Query 041464
Match_columns 198
No_of_seqs 137 out of 179
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 07:22:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041464.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041464hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04450 BSP: Peptidase of pla 100.0 3.2E-56 7E-61 377.7 15.8 165 24-192 2-205 (205)
2 PF10263 SprT-like: SprT-like 95.9 0.011 2.5E-07 46.9 4.2 46 72-121 20-70 (157)
3 COG3091 SprT Zn-dependent meta 95.6 0.0065 1.4E-07 50.2 1.8 98 68-170 23-138 (156)
4 PF13699 DUF4157: Domain of un 94.6 0.043 9.2E-07 40.2 3.5 46 68-121 17-71 (79)
5 PF13203 DUF2201_N: Putative m 94.6 0.042 9E-07 48.2 4.0 36 82-121 35-70 (292)
6 PRK04860 hypothetical protein; 94.4 0.034 7.3E-07 46.0 2.8 47 70-121 27-73 (160)
7 PRK04351 hypothetical protein; 93.7 0.088 1.9E-06 43.0 4.0 46 71-121 25-71 (149)
8 PRK03072 heat shock protein Ht 93.6 0.095 2.1E-06 46.6 4.4 45 70-121 88-137 (288)
9 smart00731 SprT SprT homologue 93.6 0.042 9.1E-07 44.0 1.9 46 71-121 23-69 (146)
10 PRK03001 M48 family peptidase; 93.3 0.13 2.7E-06 45.5 4.6 46 69-121 84-134 (283)
11 COG0501 HtpX Zn-dependent prot 93.3 0.064 1.4E-06 46.4 2.6 33 85-121 130-167 (302)
12 PRK05457 heat shock protein Ht 93.1 0.14 3.1E-06 45.5 4.7 47 68-121 93-144 (284)
13 PRK01345 heat shock protein Ht 93.0 0.14 3E-06 46.3 4.5 36 82-121 94-134 (317)
14 PRK03982 heat shock protein Ht 92.6 0.19 4.1E-06 44.5 4.7 36 82-121 95-135 (288)
15 PRK04897 heat shock protein Ht 92.6 0.14 3E-06 45.7 3.9 47 68-121 96-147 (298)
16 COG4783 Putative Zn-dependent 91.9 0.32 7E-06 46.7 5.6 48 69-121 91-140 (484)
17 PF01435 Peptidase_M48: Peptid 91.8 0.25 5.4E-06 40.6 4.2 34 84-121 62-99 (226)
18 PRK02391 heat shock protein Ht 90.8 0.28 6.1E-06 43.9 3.8 45 70-121 94-143 (296)
19 PRK02870 heat shock protein Ht 90.4 0.34 7.4E-06 44.4 4.1 46 69-121 133-183 (336)
20 PRK01265 heat shock protein Ht 90.0 0.37 8E-06 44.0 3.9 36 82-121 110-150 (324)
21 PF05569 Peptidase_M56: BlaR1 80.8 2.7 5.9E-05 36.8 4.6 94 69-176 157-266 (299)
22 PF10460 Peptidase_M30: Peptid 80.6 8 0.00017 36.1 7.8 56 140-196 224-285 (366)
23 PF07580 Peptidase_M26_C: M26 77.0 0.61 1.3E-05 47.0 -0.7 29 85-121 372-401 (737)
24 PF01457 Peptidase_M8: Leishma 74.9 8.2 0.00018 37.1 6.3 27 91-121 194-220 (521)
25 PF13485 Peptidase_MA_2: Pepti 73.1 4 8.7E-05 29.7 3.0 33 82-121 3-35 (128)
26 PF09768 Peptidase_M76: Peptid 71.8 3.9 8.5E-05 34.3 3.0 47 68-121 34-81 (173)
27 PF12725 DUF3810: Protein of u 69.3 19 0.00041 32.7 7.0 77 111-189 196-289 (318)
28 PF01863 DUF45: Protein of unk 68.1 7.2 0.00016 31.9 3.8 46 70-121 128-174 (205)
29 PF08325 WLM: WLM domain; Int 64.1 8 0.00017 32.6 3.3 39 82-121 54-92 (186)
30 PTZ00337 surface protease GP63 63.9 8.6 0.00019 37.8 4.0 25 91-121 215-239 (567)
31 KOG1675 Predicted cyclin [Gene 61.6 6.3 0.00014 36.3 2.4 65 126-196 231-297 (343)
32 PF14891 Peptidase_M91: Effect 55.1 6 0.00013 32.5 1.0 32 90-121 74-113 (174)
33 cd04327 ZnMc_MMP_like_3 Zinc-d 52.5 14 0.00031 30.6 3.0 30 110-140 91-121 (198)
34 COG1644 RPB10 DNA-directed RNA 50.2 14 0.0003 26.4 2.1 16 181-196 10-25 (63)
35 COG1451 Predicted metal-depend 48.6 26 0.00056 30.3 4.0 57 68-129 137-196 (223)
36 PF02102 Peptidase_M35: Deuter 48.1 12 0.00026 34.9 2.0 54 70-123 247-309 (359)
37 PF02130 UPF0054: Uncharacteri 46.7 20 0.00043 28.8 2.8 58 67-125 59-123 (145)
38 smart00235 ZnMc Zinc-dependent 45.9 17 0.00038 27.9 2.3 32 89-129 73-105 (140)
39 KOG3314 Ku70-binding protein [ 45.1 22 0.00047 30.3 2.9 46 69-121 56-101 (194)
40 cd04268 ZnMc_MMP_like Zinc-dep 45.1 17 0.00037 28.5 2.2 40 90-129 73-113 (165)
41 PTZ00257 Glycoprotein GP63 (le 42.6 39 0.00085 33.8 4.6 27 91-121 240-266 (622)
42 PF14521 Aspzincin_M35: Lysine 41.1 15 0.00033 29.4 1.4 35 84-121 67-106 (148)
43 PF05299 Peptidase_M61: M61 gl 41.0 15 0.00032 29.1 1.2 58 110-169 3-75 (122)
44 PF01447 Peptidase_M4: Thermol 38.9 17 0.00038 29.5 1.4 10 112-121 136-145 (150)
45 PRK04016 DNA-directed RNA poly 38.2 26 0.00055 25.0 1.9 16 181-196 10-25 (62)
46 PF13076 DUF3940: Protein of u 38.2 38 0.00083 21.7 2.6 30 164-194 7-37 (38)
47 PF07700 HNOB: Heme NO binding 36.5 57 0.0012 26.4 4.1 49 147-195 7-73 (171)
48 PF14162 YozD: YozD-like prote 36.4 38 0.00082 23.5 2.5 21 108-128 10-30 (57)
49 PLN00032 DNA-directed RNA poly 34.5 31 0.00066 25.2 1.9 16 181-196 10-25 (71)
50 COG3864 Uncharacterized protei 33.8 31 0.00068 32.2 2.3 33 85-121 47-79 (396)
51 PF08014 DUF1704: Domain of un 33.5 64 0.0014 29.8 4.3 111 71-191 132-261 (349)
52 PF02449 Glyco_hydro_42: Beta- 31.9 36 0.00078 30.9 2.4 53 140-194 142-205 (374)
53 PF11444 DUF2895: Protein of u 31.8 78 0.0017 27.3 4.3 37 25-61 38-74 (199)
54 PF10023 DUF2265: Predicted am 31.5 28 0.0006 32.3 1.6 14 108-121 162-175 (337)
55 PF01433 Peptidase_M1: Peptida 31.5 1.5E+02 0.0032 26.3 6.3 68 52-126 239-313 (390)
56 TIGR00043 metalloprotein, YbeY 30.4 31 0.00067 26.6 1.5 36 90-125 49-88 (110)
57 TIGR03746 conj_TIGR03746 integ 29.2 79 0.0017 27.4 3.8 38 25-62 39-76 (202)
58 TIGR02412 pepN_strep_liv amino 28.9 70 0.0015 32.6 4.1 39 91-129 266-308 (831)
59 cd04278 ZnMc_MMP Zinc-dependen 28.5 47 0.001 26.2 2.3 37 89-125 85-122 (157)
60 PRK00016 metal-binding heat sh 28.2 32 0.0007 28.1 1.3 36 90-125 89-128 (159)
61 COG4219 MecR1 Antirepressor re 26.6 74 0.0016 29.6 3.4 48 68-121 150-200 (337)
62 PF10005 DUF2248: Uncharacteri 26.1 36 0.00079 31.6 1.4 53 68-121 126-189 (343)
63 PF14247 DUF4344: Domain of un 26.0 1.3E+02 0.0027 26.2 4.6 52 70-121 37-102 (220)
64 PTZ00391 transport protein par 23.4 48 0.001 27.7 1.5 48 139-189 33-83 (168)
65 PF06262 DUF1025: Possibl zinc 23.4 64 0.0014 24.5 2.1 31 91-121 51-83 (97)
66 PF06114 DUF955: Domain of unk 22.9 1.3E+02 0.0028 21.3 3.6 25 89-121 28-52 (122)
67 PRK11901 hypothetical protein; 22.2 56 0.0012 30.3 1.8 40 1-40 38-77 (327)
68 cd04281 ZnMc_BMP1_TLD Zinc-dep 21.7 41 0.0009 28.6 0.8 10 112-121 88-97 (200)
69 COG4784 Putative Zn-dependent 20.7 1.7E+02 0.0037 28.0 4.6 51 67-121 83-134 (479)
70 PF02607 B12-binding_2: B12 bi 20.6 1.2E+02 0.0025 20.9 2.8 45 146-190 5-54 (79)
71 cd04277 ZnMc_serralysin_like Z 20.6 1.9E+02 0.0041 23.3 4.5 56 70-127 63-130 (186)
No 1
>PF04450 BSP: Peptidase of plants and bacteria; InterPro: IPR007541 These basic secretory proteins (BSPs) are believed to be part of the plants defence mechanism against pathogens [].
Probab=100.00 E-value=3.2e-56 Score=377.66 Aligned_cols=165 Identities=41% Similarity=0.847 Sum_probs=149.0
Q ss_pred eEEEEEeCCCCCcccchhhhccCCCchh-----HHHHHHhccCCCCCCCCCCeEEEEEccCCCCceeEecC----CeEEE
Q 041464 24 VDYTVSNRAATTPGGMRFANEIGAEYTP-----NFIWRLFQQNTEADRKNIPQVDLFIDDMKPGEIAFTSN----NGIHY 94 (198)
Q Consensus 24 ~~~~~~n~a~~t~gg~rF~~~i~~~~a~-----~~i~~lf~y~~p~~rk~v~~Vtl~l~d~~~~GVA~t~g----~~I~~ 94 (198)
+++++++.+++||||+||++.|+++... .+|+++| |++|+++|+|++|||+|++| +|||||+| .+|||
T Consensus 2 p~~~l~v~n~~s~Gg~~F~~~~~~a~~~L~~a~~~V~~~l-y~~~~~~~~v~~Vt~~~~~~--~gVA~t~gd~~~~~I~~ 78 (205)
T PF04450_consen 2 PKFRLEVNNLDSPGGRRFDRFIPDAEQVLRDASRFVWRLL-YQSPADRKPVRSVTLILDDM--DGVAYTSGDDDHKEIHF 78 (205)
T ss_pred CeEEEEeeCCCCHHHHHHHHHhcCHHHHHHHHHHHHHHHh-CCCCCCCCcccEEEEEEECC--CeeEEEecCCCccEEEE
Confidence 3445555559999999999999555433 8999998 66699999999999999999 99999999 79999
Q ss_pred cccccccCCc-hhhhHHHHHHHHHHHhh-------------------------cCCCCCCCcCCCCCCCCCCCcchhHhH
Q 041464 95 GDDFIQNIPV-DLIKQEFSGVMYHEMTH-------------------------ANYVPEGWAKPGEGTMWNQGHSSVAAR 148 (198)
Q Consensus 95 S~~~i~~~~~-d~~~~Ei~GVl~HE~vH-------------------------Ag~ap~hw~~p~~g~~wd~GY~~~TA~ 148 (198)
|++||+++++ +++++||+|||+||||| |||+|+||++|+.|++||+|| ++|||
T Consensus 79 S~~~i~~~~~~~~~~~Ei~Gvl~HE~~H~~Q~~~~~~~P~~liEGIADyVRl~aG~~~~~w~~p~~~~~wd~gY-~~TA~ 157 (205)
T PF04450_consen 79 SARYIAKYPADGDVRDEIIGVLYHEMVHCWQWDGRGTAPGGLIEGIADYVRLKAGYAPPHWKRPGGGDSWDDGY-RTTAR 157 (205)
T ss_pred eHHHHhhcccccchHHHHHHHHHHHHHHHhhcCCCCCCChhheecHHHHHHHHcCCCCccccCCCCCCCccccc-HHHHH
Confidence 9999999984 34999999999999999 899999999998888999999 99999
Q ss_pred HHHHHhh--cCCCHHHHHHHHHhc-cC-CHHHHHHHhCCCHHHHHHHH
Q 041464 149 FLDYCND--LRNGFVAELNKKMRD-GY-NDNFFMELLGKSIDQLWNDY 192 (198)
Q Consensus 149 FL~wle~--~~~gfV~~LN~~mr~-~y-sd~~~~~l~G~~v~~LW~eY 192 (198)
||+|||+ +++|||++||++||+ +| ++++|+++||++|++||+||
T Consensus 158 FL~wle~~~~~~gfV~~LN~~m~~~~y~~~~~~~~l~G~~v~~LW~eY 205 (205)
T PF04450_consen 158 FLDWLEDNRYGKGFVRRLNEAMRRDKYSSDDFWKELLGKPVDELWAEY 205 (205)
T ss_pred HHHHHHhcccCccHHHHHHHHHhhCCCCcHhHHHHHHCcCHHHHHhhC
Confidence 9999997 799999999999965 59 89999999999999999998
No 2
>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=95.90 E-value=0.011 Score=46.88 Aligned_cols=46 Identities=20% Similarity=0.344 Sum_probs=35.3
Q ss_pred EEEEEc-cCC-CCceeEecCC---eEEEcccccccCCchhhhHHHHHHHHHHHhh
Q 041464 72 VDLFID-DMK-PGEIAFTSNN---GIHYGDDFIQNIPVDLIKQEFSGVMYHEMTH 121 (198)
Q Consensus 72 Vtl~l~-d~~-~~GVA~t~g~---~I~~S~~~i~~~~~d~~~~Ei~GVl~HE~vH 121 (198)
+.+++. .+. .-|.....+. +|.+|+.+++..+ ..|+..+|.|||+|
T Consensus 20 ~~i~~~~~~~~~~G~~~~~~~~~~~I~ls~~~~~~~~----~~~~~~tL~HEm~H 70 (157)
T PF10263_consen 20 IPITWSKRMKRTAGRCRYKRRSPCEIRLSPKLLDRNP----EEELIDTLLHEMAH 70 (157)
T ss_pred eEEEEECCCCCceEEEEECCCCceEEEECHHHHHhhH----HHHHHHHHHHHHHH
Confidence 666666 442 3677666666 9999999998843 45899999999999
No 3
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=95.61 E-value=0.0065 Score=50.17 Aligned_cols=98 Identities=16% Similarity=0.197 Sum_probs=63.2
Q ss_pred CCCeEEEEEccCCCCceeEecCCeEEEcccccccCCchhhhHHHHHHHHHHHhh-------cCCCCC--CCcC---CCCC
Q 041464 68 NIPQVDLFIDDMKPGEIAFTSNNGIHYGDDFIQNIPVDLIKQEFSGVMYHEMTH-------ANYVPE--GWAK---PGEG 135 (198)
Q Consensus 68 ~v~~Vtl~l~d~~~~GVA~t~g~~I~~S~~~i~~~~~d~~~~Ei~GVl~HE~vH-------Ag~ap~--hw~~---p~~g 135 (198)
+-.++.+..+-.+ .|+||---++|.|+|.++.....| +|.+|+-||++| -||.|- -|+. .-.|
T Consensus 23 ~~p~~~~n~Rg~t-aG~ayL~~~~I~lNP~ll~en~~~----f~~~vV~HELaHl~ly~~~gr~~phg~ewk~lm~qV~~ 97 (156)
T COG3091 23 FRPKASYNQRGRT-AGGAYLLKSEIRLNPKLLEENGED----FIEQVVPHELAHLHLYQEFGRYKPHGKEWKLLMQQVLG 97 (156)
T ss_pred CCcceehhhhhhh-cchhhccccccccCHHHHHHccHH----HHHHHHHHHHHHHHHHHHcCCCCCCchhHHHHHHHhCC
Confidence 3345777777643 899999888999999999987654 799999999999 677763 4531 0011
Q ss_pred CCCCC--Cc---chhHhHHHHHHh-hcCCCHHHHHHHHHhc
Q 041464 136 TMWNQ--GH---SSVAARFLDYCN-DLRNGFVAELNKKMRD 170 (198)
Q Consensus 136 ~~wd~--GY---~~~TA~FL~wle-~~~~gfV~~LN~~mr~ 170 (198)
-+.+. .+ +..+..|+-.|. ....=.||+.|..+|.
T Consensus 98 l~~~~~h~~~~~~v~~~~~~Y~C~C~q~~l~~RRhn~~~~g 138 (156)
T COG3091 98 LRFCRTHQFEVQSVRRTTYPYRCQCQQHYLRIRRHNTVRRG 138 (156)
T ss_pred CCCCccchHHHhhccccceeEEeecCCccchhhhccccccc
Confidence 11111 11 012256666666 3345567888877753
No 4
>PF13699 DUF4157: Domain of unknown function (DUF4157)
Probab=94.62 E-value=0.043 Score=40.21 Aligned_cols=46 Identities=24% Similarity=0.464 Sum_probs=32.9
Q ss_pred CCCeEEEEEc--------cCCCCceeEecCCeEEEcccccc-cCCchhhhHHHHHHHHHHHhh
Q 041464 68 NIPQVDLFID--------DMKPGEIAFTSNNGIHYGDDFIQ-NIPVDLIKQEFSGVMYHEMTH 121 (198)
Q Consensus 68 ~v~~Vtl~l~--------d~~~~GVA~t~g~~I~~S~~~i~-~~~~d~~~~Ei~GVl~HE~vH 121 (198)
+...|.+-.. .+ .-.|+|.|+.|+|.+.-.. ..+.+ ..+|.||++|
T Consensus 17 dl~~Vrvh~~~~a~~~~~~~--~A~A~T~G~~I~f~~g~~~~~s~~~------~~llaHEl~H 71 (79)
T PF13699_consen 17 DLSDVRVHTGPAASRAAAAL--GARAFTVGNDIYFAPGKYNPDSPEG------RALLAHELAH 71 (79)
T ss_pred CccceEEEeCCchhhhhhcc--CCeEEEECCEEEEcCCCcCCCCCCc------chhHhHHHHH
Confidence 3566776665 23 4589999999999765432 33445 5899999999
No 5
>PF13203 DUF2201_N: Putative metallopeptidase domain
Probab=94.58 E-value=0.042 Score=48.23 Aligned_cols=36 Identities=25% Similarity=0.464 Sum_probs=31.1
Q ss_pred CceeEecCCeEEEcccccccCCchhhhHHHHHHHHHHHhh
Q 041464 82 GEIAFTSNNGIHYGDDFIQNIPVDLIKQEFSGVMYHEMTH 121 (198)
Q Consensus 82 ~GVA~t~g~~I~~S~~~i~~~~~d~~~~Ei~GVl~HE~vH 121 (198)
-..++|.|..|+|++.|+.+.+. .|+.+||.||+.|
T Consensus 35 ~~t~~tDg~~l~~nP~~~~~l~~----~~~~~~l~HevlH 70 (292)
T PF13203_consen 35 IPTAATDGRRLYYNPEFLESLSP----EERVGLLLHEVLH 70 (292)
T ss_pred CceeeEcCcEEEECcHHHhcCCH----HHHHHHHHHHHHH
Confidence 35788899999999999987764 3789999999999
No 6
>PRK04860 hypothetical protein; Provisional
Probab=94.40 E-value=0.034 Score=46.02 Aligned_cols=47 Identities=19% Similarity=0.247 Sum_probs=38.5
Q ss_pred CeEEEEEccCCCCceeEecCCeEEEcccccccCCchhhhHHHHHHHHHHHhh
Q 041464 70 PQVDLFIDDMKPGEIAFTSNNGIHYGDDFIQNIPVDLIKQEFSGVMYHEMTH 121 (198)
Q Consensus 70 ~~Vtl~l~d~~~~GVA~t~g~~I~~S~~~i~~~~~d~~~~Ei~GVl~HE~vH 121 (198)
..|++..+.-+ .|.|+-..++|.||+..++..+. .++.+||-|||+|
T Consensus 27 p~~~f~~R~rt-aG~~~l~~~~I~~Np~ll~~~~~----~~l~~~v~HEl~H 73 (160)
T PRK04860 27 PKVSYTQRGTS-AGTAWLQSNEIRLNPVLLLENQQ----AFIDEVVPHELAH 73 (160)
T ss_pred CEEEEeecchh-hcchhHhcCCeeeCHHHHhhCcH----HHHHhHHHHHHHH
Confidence 36788877532 78888888899999999887754 4789999999999
No 7
>PRK04351 hypothetical protein; Provisional
Probab=93.73 E-value=0.088 Score=43.02 Aligned_cols=46 Identities=15% Similarity=0.295 Sum_probs=35.1
Q ss_pred eEEEEEccCCCCceeE-ecCCeEEEcccccccCCchhhhHHHHHHHHHHHhh
Q 041464 71 QVDLFIDDMKPGEIAF-TSNNGIHYGDDFIQNIPVDLIKQEFSGVMYHEMTH 121 (198)
Q Consensus 71 ~Vtl~l~d~~~~GVA~-t~g~~I~~S~~~i~~~~~d~~~~Ei~GVl~HE~vH 121 (198)
+|++..+-- ..|.+| -..+.|.||+..+..++.+ +|.+||-|||.|
T Consensus 25 ~v~~n~Rlr-ttgG~~~l~~~~I~lnp~ll~~~~~~----~l~~vv~HElcH 71 (149)
T PRK04351 25 QAYFNKRLR-TTGGRYLLKDHHIEFNPKMLEEYGLE----ELIGIIKHELCH 71 (149)
T ss_pred EEEEeccch-hhhheeecCCCeEEeCHHHHhhccHH----HHHhhHHHHHHH
Confidence 677766642 255555 5567999999999887654 689999999999
No 8
>PRK03072 heat shock protein HtpX; Provisional
Probab=93.63 E-value=0.095 Score=46.63 Aligned_cols=45 Identities=22% Similarity=0.452 Sum_probs=32.3
Q ss_pred CeEEEEEccCCCCceeEecCC-----eEEEcccccccCCchhhhHHHHHHHHHHHhh
Q 041464 70 PQVDLFIDDMKPGEIAFTSNN-----GIHYGDDFIQNIPVDLIKQEFSGVMYHEMTH 121 (198)
Q Consensus 70 ~~Vtl~l~d~~~~GVA~t~g~-----~I~~S~~~i~~~~~d~~~~Ei~GVl~HE~vH 121 (198)
.+| +++++- ..-||++|. .|-++...++..+. +|+.|||.||+.|
T Consensus 88 p~v-yv~~~~--~~NAFa~G~~~~~~~v~vt~gLl~~l~~----~El~aVlAHElgH 137 (288)
T PRK03072 88 PRL-YISPTA--APNAFATGRNPRNAAVCCTEGILQILNE----RELRGVLGHELSH 137 (288)
T ss_pred CCE-EEecCC--CCceEEecCCCCCcEEEecHHHHHhCCH----HHHHHHHHHHHHH
Confidence 344 345543 456888884 37777777766653 5999999999999
No 9
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=93.58 E-value=0.042 Score=43.96 Aligned_cols=46 Identities=13% Similarity=0.148 Sum_probs=31.3
Q ss_pred eEEEEEccCCCCceeEec-CCeEEEcccccccCCchhhhHHHHHHHHHHHhh
Q 041464 71 QVDLFIDDMKPGEIAFTS-NNGIHYGDDFIQNIPVDLIKQEFSGVMYHEMTH 121 (198)
Q Consensus 71 ~Vtl~l~d~~~~GVA~t~-g~~I~~S~~~i~~~~~d~~~~Ei~GVl~HE~vH 121 (198)
.|++.-+ |+..|=++.. ..+|.||+..+...+.+ +|.+||.|||+|
T Consensus 23 ~i~w~~r-~~~~~G~~~~~~~~I~ln~~l~~~~~~~----~l~~~l~HEm~H 69 (146)
T smart00731 23 KVVWNKR-LRKTGGRCLLKSAEIRLNPKLLTENGRD----RLRETLLHELCH 69 (146)
T ss_pred EEEEehh-hhhhhHHhhcCCCEEEeCHHHHhhccHH----HHHhhHHHHHHH
Confidence 5555444 2212223443 56999999999876643 688999999999
No 10
>PRK03001 M48 family peptidase; Provisional
Probab=93.33 E-value=0.13 Score=45.47 Aligned_cols=46 Identities=26% Similarity=0.543 Sum_probs=33.7
Q ss_pred CCeEEEEEccCCCCceeEecCC-----eEEEcccccccCCchhhhHHHHHHHHHHHhh
Q 041464 69 IPQVDLFIDDMKPGEIAFTSNN-----GIHYGDDFIQNIPVDLIKQEFSGVMYHEMTH 121 (198)
Q Consensus 69 v~~Vtl~l~d~~~~GVA~t~g~-----~I~~S~~~i~~~~~d~~~~Ei~GVl~HE~vH 121 (198)
..+| +++++- .--||+.|. .|-++...++..+ ++|+.+||.||+.|
T Consensus 84 ~p~v-~v~~~~--~~NAfa~G~~~~~~~Ivvt~gLl~~l~----~~El~aVlAHElgH 134 (283)
T PRK03001 84 MPKV-YLINED--QPNAFATGRNPEHAAVAATTGILRVLS----EREIRGVMAHELAH 134 (283)
T ss_pred CCeE-EEecCC--CcceEEecCCCCCeEEEecHHHHhhCC----HHHHHHHHHHHHHH
Confidence 3444 344542 346888873 6999999998775 35999999999999
No 11
>COG0501 HtpX Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]
Probab=93.26 E-value=0.064 Score=46.38 Aligned_cols=33 Identities=21% Similarity=0.374 Sum_probs=27.0
Q ss_pred eEecCC-----eEEEcccccccCCchhhhHHHHHHHHHHHhh
Q 041464 85 AFTSNN-----GIHYGDDFIQNIPVDLIKQEFSGVMYHEMTH 121 (198)
Q Consensus 85 A~t~g~-----~I~~S~~~i~~~~~d~~~~Ei~GVl~HE~vH 121 (198)
|++.|+ .|-++..-++.-++ +||.+||.||+.|
T Consensus 130 AFa~g~~~~~~~V~vt~gLl~~l~~----dEl~aVlaHElgH 167 (302)
T COG0501 130 AFALGGGPKNGRVVVTTGLLDLLND----DELEAVLAHELGH 167 (302)
T ss_pred ceecCCCCCCeeEEecHHHHhhCCH----HHHHHHHHHHHHH
Confidence 555543 99999999995554 4999999999999
No 12
>PRK05457 heat shock protein HtpX; Provisional
Probab=93.14 E-value=0.14 Score=45.51 Aligned_cols=47 Identities=23% Similarity=0.411 Sum_probs=33.8
Q ss_pred CCCeEEEEEccCCCCceeEecCC-----eEEEcccccccCCchhhhHHHHHHHHHHHhh
Q 041464 68 NIPQVDLFIDDMKPGEIAFTSNN-----GIHYGDDFIQNIPVDLIKQEFSGVMYHEMTH 121 (198)
Q Consensus 68 ~v~~Vtl~l~d~~~~GVA~t~g~-----~I~~S~~~i~~~~~d~~~~Ei~GVl~HE~vH 121 (198)
|+.+|- ++++- .--|+++|. .|-++...++.-+. +|+.|||.||+.|
T Consensus 93 p~p~v~-v~~~~--~~NAfa~G~~~~~~~V~vt~gLl~~L~~----~El~aVlAHElgH 144 (284)
T PRK05457 93 GMPEVA-IYHSP--EINAFATGASKNNSLVAVSTGLLQNMSR----DEVEAVLAHEISH 144 (284)
T ss_pred CCCCEE-EEeCC--CceEEEecCCCCCeEEEeehHHhhhCCH----HHHHHHHHHHHHH
Confidence 345554 33432 457888883 58888888887653 5999999999999
No 13
>PRK01345 heat shock protein HtpX; Provisional
Probab=93.02 E-value=0.14 Score=46.30 Aligned_cols=36 Identities=28% Similarity=0.504 Sum_probs=29.5
Q ss_pred CceeEecCC-----eEEEcccccccCCchhhhHHHHHHHHHHHhh
Q 041464 82 GEIAFTSNN-----GIHYGDDFIQNIPVDLIKQEFSGVMYHEMTH 121 (198)
Q Consensus 82 ~GVA~t~g~-----~I~~S~~~i~~~~~d~~~~Ei~GVl~HE~vH 121 (198)
.--||++|. .|-++...++..++ +|+.|||.||+.|
T Consensus 94 ~~NAFa~G~~~~~~~V~vt~gLL~~L~~----dEL~aVlAHElgH 134 (317)
T PRK01345 94 QPNAFATGRNPENAAVAATTGLLQRLSP----EEVAGVMAHELAH 134 (317)
T ss_pred CcceEEecCCCCCeEEEechHHHhhCCH----HHHHHHHHHHHHH
Confidence 346888873 69999999987643 5999999999999
No 14
>PRK03982 heat shock protein HtpX; Provisional
Probab=92.63 E-value=0.19 Score=44.49 Aligned_cols=36 Identities=25% Similarity=0.434 Sum_probs=29.4
Q ss_pred CceeEecCC-----eEEEcccccccCCchhhhHHHHHHHHHHHhh
Q 041464 82 GEIAFTSNN-----GIHYGDDFIQNIPVDLIKQEFSGVMYHEMTH 121 (198)
Q Consensus 82 ~GVA~t~g~-----~I~~S~~~i~~~~~d~~~~Ei~GVl~HE~vH 121 (198)
.--||++|. .|.++...++..++ +|+.+||.||+.|
T Consensus 95 ~~NAfa~G~~~~~~~V~vt~gLl~~l~~----~El~AVlAHElgH 135 (288)
T PRK03982 95 TPNAFATGRDPKHAVVAVTEGILNLLNE----DELEGVIAHELTH 135 (288)
T ss_pred CcceEEeccCCCCeEEEeehHHHhhCCH----HHHHHHHHHHHHH
Confidence 347888862 68899999987653 5999999999999
No 15
>PRK04897 heat shock protein HtpX; Provisional
Probab=92.60 E-value=0.14 Score=45.75 Aligned_cols=47 Identities=28% Similarity=0.492 Sum_probs=35.0
Q ss_pred CCCeEEEEEccCCCCceeEecCC-----eEEEcccccccCCchhhhHHHHHHHHHHHhh
Q 041464 68 NIPQVDLFIDDMKPGEIAFTSNN-----GIHYGDDFIQNIPVDLIKQEFSGVMYHEMTH 121 (198)
Q Consensus 68 ~v~~Vtl~l~d~~~~GVA~t~g~-----~I~~S~~~i~~~~~d~~~~Ei~GVl~HE~vH 121 (198)
|..+|- ++++- ..-||++|. .|-++...++..+. +|+.+||.||+.|
T Consensus 96 p~p~v~-v~~~~--~~NAfa~G~~~~~~~v~vt~gLl~~l~~----~El~aVlAHElgH 147 (298)
T PRK04897 96 PMPRVF-IIDDP--SPNAFATGSSPKNAAVAVTTGLLAIMNR----EELEGVIGHEISH 147 (298)
T ss_pred CCCcEE-EecCC--CCceEEeccCCCCcEEEeehHHHhhCCH----HHHHHHHHHHHHH
Confidence 345554 34543 567888873 68899888887653 5999999999999
No 16
>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]
Probab=91.94 E-value=0.32 Score=46.68 Aligned_cols=48 Identities=21% Similarity=0.381 Sum_probs=37.7
Q ss_pred CCeEEEEEccCCCCce-eEec-CCeEEEcccccccCCchhhhHHHHHHHHHHHhh
Q 041464 69 IPQVDLFIDDMKPGEI-AFTS-NNGIHYGDDFIQNIPVDLIKQEFSGVMYHEMTH 121 (198)
Q Consensus 69 v~~Vtl~l~d~~~~GV-A~t~-g~~I~~S~~~i~~~~~d~~~~Ei~GVl~HE~vH 121 (198)
-..++|+|-+- +.+ |+++ |+.|.+++..|-...+ ..|+.|||.||+-|
T Consensus 91 ~~~f~f~lV~d--~~iNAFA~~Gg~v~vntGLll~ae~---esElagViAHEigH 140 (484)
T COG4783 91 KTPFTFFLVND--DSINAFATPGGYVVVNTGLLLTAEN---ESELAGVIAHEIGH 140 (484)
T ss_pred CCCeEEEEecC--CccchhhcCCceEEEehHHHHhcCC---HHHHHHHHHHHHHH
Confidence 34588887764 564 6666 9999999999877543 36899999999999
No 17
>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=91.81 E-value=0.25 Score=40.62 Aligned_cols=34 Identities=24% Similarity=0.486 Sum_probs=26.6
Q ss_pred eeEecCC-e---EEEcccccccCCchhhhHHHHHHHHHHHhh
Q 041464 84 IAFTSNN-G---IHYGDDFIQNIPVDLIKQEFSGVMYHEMTH 121 (198)
Q Consensus 84 VA~t~g~-~---I~~S~~~i~~~~~d~~~~Ei~GVl~HE~vH 121 (198)
=|++.|. . |.++...+...+ .+|+.+||.||+.|
T Consensus 62 NA~~~g~~~~~~I~v~~~ll~~~~----~~el~aVlaHElgH 99 (226)
T PF01435_consen 62 NAFATGGGPRKRIVVTSGLLESLS----EDELAAVLAHELGH 99 (226)
T ss_dssp EEEEETTTC--EEEEEHHHHHHSS----HHHHHHHHHHHHHH
T ss_pred cEEEEccCCCcEEEEeChhhhccc----HHHHHHHHHHHHHH
Confidence 4666554 4 999999995544 35999999999999
No 18
>PRK02391 heat shock protein HtpX; Provisional
Probab=90.79 E-value=0.28 Score=43.92 Aligned_cols=45 Identities=22% Similarity=0.397 Sum_probs=33.4
Q ss_pred CeEEEEEccCCCCceeEecCC-----eEEEcccccccCCchhhhHHHHHHHHHHHhh
Q 041464 70 PQVDLFIDDMKPGEIAFTSNN-----GIHYGDDFIQNIPVDLIKQEFSGVMYHEMTH 121 (198)
Q Consensus 70 ~~Vtl~l~d~~~~GVA~t~g~-----~I~~S~~~i~~~~~d~~~~Ei~GVl~HE~vH 121 (198)
.+|- ++++- ..-||++|. .|-++...++.-++ +|+.+||.||+.|
T Consensus 94 p~v~-v~~~~--~~NAfa~G~~~~~~~V~vt~gLl~~L~~----~El~aVlaHElgH 143 (296)
T PRK02391 94 PRVA-VADSD--VPNAFATGRSPKNAVVCVTTGLMRRLDP----DELEAVLAHELSH 143 (296)
T ss_pred CcEE-EEeCC--CCceEEecCCCCCcEEEecHHHHhhCCH----HHHHHHHHHHHHH
Confidence 3443 44542 567888873 58888888887653 5999999999999
No 19
>PRK02870 heat shock protein HtpX; Provisional
Probab=90.39 E-value=0.34 Score=44.40 Aligned_cols=46 Identities=28% Similarity=0.481 Sum_probs=34.1
Q ss_pred CCeEEEEEccCCCCceeEecC-----CeEEEcccccccCCchhhhHHHHHHHHHHHhh
Q 041464 69 IPQVDLFIDDMKPGEIAFTSN-----NGIHYGDDFIQNIPVDLIKQEFSGVMYHEMTH 121 (198)
Q Consensus 69 v~~Vtl~l~d~~~~GVA~t~g-----~~I~~S~~~i~~~~~d~~~~Ei~GVl~HE~vH 121 (198)
..+|-+ +++- .--|+++| ..|-++...++..+ ++|+.|||.||+.|
T Consensus 133 ~p~V~v-i~~~--~~NAFA~G~~~~~~~Ivvt~GLL~~L~----~dEL~aVlAHELgH 183 (336)
T PRK02870 133 MPKVYI-IDAP--YMNAFASGYSEKSAMVAITTGLLEKLD----RDELQAVMAHELSH 183 (336)
T ss_pred CCeEEE-EcCC--CCceEEecCCCCCcEEEEehHHhhhCC----HHHHHHHHHHHHHH
Confidence 345543 3432 45688876 38999999998765 36999999999999
No 20
>PRK01265 heat shock protein HtpX; Provisional
Probab=90.03 E-value=0.37 Score=44.02 Aligned_cols=36 Identities=22% Similarity=0.205 Sum_probs=29.2
Q ss_pred CceeEecC-----CeEEEcccccccCCchhhhHHHHHHHHHHHhh
Q 041464 82 GEIAFTSN-----NGIHYGDDFIQNIPVDLIKQEFSGVMYHEMTH 121 (198)
Q Consensus 82 ~GVA~t~g-----~~I~~S~~~i~~~~~d~~~~Ei~GVl~HE~vH 121 (198)
..-|+++| ..|-++...++..+. +|+.|||.||+.|
T Consensus 110 ~~NAfa~G~~~~~~~Ivvt~gLl~~l~~----~El~aVlAHElgH 150 (324)
T PRK01265 110 FPNAFAYGSPIAGKRIAITLPLLKILNR----DEIKAVAGHELGH 150 (324)
T ss_pred CCCeEEeccCCCCCEEEEehHHHhhCCH----HHHHHHHHHHHHH
Confidence 35677765 389999998888754 5999999999999
No 21
>PF05569 Peptidase_M56: BlaR1 peptidase M56; InterPro: IPR008756 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 M56 (clan M-). The predicted active site residues for members of this family occur in the motif HEXXH. The type example is BlaR1 peptidase from Bacillus licheniformis. Production of beta-Lactamase and penicillin-binding protein 2a (which mediate staphylococcal resistance to beta-lactam antibiotics) is regulated by a signal-transducing integral membrane protein and a transcriptional repressor. The signal transducer is a fusion protein with penicillin-binding and zinc metalloprotease domains. The signal for protein expression is transmitted by site-specific proteolytic cleavage of both the transducer, which auto-activates, and the repressor, which is inactivated, unblocking gene transcription.
Probab=80.84 E-value=2.7 Score=36.79 Aligned_cols=94 Identities=14% Similarity=0.274 Sum_probs=53.8
Q ss_pred CCeEEEEEccCCCCceeEecC---CeEEEcccccccCCchhhhHHHHHHHHHHHhh---cCC---------CCCCCcCCC
Q 041464 69 IPQVDLFIDDMKPGEIAFTSN---NGIHYGDDFIQNIPVDLIKQEFSGVMYHEMTH---ANY---------VPEGWAKPG 133 (198)
Q Consensus 69 v~~Vtl~l~d~~~~GVA~t~g---~~I~~S~~~i~~~~~d~~~~Ei~GVl~HE~vH---Ag~---------ap~hw~~p~ 133 (198)
-++|.+.+.+. --..++.| ..|-++.+..++.+++ |+.-||.||++| -|. ..-||--|.
T Consensus 157 ~~~~~i~~s~~--i~sP~~~G~~~p~I~lP~~~~~~~~~~----el~~il~HEl~Hikr~D~~~~~l~~l~~~l~WfnP~ 230 (299)
T PF05569_consen 157 KRPIRIRVSSG--ISSPFVFGFLRPVIVLPESLLEDLSEE----ELRAILLHELAHIKRRDLLWKLLAELLCALHWFNPL 230 (299)
T ss_pred CCceEEEEcCC--CCCCeeecCcceEEEecCccccccCHH----HHHHHHHHHHHHHHCCChHHHHHHHHHHHHHHhhHH
Confidence 35566666553 22456667 3899998877776644 788999999999 111 123554331
Q ss_pred CCCCCCCCcchhHhHHHHHHh-hcCCCHHHHHHHHHhccCCHHH
Q 041464 134 EGTMWNQGHSSVAARFLDYCN-DLRNGFVAELNKKMRDGYNDNF 176 (198)
Q Consensus 134 ~g~~wd~GY~~~TA~FL~wle-~~~~gfV~~LN~~mr~~ysd~~ 176 (198)
- | -...++-..+| ..|...++.+|..=+..|.+..
T Consensus 231 ~-------~-~~~~~~~~~~E~~cD~~vl~~l~~~~~~~Y~~~L 266 (299)
T PF05569_consen 231 V-------W-LLRRRIRRDRELACDEAVLRNLGKEERKAYAETL 266 (299)
T ss_pred H-------H-HHHHHHHHHHHHhhhHHHHHhcCchhHHHHHHHH
Confidence 0 1 13334444555 5566666666555444454433
No 22
>PF10460 Peptidase_M30: Peptidase M30; InterPro: IPR019501 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 family contains metallopeptidases belonging to MEROPS peptidase family M30 (hyicolysin family, clan MA). Hyicolysin has a zinc ion which is liganded by two histidine and one glutamate residue.
Probab=80.60 E-value=8 Score=36.15 Aligned_cols=56 Identities=14% Similarity=0.159 Sum_probs=33.0
Q ss_pred CCcchhHhHHHHHHh-hcCCCHHHHHHHHHhccCCHHHHHH----H-hCCCHHHHHHHHHHHh
Q 041464 140 QGHSSVAARFLDYCN-DLRNGFVAELNKKMRDGYNDNFFME----L-LGKSIDQLWNDYKAKY 196 (198)
Q Consensus 140 ~GY~~~TA~FL~wle-~~~~gfV~~LN~~mr~~ysd~~~~~----l-~G~~v~~LW~eY~~~~ 196 (198)
.+| ..+.-|..||. +++.+|++++=..-...=+++.... + .|.+.+++-.++...+
T Consensus 224 ~sY-s~s~~Fg~~L~rQ~G~~~~~~~l~~~~~tds~avl~aa~~~~~~~~sf~~~l~~w~~A~ 285 (366)
T PF10460_consen 224 ASY-SSSYSFGAYLYRQYGGDFYKKLLTNSSSTDSEAVLDAAIKQAGPGNSFGELLRRWGVAL 285 (366)
T ss_pred ccc-hhHHHHHHHHHHHcChHHHHHHHhcCCCCcHHHHHHHHHHhhcCCCCHHHHHHHHHHHH
Confidence 479 89999999998 6788888764221111111222222 2 2456777777666544
No 23
>PF07580 Peptidase_M26_C: M26 IgA1-specific Metallo-endopeptidase C-terminal region; InterPro: IPR011505 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 metallopeptidases belonging to MEROPS peptidase family M26 (IgA1-specific metallopeptidase, clan MA). They are extracellular enzymes, which cleave mammalian IgA. They are only found in Gram-positive bacteria and are often found associated with IPR001899 from INTERPRO; they may be attached to the cell wall. This entry also contains the metallopeptidases ZmpB and ZmpC from Streptococcus pneumoniae. These metallopeptidases are thought to contribute to the inflammatory response to Streptococcal infection [, ].; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding, 0005576 extracellular region, 0005618 cell wall
Probab=76.98 E-value=0.61 Score=47.01 Aligned_cols=29 Identities=24% Similarity=0.431 Sum_probs=18.8
Q ss_pred eEecCCeEEEcc-cccccCCchhhhHHHHHHHHHHHhh
Q 041464 85 AFTSNNGIHYGD-DFIQNIPVDLIKQEFSGVMYHEMTH 121 (198)
Q Consensus 85 A~t~g~~I~~S~-~~i~~~~~d~~~~Ei~GVl~HE~vH 121 (198)
||+.|..|++.. +.|.... ..+.+|||||
T Consensus 372 AyA~g~~V~y~~~~ml~d~G--------~s~yTHEmTH 401 (737)
T PF07580_consen 372 AYANGYAVYYVAYRMLDDYG--------ISTYTHEMTH 401 (737)
T ss_pred ceeeeeeEEEehhhhccccc--------hhhheeeccc
Confidence 677777666643 3333321 4789999999
No 24
>PF01457 Peptidase_M8: Leishmanolysin This Prosite motif covers only the active site. This is family M8 in the peptidase classification. ; InterPro: IPR001577 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 M8 (leishmanolysin 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. Leishmanolysin is an enzyme found in the eukaryotes including Leishmania and related parasitic protozoa []. The endopeptidase is the most abundant protein on the cell surface during the promastigote stage of the parasite, and is attached to the membrane by a glycosylphosphatidylinositol anchor []. In the amastigote form, the parasite lives in lysosomes of host macrophages, producing a form of the protease that has an acidic pH optimum []. This differs from most other metalloproteases and may be an adaptation to the environment in which the organism survives [].; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis, 0007155 cell adhesion, 0016020 membrane; PDB: 1LML_A.
Probab=74.89 E-value=8.2 Score=37.14 Aligned_cols=27 Identities=30% Similarity=0.432 Sum_probs=17.3
Q ss_pred eEEEcccccccCCchhhhHHHHHHHHHHHhh
Q 041464 91 GIHYGDDFIQNIPVDLIKQEFSGVMYHEMTH 121 (198)
Q Consensus 91 ~I~~S~~~i~~~~~d~~~~Ei~GVl~HE~vH 121 (198)
.|.|++++|.... ..+...++.|||+|
T Consensus 194 ~in~~p~~i~~~~----~~~~~~~~~HEi~H 220 (521)
T PF01457_consen 194 VININPSYIPSFY----FQEFFRTVIHEIAH 220 (521)
T ss_dssp EEE--GGG---S------HHHHHHHHHHHHH
T ss_pred EEEEchhHccchh----hhcccceeeeeeee
Confidence 8999999988752 34567899999999
No 25
>PF13485 Peptidase_MA_2: Peptidase MA superfamily
Probab=73.07 E-value=4 Score=29.72 Aligned_cols=33 Identities=24% Similarity=0.246 Sum_probs=21.9
Q ss_pred CceeEecCCeEEEcccccccCCchhhhHHHHHHHHHHHhh
Q 041464 82 GEIAFTSNNGIHYGDDFIQNIPVDLIKQEFSGVMYHEMTH 121 (198)
Q Consensus 82 ~GVA~t~g~~I~~S~~~i~~~~~d~~~~Ei~GVl~HE~vH 121 (198)
.||++...+.|.+.. ... -.+.+..+|.||++|
T Consensus 3 ~G~~~~~~~~i~~~~---~~~----~~~~~~~~l~HE~~H 35 (128)
T PF13485_consen 3 GGVYYPGFNRIVVYF---QGS----DEDWLDRVLAHELAH 35 (128)
T ss_pred eEEEecCCCEEEEec---CCC----CHHHHHHHHHHHHHH
Confidence 678887777777432 121 223356999999999
No 26
>PF09768 Peptidase_M76: Peptidase M76 family; InterPro: IPR019165 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 []. Mitochondrial inner membrane protease ATP23 has two roles in the assembly of mitochondrial ATPase. Firstly, it acts as a protease that removes the N-terminal 10 residues of mitochondrial ATPase CF(0) subunit 6 (ATP6) at the intermembrane space side. Secondly, it is involved in the correct assembly of the membrane-embedded ATPase CF(0) particle, probably mediating association of ATP6 with the subunit 9 ring [, ].; GO: 0004222 metalloendopeptidase activity
Probab=71.82 E-value=3.9 Score=34.31 Aligned_cols=47 Identities=17% Similarity=0.248 Sum_probs=31.0
Q ss_pred CCCeEEEEEccCCCCceeEec-CCeEEEcccccccCCchhhhHHHHHHHHHHHhh
Q 041464 68 NIPQVDLFIDDMKPGEIAFTS-NNGIHYGDDFIQNIPVDLIKQEFSGVMYHEMTH 121 (198)
Q Consensus 68 ~v~~Vtl~l~d~~~~GVA~t~-g~~I~~S~~~i~~~~~d~~~~Ei~GVl~HE~vH 121 (198)
+-+.|.....+.+..| .|.. ...|.+-..+|.+ +.++..+|.|||+|
T Consensus 34 ~~~~i~c~~C~~~~~G-gf~p~~~~I~lC~N~~~~------~~~l~~~l~HELIH 81 (173)
T PF09768_consen 34 PPRHIKCEPCDSSVSG-GFDPSKKGIVLCQNRIRS------QGHLEDTLTHELIH 81 (173)
T ss_pred CCCCeEEEECcCCCcC-CccCCCCCEEEeeCCCCC------HHHHHHHHHHHHHH
Confidence 4455666655431011 2444 5689998888744 56789999999999
No 27
>PF12725 DUF3810: Protein of unknown function (DUF3810); InterPro: IPR024294 This family of bacterial proteins is functionally uncharacterised. Proteins in this family are typically between 333 and 377 amino acids in length and contain a conserved HEXXH sequence motif that is characteristic of metallopeptidases. This family may therefore belong to an as yet uncharacterised family of peptidase enzymes.
Probab=69.34 E-value=19 Score=32.70 Aligned_cols=77 Identities=12% Similarity=0.221 Sum_probs=41.8
Q ss_pred HHHHHHHHHhh-cCCCCC---CCc-CCCCCCCCCCCcchhHhHHHHH--Hh----hcCCC----HHHHHHHHHhccCC--
Q 041464 111 FSGVMYHEMTH-ANYVPE---GWA-KPGEGTMWNQGHSSVAARFLDY--CN----DLRNG----FVAELNKKMRDGYN-- 173 (198)
Q Consensus 111 i~GVl~HE~vH-Ag~ap~---hw~-~p~~g~~wd~GY~~~TA~FL~w--le----~~~~g----fV~~LN~~mr~~ys-- 173 (198)
+=-.+.|||.| .|++.- .+- -=..-.+=|--+ +.+|++..| |- +.++. +..+||..++..+.
T Consensus 196 ~P~T~~HElAHq~G~a~E~EANFiayLac~~s~d~~f-rYSgy~~~l~y~l~~l~~~d~e~~~~l~~~l~~~v~~d~~~~ 274 (318)
T PF12725_consen 196 LPFTICHELAHQLGFASEDEANFIAYLACINSPDPYF-RYSGYLFALRYCLNALYRKDPEAYKELYSQLSPGVKKDLKEN 274 (318)
T ss_pred ccHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCChhe-eHHHHHHHHHHHHHHHHhcCHHHHHHHHHhCCHHHHHHHHHH
Confidence 44678999999 777742 000 000111112233 778888555 43 33444 44555555544444
Q ss_pred HHHHHHHhCCCHHHHH
Q 041464 174 DNFFMELLGKSIDQLW 189 (198)
Q Consensus 174 d~~~~~l~G~~v~~LW 189 (198)
..+|++.-| +++++=
T Consensus 275 ~~fW~~y~~-~i~~~~ 289 (318)
T PF12725_consen 275 RAFWQKYEG-PIEEVS 289 (318)
T ss_pred HHHHHHhcc-hHHHHH
Confidence 478888888 666653
No 28
>PF01863 DUF45: Protein of unknown function DUF45; InterPro: IPR002725 Members of this family are found in some archaebacteria, as well as Helicobacter pylori. The proteins are 190-240 amino acids long, with the C terminus being the most conserved region, containing three conserved histidines.
Probab=68.13 E-value=7.2 Score=31.89 Aligned_cols=46 Identities=26% Similarity=0.350 Sum_probs=30.1
Q ss_pred CeEEEEEccCCC-CceeEecCCeEEEcccccccCCchhhhHHHHHHHHHHHhh
Q 041464 70 PQVDLFIDDMKP-GEIAFTSNNGIHYGDDFIQNIPVDLIKQEFSGVMYHEMTH 121 (198)
Q Consensus 70 ~~Vtl~l~d~~~-~GVA~t~g~~I~~S~~~i~~~~~d~~~~Ei~GVl~HE~vH 121 (198)
+--.+.|++|+. =|. ++..+.|.||.+.+.- |.. -|.=|+.|||+|
T Consensus 128 ~~~~i~ir~~ksrWGs-c~~~~~I~ln~~L~~~-P~~----~idYVvvHEL~H 174 (205)
T PF01863_consen 128 PPPKIKIRDMKSRWGS-CSSKGNITLNWRLVMA-PPE----VIDYVVVHELCH 174 (205)
T ss_pred CcceEEEeehhhcccc-CCCCCcEEeecccccC-Ccc----HHHHHHHHHHHH
Confidence 334456677731 222 2556699999888774 322 366899999999
No 29
>PF08325 WLM: WLM domain; InterPro: IPR013536 The WLM (WSS1-like metalloprotease) domain is a globular domain related to the zincin-like superfamily of Zn-dependent peptidase. Since the WLM domain contains all known active site residues of zincins, it is predicted to be a catalytically active peptidase domain. The WLM domain is a eukaryotic domain represented in plants, fungi, Plasmodium, and kinetoplastids. By contrast, it is absent in animals, Cryptosporidium, and Microsporidia, suggesting that it has been lost on multiple occasions during the evolution of eukaryotes. The WLM domain is found either in stand-alone form or in association with other domains such as the RanBP2 zinc finger , the ubiquitin domain, or the PUB/PUG domain. This domain could function as a specific de-SUMOylating domain of distinct protein complexes in the nucleus and the cytoplasm []. It has been suggested to form a segregated alpha/beta structure with eight helices and five strands. Proteins containign this domain include yeast WSS1 (a weak suppressor of the Ub-related protein SMT3), and various putative metalloproteases from plant and fungal species.
Probab=64.13 E-value=8 Score=32.63 Aligned_cols=39 Identities=18% Similarity=0.124 Sum_probs=25.4
Q ss_pred CceeEecCCeEEEcccccccCCchhhhHHHHHHHHHHHhh
Q 041464 82 GEIAFTSNNGIHYGDDFIQNIPVDLIKQEFSGVMYHEMTH 121 (198)
Q Consensus 82 ~GVA~t~g~~I~~S~~~i~~~~~d~~~~Ei~GVl~HE~vH 121 (198)
-|.-+-.|.+|.+-.+.=.. .+=.--.+|.+|+.|||+|
T Consensus 54 lG~N~N~G~~I~lrLR~~~~-~~fl~~~~i~~t~lHELaH 92 (186)
T PF08325_consen 54 LGLNVNKGEKICLRLRTPDD-GGFLPYETILGTMLHELAH 92 (186)
T ss_pred cceecCCCcEEEEEeCCCCC-CCEeeHHHHHHHHHHHHHh
Confidence 34444556688877664443 2112346799999999999
No 30
>PTZ00337 surface protease GP63; Provisional
Probab=63.90 E-value=8.6 Score=37.84 Aligned_cols=25 Identities=20% Similarity=0.228 Sum_probs=20.4
Q ss_pred eEEEcccccccCCchhhhHHHHHHHHHHHhh
Q 041464 91 GIHYGDDFIQNIPVDLIKQEFSGVMYHEMTH 121 (198)
Q Consensus 91 ~I~~S~~~i~~~~~d~~~~Ei~GVl~HE~vH 121 (198)
.|.|++++|...+ +...|+.|||+|
T Consensus 215 ~in~np~~i~~~~------~~~~v~~HEi~H 239 (567)
T PTZ00337 215 AVNFDPRQIAVTN------GDVRVAAHELGH 239 (567)
T ss_pred EEEECHHHccchh------HHHHHHHHHHHH
Confidence 8999999886533 346899999999
No 31
>KOG1675 consensus Predicted cyclin [General function prediction only]
Probab=61.60 E-value=6.3 Score=36.33 Aligned_cols=65 Identities=25% Similarity=0.456 Sum_probs=49.4
Q ss_pred CCCCcCCCCCCCC--CCCcchhHhHHHHHHhhcCCCHHHHHHHHHhccCCHHHHHHHhCCCHHHHHHHHHHHh
Q 041464 126 PEGWAKPGEGTMW--NQGHSSVAARFLDYCNDLRNGFVAELNKKMRDGYNDNFFMELLGKSIDQLWNDYKAKY 196 (198)
Q Consensus 126 p~hw~~p~~g~~w--d~GY~~~TA~FL~wle~~~~gfV~~LN~~mr~~ysd~~~~~l~G~~v~~LW~eY~~~~ 196 (198)
|..|+++..|..| +.+|-+-.+-=.|||+-++.+.|..+|+.= +-|-++++-.+..=|.+|++.|
T Consensus 231 p~~w~r~~~g~il~sskv~~dqs~wnvdycqIlKd~tveDmNe~E------RqfLelLqfNinvp~svYAKyY 297 (343)
T KOG1675|consen 231 PRNWSRAVLGEILLSSKVYDDQSVWNVDYCEILKDQSVDDMNALE------RQFLELLQFNINVPSSEYAKYY 297 (343)
T ss_pred cchhhhhhhhhheehhhhhhhhhcccHHHHHHHhhccHhhHHHHH------HHHHHHHhhccCccHHHHHHHH
Confidence 7899988666555 233411222229999999999999999874 4688999999999999999986
No 32
>PF14891 Peptidase_M91: Effector protein
Probab=55.11 E-value=6 Score=32.48 Aligned_cols=32 Identities=22% Similarity=0.254 Sum_probs=18.8
Q ss_pred CeEEEccc--ccc-cCCc-----hhhhHHHHHHHHHHHhh
Q 041464 90 NGIHYGDD--FIQ-NIPV-----DLIKQEFSGVMYHEMTH 121 (198)
Q Consensus 90 ~~I~~S~~--~i~-~~~~-----d~~~~Ei~GVl~HE~vH 121 (198)
..|.+++. .+. ...+ .....+=.=+|+|||+|
T Consensus 74 ~~I~~np~~~~~~~~~~~~~~~~~~~~~~p~v~L~HEL~H 113 (174)
T PF14891_consen 74 ATINWNPSKYSIGDGTEGSPINGGWSPRPPFVVLYHELIH 113 (174)
T ss_pred eEEEECCCcccccCCCCcccccccchhHHHHHHHHHHHHH
Confidence 49999998 222 1111 11122334689999999
No 33
>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=52.54 E-value=14 Score=30.63 Aligned_cols=30 Identities=33% Similarity=0.691 Sum_probs=21.6
Q ss_pred HHHHHHHHHHhh-cCCCCCCCcCCCCCCCCCC
Q 041464 110 EFSGVMYHEMTH-ANYVPEGWAKPGEGTMWNQ 140 (198)
Q Consensus 110 Ei~GVl~HE~vH-Ag~ap~hw~~p~~g~~wd~ 140 (198)
+..|++.||+.| -|+.-.|- +|..+..|+.
T Consensus 91 ~~~~~i~HElgHaLG~~HEh~-rpdrdi~w~~ 121 (198)
T cd04327 91 EFSRVVLHEFGHALGFIHEHQ-SPAANIPWDK 121 (198)
T ss_pred hHHHHHHHHHHHHhcCccccc-CCCCCCCcCH
Confidence 457999999999 47775555 5655566764
No 34
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=50.16 E-value=14 Score=26.40 Aligned_cols=16 Identities=38% Similarity=0.839 Sum_probs=14.3
Q ss_pred hCCCHHHHHHHHHHHh
Q 041464 181 LGKSIDQLWNDYKAKY 196 (198)
Q Consensus 181 ~G~~v~~LW~eY~~~~ 196 (198)
+|+.+-++|++|++..
T Consensus 10 CGkvi~~~w~~y~~rv 25 (63)
T COG1644 10 CGKVIGHKWEEYKRRV 25 (63)
T ss_pred CCCCHHHHHHHHHHHH
Confidence 6999999999999854
No 35
>COG1451 Predicted metal-dependent hydrolase [General function prediction only]
Probab=48.60 E-value=26 Score=30.33 Aligned_cols=57 Identities=18% Similarity=0.281 Sum_probs=34.4
Q ss_pred CCCeEEEEEccCCCCceeEecCCeEEEcccccccCCchhhhHHHHHHHHHHHhh---cCCCCCCC
Q 041464 68 NIPQVDLFIDDMKPGEIAFTSNNGIHYGDDFIQNIPVDLIKQEFSGVMYHEMTH---ANYVPEGW 129 (198)
Q Consensus 68 ~v~~Vtl~l~d~~~~GVA~t~g~~I~~S~~~i~~~~~d~~~~Ei~GVl~HE~vH---Ag~ap~hw 129 (198)
++....+.|.+|+.-=-.++..+.|.+|...+.. ....|.=|+.|||+| ++-.|..|
T Consensus 137 ~~~~~~~~ik~~k~~WGScs~~~~i~~~~~l~~~-----p~~~i~YVvvHELaHLke~nHs~~Fw 196 (223)
T COG1451 137 GVPPRAIKLKNMKRRWGSCSKAGEIRFNWRLVMA-----PEEVIDYVVVHELAHLKEKNHSKRFW 196 (223)
T ss_pred CCCccceeeeeccceeeeecCCCcEEeehhhhcC-----CHHHHHHHHHHHHHHHhhhhccHHHH
Confidence 3334444555773211234444489888776654 344677899999999 55555555
No 36
>PF02102 Peptidase_M35: Deuterolysin metalloprotease (M35) family; InterPro: IPR001384 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 M35 (deuterolysin 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. Deuterolysin is a microbial zinc-containing metalloprotease that shows some similarity to thermolysin []. The protein is expressed with a possible 19-residue signal sequence, a 155-residue propeptide, and an active peptide of 177 residues []. The latter contains an HEXXH motif towards the C terminus, but the other zinc ligands are as yet undetermined [, ].; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 1EB6_A.
Probab=48.15 E-value=12 Score=34.86 Aligned_cols=54 Identities=26% Similarity=0.287 Sum_probs=29.5
Q ss_pred CeEEEEEccCC-C--Cc-eeEecC--CeEEEcccccccCC---chhhhHHHHHHHHHHHhhcC
Q 041464 70 PQVDLFIDDMK-P--GE-IAFTSN--NGIHYGDDFIQNIP---VDLIKQEFSGVMYHEMTHAN 123 (198)
Q Consensus 70 ~~Vtl~l~d~~-~--~G-VA~t~g--~~I~~S~~~i~~~~---~d~~~~Ei~GVl~HE~vHAg 123 (198)
.++++--.|.- + .| +|||.. +.|.+.+.|....| ...-.+--.+++.|||+|+.
T Consensus 247 g~~t~~C~D~~~~C~~~vlAYT~p~~~~I~~Cp~ff~~lp~~~~~C~~qDqatt~LHE~TH~~ 309 (359)
T PF02102_consen 247 GSTTYYCTDPYGYCSSGVLAYTLPSQNQIVNCPIFFSDLPALSNRCHAQDQATTTLHEMTHAP 309 (359)
T ss_dssp SS-EEESS-SSS---TT--EEEEGGGTEEEE-HHHHHH--SS--STT---HHHHHHHHHHT-T
T ss_pred CceEEEEECCCCccCCCeEEEEEcCCCeEEECchhhccCCCccccccCCCccchhhhhhhccc
Confidence 45666666521 0 33 789975 59999999986543 21122334689999999953
No 37
>PF02130 UPF0054: Uncharacterized protein family UPF0054; InterPro: IPR002036 These, as yet, uncharacterised proteins are of 17 to 21 kDa. They contain a conserved region with three histidines at the C terminus. The protein family is represented by a single member sequence only in nearly every bacterium. The crystal structure of the protein from the hyperthermophilic bacteria Aquifex aeolicus has been determined. The overall fold consists of one central alpha-helix surrounded by a four-stranded beta-sheet and four other alpha-helices. Structure-based homology analysis reveals a good resemblance to the metal-dependent proteinases such as collagenases and gelatinases. However, experimental tests for collagenase and gelatinase-type function show no detectable activity under standard assay conditions [].; GO: 0046872 metal ion binding; PDB: 1TVI_A 1OZ9_A 1XM5_A 1XAX_A.
Probab=46.67 E-value=20 Score=28.78 Aligned_cols=58 Identities=14% Similarity=0.146 Sum_probs=37.6
Q ss_pred CCCCeEEEEEccCCCCceeEec---CCeEEEcccccccCC---chhhhHHHHHHHHHHHhh-cCCC
Q 041464 67 KNIPQVDLFIDDMKPGEIAFTS---NNGIHYGDDFIQNIP---VDLIKQEFSGVMYHEMTH-ANYV 125 (198)
Q Consensus 67 k~v~~Vtl~l~d~~~~GVA~t~---g~~I~~S~~~i~~~~---~d~~~~Ei~GVl~HE~vH-Ag~a 125 (198)
+|++=++|-..+- ..+...-. -++|.+|++++.+.. +..+.+|+.=++.|.+-| +||-
T Consensus 59 ~pTDVLSFp~~~~-~~~~~~~~~~~lGdI~Is~~~~~~qA~e~~~~~~~el~~l~vHG~LHLlGyD 123 (145)
T PF02130_consen 59 YPTDVLSFPYDEP-EEPISPLPFEYLGDIFISPDTAERQAEEYGHSFEEELARLLVHGLLHLLGYD 123 (145)
T ss_dssp SS-SEEEEE--SS-STTEE-E---EEEEEEEEHHHHHHHHHHCTS-HHHHHHHHHHHHHHHHTT-S
T ss_pred CCCeEEeECCCCC-cccccccccccCceEEECHHHHHHHHHHccCChHHHHhHHHHHHHHHHcCCC
Confidence 4667778777653 13332222 369999999998752 224999999999999999 7874
No 38
>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=45.87 E-value=17 Score=27.91 Aligned_cols=32 Identities=25% Similarity=0.306 Sum_probs=20.6
Q ss_pred CCeEEEcccccccCCchhhhHHHHHHHHHHHhh-cCCCCCCC
Q 041464 89 NNGIHYGDDFIQNIPVDLIKQEFSGVMYHEMTH-ANYVPEGW 129 (198)
Q Consensus 89 g~~I~~S~~~i~~~~~d~~~~Ei~GVl~HE~vH-Ag~ap~hw 129 (198)
|+.++++. ...... .||+.||+.| -|+.-+|.
T Consensus 73 ~g~~~~~~---~~~~~~------~~~~~HEigHaLGl~H~~~ 105 (140)
T smart00235 73 GGDQHFSL---GNGCIN------TGVAAHELGHALGLYHEQS 105 (140)
T ss_pred CCceEEEc---cCCcCC------cccHHHHHHHHhcCCcCCC
Confidence 56788864 111111 5899999999 47765555
No 39
>KOG3314 consensus Ku70-binding protein [Replication, recombination and repair]
Probab=45.10 E-value=22 Score=30.28 Aligned_cols=46 Identities=20% Similarity=0.281 Sum_probs=31.5
Q ss_pred CCeEEEEEccCCCCceeEecCCeEEEcccccccCCchhhhHHHHHHHHHHHhh
Q 041464 69 IPQVDLFIDDMKPGEIAFTSNNGIHYGDDFIQNIPVDLIKQEFSGVMYHEMTH 121 (198)
Q Consensus 69 v~~Vtl~l~d~~~~GVA~t~g~~I~~S~~~i~~~~~d~~~~Ei~GVl~HE~vH 121 (198)
-+.|.....+- .-+=.|+.|..|.+-..+|. .+.++.-||.|||.|
T Consensus 56 d~~isc~~C~~-~~~GGy~~~~gIvlCqN~l~------~q~h~n~vv~HElIH 101 (194)
T KOG3314|consen 56 DNFISCVVCTG-PVAGGYTPGRGIVLCQNRLT------IQDHVNQVVIHELIH 101 (194)
T ss_pred CCceEEeeCCC-CccCCccCCCceEEeccccc------hHHHHHHHHHHHHHH
Confidence 34455555431 12234777878999887775 356788999999999
No 40
>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=45.10 E-value=17 Score=28.48 Aligned_cols=40 Identities=13% Similarity=0.071 Sum_probs=26.2
Q ss_pred CeEEEcccccccCCchhhhHHHHHHHHHHHhh-cCCCCCCC
Q 041464 90 NGIHYGDDFIQNIPVDLIKQEFSGVMYHEMTH-ANYVPEGW 129 (198)
Q Consensus 90 ~~I~~S~~~i~~~~~d~~~~Ei~GVl~HE~vH-Ag~ap~hw 129 (198)
.+|+++...+.....+....+..+++.||+-| -|+.-++-
T Consensus 73 g~i~~~~~~~~~~~~~~~~~~~~~~~~HEiGHaLGL~H~~~ 113 (165)
T cd04268 73 GEILLARVYLYSSFVEYSGARLRNTAEHELGHALGLRHNFA 113 (165)
T ss_pred ccEEeeEEEEchhHHHHHHHHHHHHHHHHHHHHhcccccCc
Confidence 48888877664421111345678999999999 47765543
No 41
>PTZ00257 Glycoprotein GP63 (leishmanolysin); Provisional
Probab=42.61 E-value=39 Score=33.82 Aligned_cols=27 Identities=19% Similarity=0.161 Sum_probs=20.5
Q ss_pred eEEEcccccccCCchhhhHHHHHHHHHHHhh
Q 041464 91 GIHYGDDFIQNIPVDLIKQEFSGVMYHEMTH 121 (198)
Q Consensus 91 ~I~~S~~~i~~~~~d~~~~Ei~GVl~HE~vH 121 (198)
.|-|++++|... ...+...++.|||+|
T Consensus 240 ~iNinp~~i~s~----~~~~~~rv~~HEi~H 266 (622)
T PTZ00257 240 VMNIPAANIVSR----YDQGTTRTVTHEVAH 266 (622)
T ss_pred EEeeCHHHCCCc----cchHHHHHHHHHHHH
Confidence 788888877532 234567999999999
No 42
>PF14521 Aspzincin_M35: Lysine-specific metallo-endopeptidase ; PDB: 2X3C_A 2X3A_A 2X3B_A 1GE7_B 1GE6_A 1GE5_A 1G12_A.
Probab=41.14 E-value=15 Score=29.43 Aligned_cols=35 Identities=20% Similarity=0.281 Sum_probs=22.1
Q ss_pred eeEecCC----eEEEcccccccC-CchhhhHHHHHHHHHHHhh
Q 041464 84 IAFTSNN----GIHYGDDFIQNI-PVDLIKQEFSGVMYHEMTH 121 (198)
Q Consensus 84 VA~t~g~----~I~~S~~~i~~~-~~d~~~~Ei~GVl~HE~vH 121 (198)
.||+.-+ +|.|.+.|...- .+. .--.|.|.||++|
T Consensus 67 ~a~~~~~~~~~~IyLc~~F~~~p~~g~---~Sk~~TLiHE~SH 106 (148)
T PF14521_consen 67 YAYVYPDSPTYTIYLCPAFFSAPTTGK---DSKEGTLIHEWSH 106 (148)
T ss_dssp SEEE-TTST-TEEEE-HHHHHS-SSST---T-HHHHHHHHHHH
T ss_pred EEEEECCCCceEEEEChhhcCCCCCCC---CchHHHHHHhhhh
Confidence 5565532 899999999842 221 1126999999999
No 43
>PF05299 Peptidase_M61: M61 glycyl aminopeptidase; InterPro: IPR007963 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 M61 (glycyl aminopeptidase 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 type example is glycyl aminopeptidase from Sphingomonas capsulata.
Probab=40.97 E-value=15 Score=29.15 Aligned_cols=58 Identities=24% Similarity=0.435 Sum_probs=37.6
Q ss_pred HHHHHHHHHHhh---------cCCCCCCCcCCCCCCC-CCCCcchhHhHHHHHHh-hc----CCCHHHHHHHHHh
Q 041464 110 EFSGVMYHEMTH---------ANYVPEGWAKPGEGTM-WNQGHSSVAARFLDYCN-DL----RNGFVAELNKKMR 169 (198)
Q Consensus 110 Ei~GVl~HE~vH---------Ag~ap~hw~~p~~g~~-wd~GY~~~TA~FL~wle-~~----~~gfV~~LN~~mr 169 (198)
...|++.||..| +++.|....+|..... |-.- ..|-|+=+.+- +- ...+..+|++.+.
T Consensus 3 ~~l~l~sHEffH~WnvkrirP~~l~p~dy~~~~~t~~LWv~E--G~T~Y~~~l~l~RaGl~~~~~yl~~L~~~~~ 75 (122)
T PF05299_consen 3 RFLGLLSHEFFHSWNVKRIRPAELGPFDYEKPNYTELLWVYE--GFTSYYGDLLLVRAGLISPEEYLEELAKTIA 75 (122)
T ss_pred chhhhhhhhccccccceEeccccccCCCCCCCCCCCCEeeee--CcHHHHHHHHHHHcCCCCHHHHHHHHHHHHH
Confidence 457999999999 7888887777743222 6421 35766655543 21 2457777777774
No 44
>PF01447 Peptidase_M4: Thermolysin metallopeptidase, catalytic domain This Prosite motif covers only the active site. This is family M4 in the peptidase classification. ; InterPro: IPR013856 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases that belong to the MEROPS peptidase family M4 (thermolysin family, clan MA(E)). The protein fold of the peptidase domain of thermolysin, is the type example for members of the clan MA. The thermolysin family is composed only of secreted eubacterial endopeptidases. The zinc-binding residues are H-142, H-146 and E-166, with E-143 acting as the catalytic residue. Thermolysin also contains 4 calcium-binding sites, which contribute to its unusual thermostability. The family also includes enzymes from a number of pathogens, including Legionella and Listeria, and the protein pseudolysin, all with a substrate specificity for an aromatic residue in the P1' position. Three-dimensional structure analysis has shown that the enzymes undergo a hinge-bend motion during catalysis. Pseudolysin has a broader specificity, acting on large molecules such as elastin and collagen, possibly due to its wider active site cleft []. This entry represents a domain found in peptidase M4 family members.; GO: 0004222 metalloendopeptidase activity; PDB: 3NQX_A 3NQZ_B 3NQY_B 1BQB_A 1U4G_A 1EZM_A 3DBK_A 1ESP_A 1NPC_A 1LND_E ....
Probab=38.95 E-value=17 Score=29.52 Aligned_cols=10 Identities=50% Similarity=0.723 Sum_probs=9.1
Q ss_pred HHHHHHHHhh
Q 041464 112 SGVMYHEMTH 121 (198)
Q Consensus 112 ~GVl~HE~vH 121 (198)
..|+.|||+|
T Consensus 136 lDVvaHEltH 145 (150)
T PF01447_consen 136 LDVVAHELTH 145 (150)
T ss_dssp HHHHHHHHHH
T ss_pred cceeeecccc
Confidence 4899999999
No 45
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=38.23 E-value=26 Score=24.96 Aligned_cols=16 Identities=31% Similarity=0.798 Sum_probs=14.3
Q ss_pred hCCCHHHHHHHHHHHh
Q 041464 181 LGKSIDQLWNDYKAKY 196 (198)
Q Consensus 181 ~G~~v~~LW~eY~~~~ 196 (198)
+|+.+.++|++|+...
T Consensus 10 CGkvi~~~we~y~~~~ 25 (62)
T PRK04016 10 CGKVIAEKWEEFKERV 25 (62)
T ss_pred CCCChHHHHHHHHHHH
Confidence 6999999999999865
No 46
>PF13076 DUF3940: Protein of unknown function (DUF3940)
Probab=38.20 E-value=38 Score=21.68 Aligned_cols=30 Identities=20% Similarity=0.452 Sum_probs=23.0
Q ss_pred HHHHHhcc-CCHHHHHHHhCCCHHHHHHHHHH
Q 041464 164 LNKKMRDG-YNDNFFMELLGKSIDQLWNDYKA 194 (198)
Q Consensus 164 LN~~mr~~-ysd~~~~~l~G~~v~~LW~eY~~ 194 (198)
+++-++.| |...- .++..-++.+|+++|++
T Consensus 7 I~~Li~~Giyk~~d-rqL~Eltl~ELe~ey~~ 37 (38)
T PF13076_consen 7 IEKLIQSGIYKKED-RQLYELTLSELEKEYER 37 (38)
T ss_pred HHHHHHcCCcCccc-hHHHHcCHHHHHHHHHc
Confidence 34555677 87433 88888999999999985
No 47
>PF07700 HNOB: Heme NO binding; InterPro: IPR011644 This ligand-binding domain is found in soluble guanylate cyclases. In soluble guanylate cyclases this domain binds heme via a covalent linkage to histidine []. Soluble guanylate cyclases are nitric oxide-responsive signaling proteins.; GO: 0020037 heme binding; PDB: 3TFE_A 2O0C_B 3TFA_A 2O09_B 2O0G_B 3L6J_A 3TFG_B 3TF8_A 3TFF_A 3TF9_B ....
Probab=36.48 E-value=57 Score=26.36 Aligned_cols=49 Identities=18% Similarity=0.398 Sum_probs=34.3
Q ss_pred hHHHHHHh-hcCCCHHHHHHHHH--h-c------c-CCHHH-------HHHHhCCCHHHHHHHHHHH
Q 041464 147 ARFLDYCN-DLRNGFVAELNKKM--R-D------G-YNDNF-------FMELLGKSIDQLWNDYKAK 195 (198)
Q Consensus 147 A~FL~wle-~~~~gfV~~LN~~m--r-~------~-ysd~~-------~~~l~G~~v~~LW~eY~~~ 195 (198)
--|.++++ ++++....++=++. . + + |+|.. ..+.+|.+++++|.+|.+.
T Consensus 7 ~~~~~~v~~~~G~~~w~~i~~~~~~~~~~~f~~~~~Y~D~~~~~lv~a~a~~~g~~~~~~l~~fG~~ 73 (171)
T PF07700_consen 7 KALQEFVEEKYGEEVWDEILERAGLDSDGIFTSHGNYDDEETYKLVEAAAEVTGISVEELLEEFGEY 73 (171)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHTTSSTTSS--TTSBTTHHHHHHHHHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHcCHHHHHHHHHHhCCCcCCccccccccCHHHHHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence 34778887 77888887776655 2 1 2 78654 3456899999999999875
No 48
>PF14162 YozD: YozD-like protein
Probab=36.37 E-value=38 Score=23.52 Aligned_cols=21 Identities=33% Similarity=0.744 Sum_probs=18.4
Q ss_pred hHHHHHHHHHHHhhcCCCCCC
Q 041464 108 KQEFSGVMYHEMTHANYVPEG 128 (198)
Q Consensus 108 ~~Ei~GVl~HE~vHAg~ap~h 128 (198)
..||.--.+||++..||+|.-
T Consensus 10 TEEIAefFy~eL~kRGyvP~e 30 (57)
T PF14162_consen 10 TEEIAEFFYHELVKRGYVPTE 30 (57)
T ss_pred HHHHHHHHHHHHHHccCCCcH
Confidence 468999999999999999863
No 49
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=34.48 E-value=31 Score=25.22 Aligned_cols=16 Identities=31% Similarity=0.619 Sum_probs=14.4
Q ss_pred hCCCHHHHHHHHHHHh
Q 041464 181 LGKSIDQLWNDYKAKY 196 (198)
Q Consensus 181 ~G~~v~~LW~eY~~~~ 196 (198)
+||.+-++|++|++.+
T Consensus 10 CGkvig~~we~y~~~~ 25 (71)
T PLN00032 10 CGKVIGNKWDTYLDLL 25 (71)
T ss_pred CCCCcHHHHHHHHHHH
Confidence 6999999999999865
No 50
>COG3864 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.83 E-value=31 Score=32.21 Aligned_cols=33 Identities=27% Similarity=0.450 Sum_probs=26.6
Q ss_pred eEecCCeEEEcccccccCCchhhhHHHHHHHHHHHhh
Q 041464 85 AFTSNNGIHYGDDFIQNIPVDLIKQEFSGVMYHEMTH 121 (198)
Q Consensus 85 A~t~g~~I~~S~~~i~~~~~d~~~~Ei~GVl~HE~vH 121 (198)
|-|++-.+.++|.-+.+.|-+ |+.|.|.||+.|
T Consensus 47 a~t~~~~~y~NPei~~~~p~~----~~~aLl~HEV~H 79 (396)
T COG3864 47 ASTSYFTMYFNPEIFLNCPIS----EMKALLKHEVYH 79 (396)
T ss_pred ccCCceEEEeCHHHHccCCHH----HHHHHHHHHHHH
Confidence 334445899999988888754 789999999999
No 51
>PF08014 DUF1704: Domain of unknown function (DUF1704); InterPro: IPR012548 This family contains many hypothetical proteins.
Probab=33.53 E-value=64 Score=29.84 Aligned_cols=111 Identities=16% Similarity=0.225 Sum_probs=59.2
Q ss_pred eEEEEEcc-CCCCceeEecCCeEEEcccccccCCchhhhHHHHHHHHHHH-hh-----cC-CCCCCCcCCCCCCCCCCCc
Q 041464 71 QVDLFIDD-MKPGEIAFTSNNGIHYGDDFIQNIPVDLIKQEFSGVMYHEM-TH-----AN-YVPEGWAKPGEGTMWNQGH 142 (198)
Q Consensus 71 ~Vtl~l~d-~~~~GVA~t~g~~I~~S~~~i~~~~~d~~~~Ei~GVl~HE~-vH-----Ag-~ap~hw~~p~~g~~wd~GY 142 (198)
.|++.++| + -.-|..+++.|.++.+.. . -+.++.+++.||. || -| .-|-+|-+-|.. ..+.-=
T Consensus 132 ~~~V~~sddl--~a~A~v~~~~l~I~~~~~--f----s~~~l~~L~~HEigvH~lt~~Ng~~QPl~~l~~Glp-~~~~TQ 202 (349)
T PF08014_consen 132 EVKVELSDDL--LARAMVSGDRLKINKNAM--F----SERDLEALLHHEIGVHLLTTLNGRAQPLKILSLGLP-GYTPTQ 202 (349)
T ss_pred eEEEEEcCCc--chhhcccCCeeEEcCCCC--c----CHHHHHHHHHHhhhhhhccccccccCCcHHhCCCCC-CCCCCc
Confidence 57787774 4 334556677788876421 1 1356899999999 99 22 234333221110 011111
Q ss_pred chhHhHHHHHHh-hcCCCHHHHHHH------HHhccCC-HHHHHHH---hCCCHHHHHHH
Q 041464 143 SSVAARFLDYCN-DLRNGFVAELNK------KMRDGYN-DNFFMEL---LGKSIDQLWND 191 (198)
Q Consensus 143 ~~~TA~FL~wle-~~~~gfV~~LN~------~mr~~ys-d~~~~~l---~G~~v~~LW~e 191 (198)
+-=|=|-+++. ...+.-.++|-. +|.+|.| -+.|..+ .|.+-++=|.-
T Consensus 203 -EGLAvl~E~l~g~~~~~Rl~~La~RV~Av~~m~~ga~F~e~F~~l~~~y~~~~~~af~~ 261 (349)
T PF08014_consen 203 -EGLAVLSEYLSGSLTPWRLRLLAYRVIAVDSMEKGASFSETFRYLREFYGQDPEDAFTI 261 (349)
T ss_pred -hHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHhCCCHHHHHHH
Confidence 34466777765 334444444432 3445666 3444433 47777777753
No 52
>PF02449 Glyco_hydro_42: Beta-galactosidase; InterPro: IPR013529 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. This group of beta-galactosidase enzymes (3.2.1.23 from EC) belong to the glycosyl hydrolase 42 family GH42 from CAZY. The enzyme catalyses the hydrolysis of terminal, non-reducing terminal beta-D-galactosidase residues.; GO: 0004565 beta-galactosidase activity, 0005975 carbohydrate metabolic process, 0009341 beta-galactosidase complex; PDB: 1KWK_A 1KWG_A 3U7V_A.
Probab=31.91 E-value=36 Score=30.86 Aligned_cols=53 Identities=15% Similarity=0.280 Sum_probs=32.2
Q ss_pred CCc-chhHhHHHHHHh-hcCCCHHHHHHHHHhcc-CCH--HHHHHHh-----C-CCHHHHHHHHHH
Q 041464 140 QGH-SSVAARFLDYCN-DLRNGFVAELNKKMRDG-YND--NFFMELL-----G-KSIDQLWNDYKA 194 (198)
Q Consensus 140 ~GY-~~~TA~FL~wle-~~~~gfV~~LN~~mr~~-ysd--~~~~~l~-----G-~~v~~LW~eY~~ 194 (198)
..| +...+.|-+||+ +++. |.+||++-... ||. .-|.++. + ..-..+|-||..
T Consensus 142 ~~~~~~~~~~f~~wLk~kY~t--i~~LN~aWgt~~ws~~~~~f~~v~~P~~~~~~~~~~~~~D~~r 205 (374)
T PF02449_consen 142 RCYSPACQAAFRQWLKEKYGT--IEALNRAWGTAFWSQRYSSFDEVPPPRPTSSPENPAQWLDWYR 205 (374)
T ss_dssp S--SHHHHHHHHHHHHHHHSS--HHHHHHHHTTTGGG---SSGGG---S-S-SS---HHHHHHHHH
T ss_pred cCCChHHHHHHHHHHHHHhCC--HHHHHHHHcCCcccCccCcHHhcCCCCCCCCCCChHHHHHHHH
Confidence 455 468889999998 6765 99999999765 663 3355553 1 123345666654
No 53
>PF11444 DUF2895: Protein of unknown function (DUF2895); InterPro: IPR021548 This is a bacterial family of uncharacterised proteins.
Probab=31.84 E-value=78 Score=27.30 Aligned_cols=37 Identities=27% Similarity=0.284 Sum_probs=25.4
Q ss_pred EEEEEeCCCCCcccchhhhccCCCchhHHHHHHhccC
Q 041464 25 DYTVSNRAATTPGGMRFANEIGAEYTPNFIWRLFQQN 61 (198)
Q Consensus 25 ~~~~~n~a~~t~gg~rF~~~i~~~~a~~~i~~lf~y~ 61 (198)
++++.+.--=..|+.|=..+||.++.-+|...+|||-
T Consensus 38 ~ltih~PPDLrsGstr~~~eVP~~~VYaFa~yIfQQl 74 (199)
T PF11444_consen 38 RLTIHNPPDLRSGSTRKWWEVPPETVYAFAFYIFQQL 74 (199)
T ss_pred ceEEECCCccCCCceeEcccCChHHHHHHHHHHHHHH
Confidence 4666554333669999888999887766666676553
No 54
>PF10023 DUF2265: Predicted aminopeptidase (DUF2265); InterPro: IPR014553 This group represents a predicted aminopeptidase.
Probab=31.51 E-value=28 Score=32.31 Aligned_cols=14 Identities=29% Similarity=0.800 Sum_probs=12.8
Q ss_pred hHHHHHHHHHHHhh
Q 041464 108 KQEFSGVMYHEMTH 121 (198)
Q Consensus 108 ~~Ei~GVl~HE~vH 121 (198)
..|+.++|.|||+|
T Consensus 162 ~~~LA~LIfHELaH 175 (337)
T PF10023_consen 162 DGELARLIFHELAH 175 (337)
T ss_pred chHHHHHHHHHHhh
Confidence 46899999999999
No 55
>PF01433 Peptidase_M1: Peptidase family M1 This is family M1 in the peptidase classification.; InterPro: IPR014782 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 M1 (clan MA(E)), the type example being aminopeptidase N from Homo sapiens (Human). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA. Membrane alanine aminopeptidase (3.4.11.2 from EC) is part of the HEXXH+E group; it consists entirely of aminopeptidases, spread across a wide variety of species []. Functional studies show that CD13/APN catalyzes the removal of single amino acids from the amino terminus of small peptides and probably plays a role in their final digestion; one family member (leukotriene-A4 hydrolase) is known to hydrolyse the epoxide leukotriene-A4 to form an inflammatory mediator []. This hydrolase has been shown to have aminopeptidase activity [], and the zinc ligands of the M1 family were identified by site-directed mutagenesis on this enzyme [] CD13 participates in trimming peptides bound to MHC class II molecules [] and cleaves MIP-1 chemokine, which alters target cell specificity from basophils to eosinophils []. CD13 acts as a receptor for specific strains of RNA viruses (coronaviruses) which cause a relatively large percentage of upper respiratory trace infections. 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: 0008237 metallopeptidase activity, 0008270 zinc ion binding; PDB: 2XQ0_A 2XPY_A 2XPZ_A 3SE6_B 3EBH_A 3EBG_A 3T8V_A 3Q44_A 3Q43_A 3EBI_A ....
Probab=31.49 E-value=1.5e+02 Score=26.29 Aligned_cols=68 Identities=21% Similarity=0.281 Sum_probs=36.5
Q ss_pred HHHHHHhccCCCCCCCCCCeEEEEEc-cCCCCceeEecCCeEEEcccccccC---CchhhhHHHHHHHHHHHhh---cCC
Q 041464 52 NFIWRLFQQNTEADRKNIPQVDLFID-DMKPGEIAFTSNNGIHYGDDFIQNI---PVDLIKQEFSGVMYHEMTH---ANY 124 (198)
Q Consensus 52 ~~i~~lf~y~~p~~rk~v~~Vtl~l~-d~~~~GVA~t~g~~I~~S~~~i~~~---~~d~~~~Ei~GVl~HE~vH---Ag~ 124 (198)
.+..++|..+= |.++..++.- ++...|.. .=+-|.++.+++-.. +....+.++..+|.|||+| .++
T Consensus 239 ~~~~~~~g~~y-----p~~k~~~v~~p~~~~~~me--~~g~i~~~~~~l~~~~~~~~~~~~~~~~~~iahElahqWfGn~ 311 (390)
T PF01433_consen 239 EYYEEYFGIPY-----PFKKLDIVAVPDFPFGGME--NWGLITYRESYLLYDPDISTIGDKQEIASLIAHELAHQWFGNL 311 (390)
T ss_dssp HHHHHHHTS-------SSSEEEEEEEST-SSSEE----TTEEEEEGGGTS-STTTS-HHHHHHHHHHHHHHHHTTTBTTT
T ss_pred HHHHhhccccc-----eecceeEEEEecccccccc--ccccccccccccccCcccccchhhhhhHHHHHHHHHHHHhccC
Confidence 56666663332 3446665554 43112221 123567777776432 2223578899999999999 556
Q ss_pred CC
Q 041464 125 VP 126 (198)
Q Consensus 125 ap 126 (198)
+.
T Consensus 312 vt 313 (390)
T PF01433_consen 312 VT 313 (390)
T ss_dssp EE
T ss_pred Cc
Confidence 53
No 56
>TIGR00043 metalloprotein, YbeY/UPF0054 family. This minimally protein family is represented by a single member sequence only in nearly every bacterium. Crystallography demonstrates metal-binding activity, possibly to nickel. It is a predicted to be a metallohydrolase, and somewhat more weakly to be a metalloproteinase.
Probab=30.42 E-value=31 Score=26.58 Aligned_cols=36 Identities=14% Similarity=0.221 Sum_probs=29.8
Q ss_pred CeEEEcccccccCC---chhhhHHHHHHHHHHHhh-cCCC
Q 041464 90 NGIHYGDDFIQNIP---VDLIKQEFSGVMYHEMTH-ANYV 125 (198)
Q Consensus 90 ~~I~~S~~~i~~~~---~d~~~~Ei~GVl~HE~vH-Ag~a 125 (198)
++|.+|+..+.+.+ +-.+.+|+.=++.|.+-| .||-
T Consensus 49 GdI~Is~~~~~~qa~~~~~~~~~e~~~l~iHG~LHLlGyD 88 (110)
T TIGR00043 49 GDIVISLEVAKEQAKEYGHSLERELAHLTVHGLLHLLGYD 88 (110)
T ss_pred eeEEEcHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHcCCC
Confidence 49999999998753 223899999999999999 7774
No 57
>TIGR03746 conj_TIGR03746 integrating conjugative element protein, PFL_4703 family. Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. The function is unknown.
Probab=29.21 E-value=79 Score=27.42 Aligned_cols=38 Identities=26% Similarity=0.277 Sum_probs=24.6
Q ss_pred EEEEEeCCCCCcccchhhhccCCCchhHHHHHHhccCC
Q 041464 25 DYTVSNRAATTPGGMRFANEIGAEYTPNFIWRLFQQNT 62 (198)
Q Consensus 25 ~~~~~n~a~~t~gg~rF~~~i~~~~a~~~i~~lf~y~~ 62 (198)
+++++|.---..||.|=..+||.++.-+|...+|||-+
T Consensus 39 ~ltih~PPDlrsGstr~~~eVP~~~VYaFa~yI~QQlN 76 (202)
T TIGR03746 39 DLTIHVPPDLRSGSTRKWWEVPPENVYAFAFYIFQQLN 76 (202)
T ss_pred ccEEECCCccCCCCccCcccCCchhhhhhHHHHHHHHh
Confidence 35555543336699998889988876655556665533
No 58
>TIGR02412 pepN_strep_liv aminopeptidase N, Streptomyces lividans type. This family is a subset of the members of the zinc metallopeptidase family M1 (pfam01433), with a single member characterized in Streptomyces lividans 66 and designated aminopeptidase N. The spectrum of activity may differ somewhat from the aminopeptidase N clade of E. coli and most other Proteobacteria, well separated phylogenetically within the M1 family. The M1 family also includes leukotriene A-4 hydrolase/aminopeptidase (with a bifunctional active site).
Probab=28.86 E-value=70 Score=32.61 Aligned_cols=39 Identities=26% Similarity=0.609 Sum_probs=25.7
Q ss_pred eEEEcccccccCC-chhhhHHHHHHHHHHHhh---cCCCCCCC
Q 041464 91 GIHYGDDFIQNIP-VDLIKQEFSGVMYHEMTH---ANYVPEGW 129 (198)
Q Consensus 91 ~I~~S~~~i~~~~-~d~~~~Ei~GVl~HE~vH---Ag~ap~hw 129 (198)
-|.++..++-... .+..+..+..|+.|||+| .+++-+.|
T Consensus 266 lit~~e~~l~~~~~~~~~~~~~~~viaHElAHqWFGnlVT~~w 308 (831)
T TIGR02412 266 CVTFAENFLHRAEATRAEKENRAGVILHEMAHMWFGDLVTMRW 308 (831)
T ss_pred eeeechhhccCCcCCHHHHHHHHHHHHHHHHHHHhCCEecccc
Confidence 6777777764321 122455678999999999 66775544
No 59
>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=28.54 E-value=47 Score=26.21 Aligned_cols=37 Identities=24% Similarity=0.276 Sum_probs=24.2
Q ss_pred CCeEEEcccccccCCchhhhHHHHHHHHHHHhh-cCCC
Q 041464 89 NNGIHYGDDFIQNIPVDLIKQEFSGVMYHEMTH-ANYV 125 (198)
Q Consensus 89 g~~I~~S~~~i~~~~~d~~~~Ei~GVl~HE~vH-Ag~a 125 (198)
.+.|+|+.+..-..+...-...+..|+.||+=| -|+.
T Consensus 85 ~g~i~~~~~~~~~~~~~~~~~~~~~~~~HEiGHaLGL~ 122 (157)
T cd04278 85 GGDIHFDDDEQWTLGSDSGGTDLFSVAAHEIGHALGLG 122 (157)
T ss_pred ceeEEECCCcccccCCCCccchHHHHHHHHhccccccC
Confidence 458999876654433210223478999999999 4774
No 60
>PRK00016 metal-binding heat shock protein; Provisional
Probab=28.22 E-value=32 Score=28.13 Aligned_cols=36 Identities=14% Similarity=0.242 Sum_probs=29.7
Q ss_pred CeEEEcccccccCCc---hhhhHHHHHHHHHHHhh-cCCC
Q 041464 90 NGIHYGDDFIQNIPV---DLIKQEFSGVMYHEMTH-ANYV 125 (198)
Q Consensus 90 ~~I~~S~~~i~~~~~---d~~~~Ei~GVl~HE~vH-Ag~a 125 (198)
++|.+|++++.+... ..+.+|+.=++.|.+-| .||-
T Consensus 89 GDI~Is~~~~~~qa~~~~~s~~~e~~~l~iHG~LHLlGYD 128 (159)
T PRK00016 89 GDIVICPEVAEEQAEEQGHSLERELAHLTVHGILHLLGYD 128 (159)
T ss_pred eeEEEcHHHHHHHHHHcCCCHHHHHHHHHHHhhHHhcCCC
Confidence 599999999987542 23889999999999999 7774
No 61
>COG4219 MecR1 Antirepressor regulating drug resistance, predicted signal transduction N-terminal membrane component [Transcription / Signal transduction mechanisms]
Probab=26.64 E-value=74 Score=29.59 Aligned_cols=48 Identities=15% Similarity=0.227 Sum_probs=36.1
Q ss_pred CCCeEEEEEcc-CCCCceeEecC--CeEEEcccccccCCchhhhHHHHHHHHHHHhh
Q 041464 68 NIPQVDLFIDD-MKPGEIAFTSN--NGIHYGDDFIQNIPVDLIKQEFSGVMYHEMTH 121 (198)
Q Consensus 68 ~v~~Vtl~l~d-~~~~GVA~t~g--~~I~~S~~~i~~~~~d~~~~Ei~GVl~HE~vH 121 (198)
..++++++-++ . +|...+.= -.|-+-+++.++.+++ |+.=++.||+.|
T Consensus 150 ~~k~i~ir~s~~i--~~P~v~gl~kp~IvlP~d~~~r~~~e----e~~yIilHEl~H 200 (337)
T COG4219 150 YKKHILIRKSKAI--DGPMVFGLVKPCIVLPADFVERLTDE----ELKYIILHELSH 200 (337)
T ss_pred hccCeeEeecccC--CCceeeccCcceEEccHHHHhhcCHH----hhhhhHhHHHhh
Confidence 45678887774 4 77555442 3888888888887744 788999999999
No 62
>PF10005 DUF2248: Uncharacterized protein conserved in bacteria (DUF2248); InterPro: IPR011201 This is a family of uncharacterised bacterial proteins.
Probab=26.12 E-value=36 Score=31.65 Aligned_cols=53 Identities=13% Similarity=0.086 Sum_probs=29.7
Q ss_pred CCCeEEEE-EccCCCCceeEecC---CeEEEcccccccCCchh-------hhHHHHHHHHHHHhh
Q 041464 68 NIPQVDLF-IDDMKPGEIAFTSN---NGIHYGDDFIQNIPVDL-------IKQEFSGVMYHEMTH 121 (198)
Q Consensus 68 ~v~~Vtl~-l~d~~~~GVA~t~g---~~I~~S~~~i~~~~~d~-------~~~Ei~GVl~HE~vH 121 (198)
+..-..|- |.|. .++-...+| +.|+|+..=-.....++ .-+-+.|=+.||+-|
T Consensus 126 ~~~GL~FdfL~d~-~~~~~V~TGHa~GvITinlaEADda~RE~~R~~m~EpYRTLLGHfRHE~GH 189 (343)
T PF10005_consen 126 PERGLAFDFLADP-SGGEPVMTGHANGVITINLAEADDAERERRRVQMGEPYRTLLGHFRHEIGH 189 (343)
T ss_pred CCCCceEEecccC-CCCCCceeccCCceEEEEecccChHHHHHHHHHhccHHHHHHHHhcchhHH
Confidence 44555553 3342 255666666 39999754111111111 225567999999999
No 63
>PF14247 DUF4344: Domain of unknown function (DUF4344)
Probab=25.96 E-value=1.3e+02 Score=26.24 Aligned_cols=52 Identities=15% Similarity=0.309 Sum_probs=32.3
Q ss_pred CeEEEEEccCCCCceeEecC-CeEEEcccccccC---------Cch----hhhHHHHHHHHHHHhh
Q 041464 70 PQVDLFIDDMKPGEIAFTSN-NGIHYGDDFIQNI---------PVD----LIKQEFSGVMYHEMTH 121 (198)
Q Consensus 70 ~~Vtl~l~d~~~~GVA~t~g-~~I~~S~~~i~~~---------~~d----~~~~Ei~GVl~HE~vH 121 (198)
+.|+|+...-..+|-=|-.. .+|+|.-.++... +.+ .+..-+.-+|+||+-|
T Consensus 37 ~~l~i~~~~CGe~nA~ydPe~~~I~iCYEf~~~~~~~f~~~~~~~~~~~~~~~~~~~~~l~HE~GH 102 (220)
T PF14247_consen 37 RDLTIRFAECGEDNAFYDPENRSITICYEFVDEILDRFAKANDPDEEYGQAAIGNVLFTLYHELGH 102 (220)
T ss_pred CCeEEEEeecCCCCCccCCCCCEEEECHHHHHHHHHHHHhCCcCcchHHHHHHHHHHHHHHHHHHH
Confidence 34888885421144444443 4999988887642 111 2445566788999999
No 64
>PTZ00391 transport protein particle component (TRAPP) superfamily; Provisional
Probab=23.36 E-value=48 Score=27.73 Aligned_cols=48 Identities=17% Similarity=0.079 Sum_probs=31.4
Q ss_pred CCCcchhHhHHHHHHhhc---CCCHHHHHHHHHhccCCHHHHHHHhCCCHHHHH
Q 041464 139 NQGHSSVAARFLDYCNDL---RNGFVAELNKKMRDGYNDNFFMELLGKSIDQLW 189 (198)
Q Consensus 139 d~GY~~~TA~FL~wle~~---~~gfV~~LN~~mr~~ysd~~~~~l~G~~v~~LW 189 (198)
.-|| ++--+.|+.+.-+ .+-+++-|+--. ==...+|+.++||.+|.|.
T Consensus 33 ~~G~-~VG~rllE~l~~r~~~~~R~~~~L~iLk--FI~~~~W~~lFgk~aD~Lk 83 (168)
T PTZ00391 33 EMGL-RVGYKLNELLPYREKNQKRETKILSILT--FISKHVWKYLFGHSSDLLK 83 (168)
T ss_pred HHhH-HHhHHHHHHHHHhccCCCccchHHHHHH--HHHHHHHHHHhCchhhhhc
Confidence 3578 8888888888722 234444444211 0135899999999999993
No 65
>PF06262 DUF1025: Possibl zinc metallo-peptidase; InterPro: IPR010428 This is a family of bacterial protein with undetermined function.; PDB: 3E11_A.
Probab=23.36 E-value=64 Score=24.52 Aligned_cols=31 Identities=13% Similarity=0.172 Sum_probs=20.9
Q ss_pred eEEEcccccccCC--chhhhHHHHHHHHHHHhh
Q 041464 91 GIHYGDDFIQNIP--VDLIKQEFSGVMYHEMTH 121 (198)
Q Consensus 91 ~I~~S~~~i~~~~--~d~~~~Ei~GVl~HE~vH 121 (198)
.|.+=-+=|.... .+.++.+|.-+|.||+.|
T Consensus 51 rI~lyR~pl~~~~~~~~eL~~~I~~tlvhEiah 83 (97)
T PF06262_consen 51 RIVLYRRPLERRARSREELAELIRDTLVHEIAH 83 (97)
T ss_dssp EEEEEHHHHHHT-SSHHHHHHHHHHHHHHHHHH
T ss_pred EEEEehHHHHHHhCCHHHHHHHHHHHHHHHHHH
Confidence 5555444444332 223999999999999999
No 66
>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=22.87 E-value=1.3e+02 Score=21.34 Aligned_cols=25 Identities=20% Similarity=0.243 Sum_probs=16.1
Q ss_pred CCeEEEcccccccCCchhhhHHHHHHHHHHHhh
Q 041464 89 NNGIHYGDDFIQNIPVDLIKQEFSGVMYHEMTH 121 (198)
Q Consensus 89 g~~I~~S~~~i~~~~~d~~~~Ei~GVl~HE~vH 121 (198)
...|.++++ . +. .+-.=++.||+.|
T Consensus 28 ~~~I~in~~-~---~~----~~~~f~laHELgH 52 (122)
T PF06114_consen 28 NPIIFINSN-L---SP----ERQRFTLAHELGH 52 (122)
T ss_dssp TTEEEEESS-S----H----HHHHHHHHHHHHH
T ss_pred CCEEEECCC-C---CH----HHHHHHHHHHHHH
Confidence 458888866 1 11 1124588999999
No 67
>PRK11901 hypothetical protein; Reviewed
Probab=22.22 E-value=56 Score=30.28 Aligned_cols=40 Identities=13% Similarity=0.196 Sum_probs=23.4
Q ss_pred CchhhHHHHHHHHHHHHhhcccceEEEEEeCCCCCcccch
Q 041464 1 MADHSAFFLISLLTLTAMQGIHAVDYTVSNRAATTPGGMR 40 (198)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~a~~t~gg~r 40 (198)
||+-+-++++||+++++.++.|+++=.=...+..+.|+.|
T Consensus 38 ~MiGiGilVLlLLIi~IgSALksP~~~~~~q~~~~~~~~k 77 (327)
T PRK11901 38 MMIGIGILVLLLLIIAIGSALKSPTEHESQQSSNNAGAEK 77 (327)
T ss_pred HHHHHHHHHHHHHHHHHhhhccCCCCCccccccccccccc
Confidence 5555544555666788888888887544444444444443
No 68
>cd04281 ZnMc_BMP1_TLD Zinc-dependent metalloprotease; BMP1/TLD-like subfamily. BMP1 (Bone morphogenetic protein 1) and TLD (tolloid)-like metalloproteases play vital roles in extracellular matrix formation, by cleaving precursor proteins such as enzymes, structural proteins, and proteins involved in the mineralization of the extracellular matrix. The drosophila protein tolloid and its Xenopus homologue xolloid cleave and inactivate Sog and chordin, respectively, which are inhibitors of Dpp (the Drosophila decapentaplegic gene product) and its homologue BMP4, involved in dorso-ventral patterning.
Probab=21.71 E-value=41 Score=28.60 Aligned_cols=10 Identities=40% Similarity=0.823 Sum_probs=9.4
Q ss_pred HHHHHHHHhh
Q 041464 112 SGVMYHEMTH 121 (198)
Q Consensus 112 ~GVl~HE~vH 121 (198)
.|++.|||.|
T Consensus 88 ~Gti~HEl~H 97 (200)
T cd04281 88 FGIVVHELGH 97 (200)
T ss_pred CchHHHHHHH
Confidence 5999999999
No 69
>COG4784 Putative Zn-dependent protease [General function prediction only]
Probab=20.66 E-value=1.7e+02 Score=27.95 Aligned_cols=51 Identities=22% Similarity=0.266 Sum_probs=31.4
Q ss_pred CCCCeEEEEEccCCCCceeEe-cCCeEEEcccccccCCchhhhHHHHHHHHHHHhh
Q 041464 67 KNIPQVDLFIDDMKPGEIAFT-SNNGIHYGDDFIQNIPVDLIKQEFSGVMYHEMTH 121 (198)
Q Consensus 67 k~v~~Vtl~l~d~~~~GVA~t-~g~~I~~S~~~i~~~~~d~~~~Ei~GVl~HE~vH 121 (198)
+|-++-.++|-| +++-=|++ .|+-|.+--..|+= .+| ..|+.-||.|||-|
T Consensus 83 ~p~q~YriTiln-SP~INAFALPGGYlYitRGLlAl-and--~sEvAAVl~HEmgH 134 (479)
T COG4784 83 NPQQTYRITILN-SPNINAFALPGGYLYITRGLLAL-AND--SSEVAAVLAHEMGH 134 (479)
T ss_pred CCCceEEEEEec-CCCccccccCCceEEEehhHHHH-cCC--HHHHHHHHHhhhhh
Confidence 355566666655 23333444 36666665454443 334 57899999999999
No 70
>PF02607 B12-binding_2: B12 binding domain; InterPro: IPR003759 Cobalamin-dependent methionine synthase (2.1.1.13 from EC) is a large modular protein that catalyses methyl transfer from methyltetrahydrofolate (CH3-H4folate) to homocysteine. During the catalytic cycle, it supports three distinct methyl transfer reactions, each involving the cobalamin (vitamin B12) cofactor and a substrate bound to its own functional unit []. The cobalamin cofactor plays an essential role in this reaction, accepting the methyl group from CH3-H4folate to form methylcob(III)alamin, and in turn donating the methyl group to homocysteine to generate methionine and cob(I)alamin. Methionine synthase is a large enzyme composed of four structurally and functionally distinct modules: the first two modules bind homocysteine and CH3-H4folate, the third module binds the cobalamin cofactor and the C-terminal module binds S-adenosylmethionine. The cobalamin-binding module is composed of two structurally distinct domains: a 4-helical bundle cap domain (residues 651-740 in the Escherichia coli enzyme) and an alpha/beta B12-binding domain (residues 741-896) (IPR006158 from INTERPRO). The 4-helical bundle forms a cap over the alpha/beta domain, which acts to shield the methyl ligand of cobalamin from solvent []. Furthermore, in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO). The alpha/beta domain is a common cobalamin-binding motif, whereas the 4-helical bundle domain with its methyl cap is a distinctive feature of methionine synthases. This entry represents the 4-helical bundle cap domain. This domain is also present in other shorter proteins that bind to B12, and is always found N terminus to the alpha/beta B12-binding domain.; GO: 0008705 methionine synthase activity, 0031419 cobalamin binding, 0046872 metal ion binding, 0009086 methionine biosynthetic process; PDB: 3EZX_A 3BUL_A 1K7Y_A 1BMT_A 3IV9_A 1K98_A 3IVA_A 2I2X_P.
Probab=20.63 E-value=1.2e+02 Score=20.89 Aligned_cols=45 Identities=27% Similarity=0.431 Sum_probs=32.5
Q ss_pred HhHHHHHHhh-cCCCHHHHHHHHHhccCC-HHHHHHHhCC---CHHHHHH
Q 041464 146 AARFLDYCND-LRNGFVAELNKKMRDGYN-DNFFMELLGK---SIDQLWN 190 (198)
Q Consensus 146 TA~FL~wle~-~~~gfV~~LN~~mr~~ys-d~~~~~l~G~---~v~~LW~ 190 (198)
.-.|++.+-+ ...++.+-+|+.+..|++ ..++.+++-. .|.++|+
T Consensus 5 ~~~l~~al~~~d~~~~~~~~~~~l~~g~~~~~i~~~~l~p~m~~iG~~w~ 54 (79)
T PF02607_consen 5 IERLLDALLAGDEEEAEALLEEALAQGYPPEDIIEEILMPAMEEIGELWE 54 (79)
T ss_dssp HHHHHHHHHTT-CCHHHHHHHHHHHCSSSTTHHHHHTHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 4567777764 467788999999988888 5788776643 5666775
No 71
>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=20.55 E-value=1.9e+02 Score=23.31 Aligned_cols=56 Identities=11% Similarity=0.073 Sum_probs=32.1
Q ss_pred CeEEEEEccCC---CCceeEecC--------CeEEEcccccccCCchhhhHHHHHHHHHHHhh-cCCCCC
Q 041464 70 PQVDLFIDDMK---PGEIAFTSN--------NGIHYGDDFIQNIPVDLIKQEFSGVMYHEMTH-ANYVPE 127 (198)
Q Consensus 70 ~~Vtl~l~d~~---~~GVA~t~g--------~~I~~S~~~i~~~~~d~~~~Ei~GVl~HE~vH-Ag~ap~ 127 (198)
..|.+...+.. ..|.|+..+ +.|+++..+..... ........++.||+-| -||.-+
T Consensus 63 adI~i~~~~~~~~~~~g~a~~p~~~~~~~~~g~i~~~~~~~~~~~--~~g~~~~~t~~HEiGHaLGL~H~ 130 (186)
T cd04277 63 ADIRFGNSSDPDGNTAGYAYYPGSGSGTAYGGDIWFNSSYDTNSD--SPGSYGYQTIIHEIGHALGLEHP 130 (186)
T ss_pred ceEEEEeccCCCCCccEEEECCCCCccccccceeEEecCcccccC--CCChhhHHHHHHHHHHHhcCCCC
Confidence 44555555421 134666543 37888877665421 1223457999999999 355433
Done!