Query 019897
Match_columns 334
No_of_seqs 175 out of 286
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 05:24:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019897.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019897hhsearch_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 99.2 2.1E-11 4.5E-16 109.9 5.3 77 253-333 2-78 (183)
2 cd06164 S2P-M50_SpoIVFB_CBS Sp 97.8 6E-05 1.3E-09 70.0 7.1 46 279-324 37-82 (227)
3 cd06161 S2P-M50_SpoIVFB SpoIVF 97.3 0.00025 5.5E-09 64.7 4.6 43 282-324 25-67 (208)
4 cd06159 S2P-M50_PDZ_Arch Uncha 97.2 0.001 2.2E-08 63.6 7.0 34 285-318 108-141 (263)
5 cd06162 S2P-M50_PDZ_SREBP Ster 95.4 0.016 3.5E-07 56.2 3.9 27 292-318 132-158 (277)
6 KOG2921 Intramembrane metallop 91.3 0.16 3.5E-06 52.2 3.1 33 285-317 120-153 (484)
7 PF05572 Peptidase_M43: Pregna 78.4 0.98 2.1E-05 40.0 1.1 12 297-308 71-82 (154)
8 PF13398 Peptidase_M50B: Pepti 69.0 4.4 9.4E-05 37.1 2.9 26 298-323 25-50 (200)
9 PF06114 DUF955: Domain of unk 65.9 3.7 8E-05 32.0 1.5 14 299-312 46-59 (122)
10 PF07423 DUF1510: Protein of u 58.6 5.4 0.00012 37.8 1.5 61 159-230 150-213 (217)
11 PRK03982 heat shock protein Ht 54.9 7.6 0.00017 37.2 1.9 13 294-307 125-137 (288)
12 PRK03001 M48 family peptidase; 54.9 7.6 0.00017 37.1 1.9 13 294-307 124-136 (283)
13 PF13485 Peptidase_MA_2: Pepti 54.6 10 0.00022 29.8 2.2 17 297-313 27-43 (128)
14 COG0501 HtpX Zn-dependent prot 53.8 8.3 0.00018 35.8 1.9 13 294-307 157-169 (302)
15 COG1994 SpoIVFB Zn-dependent p 53.0 11 0.00024 35.0 2.6 41 283-323 40-80 (230)
16 PF13688 Reprolysin_5: Metallo 52.6 7.7 0.00017 34.1 1.4 18 296-313 143-160 (196)
17 PF13582 Reprolysin_3: Metallo 52.4 7.1 0.00015 31.7 1.1 14 297-310 109-122 (124)
18 PF01435 Peptidase_M48: Peptid 51.8 10 0.00022 33.4 2.1 17 298-316 92-108 (226)
19 cd04267 ZnMc_ADAM_like Zinc-de 51.5 6.8 0.00015 34.5 0.9 19 296-314 134-152 (192)
20 PRK11037 hypothetical protein; 51.3 51 0.0011 27.3 5.7 65 152-217 4-81 (83)
21 PRK02870 heat shock protein Ht 51.1 7.7 0.00017 38.7 1.3 17 296-316 175-191 (336)
22 PRK04897 heat shock protein Ht 50.5 9.8 0.00021 36.9 1.9 13 294-307 137-149 (298)
23 PF13574 Reprolysin_2: Metallo 49.3 7.6 0.00017 34.5 0.9 20 295-314 111-130 (173)
24 PF00413 Peptidase_M10: Matrix 49.0 11 0.00024 31.5 1.8 14 298-311 108-121 (154)
25 cd04279 ZnMc_MMP_like_1 Zinc-d 48.3 11 0.00024 32.3 1.7 19 298-316 107-125 (156)
26 cd04269 ZnMc_adamalysin_II_lik 48.3 12 0.00027 33.0 2.0 20 294-313 130-149 (194)
27 PRK01345 heat shock protein Ht 47.7 12 0.00025 36.9 1.9 13 294-307 124-136 (317)
28 COG5309 Exo-beta-1,3-glucanase 47.1 36 0.00079 34.0 5.2 61 158-222 218-281 (305)
29 PF10692 DUF2498: Protein of u 46.4 62 0.0014 26.7 5.5 64 153-217 4-80 (82)
30 cd04275 ZnMc_pappalysin_like Z 46.4 3.4 7.3E-05 38.9 -1.9 12 297-308 139-150 (225)
31 PRK03072 heat shock protein Ht 46.4 12 0.00027 36.0 1.9 12 295-307 128-139 (288)
32 KOG2719 Metalloprotease [Gener 45.6 12 0.00025 39.0 1.6 11 296-307 282-292 (428)
33 COG2856 Predicted Zn peptidase 45.1 11 0.00025 35.4 1.3 13 300-312 77-89 (213)
34 PRK05457 heat shock protein Ht 45.1 13 0.00029 35.8 1.9 11 295-306 135-145 (284)
35 PF02031 Peptidase_M7: Strepto 45.0 13 0.00028 33.1 1.6 10 298-307 80-89 (132)
36 PRK02391 heat shock protein Ht 44.6 14 0.0003 36.0 1.9 11 295-306 134-144 (296)
37 PRK12462 phosphoserine aminotr 44.2 47 0.001 33.6 5.6 67 149-223 8-76 (364)
38 PRK01265 heat shock protein Ht 43.5 15 0.00032 36.7 1.9 11 295-306 141-151 (324)
39 COG3824 Predicted Zn-dependent 42.5 11 0.00025 33.4 0.8 18 196-213 21-38 (136)
40 cd00203 ZnMc Zinc-dependent me 41.4 14 0.00029 31.3 1.1 18 295-312 96-113 (167)
41 PLN02452 phosphoserine transam 40.0 61 0.0013 32.4 5.6 67 149-223 11-79 (365)
42 PF04315 DUF462: Protein of un 39.0 16 0.00035 33.5 1.3 11 299-309 45-55 (164)
43 PF01434 Peptidase_M41: Peptid 38.8 21 0.00046 32.8 2.0 19 295-313 28-46 (213)
44 cd04278 ZnMc_MMP Zinc-dependen 37.0 13 0.00027 32.1 0.3 13 299-311 111-123 (157)
45 PF01421 Reprolysin: Reprolysi 36.4 27 0.00058 31.1 2.3 22 293-314 129-150 (199)
46 cd04268 ZnMc_MMP_like Zinc-dep 35.7 34 0.00073 29.0 2.7 16 295-310 94-109 (165)
47 smart00235 ZnMc Zinc-dependent 35.3 20 0.00043 30.0 1.2 13 298-310 89-101 (140)
48 PF13699 DUF4157: Domain of un 35.2 22 0.00047 28.4 1.4 11 202-212 5-15 (79)
49 PF12046 DUF3529: Protein of u 34.3 2E+02 0.0044 26.7 7.6 20 194-216 40-59 (173)
50 cd04270 ZnMc_TACE_like Zinc-de 33.7 26 0.00057 32.9 1.9 19 294-312 166-184 (244)
51 KOG1832 HIV-1 Vpr-binding prot 32.9 45 0.00098 38.4 3.7 15 5-19 1354-1368(1516)
52 cd04277 ZnMc_serralysin_like Z 31.6 24 0.00053 31.1 1.2 14 297-310 115-128 (186)
53 PF12315 DUF3633: Protein of u 31.4 35 0.00075 32.6 2.2 27 284-313 84-110 (212)
54 PF04228 Zn_peptidase: Putativ 31.2 41 0.00088 33.2 2.8 12 299-310 174-185 (292)
55 KOG2987 Fatty acid desaturase 29.7 1.3E+02 0.0028 30.2 5.8 29 296-324 84-120 (324)
56 PLN02598 omega-6 fatty acid de 29.0 49 0.0011 34.1 3.0 16 299-314 142-157 (421)
57 cd04272 ZnMc_salivary_gland_MP 28.8 34 0.00074 31.2 1.7 19 296-314 146-164 (220)
58 PF13583 Reprolysin_4: Metallo 28.2 22 0.00047 32.6 0.3 15 299-313 141-155 (206)
59 PF10263 SprT-like: SprT-like 27.5 34 0.00075 29.1 1.4 11 299-309 64-74 (157)
60 PF08219 TOM13: Outer membrane 25.9 54 0.0012 26.9 2.1 20 297-318 54-73 (77)
61 TIGR02500 type_III_yscD type I 25.4 1.7E+02 0.0037 29.6 6.1 40 181-220 302-341 (410)
62 PF05683 Fumerase_C: Fumarase 25.4 94 0.002 29.5 4.0 43 152-210 31-73 (205)
63 PF01990 ATP-synt_F: ATP synth 24.5 3.3E+02 0.0072 21.7 6.5 51 168-237 15-79 (95)
64 PF15281 Consortin_C: Consorti 24.4 1.7E+02 0.0036 25.6 4.9 12 297-308 101-112 (113)
65 cd04927 ACT_ACR-like_2 Second 23.9 1E+02 0.0022 23.8 3.3 34 169-213 40-73 (76)
66 PF14891 Peptidase_M91: Effect 23.7 51 0.0011 29.4 1.9 16 296-311 104-119 (174)
67 PF12388 Peptidase_M57: Dual-a 23.7 46 0.00099 31.7 1.6 24 288-311 126-149 (211)
68 PLN03199 delta6-acyl-lipid des 23.5 2.8E+02 0.0061 28.9 7.4 17 195-212 109-125 (485)
69 PF11667 DUF3267: Protein of u 23.3 26 0.00057 28.8 -0.1 21 295-315 4-24 (111)
70 PRK06842 fumarate hydratase; P 23.0 84 0.0018 29.4 3.1 62 153-237 6-67 (185)
71 PF13492 GAF_3: GAF domain; PD 22.9 1.7E+02 0.0037 22.4 4.5 28 195-222 1-29 (129)
72 PF01431 Peptidase_M13: Peptid 22.9 60 0.0013 28.9 2.1 19 290-308 31-49 (206)
73 PRK13267 archaemetzincin-like 22.7 43 0.00094 30.6 1.2 10 299-308 129-138 (179)
74 cd03508 Delta4-sphingolipid-FA 22.6 2E+02 0.0043 28.1 5.8 16 298-313 61-76 (289)
75 PF09471 Peptidase_M64: IgA Pe 22.2 42 0.00092 32.5 1.1 12 297-308 218-229 (264)
76 PF06262 DUF1025: Possibl zinc 22.2 63 0.0014 27.0 1.9 13 295-307 73-85 (97)
77 PF07998 Peptidase_M54: Peptid 22.1 43 0.00094 31.3 1.1 31 185-216 5-37 (194)
78 PF07817 GLE1: GLE1-like prote 22.0 68 0.0015 30.5 2.4 38 285-325 103-141 (256)
79 PHA02456 zinc metallopeptidase 22.0 54 0.0012 29.1 1.6 23 299-321 83-107 (141)
80 PTZ00429 beta-adaptin; Provisi 21.7 1.2E+02 0.0025 33.8 4.3 32 75-106 608-639 (746)
81 PF08800 VirE_N: VirE N-termin 20.8 3.1E+02 0.0066 23.7 6.0 60 153-212 38-112 (136)
82 TIGR01364 serC_1 phosphoserine 20.8 1.5E+02 0.0032 29.2 4.5 60 155-222 2-63 (349)
83 COG4783 Putative Zn-dependent 20.8 56 0.0012 34.7 1.7 10 296-306 132-141 (484)
84 cd04271 ZnMc_ADAM_fungal Zinc- 20.4 40 0.00086 31.6 0.5 14 297-310 147-160 (228)
85 PF04155 Ground-like: Ground-l 20.3 83 0.0018 24.5 2.2 26 194-219 22-47 (76)
86 smart00731 SprT SprT homologue 20.3 59 0.0013 28.1 1.5 11 300-310 64-74 (146)
87 COG3101 Uncharacterized protei 20.3 48 0.001 30.5 1.0 34 200-237 5-38 (180)
88 PF05265 DUF723: Protein of un 20.2 1.9E+02 0.0042 22.7 4.1 36 199-237 4-39 (60)
89 cd04327 ZnMc_MMP_like_3 Zinc-d 20.2 54 0.0012 29.6 1.3 10 300-309 97-106 (198)
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=99.18 E-value=2.1e-11 Score=109.89 Aligned_cols=77 Identities=35% Similarity=0.484 Sum_probs=64.4
Q ss_pred HHHHHHHHHHHHhccccccccchhcccchhHhhhchhhHHHHHHHHHHHHHHHHHHHHHcCcccccceeecccccccCCC
Q 019897 253 AFGLVTVFTLLLRNVPALQSNLLSTFDNLNLLTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVPSWQVICSVP 332 (334)
Q Consensus 253 LLfllTl~TT~~aG~~~L~~~~L~~f~~p~~l~~gLP~al~ll~ILgvHE~GHylaArr~gVklSlPYFIP~pqi~GTig 332 (334)
+++++|++|....++..... .+.++++.+..+++++++++.++.+||+||+++||++|+|...|+|+|+|. .||+|
T Consensus 2 ~~~~~s~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~l~l~~~l~iHElgH~~~A~~~G~~~~~~~l~P~~~-~G~~G 77 (183)
T cd06160 2 LLLVLTLLTTLLVGAWLSGN---DVPGNPLLLLQGLPFALALLAILGIHEMGHYLAARRHGVKASLPYFIPFPF-IGTFG 77 (183)
T ss_pred HHHHHHHHHHHHHHHHHhcc---cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCccceeeeehHh-cCcEE
Confidence 56789999988887532111 233678889999999999999999999999999999999999999999988 67776
Q ss_pred C
Q 019897 333 N 333 (334)
Q Consensus 333 ~ 333 (334)
.
T Consensus 78 ~ 78 (183)
T cd06160 78 A 78 (183)
T ss_pred E
Confidence 4
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=97.78 E-value=6e-05 Score=70.04 Aligned_cols=46 Identities=26% Similarity=0.249 Sum_probs=39.8
Q ss_pred cchhHhhhchhhHHHHHHHHHHHHHHHHHHHHHcCcccccceeecc
Q 019897 279 DNLNLLTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVPS 324 (334)
Q Consensus 279 ~~p~~l~~gLP~al~ll~ILgvHE~GHylaArr~gVklSlPYFIP~ 324 (334)
.++..+.-|+.++++++.++.+||+||+++||++|+|+.--.+.|.
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 3455678899999999999999999999999999999987667664
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=97.32 E-value=0.00025 Score=64.69 Aligned_cols=43 Identities=33% Similarity=0.417 Sum_probs=37.3
Q ss_pred hHhhhchhhHHHHHHHHHHHHHHHHHHHHHcCcccccceeecc
Q 019897 282 NLLTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVPS 324 (334)
Q Consensus 282 ~~l~~gLP~al~ll~ILgvHE~GHylaArr~gVklSlPYFIP~ 324 (334)
..+..++.+++.++.++.+||+||+++||++|+++.--.+.|.
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 4567889999999999999999999999999999886666664
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=97.17 E-value=0.001 Score=63.61 Aligned_cols=34 Identities=24% Similarity=0.292 Sum_probs=28.2
Q ss_pred hhchhhHHHHHHHHHHHHHHHHHHHHHcCccccc
Q 019897 285 TNGLPGALVTALVIGVHELGHILAAKSTGVELGV 318 (334)
Q Consensus 285 ~~gLP~al~ll~ILgvHE~GHylaArr~gVklSl 318 (334)
...+.+.++++..+.+||+||.++||++|+++..
T Consensus 108 i~~~~~~iaL~isv~iHElgHa~~Ar~~G~~V~~ 141 (263)
T cd06159 108 IPLPYGIIALVVGVVVHELSHGILARVEGIKVKS 141 (263)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHcCCEECc
Confidence 3555666777778889999999999999999875
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=95.37 E-value=0.016 Score=56.21 Aligned_cols=27 Identities=30% Similarity=0.255 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHcCccccc
Q 019897 292 LVTALVIGVHELGHILAAKSTGVELGV 318 (334)
Q Consensus 292 l~ll~ILgvHE~GHylaArr~gVklSl 318 (334)
++++....+||+||.++|+++|+++.-
T Consensus 132 ~al~isvvvHElgHal~A~~~gi~V~~ 158 (277)
T cd06162 132 TALLISGVVHEMGHGVAAVREQVRVNG 158 (277)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCeece
Confidence 455566778999999999999999875
No 6
>KOG2921 consensus Intramembrane metalloprotease (sterol-regulatory element-binding protein (SREBP) protease) [Posttranslational modification, protein turnover, chaperones]
Probab=91.30 E-value=0.16 Score=52.15 Aligned_cols=33 Identities=42% Similarity=0.622 Sum_probs=26.7
Q ss_pred hhchhhHHHHHHHHH-HHHHHHHHHHHHcCcccc
Q 019897 285 TNGLPGALVTALVIG-VHELGHILAAKSTGVELG 317 (334)
Q Consensus 285 ~~gLP~al~ll~ILg-vHE~GHylaArr~gVklS 317 (334)
+++++|-+..+.|-+ +|||||-|||.+.||++.
T Consensus 120 l~~I~yf~t~lvi~~vvHElGHalAA~segV~vn 153 (484)
T KOG2921|consen 120 LSGIAYFLTSLVITVVVHELGHALAAASEGVQVN 153 (484)
T ss_pred cccchhhhhhHHHHHHHHHhhHHHHHHhcCceee
Confidence 568887776655544 799999999999999875
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=78.43 E-value=0.98 Score=39.96 Aligned_cols=12 Identities=42% Similarity=0.556 Sum_probs=9.8
Q ss_pred HHHHHHHHHHHH
Q 019897 297 VIGVHELGHILA 308 (334)
Q Consensus 297 ILgvHE~GHyla 308 (334)
-.++||+|||+=
T Consensus 71 ~TltHEvGH~LG 82 (154)
T PF05572_consen 71 KTLTHEVGHWLG 82 (154)
T ss_dssp HHHHHHHHHHTT
T ss_pred cchhhhhhhhhc
Confidence 556999999974
No 8
>PF13398 Peptidase_M50B: Peptidase M50B-like
Probab=69.00 E-value=4.4 Score=37.07 Aligned_cols=26 Identities=46% Similarity=0.478 Sum_probs=18.4
Q ss_pred HHHHHHHHHHHHHHcCcccccceeec
Q 019897 298 IGVHELGHILAAKSTGVELGVPYFVP 323 (334)
Q Consensus 298 LgvHE~GHylaArr~gVklSlPYFIP 323 (334)
..+||+||-++|.-.|=|+.-=...|
T Consensus 25 t~~HE~gHal~a~l~G~~v~~i~l~~ 50 (200)
T PF13398_consen 25 TFVHELGHALAALLTGGRVKGIVLFP 50 (200)
T ss_pred HHHHHHHHHHHHHHhCCCcceEEEEe
Confidence 56999999999987666554333333
No 9
>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=65.94 E-value=3.7 Score=31.98 Aligned_cols=14 Identities=50% Similarity=0.688 Sum_probs=10.6
Q ss_pred HHHHHHHHHHHHHc
Q 019897 299 GVHELGHILAAKST 312 (334)
Q Consensus 299 gvHE~GHylaArr~ 312 (334)
.+||+||++.-...
T Consensus 46 laHELgH~~~~~~~ 59 (122)
T PF06114_consen 46 LAHELGHILLHHGD 59 (122)
T ss_dssp HHHHHHHHHHHH-H
T ss_pred HHHHHHHHHhhhcc
Confidence 38999999986554
No 10
>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=5.4 Score=37.85 Aligned_cols=61 Identities=21% Similarity=0.349 Sum_probs=43.5
Q ss_pred hHHHHHhhcccccceEEEEeeeeeCCeEEEEcccCChHHHHHHHHHHHHHHhcCCceeEEEee--cCCCC-CCeE
Q 019897 159 ETIDILKDQVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFGDQYKLFLLV--NPEDD-KPVA 230 (334)
Q Consensus 159 EdL~~IK~~~FG~dTFfvT~~e~~~qGVIfRGNLRg~pEevy~kL~~kLee~fGDrY~LfLve--e~edg-KPV~ 230 (334)
-|++-|+.. ..|+|++..-+--+.|.||= |.|.+++..|+.+= . |.+|+++| + +. .| ||+-
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-GKKYRVYI-EWVDN-EGWKPVK 213 (217)
T ss_pred cCHHHHHHH-----HHHhhCCChhheEEEhhhcC-CcccceeEEeccCC--C-CceEEEEE-EEecC-CCcccee
Confidence 455544443 67899998888889999994 77799999988753 3 67899775 4 22 23 7874
No 11
>PRK03982 heat shock protein HtpX; Provisional
Probab=54.94 E-value=7.6 Score=37.19 Aligned_cols=13 Identities=54% Similarity=0.570 Sum_probs=9.5
Q ss_pred HHHHHHHHHHHHHH
Q 019897 294 TALVIGVHELGHIL 307 (334)
Q Consensus 294 ll~ILgvHE~GHyl 307 (334)
+.+|| +||+||+-
T Consensus 125 l~AVl-AHElgHi~ 137 (288)
T PRK03982 125 LEGVI-AHELTHIK 137 (288)
T ss_pred HHHHH-HHHHHHHH
Confidence 34455 89999985
No 12
>PRK03001 M48 family peptidase; Provisional
Probab=54.88 E-value=7.6 Score=37.09 Aligned_cols=13 Identities=38% Similarity=0.552 Sum_probs=9.3
Q ss_pred HHHHHHHHHHHHHH
Q 019897 294 TALVIGVHELGHIL 307 (334)
Q Consensus 294 ll~ILgvHE~GHyl 307 (334)
+.+|| +||+||+-
T Consensus 124 l~aVl-AHElgHi~ 136 (283)
T PRK03001 124 IRGVM-AHELAHVK 136 (283)
T ss_pred HHHHH-HHHHHHHh
Confidence 33444 89999984
No 13
>PF13485 Peptidase_MA_2: Peptidase MA superfamily
Probab=54.59 E-value=10 Score=29.78 Aligned_cols=17 Identities=29% Similarity=0.311 Sum_probs=13.9
Q ss_pred HHHHHHHHHHHHHHHcC
Q 019897 297 VIGVHELGHILAAKSTG 313 (334)
Q Consensus 297 ILgvHE~GHylaArr~g 313 (334)
-+.+||++|.|.....+
T Consensus 27 ~~l~HE~~H~~~~~~~~ 43 (128)
T PF13485_consen 27 RVLAHELAHQWFGNYFG 43 (128)
T ss_pred HHHHHHHHHHHHHHHcC
Confidence 45699999999988754
No 14
>COG0501 HtpX Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]
Probab=53.82 E-value=8.3 Score=35.85 Aligned_cols=13 Identities=54% Similarity=0.818 Sum_probs=9.5
Q ss_pred HHHHHHHHHHHHHH
Q 019897 294 TALVIGVHELGHIL 307 (334)
Q Consensus 294 ll~ILgvHE~GHyl 307 (334)
+.+|| +||+||+.
T Consensus 157 l~aVl-aHElgHi~ 169 (302)
T COG0501 157 LEAVL-AHELGHIK 169 (302)
T ss_pred HHHHH-HHHHHHHh
Confidence 44555 89999973
No 15
>COG1994 SpoIVFB Zn-dependent proteases [General function prediction only]
Probab=52.99 E-value=11 Score=35.05 Aligned_cols=41 Identities=24% Similarity=0.259 Sum_probs=31.8
Q ss_pred HhhhchhhHHHHHHHHHHHHHHHHHHHHHcCcccccceeec
Q 019897 283 LLTNGLPGALVTALVIGVHELGHILAAKSTGVELGVPYFVP 323 (334)
Q Consensus 283 ~l~~gLP~al~ll~ILgvHE~GHylaArr~gVklSlPYFIP 323 (334)
.+.++....++++.-+..||+||+..++++++++-+-.+.+
T Consensus 40 ~~~~~~~~~~~l~~rl~l~~~gh~~~~~~~~~~l~~~~i~~ 80 (230)
T COG1994 40 SLGDGTAAFVGLAHRLVLHPLGHSDEAGRLGLKLLLALLFG 80 (230)
T ss_pred HHhhhHHHHHHHhHHHhhhHhhHHHHHHHHHHHHHHHHHHh
Confidence 35556666666666778999999999999999988777663
No 16
>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=52.62 E-value=7.7 Score=34.12 Aligned_cols=18 Identities=39% Similarity=0.576 Sum_probs=11.3
Q ss_pred HHHHHHHHHHHHHHHHcC
Q 019897 296 LVIGVHELGHILAAKSTG 313 (334)
Q Consensus 296 ~ILgvHE~GHylaArr~g 313 (334)
.+..+||+||-|=|..=+
T Consensus 143 ~~~~AHEiGH~lGa~HD~ 160 (196)
T PF13688_consen 143 AITFAHEIGHNLGAPHDG 160 (196)
T ss_dssp HHHHHHHHHHHTT-----
T ss_pred ehhhHHhHHHhcCCCCCC
Confidence 467799999999887533
No 17
>PF13582 Reprolysin_3: Metallo-peptidase family M12B Reprolysin-like; PDB: 3P24_C.
Probab=52.43 E-value=7.1 Score=31.75 Aligned_cols=14 Identities=36% Similarity=0.423 Sum_probs=9.5
Q ss_pred HHHHHHHHHHHHHH
Q 019897 297 VIGVHELGHILAAK 310 (334)
Q Consensus 297 ILgvHE~GHylaAr 310 (334)
-..+||+||-+=+.
T Consensus 109 ~~~~HEiGH~lGl~ 122 (124)
T PF13582_consen 109 DTFAHEIGHNLGLN 122 (124)
T ss_dssp THHHHHHHHHTT--
T ss_pred eEeeehhhHhcCCC
Confidence 45589999987543
No 18
>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=51.81 E-value=10 Score=33.42 Aligned_cols=17 Identities=35% Similarity=0.460 Sum_probs=11.6
Q ss_pred HHHHHHHHHHHHHHcCccc
Q 019897 298 IGVHELGHILAAKSTGVEL 316 (334)
Q Consensus 298 LgvHE~GHylaArr~gVkl 316 (334)
+.+||+||+. .+|..+.
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 4555444
No 19
>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=51.48 E-value=6.8 Score=34.52 Aligned_cols=19 Identities=42% Similarity=0.548 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHHHHHcCc
Q 019897 296 LVIGVHELGHILAAKSTGV 314 (334)
Q Consensus 296 ~ILgvHE~GHylaArr~gV 314 (334)
+...+||+||.+=+..-+-
T Consensus 134 ~~~~aHElGH~lG~~HD~~ 152 (192)
T cd04267 134 ALTMAHELGHNLGAEHDGG 152 (192)
T ss_pred hhhhhhhHHhhcCCcCCCC
Confidence 4567999999998776553
No 20
>PRK11037 hypothetical protein; Provisional
Probab=51.34 E-value=51 Score=27.31 Aligned_cols=65 Identities=18% Similarity=0.383 Sum_probs=44.8
Q ss_pred cccCCCHhHH-----HHHhhcccccceEEEEeeeeeCCeEEEEccc--CC------hHHHHHHHHHHHHHHhcCCceeE
Q 019897 152 EYIRIPKETI-----DILKDQVFGFDTFFVTNQEPYEGGVLFKGNL--RG------QAAKTYEKISTRMKNKFGDQYKL 217 (334)
Q Consensus 152 ~~~~ip~EdL-----~~IK~~~FG~dTFfvT~~e~~~qGVIfRGNL--Rg------~pEevy~kL~~kLee~fGDrY~L 217 (334)
+..+|++++| ++||+.===+...++|+++..++..+|||.. .. +...||+ +-+.|+-.+..+|.|
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 4567888887 4555432234457899999999999999983 22 2455554 566777777888984
No 21
>PRK02870 heat shock protein HtpX; Provisional
Probab=51.10 E-value=7.7 Score=38.73 Aligned_cols=17 Identities=41% Similarity=0.741 Sum_probs=11.2
Q ss_pred HHHHHHHHHHHHHHHHcCccc
Q 019897 296 LVIGVHELGHILAAKSTGVEL 316 (334)
Q Consensus 296 ~ILgvHE~GHylaArr~gVkl 316 (334)
+|+ +||+||+ +.+.++.
T Consensus 175 aVl-AHELgHi---k~~di~~ 191 (336)
T PRK02870 175 AVM-AHELSHI---RHGDIRL 191 (336)
T ss_pred HHH-HHHHHHH---HcccHHH
Confidence 444 8999998 4444444
No 22
>PRK04897 heat shock protein HtpX; Provisional
Probab=50.47 E-value=9.8 Score=36.86 Aligned_cols=13 Identities=46% Similarity=0.488 Sum_probs=9.2
Q ss_pred HHHHHHHHHHHHHH
Q 019897 294 TALVIGVHELGHIL 307 (334)
Q Consensus 294 ll~ILgvHE~GHyl 307 (334)
+.+|+ +||+||+-
T Consensus 137 l~aVl-AHElgHi~ 149 (298)
T PRK04897 137 LEGVI-GHEISHIR 149 (298)
T ss_pred HHHHH-HHHHHHHh
Confidence 33444 89999974
No 23
>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=49.30 E-value=7.6 Score=34.51 Aligned_cols=20 Identities=35% Similarity=0.285 Sum_probs=12.4
Q ss_pred HHHHHHHHHHHHHHHHHcCc
Q 019897 295 ALVIGVHELGHILAAKSTGV 314 (334)
Q Consensus 295 l~ILgvHE~GHylaArr~gV 314 (334)
.....+|||||-|=|..-+=
T Consensus 111 ~~~~~aHElGH~lGa~Hd~~ 130 (173)
T PF13574_consen 111 GIDTFAHELGHQLGAPHDFD 130 (173)
T ss_dssp HHHHHHHHHHHHHT---SSS
T ss_pred eeeeehhhhHhhcCCCCCCC
Confidence 33447999999998875443
No 24
>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=49.01 E-value=11 Score=31.51 Aligned_cols=14 Identities=36% Similarity=0.821 Sum_probs=10.1
Q ss_pred HHHHHHHHHHHHHH
Q 019897 298 IGVHELGHILAAKS 311 (334)
Q Consensus 298 LgvHE~GHylaArr 311 (334)
.++|||||-+=-..
T Consensus 108 v~~HEiGHaLGL~H 121 (154)
T PF00413_consen 108 VAIHEIGHALGLDH 121 (154)
T ss_dssp HHHHHHHHHTTBES
T ss_pred hhhhccccccCcCc
Confidence 34899999875433
No 25
>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=48.35 E-value=11 Score=32.30 Aligned_cols=19 Identities=37% Similarity=0.468 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHHHHcCccc
Q 019897 298 IGVHELGHILAAKSTGVEL 316 (334)
Q Consensus 298 LgvHE~GHylaArr~gVkl 316 (334)
..+|||||-+=.+...-+-
T Consensus 107 ~~~HEiGHaLGL~H~~~~~ 125 (156)
T cd04279 107 IALHELGHALGLWHHSDRP 125 (156)
T ss_pred HHHHHhhhhhcCCCCCCCc
Confidence 4489999999888777654
No 26
>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=48.31 E-value=12 Score=33.04 Aligned_cols=20 Identities=35% Similarity=0.383 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHHHHHcC
Q 019897 294 TALVIGVHELGHILAAKSTG 313 (334)
Q Consensus 294 ll~ILgvHE~GHylaArr~g 313 (334)
..++..+||+||-+=+..-+
T Consensus 130 ~~a~~~AHElGH~lG~~HD~ 149 (194)
T cd04269 130 LFAVTMAHELGHNLGMEHDD 149 (194)
T ss_pred HHHHHHHHHHHhhcCCCcCC
Confidence 34577899999998766443
No 27
>PRK01345 heat shock protein HtpX; Provisional
Probab=47.66 E-value=12 Score=36.91 Aligned_cols=13 Identities=46% Similarity=0.644 Sum_probs=9.7
Q ss_pred HHHHHHHHHHHHHH
Q 019897 294 TALVIGVHELGHIL 307 (334)
Q Consensus 294 ll~ILgvHE~GHyl 307 (334)
+.+|| +||+||+-
T Consensus 124 L~aVl-AHElgHi~ 136 (317)
T PRK01345 124 VAGVM-AHELAHVK 136 (317)
T ss_pred HHHHH-HHHHHHHH
Confidence 44455 89999985
No 28
>COG5309 Exo-beta-1,3-glucanase [Carbohydrate transport and metabolism]
Probab=47.14 E-value=36 Score=33.95 Aligned_cols=61 Identities=16% Similarity=0.312 Sum_probs=45.7
Q ss_pred HhHHHHHhhccccc-ceEEEEeeeeeCCeEEEEcccCC--hHHHHHHHHHHHHHHhcCCceeEEEeec
Q 019897 158 KETIDILKDQVFGF-DTFFVTNQEPYEGGVLFKGNLRG--QAAKTYEKISTRMKNKFGDQYKLFLLVN 222 (334)
Q Consensus 158 ~EdL~~IK~~~FG~-dTFfvT~~e~~~qGVIfRGNLRg--~pEevy~kL~~kLee~fGDrY~LfLvee 222 (334)
.|.|++||+ .||= .+|||||+-.--.|.-+-++.-. +..+.++++...|+.. | |..|+++-
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 7777 99999999654455444444332 4678889999999888 9 77788763
No 29
>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=46.43 E-value=62 Score=26.74 Aligned_cols=64 Identities=14% Similarity=0.304 Sum_probs=39.1
Q ss_pred ccCCCHhHH-----HHHhhcccccceEEEEeeeeeCCeEEEEccc--CC------hHHHHHHHHHHHHHHhcCCceeE
Q 019897 153 YIRIPKETI-----DILKDQVFGFDTFFVTNQEPYEGGVLFKGNL--RG------QAAKTYEKISTRMKNKFGDQYKL 217 (334)
Q Consensus 153 ~~~ip~EdL-----~~IK~~~FG~dTFfvT~~e~~~qGVIfRGNL--Rg------~pEevy~kL~~kLee~fGDrY~L 217 (334)
..+|++++| ++||+.===+....+|+++..++..+|||+. .. +...||+ +-+.|+-.+..||.|
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 346777776 3444321123346799999999999999983 22 2345554 667788888999984
No 30
>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=46.42 E-value=3.4 Score=38.89 Aligned_cols=12 Identities=42% Similarity=0.659 Sum_probs=9.8
Q ss_pred HHHHHHHHHHHH
Q 019897 297 VIGVHELGHILA 308 (334)
Q Consensus 297 ILgvHE~GHyla 308 (334)
..++||+|||+-
T Consensus 139 ~t~~HEvGH~lG 150 (225)
T cd04275 139 DTATHEVGHWLG 150 (225)
T ss_pred ceeEEeccceee
Confidence 456999999984
No 31
>PRK03072 heat shock protein HtpX; Provisional
Probab=46.40 E-value=12 Score=36.04 Aligned_cols=12 Identities=42% Similarity=0.584 Sum_probs=8.7
Q ss_pred HHHHHHHHHHHHH
Q 019897 295 ALVIGVHELGHIL 307 (334)
Q Consensus 295 l~ILgvHE~GHyl 307 (334)
.+|+ +||+||+-
T Consensus 128 ~aVl-AHElgHi~ 139 (288)
T PRK03072 128 RGVL-GHELSHVY 139 (288)
T ss_pred HHHH-HHHHHHHh
Confidence 3444 89999973
No 32
>KOG2719 consensus Metalloprotease [General function prediction only]
Probab=45.58 E-value=12 Score=38.99 Aligned_cols=11 Identities=55% Similarity=0.830 Sum_probs=8.5
Q ss_pred HHHHHHHHHHHH
Q 019897 296 LVIGVHELGHIL 307 (334)
Q Consensus 296 ~ILgvHE~GHyl 307 (334)
+|| +||+|||-
T Consensus 282 AVl-~HELGHW~ 292 (428)
T KOG2719|consen 282 AVL-AHELGHWK 292 (428)
T ss_pred HHH-HHHhhHHH
Confidence 444 89999985
No 33
>COG2856 Predicted Zn peptidase [Amino acid transport and metabolism]
Probab=45.13 E-value=11 Score=35.43 Aligned_cols=13 Identities=46% Similarity=0.687 Sum_probs=10.5
Q ss_pred HHHHHHHHHHHHc
Q 019897 300 VHELGHILAAKST 312 (334)
Q Consensus 300 vHE~GHylaArr~ 312 (334)
+||+||+|.=++-
T Consensus 77 AHELGH~llH~~~ 89 (213)
T COG2856 77 AHELGHALLHTDL 89 (213)
T ss_pred HHHHhHHHhcccc
Confidence 8999999975543
No 34
>PRK05457 heat shock protein HtpX; Provisional
Probab=45.10 E-value=13 Score=35.84 Aligned_cols=11 Identities=45% Similarity=0.845 Sum_probs=8.3
Q ss_pred HHHHHHHHHHHH
Q 019897 295 ALVIGVHELGHI 306 (334)
Q Consensus 295 l~ILgvHE~GHy 306 (334)
.+|+ +||+||+
T Consensus 135 ~aVl-AHElgHi 145 (284)
T PRK05457 135 EAVL-AHEISHI 145 (284)
T ss_pred HHHH-HHHHHHH
Confidence 3444 8999997
No 35
>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=45.03 E-value=13 Score=33.14 Aligned_cols=10 Identities=80% Similarity=1.291 Sum_probs=8.4
Q ss_pred HHHHHHHHHH
Q 019897 298 IGVHELGHIL 307 (334)
Q Consensus 298 LgvHE~GHyl 307 (334)
..+||+||.+
T Consensus 80 IaaHE~GHiL 89 (132)
T PF02031_consen 80 IAAHELGHIL 89 (132)
T ss_dssp HHHHHHHHHH
T ss_pred eeeehhcccc
Confidence 4589999986
No 36
>PRK02391 heat shock protein HtpX; Provisional
Probab=44.63 E-value=14 Score=36.03 Aligned_cols=11 Identities=45% Similarity=0.854 Sum_probs=8.2
Q ss_pred HHHHHHHHHHHH
Q 019897 295 ALVIGVHELGHI 306 (334)
Q Consensus 295 l~ILgvHE~GHy 306 (334)
.+|+ +||+||+
T Consensus 134 ~aVl-aHElgHi 144 (296)
T PRK02391 134 EAVL-AHELSHV 144 (296)
T ss_pred HHHH-HHHHHHH
Confidence 3444 8999996
No 37
>PRK12462 phosphoserine aminotransferase; Provisional
Probab=44.25 E-value=47 Score=33.57 Aligned_cols=67 Identities=12% Similarity=0.162 Sum_probs=48.5
Q ss_pred CcccccCCCHhHHHHHhhcccccceEEEEeeeeeCCeEEEEcccCChHHHHHHHHHHHHHHhcC--CceeEEEeecC
Q 019897 149 QLDEYIRIPKETIDILKDQVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFG--DQYKLFLLVNP 223 (334)
Q Consensus 149 ~~~~~~~ip~EdL~~IK~~~FG~dTFfvT~~e~~~qGVIfRGNLRg~pEevy~kL~~kLee~fG--DrY~LfLvee~ 223 (334)
....+..+|+|.|++++.++.-|.. -+-+|+=.+---.+-.++|+++.++|++.|+ +.|.+++++.+
T Consensus 8 F~aGPa~lp~~Vl~~~~~~~~~~~~--------~g~si~eisHRs~~F~~i~~~~~~~Lr~Ll~~P~~y~Vlfl~Gg 76 (364)
T PRK12462 8 FSGGPGALPDTVLEQVRQAVVELPE--------TGLSVLGMSHRSSWFSSLLAQAEADLRDLLGIPDEYGVVFLQGG 76 (364)
T ss_pred ecCCCcCCCHHHHHHHHHHHhcccc--------cCccccccccccHHHHHHHHHHHHHHHHHhCCCCCCeEEEEecc
Confidence 3456789999999999987544332 1223443333334778999999999999999 68999888864
No 38
>PRK01265 heat shock protein HtpX; Provisional
Probab=43.52 E-value=15 Score=36.67 Aligned_cols=11 Identities=55% Similarity=0.809 Sum_probs=8.2
Q ss_pred HHHHHHHHHHHH
Q 019897 295 ALVIGVHELGHI 306 (334)
Q Consensus 295 l~ILgvHE~GHy 306 (334)
.+|+ +||+||+
T Consensus 141 ~aVl-AHElgHi 151 (324)
T PRK01265 141 KAVA-GHELGHL 151 (324)
T ss_pred HHHH-HHHHHHH
Confidence 3444 8999996
No 39
>COG3824 Predicted Zn-dependent protease [General function prediction only]
Probab=42.55 E-value=11 Score=33.42 Aligned_cols=18 Identities=11% Similarity=0.488 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHHHHhcCC
Q 019897 196 AAKTYEKISTRMKNKFGD 213 (334)
Q Consensus 196 pEevy~kL~~kLee~fGD 213 (334)
..++|..|-+.++.+.|+
T Consensus 21 a~~A~d~lP~efr~l~~~ 38 (136)
T COG3824 21 ASDALDHLPQEFRDLMGN 38 (136)
T ss_pred HHHHHHhCcHHHHHHhcC
Confidence 456788888888888774
No 40
>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=41.40 E-value=14 Score=31.33 Aligned_cols=18 Identities=33% Similarity=0.337 Sum_probs=13.0
Q ss_pred HHHHHHHHHHHHHHHHHc
Q 019897 295 ALVIGVHELGHILAAKST 312 (334)
Q Consensus 295 l~ILgvHE~GHylaArr~ 312 (334)
.....+||+||-+=.+..
T Consensus 96 ~~~~~~HElGH~LGl~H~ 113 (167)
T cd00203 96 GAQTIAHELGHALGFYHD 113 (167)
T ss_pred chhhHHHHHHHHhCCCcc
Confidence 345668999999866543
No 41
>PLN02452 phosphoserine transaminase
Probab=39.99 E-value=61 Score=32.37 Aligned_cols=67 Identities=9% Similarity=0.186 Sum_probs=50.6
Q ss_pred CcccccCCCHhHHHHHhhcccccceEEEEeeeeeCCeEEEEcccCChHHHHHHHHHHHHHHhcC--CceeEEEeecC
Q 019897 149 QLDEYIRIPKETIDILKDQVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFG--DQYKLFLLVNP 223 (334)
Q Consensus 149 ~~~~~~~ip~EdL~~IK~~~FG~dTFfvT~~e~~~qGVIfRGNLRg~pEevy~kL~~kLee~fG--DrY~LfLvee~ 223 (334)
....+..+|++.+++++.+++.|. -.+-+++-.+---.+=.++++.++++|++.++ +.|.+++++.+
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 456688999999999988755443 22445655555555678999999999999998 67998888754
No 42
>PF04315 DUF462: Protein of unknown function, DUF462; InterPro: IPR007411 This family consists of bacterial proteins of uncharacterised function.
Probab=38.96 E-value=16 Score=33.54 Aligned_cols=11 Identities=36% Similarity=0.591 Sum_probs=9.8
Q ss_pred HHHHHHHHHHH
Q 019897 299 GVHELGHILAA 309 (334)
Q Consensus 299 gvHE~GHylaA 309 (334)
+.||++||-.|
T Consensus 45 ALHEIaHWciA 55 (164)
T PF04315_consen 45 ALHEIAHWCIA 55 (164)
T ss_pred HHHHHHHHHhc
Confidence 36999999998
No 43
>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=38.76 E-value=21 Score=32.77 Aligned_cols=19 Identities=32% Similarity=0.286 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHHHHHHcC
Q 019897 295 ALVIGVHELGHILAAKSTG 313 (334)
Q Consensus 295 l~ILgvHE~GHylaArr~g 313 (334)
.-++++||.||-++|-...
T Consensus 28 ~~~~A~HEAGhAvva~~l~ 46 (213)
T PF01434_consen 28 KRRIAYHEAGHAVVAYLLP 46 (213)
T ss_dssp HHHHHHHHHHHHHHHHHSS
T ss_pred HHHHHHHHHHHHHHHHHhc
Confidence 3478899999999998654
No 44
>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=37.01 E-value=13 Score=32.07 Aligned_cols=13 Identities=38% Similarity=0.687 Sum_probs=10.0
Q ss_pred HHHHHHHHHHHHH
Q 019897 299 GVHELGHILAAKS 311 (334)
Q Consensus 299 gvHE~GHylaArr 311 (334)
+.|||||-+=-..
T Consensus 111 ~~HEiGHaLGL~H 123 (157)
T cd04278 111 AAHEIGHALGLGH 123 (157)
T ss_pred HHHHhccccccCC
Confidence 4899999876543
No 45
>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=36.35 E-value=27 Score=31.09 Aligned_cols=22 Identities=41% Similarity=0.499 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHHHHHHHHHcCc
Q 019897 293 VTALVIGVHELGHILAAKSTGV 314 (334)
Q Consensus 293 ~ll~ILgvHE~GHylaArr~gV 314 (334)
...+...+||+||-+=...-+-
T Consensus 129 ~~~a~~~AHelGH~lGm~HD~~ 150 (199)
T PF01421_consen 129 LSFAVIIAHELGHNLGMPHDGD 150 (199)
T ss_dssp HHHHHHHHHHHHHHTT---TTT
T ss_pred HHHHHHHHHHHHHhcCCCCCCC
Confidence 3445666999999886665554
No 46
>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=35.66 E-value=34 Score=29.01 Aligned_cols=16 Identities=38% Similarity=0.497 Sum_probs=10.9
Q ss_pred HHHHHHHHHHHHHHHH
Q 019897 295 ALVIGVHELGHILAAK 310 (334)
Q Consensus 295 l~ILgvHE~GHylaAr 310 (334)
+.-..+|||||-+=-+
T Consensus 94 ~~~~~~HEiGHaLGL~ 109 (165)
T cd04268 94 LRNTAEHELGHALGLR 109 (165)
T ss_pred HHHHHHHHHHHHhccc
Confidence 3344589999987443
No 47
>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=35.31 E-value=20 Score=29.96 Aligned_cols=13 Identities=46% Similarity=0.777 Sum_probs=10.1
Q ss_pred HHHHHHHHHHHHH
Q 019897 298 IGVHELGHILAAK 310 (334)
Q Consensus 298 LgvHE~GHylaAr 310 (334)
..+|||||-+=..
T Consensus 89 ~~~HEigHaLGl~ 101 (140)
T smart00235 89 VAAHELGHALGLY 101 (140)
T ss_pred cHHHHHHHHhcCC
Confidence 3589999988554
No 48
>PF13699 DUF4157: Domain of unknown function (DUF4157)
Probab=35.19 E-value=22 Score=28.36 Aligned_cols=11 Identities=36% Similarity=0.836 Sum_probs=9.3
Q ss_pred HHHHHHHHhcC
Q 019897 202 KISTRMKNKFG 212 (334)
Q Consensus 202 kL~~kLee~fG 212 (334)
.++.+|+..||
T Consensus 5 ~~r~~~e~~~G 15 (79)
T PF13699_consen 5 SIRSRLERAFG 15 (79)
T ss_pred HHHHHHHHHhC
Confidence 57888999988
No 49
>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=34.28 E-value=2e+02 Score=26.72 Aligned_cols=20 Identities=10% Similarity=0.400 Sum_probs=18.2
Q ss_pred ChHHHHHHHHHHHHHHhcCCcee
Q 019897 194 GQAAKTYEKISTRMKNKFGDQYK 216 (334)
Q Consensus 194 g~pEevy~kL~~kLee~fGDrY~ 216 (334)
++++++-+.|++.++++ | |+
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 45999999999999999 8 88
No 50
>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=33.70 E-value=26 Score=32.92 Aligned_cols=19 Identities=26% Similarity=0.476 Sum_probs=14.1
Q ss_pred HHHHHHHHHHHHHHHHHHc
Q 019897 294 TALVIGVHELGHILAAKST 312 (334)
Q Consensus 294 ll~ILgvHE~GHylaArr~ 312 (334)
+.++..+|||||=|=+..-
T Consensus 166 ~~a~t~AHElGHnlGm~HD 184 (244)
T cd04270 166 ESDLVTAHELGHNFGSPHD 184 (244)
T ss_pred HHHHHHHHHHHHhcCCCCC
Confidence 3456679999999987643
No 51
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=32.92 E-value=45 Score=38.42 Aligned_cols=15 Identities=27% Similarity=0.414 Sum_probs=6.5
Q ss_pred cccccccccCCCCcc
Q 019897 5 TTFRGNLSLLPHCSS 19 (334)
Q Consensus 5 ~~~~~~~~~~~~~~~ 19 (334)
+||-|.-..+--|++
T Consensus 1354 aTi~v~R~~~Dlct~ 1368 (1516)
T KOG1832|consen 1354 ATIPVDRCLLDLCTE 1368 (1516)
T ss_pred eeeecccchhhhhcC
Confidence 344444344444544
No 52
>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=31.61 E-value=24 Score=31.09 Aligned_cols=14 Identities=36% Similarity=0.601 Sum_probs=10.1
Q ss_pred HHHHHHHHHHHHHH
Q 019897 297 VIGVHELGHILAAK 310 (334)
Q Consensus 297 ILgvHE~GHylaAr 310 (334)
-..+||+||-+==+
T Consensus 115 ~t~~HEiGHaLGL~ 128 (186)
T cd04277 115 QTIIHEIGHALGLE 128 (186)
T ss_pred HHHHHHHHHHhcCC
Confidence 44479999987543
No 53
>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=31.44 E-value=35 Score=32.61 Aligned_cols=27 Identities=37% Similarity=0.582 Sum_probs=17.1
Q ss_pred hhhchhhHHHHHHHHHHHHHHHHHHHHHcC
Q 019897 284 LTNGLPGALVTALVIGVHELGHILAAKSTG 313 (334)
Q Consensus 284 l~~gLP~al~ll~ILgvHE~GHylaArr~g 313 (334)
++.|||--+ +.+|| +||++|-|. |-.|
T Consensus 84 vl~GLPrll-~gsiL-AHE~mHa~L-rl~g 110 (212)
T PF12315_consen 84 VLYGLPRLL-TGSIL-AHELMHAWL-RLNG 110 (212)
T ss_pred EECCCCHHH-HhhHH-HHHHHHHHh-cccC
Confidence 456777432 22344 999999998 3344
No 54
>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=31.16 E-value=41 Score=33.18 Aligned_cols=12 Identities=33% Similarity=0.415 Sum_probs=9.8
Q ss_pred HHHHHHHHHHHH
Q 019897 299 GVHELGHILAAK 310 (334)
Q Consensus 299 gvHE~GHylaAr 310 (334)
.+||.||-+...
T Consensus 174 lAHEyGHHVQ~l 185 (292)
T PF04228_consen 174 LAHEYGHHVQNL 185 (292)
T ss_pred HHHHHHHHHHHH
Confidence 499999998654
No 55
>KOG2987 consensus Fatty acid desaturase [Lipid transport and metabolism]
Probab=29.70 E-value=1.3e+02 Score=30.19 Aligned_cols=29 Identities=34% Similarity=0.510 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHHHH--------HHcCcccccceeecc
Q 019897 296 LVIGVHELGHILAA--------KSTGVELGVPYFVPS 324 (334)
Q Consensus 296 ~ILgvHE~GHylaA--------rr~gVklSlPYFIP~ 324 (334)
.-|++||+.|-.+= |.+|+=+-||.=||+
T Consensus 84 l~LAIHeiSHN~aFg~~rpl~NR~~g~fANLPigvP~ 120 (324)
T KOG2987|consen 84 LTLAIHEISHNLAFGTNRPLYNRIFGFFANLPIGVPM 120 (324)
T ss_pred HHHHHHHhhhhhhcccCchHHHHHHHHhhcCcccCce
Confidence 47889999996642 345555555555553
No 56
>PLN02598 omega-6 fatty acid desaturase
Probab=28.99 E-value=49 Score=34.14 Aligned_cols=16 Identities=31% Similarity=0.189 Sum_probs=11.7
Q ss_pred HHHHHHHHHHHHHcCc
Q 019897 299 GVHELGHILAAKSTGV 314 (334)
Q Consensus 299 gvHE~GHylaArr~gV 314 (334)
..||.||.-..+...+
T Consensus 142 l~Hec~H~s~~~~~~l 157 (421)
T PLN02598 142 IGHDCGHNSFSKNQLV 157 (421)
T ss_pred HHHhccccCCCCCHHH
Confidence 3699999987765443
No 57
>cd04272 ZnMc_salivary_gland_MPs Zinc-dependent metalloprotease, salivary_gland_MPs. Metalloproteases secreted by the salivary glands of arthropods.
Probab=28.75 E-value=34 Score=31.18 Aligned_cols=19 Identities=37% Similarity=0.548 Sum_probs=14.2
Q ss_pred HHHHHHHHHHHHHHHHcCc
Q 019897 296 LVIGVHELGHILAAKSTGV 314 (334)
Q Consensus 296 ~ILgvHE~GHylaArr~gV 314 (334)
+...+||+||-+=+..-+-
T Consensus 146 ~~~~AHElGH~lG~~HD~~ 164 (220)
T cd04272 146 VYTMTHELAHLLGAPHDGS 164 (220)
T ss_pred HHHHHHHHHHHhCCCCCCC
Confidence 3667999999997765443
No 58
>PF13583 Reprolysin_4: Metallo-peptidase family M12B Reprolysin-like
Probab=28.20 E-value=22 Score=32.64 Aligned_cols=15 Identities=33% Similarity=0.394 Sum_probs=12.0
Q ss_pred HHHHHHHHHHHHHcC
Q 019897 299 GVHELGHILAAKSTG 313 (334)
Q Consensus 299 gvHE~GHylaArr~g 313 (334)
.+||+||-+=|+.-.
T Consensus 141 ~aHEiGH~lGl~H~~ 155 (206)
T PF13583_consen 141 FAHEIGHNLGLRHDF 155 (206)
T ss_pred HHHHHHHHhcCCCCc
Confidence 589999999887544
No 59
>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=27.47 E-value=34 Score=29.09 Aligned_cols=11 Identities=36% Similarity=0.440 Sum_probs=9.4
Q ss_pred HHHHHHHHHHH
Q 019897 299 GVHELGHILAA 309 (334)
Q Consensus 299 gvHE~GHylaA 309 (334)
..|||.|+++-
T Consensus 64 L~HEm~H~~~~ 74 (157)
T PF10263_consen 64 LLHEMAHAAAY 74 (157)
T ss_pred HHHHHHHHHhh
Confidence 38999999983
No 60
>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=25.88 E-value=54 Score=26.89 Aligned_cols=20 Identities=20% Similarity=0.183 Sum_probs=14.2
Q ss_pred HHHHHHHHHHHHHHHcCccccc
Q 019897 297 VIGVHELGHILAAKSTGVELGV 318 (334)
Q Consensus 297 ILgvHE~GHylaArr~gVklSl 318 (334)
=|.+||++++| .+.|-|+-+
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 45699999998 456666544
No 61
>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=25.41 E-value=1.7e+02 Score=29.64 Aligned_cols=40 Identities=13% Similarity=0.184 Sum_probs=35.1
Q ss_pred eeCCeEEEEcccCChHHHHHHHHHHHHHHhcCCceeEEEe
Q 019897 181 PYEGGVLFKGNLRGQAAKTYEKISTRMKNKFGDQYKLFLL 220 (334)
Q Consensus 181 ~~~qGVIfRGNLRg~pEevy~kL~~kLee~fGDrY~LfLv 220 (334)
..++.+...|.|..+-.+.|+++.+.++++||..|.+.+.
T Consensus 302 ~~~~~i~lsG~l~~~~~~~~~~~l~~f~~~~~~~~~~~~~ 341 (410)
T TIGR02500 302 ESGREIALSGQLDSEKRSRLQELLAAFKQRDGVIPDVVLQ 341 (410)
T ss_pred ecCCEEEEEecCCHHHHHHHHHHHHHHHHhCCCCceEEEe
Confidence 4467899999999999999999999999999987876643
No 62
>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=25.37 E-value=94 Score=29.51 Aligned_cols=43 Identities=16% Similarity=0.179 Sum_probs=30.3
Q ss_pred cccCCCHhHHHHHhhcccccceEEEEeeeeeCCeEEEEcccCChHHHHHHHHHHHHHHh
Q 019897 152 EYIRIPKETIDILKDQVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNK 210 (334)
Q Consensus 152 ~~~~ip~EdL~~IK~~~FG~dTFfvT~~e~~~qGVIfRGNLRg~pEevy~kL~~kLee~ 210 (334)
=..|+.+|+++.||- ++-|...|.+-.-++.+|++|.+.|++-
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 356899999999996 6777888888888899999999999865
No 63
>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=24.51 E-value=3.3e+02 Score=21.70 Aligned_cols=51 Identities=18% Similarity=0.413 Sum_probs=34.7
Q ss_pred ccccceEEEEeeeeeCCeEEEEcccCChHHHHHHHHHHHHHHhcCCceeEEEeecC--------------CCCCCeEEEe
Q 019897 168 VFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFGDQYKLFLLVNP--------------EDDKPVAVVV 233 (334)
Q Consensus 168 ~FG~dTFfvT~~e~~~qGVIfRGNLRg~pEevy~kL~~kLee~fGDrY~LfLvee~--------------edgKPV~vVv 233 (334)
..|++++++. .+++++.+.+++-+++. . |-+.++.+. +...|+++.+
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 46777777777777544 3 555666543 1357999999
Q ss_pred cCCC
Q 019897 234 PRKT 237 (334)
Q Consensus 234 P~~~ 237 (334)
|...
T Consensus 76 P~~~ 79 (95)
T PF01990_consen 76 PSKE 79 (95)
T ss_dssp STTC
T ss_pred CCCC
Confidence 9986
No 64
>PF15281 Consortin_C: Consortin C-terminus
Probab=24.35 E-value=1.7e+02 Score=25.63 Aligned_cols=12 Identities=42% Similarity=0.537 Sum_probs=9.6
Q ss_pred HHHHHHHHHHHH
Q 019897 297 VIGVHELGHILA 308 (334)
Q Consensus 297 ILgvHE~GHyla 308 (334)
-.++||+-||+.
T Consensus 101 ~q~~~~l~hW~~ 112 (113)
T PF15281_consen 101 KQGLAELKHWLT 112 (113)
T ss_pred HHHHHHhhhhhc
Confidence 456899999985
No 65
>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=23.88 E-value=1e+02 Score=23.84 Aligned_cols=34 Identities=24% Similarity=0.307 Sum_probs=23.4
Q ss_pred cccceEEEEeeeeeCCeEEEEcccCChHHHHHHHHHHHHHHhcCC
Q 019897 169 FGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFGD 213 (334)
Q Consensus 169 FG~dTFfvT~~e~~~qGVIfRGNLRg~pEevy~kL~~kLee~fGD 213 (334)
.-+|+|||++- ++ . ...++..++|++.|.+.+|+
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 35689999642 11 1 13456778899999999885
No 66
>PF14891 Peptidase_M91: Effector protein
Probab=23.74 E-value=51 Score=29.35 Aligned_cols=16 Identities=31% Similarity=0.299 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHHHHHH
Q 019897 296 LVIGVHELGHILAAKS 311 (334)
Q Consensus 296 ~ILgvHE~GHylaArr 311 (334)
+|.+.|||+|-+-...
T Consensus 104 ~v~L~HEL~HA~~~~~ 119 (174)
T PF14891_consen 104 FVVLYHELIHAYDYMN 119 (174)
T ss_pred HHHHHHHHHHHHHHHC
Confidence 4667999999886653
No 67
>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=23.67 E-value=46 Score=31.65 Aligned_cols=24 Identities=17% Similarity=0.198 Sum_probs=16.2
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHH
Q 019897 288 LPGALVTALVIGVHELGHILAAKS 311 (334)
Q Consensus 288 LP~al~ll~ILgvHE~GHylaArr 311 (334)
-+++.-+..-..+|||||-+==|.
T Consensus 126 ~~~~~~~~~hvi~HEiGH~IGfRH 149 (211)
T PF12388_consen 126 SNYSVNVIEHVITHEIGHCIGFRH 149 (211)
T ss_pred CCCchhHHHHHHHHHhhhhccccc
Confidence 344555555566999999876554
No 68
>PLN03199 delta6-acyl-lipid desaturase-like protein; Provisional
Probab=23.53 E-value=2.8e+02 Score=28.93 Aligned_cols=17 Identities=18% Similarity=0.352 Sum_probs=13.9
Q ss_pred hHHHHHHHHHHHHHHhcC
Q 019897 195 QAAKTYEKISTRMKNKFG 212 (334)
Q Consensus 195 ~pEevy~kL~~kLee~fG 212 (334)
+..+-|.+|++++++. |
T Consensus 109 ~~~~~y~~L~~~v~~~-g 125 (485)
T PLN03199 109 AFEKGYRDLRAKLIMM-G 125 (485)
T ss_pred HHHHHHHHHHHHHHHc-C
Confidence 3467899999999987 7
No 69
>PF11667 DUF3267: Protein of unknown function (DUF3267); InterPro: IPR021683 This family of proteins has no known function.
Probab=23.27 E-value=26 Score=28.76 Aligned_cols=21 Identities=38% Similarity=0.350 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHHHHHHHcCcc
Q 019897 295 ALVIGVHELGHILAAKSTGVE 315 (334)
Q Consensus 295 l~ILgvHE~GHylaArr~gVk 315 (334)
+.++.+||+=|.+..+.++.+
T Consensus 4 ~~~~~~HEliH~l~~~~~~~~ 24 (111)
T PF11667_consen 4 IVLIPLHELIHGLFFKLFGKK 24 (111)
T ss_pred EeeHHHHHHHHHHHHHHhCCC
Confidence 345579999999999988763
No 70
>PRK06842 fumarate hydratase; Provisional
Probab=22.99 E-value=84 Score=29.38 Aligned_cols=62 Identities=16% Similarity=0.272 Sum_probs=46.2
Q ss_pred ccCCCHhHHHHHhhcccccceEEEEeeeeeCCeEEEEcccCChHHHHHHHHHHHHHHhcCCceeEEEeecCCCCCCeEEE
Q 019897 153 YIRIPKETIDILKDQVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFGDQYKLFLLVNPEDDKPVAVV 232 (334)
Q Consensus 153 ~~~ip~EdL~~IK~~~FG~dTFfvT~~e~~~qGVIfRGNLRg~pEevy~kL~~kLee~fGDrY~LfLvee~edgKPV~vV 232 (334)
..|+.+||++.||- ++-|...|.+-.-++.+|++|.+.+++ |...- | + ..++.++..
T Consensus 6 ~tPl~~e~i~~L~v----------------GD~V~LsG~i~taRDaAHkrl~e~l~~--G~~lP-~---d-l~g~~Iy~~ 62 (185)
T PRK06842 6 TTPLTEEKVKDLKA----------------GDSVLISGYIYTARDAAHKRLIELLDK--GEELP-I---D-IKDQIIYYV 62 (185)
T ss_pred eCCCCHHHHhhCCC----------------CCEEEEeEEEEEEeHHHHHHHHHHHhc--CCCCC-c---C-cCCCEEEEe
Confidence 35789999999985 777888888888889999999999977 43322 2 1 246677777
Q ss_pred ecCCC
Q 019897 233 VPRKT 237 (334)
Q Consensus 233 vP~~~ 237 (334)
-|.+.
T Consensus 63 GP~~~ 67 (185)
T PRK06842 63 GPSPA 67 (185)
T ss_pred cCCCC
Confidence 77764
No 71
>PF13492 GAF_3: GAF domain; PDB: 3EEA_A 4DMZ_A 4DN0_A 1VHM_A.
Probab=22.93 E-value=1.7e+02 Score=22.43 Aligned_cols=28 Identities=29% Similarity=0.462 Sum_probs=22.5
Q ss_pred hHHHHHHHHHHHHHHhcC-CceeEEEeec
Q 019897 195 QAAKTYEKISTRMKNKFG-DQYKLFLLVN 222 (334)
Q Consensus 195 ~pEevy~kL~~kLee~fG-DrY~LfLvee 222 (334)
+++++++++.+.+.+.+| ++.-++++++
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 5666676653
No 72
>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=22.90 E-value=60 Score=28.89 Aligned_cols=19 Identities=26% Similarity=0.039 Sum_probs=13.9
Q ss_pred hHHHHHHHHHHHHHHHHHH
Q 019897 290 GALVTALVIGVHELGHILA 308 (334)
Q Consensus 290 ~al~ll~ILgvHE~GHyla 308 (334)
+-.|.++.+.+|||+|-+-
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 3346777777899999663
No 73
>PRK13267 archaemetzincin-like protein; Reviewed
Probab=22.73 E-value=43 Score=30.63 Aligned_cols=10 Identities=60% Similarity=0.893 Sum_probs=8.4
Q ss_pred HHHHHHHHHH
Q 019897 299 GVHELGHILA 308 (334)
Q Consensus 299 gvHE~GHyla 308 (334)
++||+||-+-
T Consensus 129 ~~HElGH~lG 138 (179)
T PRK13267 129 VTHELGHTLG 138 (179)
T ss_pred HHHHHHHHcC
Confidence 6999999863
No 74
>cd03508 Delta4-sphingolipid-FADS-like The Delta4-sphingolipid Fatty Acid Desaturase (Delta4-sphingolipid-FADS)-like CD includes the integral-membrane enzymes, dihydroceramide Delta-4 desaturase, involved in the synthesis of sphingosine; and the human membrane fatty acid (lipid) desaturase (MLD), reported to modulate biosynthesis of the epidermal growth factor receptor; and other related proteins. These proteins are found in various eukaryotes including vertebrates, higher plants, and fungi. Studies show that MLD is localized to the endoplasmic reticulum. As with other members of this superfamily, this domain family has extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. Comparison of sequences also reveals the existence of three regions of conserved histidine cluster motifs that contain eight histidine residues: HXXXH, HXXHH, and HXXHH. These histidine residues are reported to be catalytically essential and proposed to be the ligands for
Probab=22.59 E-value=2e+02 Score=28.10 Aligned_cols=16 Identities=31% Similarity=0.443 Sum_probs=11.9
Q ss_pred HHHHHHHHHHHHHHcC
Q 019897 298 IGVHELGHILAAKSTG 313 (334)
Q Consensus 298 LgvHE~GHylaArr~g 313 (334)
+..||.+|.-..|...
T Consensus 61 ~l~Hd~~H~~~f~~~~ 76 (289)
T cd03508 61 LAIHEISHNLAFGKPL 76 (289)
T ss_pred HHHHHhHHHhhcCChH
Confidence 4579999998876443
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=22.23 E-value=42 Score=32.49 Aligned_cols=12 Identities=42% Similarity=0.739 Sum_probs=9.2
Q ss_pred HHHHHHHHHHHH
Q 019897 297 VIGVHELGHILA 308 (334)
Q Consensus 297 ILgvHE~GHyla 308 (334)
-..+||+||-++
T Consensus 218 ~v~vHE~GHsf~ 229 (264)
T PF09471_consen 218 QVVVHEFGHSFG 229 (264)
T ss_dssp HHHHHHHHHHTT
T ss_pred ceeeeecccccc
Confidence 455999999664
No 76
>PF06262 DUF1025: Possibl zinc metallo-peptidase; InterPro: IPR010428 This is a family of bacterial protein with undetermined function.; PDB: 3E11_A.
Probab=22.15 E-value=63 Score=27.02 Aligned_cols=13 Identities=31% Similarity=0.289 Sum_probs=10.0
Q ss_pred HHHHHHHHHHHHH
Q 019897 295 ALVIGVHELGHIL 307 (334)
Q Consensus 295 l~ILgvHE~GHyl 307 (334)
+-+-.+||+||++
T Consensus 73 I~~tlvhEiah~f 85 (97)
T PF06262_consen 73 IRDTLVHEIAHHF 85 (97)
T ss_dssp HHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHc
Confidence 3455689999997
No 77
>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=22.10 E-value=43 Score=31.28 Aligned_cols=31 Identities=16% Similarity=0.267 Sum_probs=17.2
Q ss_pred eEEEEcccC--ChHHHHHHHHHHHHHHhcCCcee
Q 019897 185 GVLFKGNLR--GQAAKTYEKISTRMKNKFGDQYK 216 (334)
Q Consensus 185 GVIfRGNLR--g~pEevy~kL~~kLee~fGDrY~ 216 (334)
++.+.||-. ---.++|+++.+.+++. |-...
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 345556633 23467888888888886 53344
No 78
>PF07817 GLE1: GLE1-like protein; InterPro: IPR012476 The members of this family are sequences that are similar to the human protein GLE1 (O75458 from SWISSPROT). This protein is localised at the nuclear pore complexes and functions in poly(A)+ RNA export to the cytoplasm []. ; GO: 0016973 poly(A)+ mRNA export from nucleus, 0005643 nuclear pore; PDB: 3PEV_B 3RRN_B 3PEU_B 3RRM_B.
Probab=22.00 E-value=68 Score=30.50 Aligned_cols=38 Identities=32% Similarity=0.523 Sum_probs=26.5
Q ss_pred hhchhhHHHHHHHHHH-HHHHHHHHHHHcCcccccceeeccc
Q 019897 285 TNGLPGALVTALVIGV-HELGHILAAKSTGVELGVPYFVPSW 325 (334)
Q Consensus 285 ~~gLP~al~ll~ILgv-HE~GHylaArr~gVklSlPYFIP~p 325 (334)
..++|+|..++.|+.- +|+|=++.|+.|. .-||.||..
T Consensus 103 ~~A~PlA~v~~~l~~~~p~~~dillA~l~k---~Cp~~vP~~ 141 (256)
T PF07817_consen 103 ESAFPLARVAVQLWSQHPEFGDILLARLHK---KCPYLVPKY 141 (256)
T ss_dssp GGHHHHHHHHHHHHHHSTCHHHHHHHHHHH---H-GGGG---
T ss_pred chhhhHHHHHHHHHHcCCcHHHHHHHHHHH---cCceeEeec
Confidence 4689999888877765 5999999999883 345555543
No 79
>PHA02456 zinc metallopeptidase motif-containing protein
Probab=21.96 E-value=54 Score=29.05 Aligned_cols=23 Identities=22% Similarity=0.345 Sum_probs=17.7
Q ss_pred HHHHHHHHHHHHHcCcc--ccccee
Q 019897 299 GVHELGHILAAKSTGVE--LGVPYF 321 (334)
Q Consensus 299 gvHE~GHylaArr~gVk--lSlPYF 321 (334)
..||+.|.|.=|.||.- ++.||.
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 80
>PTZ00429 beta-adaptin; Provisional
Probab=21.69 E-value=1.2e+02 Score=33.80 Aligned_cols=32 Identities=28% Similarity=0.251 Sum_probs=14.8
Q ss_pred ChhhhhhccCCCCCCCCcccccCCCCCCCCcC
Q 019897 75 NDKEKEVHDGQENQPATASDQEDDKSQPDSQL 106 (334)
Q Consensus 75 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 106 (334)
.|||++|+++.++.+++.++...+++..+|++
T Consensus 608 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 639 (746)
T PTZ00429 608 LDEEDTEDDDAVELPSTPSMGTQDGSPAPSAA 639 (746)
T ss_pred cccccccchhhccCCCCCCCCCCCCCCCcccc
Confidence 33444444444455555555444443333433
No 81
>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=20.84 E-value=3.1e+02 Score=23.70 Aligned_cols=60 Identities=15% Similarity=0.194 Sum_probs=41.8
Q ss_pred ccCCCHhHHHHHhhcccccceEEEEeeeeeCCe--EEEEcccCChH-------------HHHHHHHHHHHHHhcC
Q 019897 153 YIRIPKETIDILKDQVFGFDTFFVTNQEPYEGG--VLFKGNLRGQA-------------AKTYEKISTRMKNKFG 212 (334)
Q Consensus 153 ~~~ip~EdL~~IK~~~FG~dTFfvT~~e~~~qG--VIfRGNLRg~p-------------Eevy~kL~~kLee~fG 212 (334)
.-.+++|+++.+|..++.-.-.++.=+-+.+.| ++++-...... ..+|+.+.+..+..+|
T Consensus 38 iD~l~~ee~~~~r~~l~~~p~t~~~f~SpSG~GvKi~v~~~~~~~~~lp~~~~~~~~~h~~~y~~~~~~y~~~~~ 112 (136)
T PF08800_consen 38 IDHLDPEEAEELRQLLFEDPYTLAAFVSPSGRGVKIIVPFDYPDGSRLPQDEEEAELFHAHAYEAAVEYYQRLLG 112 (136)
T ss_pred eCCCCHHHHHHHHHHHhcCCcEEEEEEcCCCCeEEEEEEecCCCCccccchhHHHHHHHHHHHHHHHHHHhhhcC
Confidence 334558899999987776665567777777776 45555544433 5788888888888877
No 82
>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=20.80 E-value=1.5e+02 Score=29.16 Aligned_cols=60 Identities=10% Similarity=0.208 Sum_probs=41.6
Q ss_pred CCCHhHHHHHhhcccccceEEEEeeeeeCCeEEEEcccCChHHHHHHHHHHHHHHhcC--CceeEEEeec
Q 019897 155 RIPKETIDILKDQVFGFDTFFVTNQEPYEGGVLFKGNLRGQAAKTYEKISTRMKNKFG--DQYKLFLLVN 222 (334)
Q Consensus 155 ~ip~EdL~~IK~~~FG~dTFfvT~~e~~~qGVIfRGNLRg~pEevy~kL~~kLee~fG--DrY~LfLvee 222 (334)
.+|.+.++++++ ||.+.- .-.-|+.-.+.--.+-.++|+.++++|++.|| ++|.++++..
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 333211 22334555555444556999999999999999 5788888765
No 83
>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]
Probab=20.77 E-value=56 Score=34.65 Aligned_cols=10 Identities=60% Similarity=1.039 Sum_probs=7.6
Q ss_pred HHHHHHHHHHH
Q 019897 296 LVIGVHELGHI 306 (334)
Q Consensus 296 ~ILgvHE~GHy 306 (334)
++| +||+||.
T Consensus 132 gVi-AHEigHv 141 (484)
T COG4783 132 GVI-AHEIGHV 141 (484)
T ss_pred HHH-HHHHHHH
Confidence 344 8999995
No 84
>cd04271 ZnMc_ADAM_fungal Zinc-dependent metalloprotease, ADAM_fungal subgroup. The adamalysin_like or ADAM (A Disintegrin And Metalloprotease) family of metalloproteases are integral membrane proteases acting on a variety of extracellular targets. They are involved in shedding soluble peptides or proteins from the cell surface. This subfamily contains fungal ADAMs, whose precise function has yet to be determined.
Probab=20.38 E-value=40 Score=31.57 Aligned_cols=14 Identities=36% Similarity=0.574 Sum_probs=11.3
Q ss_pred HHHHHHHHHHHHHH
Q 019897 297 VIGVHELGHILAAK 310 (334)
Q Consensus 297 ILgvHE~GHylaAr 310 (334)
+..+|||||-+=+.
T Consensus 147 ~t~AHElGHnLGm~ 160 (228)
T cd04271 147 QVFAHEIGHTFGAV 160 (228)
T ss_pred eehhhhhhhhcCCC
Confidence 35699999999775
No 85
>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=20.34 E-value=83 Score=24.46 Aligned_cols=26 Identities=12% Similarity=0.323 Sum_probs=23.4
Q ss_pred ChHHHHHHHHHHHHHHhcCCceeEEE
Q 019897 194 GQAAKTYEKISTRMKNKFGDQYKLFL 219 (334)
Q Consensus 194 g~pEevy~kL~~kLee~fGDrY~LfL 219 (334)
.++..+-+.|++.++++||.+|.++.
T Consensus 22 ~~~~~s~~~Iq~~~e~~f~~~f~vIc 47 (76)
T PF04155_consen 22 CNLSISKRAIQKAAEKRFGGSFEVIC 47 (76)
T ss_pred CCHHHHHHHHHHHHHHHhCCCEEEEE
Confidence 78899999999999999999999554
No 86
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=20.33 E-value=59 Score=28.08 Aligned_cols=11 Identities=36% Similarity=0.362 Sum_probs=9.8
Q ss_pred HHHHHHHHHHH
Q 019897 300 VHELGHILAAK 310 (334)
Q Consensus 300 vHE~GHylaAr 310 (334)
.|||.|+++-.
T Consensus 64 ~HEm~H~~~~~ 74 (146)
T smart00731 64 LHELCHAALYL 74 (146)
T ss_pred HHHHHHHHHHH
Confidence 79999999874
No 87
>COG3101 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.30 E-value=48 Score=30.49 Aligned_cols=34 Identities=29% Similarity=0.613 Sum_probs=19.2
Q ss_pred HHHHHHHHHHhcCCceeEEEeecCCCCCCeEEEecCCC
Q 019897 200 YEKISTRMKNKFGDQYKLFLLVNPEDDKPVAVVVPRKT 237 (334)
Q Consensus 200 y~kL~~kLee~fGDrY~LfLvee~edgKPV~vVvP~~~ 237 (334)
|+.|-+-+-+-|-++|.--|+.. ++.|+. +|...
T Consensus 5 y~~lI~IFNqcF~~eyNT~LvkG--~DEPiY--lPAde 38 (180)
T COG3101 5 YEQLIEIFNQCFADEYNTRLVKG--DDEPIY--LPADE 38 (180)
T ss_pred HHHHHHHHHHHHHHhhcceeeeC--CCccee--ccCcc
Confidence 44444444555666677666553 566764 66664
No 88
>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=20.16 E-value=1.9e+02 Score=22.66 Aligned_cols=36 Identities=28% Similarity=0.524 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHhcCCceeEEEeecCCCCCCeEEEecCCC
Q 019897 199 TYEKISTRMKNKFGDQYKLFLLVNPEDDKPVAVVVPRKT 237 (334)
Q Consensus 199 vy~kL~~kLee~fGDrY~LfLvee~edgKPV~vVvP~~~ 237 (334)
.++....+++++||+ |.|+ +-.....|+.|.-|.--
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 367778899999999 7744 43335789999888764
No 89
>cd04327 ZnMc_MMP_like_3 Zinc-dependent metalloprotease; MMP_like sub-family 3. A group of bacterial and fungal metalloproteinase domains similar to matrix metalloproteinases and astacin.
Probab=20.16 E-value=54 Score=29.59 Aligned_cols=10 Identities=50% Similarity=0.913 Sum_probs=8.0
Q ss_pred HHHHHHHHHH
Q 019897 300 VHELGHILAA 309 (334)
Q Consensus 300 vHE~GHylaA 309 (334)
+|||||-+=-
T Consensus 97 ~HElgHaLG~ 106 (198)
T cd04327 97 LHEFGHALGF 106 (198)
T ss_pred HHHHHHHhcC
Confidence 6999998743
Done!