-.++|+.++++|++.|| ++|.++++..
T Consensus 2 ~~p~~v~~~~~~-------~~~~~~-~~~~~~~~~~hr~~~f~~~~~~~~~~l~~l~~~~~~~~v~~~~g 63 (349)
T TIGR01364 2 ALPEEVLEQAQK-------ELLNFN-GTGMSVMEISHRSKEFEAVANEAESDLRELLNIPDNYEVLFLQG 63 (349)
T ss_pred CCCHHHHHHHHH-------HHhCcc-CCCccccccCCCchHHHHHHHHHHHHHHHHhCCCCCceEEEEcC
Confidence 468888999997 333221 22334555555444556999999999999999 5788887765
No 85
>KOG3320 consensus 40S ribosomal protein S7 [Translation, ribosomal structure and biogenesis]
Probab=20.24 E-value=1.5e+02 Score=27.89 Aligned_cols=27 Identities=15% Similarity=0.304 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHHHhcCCceEEEEEec
Q 020057 196 AAKTYEKISTRMKNKFGDQYKLFLLVN 222 (331)
Q Consensus 196 pEevy~kL~~kLee~fGDrY~LfLvee 222 (331)
=.++|.+|-..|+++|+|||.+|+-+.
T Consensus 73 fqki~~~LvreleKKF~gk~Vifia~R 99 (192)
T KOG3320|consen 73 FQKIQVRLVRELEKKFSGKHVIFIAQR 99 (192)
T ss_pred HHHHHHHHHHHHHHhcCCceEEEEEee
Confidence 345555555689999999999887554
No 86
>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]
Probab=20.16 E-value=62 Score=34.31 Aligned_cols=7 Identities=57% Similarity=1.341 Sum_probs=6.4
Q ss_pred HHHHHHH
Q 020057 300 VHELGHI 306 (331)
Q Consensus 300 vHE~GHy 306 (331)
+||+||.
T Consensus 135 AHEigHv 141 (484)
T COG4783 135 AHEIGHV 141 (484)
T ss_pred HHHHHHH
Confidence 8999996
Done!