Query 019841
Match_columns 335
No_of_seqs 189 out of 1040
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 04:58:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019841.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019841hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01434 Peptidase_M41: Peptid 100.0 3.5E-29 7.5E-34 229.7 17.6 156 145-320 6-206 (213)
2 KOG0734 AAA+-type ATPase conta 99.9 1.6E-27 3.5E-32 241.6 10.4 164 144-327 534-733 (752)
3 CHL00176 ftsH cell division pr 99.9 1.8E-26 3.9E-31 241.6 18.3 164 145-329 417-626 (638)
4 PRK10733 hflB ATP-dependent me 99.9 8.5E-26 1.9E-30 236.7 18.5 163 146-328 387-595 (644)
5 TIGR01241 FtsH_fam ATP-depende 99.9 2.9E-25 6.4E-30 225.5 18.5 162 145-326 289-494 (495)
6 COG0465 HflB ATP-dependent Zn 99.9 3.4E-25 7.3E-30 229.1 15.5 155 145-319 384-579 (596)
7 KOG0731 AAA+-type ATPase conta 99.9 1.3E-22 2.7E-27 214.0 13.0 164 144-329 546-749 (774)
8 CHL00206 ycf2 Ycf2; Provisiona 98.7 1.9E-08 4.1E-13 115.1 7.0 112 144-275 1870-1994(2281)
9 cd06163 S2P-M50_PDZ_RseP-like 97.0 0.0015 3.3E-08 59.4 5.8 24 177-200 12-35 (182)
10 cd06164 S2P-M50_SpoIVFB_CBS Sp 96.5 0.004 8.6E-08 58.4 5.2 60 176-258 55-114 (227)
11 cd06161 S2P-M50_SpoIVFB SpoIVF 96.2 0.0054 1.2E-07 56.5 4.3 60 176-258 40-99 (208)
12 TIGR00054 RIP metalloprotease 95.9 0.0066 1.4E-07 61.5 3.8 22 176-197 16-37 (420)
13 PRK10779 zinc metallopeptidase 95.8 0.01 2.2E-07 60.6 4.5 26 176-201 17-42 (449)
14 PF02163 Peptidase_M50: Peptid 95.6 0.012 2.7E-07 52.4 3.7 25 177-201 10-34 (192)
15 cd05709 S2P-M50 Site-2 proteas 95.5 0.011 2.4E-07 52.4 3.0 24 177-200 11-34 (180)
16 PF13398 Peptidase_M50B: Pepti 95.3 0.02 4.3E-07 52.6 4.2 27 177-203 25-51 (200)
17 cd06162 S2P-M50_PDZ_SREBP Ster 94.4 0.072 1.6E-06 51.8 5.4 66 177-258 138-203 (277)
18 cd06158 S2P-M50_like_1 Unchara 93.8 0.071 1.5E-06 48.3 4.0 77 177-257 12-96 (181)
19 cd06160 S2P-M50_like_2 Unchara 92.6 0.11 2.3E-06 47.4 3.2 27 176-202 43-69 (183)
20 cd06159 S2P-M50_PDZ_Arch Uncha 87.3 0.28 6.2E-06 47.2 1.4 66 177-258 121-186 (263)
21 PF14247 DUF4344: Domain of un 78.6 1.5 3.2E-05 41.4 2.4 22 176-198 94-115 (220)
22 PF00413 Peptidase_M10: Matrix 76.5 1.1 2.3E-05 38.1 0.7 17 170-186 101-117 (154)
23 cd04279 ZnMc_MMP_like_1 Zinc-d 71.4 2.6 5.7E-05 36.5 1.9 21 171-191 101-121 (156)
24 cd04786 HTH_MerR-like_sg7 Heli 69.2 26 0.00056 30.2 7.6 68 264-331 41-116 (131)
25 KOG2921 Intramembrane metallop 68.6 3.8 8.3E-05 42.1 2.6 25 177-201 134-158 (484)
26 PF04298 Zn_peptidase_2: Putat 68.3 2.7 5.8E-05 39.8 1.4 13 176-188 91-103 (222)
27 cd04268 ZnMc_MMP_like Zinc-dep 67.9 3.4 7.3E-05 35.5 1.8 20 171-190 91-110 (165)
28 COG0750 Predicted membrane-ass 64.9 4.8 0.0001 39.4 2.5 26 176-201 15-40 (375)
29 PF02031 Peptidase_M7: Strepto 64.7 4.7 0.0001 35.3 2.1 31 154-186 59-89 (132)
30 cd08316 Death_FAS_TNFRSF6 Deat 63.7 42 0.00091 27.7 7.5 62 268-330 21-92 (97)
31 cd04278 ZnMc_MMP Zinc-dependen 60.2 4.1 8.8E-05 35.3 0.9 17 171-187 104-120 (157)
32 cd04277 ZnMc_serralysin_like Z 59.4 6 0.00013 35.2 1.9 19 171-189 110-128 (186)
33 PF05572 Peptidase_M43: Pregna 59.1 4.9 0.00011 35.6 1.2 21 170-190 65-85 (154)
34 cd04769 HTH_MerR2 Helix-Turn-H 57.2 61 0.0013 26.9 7.5 66 264-329 40-115 (116)
35 cd04327 ZnMc_MMP_like_3 Zinc-d 54.1 12 0.00027 33.8 3.1 26 172-197 90-116 (198)
36 COG0501 HtpX Zn-dependent prot 53.6 8.2 0.00018 36.3 1.9 32 160-191 143-174 (302)
37 smart00005 DEATH DEATH domain, 49.9 96 0.0021 23.8 7.2 58 269-327 19-86 (88)
38 PF09278 MerR-DNA-bind: MerR, 45.5 1E+02 0.0023 22.4 6.4 42 274-315 10-57 (65)
39 smart00235 ZnMc Zinc-dependent 44.5 11 0.00025 31.6 1.2 17 176-192 88-104 (140)
40 PF06114 DUF955: Domain of unk 43.8 27 0.00059 27.3 3.3 25 168-192 36-60 (122)
41 cd00203 ZnMc Zinc-dependent me 40.8 15 0.00032 31.5 1.3 20 172-191 94-113 (167)
42 PF13485 Peptidase_MA_2: Pepti 40.0 32 0.00069 27.2 3.1 23 170-192 21-43 (128)
43 cd04782 HTH_BltR Helix-Turn-He 39.6 1.3E+02 0.0028 24.2 6.6 51 265-315 42-95 (97)
44 cd08306 Death_FADD Fas-associa 39.5 1.9E+02 0.0042 22.9 8.1 58 270-328 16-83 (86)
45 PRK02391 heat shock protein Ht 38.4 22 0.00048 34.7 2.2 28 163-190 122-149 (296)
46 cd04768 HTH_BmrR-like Helix-Tu 38.3 1.3E+02 0.0029 24.1 6.5 51 265-315 42-94 (96)
47 PF13582 Reprolysin_3: Metallo 37.4 17 0.00036 29.8 1.1 12 176-187 109-120 (124)
48 PRK05457 heat shock protein Ht 37.1 26 0.00056 34.0 2.5 22 165-186 125-146 (284)
49 cd08318 Death_NMPP84 Death dom 37.0 1.2E+02 0.0026 24.1 6.0 46 270-315 21-75 (86)
50 PRK03982 heat shock protein Ht 35.6 27 0.00058 33.6 2.3 30 161-190 112-141 (288)
51 PF00531 Death: Death domain; 35.6 1.9E+02 0.0041 21.6 7.1 57 270-328 15-81 (83)
52 cd04776 HTH_GnyR Helix-Turn-He 35.0 2.7E+02 0.0058 23.3 8.5 63 265-327 40-114 (118)
53 cd01109 HTH_YyaN Helix-Turn-He 34.2 2.4E+02 0.0052 23.1 7.5 52 264-315 41-100 (113)
54 cd04788 HTH_NolA-AlbR Helix-Tu 33.9 1.4E+02 0.003 24.0 5.9 50 264-313 41-92 (96)
55 cd04783 HTH_MerR1 Helix-Turn-H 31.6 2.2E+02 0.0047 23.9 7.0 51 265-315 42-98 (126)
56 cd04777 HTH_MerR-like_sg1 Heli 31.5 2.3E+02 0.0049 23.0 6.9 51 265-315 40-102 (107)
57 TIGR01950 SoxR redox-sensitive 31.3 2.4E+02 0.0053 24.5 7.4 60 264-323 41-110 (142)
58 cd08313 Death_TNFR1 Death doma 31.2 1.7E+02 0.0038 23.3 5.9 49 267-315 11-69 (80)
59 cd08315 Death_TRAILR_DR4_DR5 D 30.9 1.7E+02 0.0036 23.9 6.0 62 268-330 20-90 (96)
60 cd01106 HTH_TipAL-Mta Helix-Tu 30.9 1.9E+02 0.004 23.3 6.3 47 265-311 42-90 (103)
61 cd04773 HTH_TioE_rpt2 Second H 30.9 2.8E+02 0.0061 22.7 7.4 52 265-316 42-100 (108)
62 PF01435 Peptidase_M48: Peptid 30.7 41 0.00088 30.0 2.5 24 169-192 84-107 (226)
63 cd04784 HTH_CadR-PbrR Helix-Tu 30.1 2.7E+02 0.0059 23.2 7.4 51 264-314 41-99 (127)
64 cd06258 Peptidase_M3_like The 28.7 32 0.00069 33.7 1.6 17 176-192 156-172 (365)
65 PF14362 DUF4407: Domain of un 28.7 1.1E+02 0.0023 29.5 5.2 43 114-156 27-70 (301)
66 PRK04897 heat shock protein Ht 28.1 43 0.00094 32.6 2.4 25 165-189 128-152 (298)
67 cd01110 HTH_SoxR Helix-Turn-He 27.7 2.5E+02 0.0053 24.3 6.8 59 265-323 42-110 (139)
68 PF12388 Peptidase_M57: Dual-a 27.6 39 0.00085 31.8 1.9 22 170-191 129-150 (211)
69 PF10728 DUF2520: Domain of un 27.5 1.2E+02 0.0026 26.2 4.8 62 260-321 6-67 (132)
70 PF11350 DUF3152: Protein of u 27.5 32 0.0007 32.3 1.3 24 171-194 136-159 (203)
71 PRK03001 M48 family peptidase; 27.4 39 0.00084 32.5 1.9 29 162-190 112-140 (283)
72 TIGR02044 CueR Cu(I)-responsiv 26.8 2.7E+02 0.0059 23.3 6.8 51 265-315 42-100 (127)
73 PF08858 IDEAL: IDEAL domain; 26.5 1.3E+02 0.0029 20.5 3.9 26 33-58 8-33 (37)
74 PRK03072 heat shock protein Ht 25.8 42 0.0009 32.6 1.8 25 166-190 119-143 (288)
75 COG2738 Predicted Zn-dependent 25.6 37 0.0008 32.1 1.3 13 176-188 94-106 (226)
76 COG1913 Predicted Zn-dependent 24.6 47 0.001 30.7 1.8 16 171-186 118-136 (181)
77 PF07998 Peptidase_M54: Peptid 24.6 48 0.001 30.8 1.9 11 176-186 147-157 (194)
78 cd04770 HTH_HMRTR Helix-Turn-H 24.5 4E+02 0.0087 21.9 7.3 51 265-315 42-100 (123)
79 cd08311 Death_p75NR Death doma 24.4 2E+02 0.0043 22.7 5.1 33 270-303 18-50 (77)
80 COG3402 Uncharacterized conser 24.3 1.7E+02 0.0038 26.5 5.3 36 113-148 27-62 (161)
81 PF12994 DUF3878: Domain of un 24.1 15 0.00032 36.3 -1.6 17 172-188 92-108 (299)
82 cd08779 Death_PIDD Death Domai 23.7 3.8E+02 0.0081 21.3 7.8 57 272-329 18-85 (86)
83 TIGR02047 CadR-PbrR Cd(II)/Pb( 23.5 3.1E+02 0.0068 23.1 6.6 52 264-315 41-100 (127)
84 PF13583 Reprolysin_4: Metallo 23.3 42 0.00092 30.8 1.3 17 176-192 139-155 (206)
85 cd08784 Death_DRs Death Domain 23.0 2.5E+02 0.0054 21.9 5.4 48 268-315 12-68 (79)
86 PRK01265 heat shock protein Ht 22.8 54 0.0012 32.7 2.0 29 161-189 127-155 (324)
87 cd04787 HTH_HMRTR_unk Helix-Tu 22.6 3.5E+02 0.0076 22.9 6.7 51 265-315 42-100 (133)
88 PF09471 Peptidase_M64: IgA Pe 22.5 37 0.0008 32.8 0.7 20 171-190 213-232 (264)
89 cd04276 ZnMc_MMP_like_2 Zinc-d 22.2 62 0.0013 29.9 2.1 15 172-186 114-128 (197)
90 PLN02598 omega-6 fatty acid de 22.0 1.3E+02 0.0028 31.1 4.6 19 77-97 73-91 (421)
91 cd08777 Death_RIP1 Death Domai 21.9 4.2E+02 0.009 21.2 7.8 47 270-316 16-74 (86)
92 COG4317 Uncharacterized protei 21.8 1.5E+02 0.0032 24.3 3.9 32 118-149 12-43 (93)
93 PRK01345 heat shock protein Ht 21.5 58 0.0013 32.1 1.9 28 164-191 114-141 (317)
94 TIGR02051 MerR Hg(II)-responsi 21.5 3.7E+02 0.008 22.5 6.6 51 265-315 41-97 (124)
95 PRK13267 archaemetzincin-like 21.4 62 0.0013 29.5 1.9 11 176-186 127-137 (179)
96 COG2317 Zn-dependent carboxype 21.3 44 0.00095 35.2 1.0 10 178-187 263-272 (497)
97 cd04779 HTH_MerR-like_sg4 Heli 21.1 4.7E+02 0.01 22.6 7.3 9 234-242 38-46 (134)
98 cd04275 ZnMc_pappalysin_like Z 21.1 13 0.00029 34.9 -2.5 20 171-190 134-153 (225)
99 PF02074 Peptidase_M32: Carbox 20.9 51 0.0011 34.8 1.4 15 178-194 263-277 (494)
100 PF01400 Astacin: Astacin (Pep 20.2 64 0.0014 29.2 1.8 18 174-191 79-96 (191)
101 PF01890 CbiG_C: Cobalamin syn 20.2 12 0.00026 31.8 -2.8 85 33-117 11-98 (121)
102 PLN02498 omega-3 fatty acid de 20.1 1.5E+02 0.0032 31.1 4.5 15 82-97 101-115 (450)
No 1
>PF01434 Peptidase_M41: Peptidase family M41 This is family M41 in the peptidase classification. ; InterPro: IPR000642 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M41 (FtsH endopeptidase family, clan MA(E)). The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH. The peptidase M41 family belong to a larger family of zinc metalloproteases. This family includes the cell division protein FtsH, and the yeast mitochondrial respiratory chain complexes assembly protein, which is a putative ATP-dependent protease required for assembly of the mitochondrial respiratory chain and ATPase complexes. FtsH is an integral membrane protein, which seems to act as an ATP-dependent zinc metallopeptidase that binds one zinc ion.; GO: 0004222 metalloendopeptidase activity, 0005524 ATP binding, 0006508 proteolysis; PDB: 4EIW_C 2DHR_E 1IY1_A 1IY2_A 1IY0_A 1IXZ_A 2CE7_F 2CEA_F 3KDS_E 2QZ4_A ....
Probab=99.96 E-value=3.5e-29 Score=229.71 Aligned_cols=156 Identities=24% Similarity=0.310 Sum_probs=122.1
Q ss_pred HHHHHHhhhcCCCCccccccccCCCCHhHHHHHHHHHHhHHHHHHHhC--CCCceeEecchhHHhhhCccccccceeeec
Q 019841 145 LWTVDSVSYNGGVGSLVLDTIGHTFSQKYHNRVIQHEAGHFLIAYLVG--ILPKGYTLTSLEALKKEGSLNVQAGTAFVD 222 (335)
Q Consensus 145 l~aiD~v~lgg~~~~llld~l~r~~s~~~r~RIA~HEAGHaLVAylLg--~PV~~~TI~p~eal~~~G~~~~~gG~~f~~ 222 (335)
--++|+|.+|.+... +.+++++|+|+||||||||+|+|+++ .||.++||+|+ | + .+|++...
T Consensus 6 ~~a~drv~~G~~~~~-------~~~~~~~~~~~A~HEAGhAvva~~l~~~~~v~~vsi~pr------g--~-~~G~~~~~ 69 (213)
T PF01434_consen 6 EEAIDRVLMGPEKKS-------RKLSEEEKRRIAYHEAGHAVVAYLLPPADPVSKVSIVPR------G--S-ALGFTQFT 69 (213)
T ss_dssp HHHHHHHHCCSCCTT-------S---HHHHHHHHHHHHHHHHHHHHSSS---EEEEESSTT------C--C-CCHCCEEC
T ss_pred HHHHHHHhcCcCcCC-------CCCCHHHHHHHHHHHHHHHHHHHHhcccccEEEEEEecC------C--C-cceeEEec
Confidence 358999999988632 34589999999999999999999998 58999999997 5 2 55655544
Q ss_pred chhhhhhccccCCHHHHHHHHHHHhhHHHHHHHHhC--Cc-cchhhHHHHHHHHHHh----cCCCH--------------
Q 019841 223 FEFLEEVNSGKVSATTLNRFSCIALAGVATEYLLYG--YA-EGGLADINKLDALLKG----LGFTQ-------------- 281 (335)
Q Consensus 223 ~~~~~~l~~g~~s~~~L~r~~~VlLAGrAAE~LvyG--~a-~Gg~~Dl~~at~i~~~----lG~s~-------------- 281 (335)
+.. +....|++++.+.++|+|||||||+++|| +. +|+++|++++|++++. +||+.
T Consensus 70 ~~~----~~~~~t~~~l~~~i~v~LaGraAEe~~~g~~~~stGa~~DL~~At~iA~~mv~~~Gm~~~~g~~~~~~~~~~~ 145 (213)
T PF01434_consen 70 PDE----DRYIRTRSYLEDRICVLLAGRAAEELFFGEDNVSTGASSDLQQATEIARKMVASYGMGDSLGLLSYSPNDDDE 145 (213)
T ss_dssp HHT----T-SS-BHHHHHHHHHHHHHHHHHHHHHHSCCS-BGGGHHHHHHHHHHHHHHHHTST-TTTTTSS-SEEEE-S-
T ss_pred cch----hcccccHHHHHhhHHHHHHHHHHHHhhcCcceecccchhHHHHHHHHHHHHHHHhCCCCCCceeeeecccccc
Confidence 332 23458999999999999999999999999 54 5999999999999864 56642
Q ss_pred ------------------HHHHHHHH----HHHHHHHHHHHHcHHHHHHHHHHHHcccchH
Q 019841 282 ------------------KKADSQVR----WSLLNTVLLLRRHKGARAKLAEAMTMGKSLG 320 (335)
Q Consensus 282 ------------------~~~d~evR----~A~~~A~~LLr~hr~aleaLaeaLle~esl~ 320 (335)
..++.+++ .||.+|++||++||+.+++|+++|+++++|.
T Consensus 146 ~~~~~~~~~~~~~s~~~~~~i~~ev~~lL~~a~~~a~~iL~~~r~~l~~la~~Lle~~~L~ 206 (213)
T PF01434_consen 146 VFLGREWNSRRPMSEETRALIDREVRKLLEEAYARAKEILEENREALEALAEALLEKETLS 206 (213)
T ss_dssp SSS-E---EEESS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHSEEE
T ss_pred ccccccccccCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhCeeC
Confidence 12344444 6999999999999999999999999999983
No 2
>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]
Probab=99.94 E-value=1.6e-27 Score=241.64 Aligned_cols=164 Identities=20% Similarity=0.259 Sum_probs=140.1
Q ss_pred HHHHHHHhhhcCCCCccccccccCCCCHhHHHHHHHHHHhHHHHHHHhC--CCCceeEecchhHHhhhCccccccceeee
Q 019841 144 FLWTVDSVSYNGGVGSLVLDTIGHTFSQKYHNRVIQHEAGHFLIAYLVG--ILPKGYTLTSLEALKKEGSLNVQAGTAFV 221 (335)
Q Consensus 144 ~l~aiD~v~lgg~~~~llld~l~r~~s~~~r~RIA~HEAGHaLVAylLg--~PV~~~TI~p~eal~~~G~~~~~gG~~f~ 221 (335)
+=|+-|+|.||.+..+.+ ++++.|+..||||+||++||+... .|++|.||.|| | -..|.++.
T Consensus 534 LE~akDrIlMG~ERks~~-------i~~eak~~TAyHE~GHAivA~yTk~A~PlhKaTImPR------G---~sLG~t~~ 597 (752)
T KOG0734|consen 534 LEFAKDRILMGPERKSMV-------IDEEAKKITAYHEGGHAIVALYTKGAMPLHKATIMPR------G---PSLGHTSQ 597 (752)
T ss_pred Hhhhhhheeecccccccc-------cChhhhhhhhhhccCceEEEeecCCCccccceeeccC------C---ccccceee
Confidence 447899999999977654 579999999999999999999986 69999999998 6 36788887
Q ss_pred cchhhhhhccccCCHHHHHHHHHHHhhHHHHHHHHhCC--c-cchhhHHHHHHHHHHh----cCCCHH------------
Q 019841 222 DFEFLEEVNSGKVSATTLNRFSCIALAGVATEYLLYGY--A-EGGLADINKLDALLKG----LGFTQK------------ 282 (335)
Q Consensus 222 ~~~~~~~l~~g~~s~~~L~r~~~VlLAGrAAE~LvyG~--a-~Gg~~Dl~~at~i~~~----lG~s~~------------ 282 (335)
.|+. |+..+|+.++..++-|.||||+||+|+||. + +|+++|++|+|++++. +|||.+
T Consensus 598 LPe~----D~~~~Tk~q~LA~lDV~MGGRvAEELIfG~D~iTsGAssDl~qAT~lA~~MVt~fGMSd~vG~v~~~~~~~~ 673 (752)
T KOG0734|consen 598 LPEK----DRYSITKAQLLARLDVCMGGRVAEELIFGTDKITSGASSDLDQATKLARRMVTKFGMSDKVGPVTLSAEDNS 673 (752)
T ss_pred cCcc----chhhHHHHHHHHHHHHhhcchHHHHHhccCCcccccccchHHHHHHHHHHHHHHcCccccccceeeeccCCC
Confidence 7764 567899999999999999999999999996 3 5999999999998765 687632
Q ss_pred ---------HHHHHHH----HHHHHHHHHHHHcHHHHHHHHHHHHcccch--HHHHHHHH
Q 019841 283 ---------KADSQVR----WSLLNTVLLLRRHKGARAKLAEAMTMGKSL--GSCIDIIE 327 (335)
Q Consensus 283 ---------~~d~evR----~A~~~A~~LLr~hr~aleaLaeaLle~esl--~~Ci~~Ie 327 (335)
.+|.|++ .+|+||+.||+.|.+.+++||+||++.||| +|..++++
T Consensus 674 ~s~~~~t~~lidaEi~~lL~~sYeRak~iL~~h~kEl~~LA~ALleYETL~A~eik~vl~ 733 (752)
T KOG0734|consen 674 SSLSPRTQELIDAEIKRLLRDSYERAKSILKTHKKELHALAEALLEYETLDAKEIKRVLK 733 (752)
T ss_pred CCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHh
Confidence 3677655 799999999999999999999999999999 44445553
No 3
>CHL00176 ftsH cell division protein; Validated
Probab=99.94 E-value=1.8e-26 Score=241.56 Aligned_cols=164 Identities=21% Similarity=0.237 Sum_probs=136.0
Q ss_pred HHHHHHhhhcCCCCccccccccCCCCHhHHHHHHHHHHhHHHHHHHhC--CCCceeEecchhHHhhhCccccccceeeec
Q 019841 145 LWTVDSVSYNGGVGSLVLDTIGHTFSQKYHNRVIQHEAGHFLIAYLVG--ILPKGYTLTSLEALKKEGSLNVQAGTAFVD 222 (335)
Q Consensus 145 l~aiD~v~lgg~~~~llld~l~r~~s~~~r~RIA~HEAGHaLVAylLg--~PV~~~TI~p~eal~~~G~~~~~gG~~f~~ 222 (335)
-.++|++.+|.+..++ .++++|++|||||||||+|+++++ .||+++||+|| | ..+|+++..
T Consensus 417 ~~Ai~rv~~g~~~~~~--------~~~~~~~~vA~hEaGhA~v~~~l~~~~~v~kvtI~pr------g---~~~G~~~~~ 479 (638)
T CHL00176 417 DTAIDRVIAGLEGTPL--------EDSKNKRLIAYHEVGHAIVGTLLPNHDPVQKVTLIPR------G---QAKGLTWFT 479 (638)
T ss_pred HHHHHHHHhhhccCcc--------ccHHHHHHHHHHhhhhHHHHhhccCCCceEEEEEeec------C---CCCCceEec
Confidence 4578888888775432 378999999999999999999997 68999999998 4 356777766
Q ss_pred chhhhhhccccCCHHHHHHHHHHHhhHHHHHHHHhCC---ccchhhHHHHHHHHHHh----cCCCH--------------
Q 019841 223 FEFLEEVNSGKVSATTLNRFSCIALAGVATEYLLYGY---AEGGLADINKLDALLKG----LGFTQ-------------- 281 (335)
Q Consensus 223 ~~~~~~l~~g~~s~~~L~r~~~VlLAGrAAE~LvyG~---a~Gg~~Dl~~at~i~~~----lG~s~-------------- 281 (335)
|+. +...+|+.++...++++|||||||+++||+ .+|+++|++++|++++. +||+.
T Consensus 480 p~~----~~~~~t~~~l~~~i~~~LgGraAE~~~fg~~~~~~Ga~~Dl~~AT~iA~~mv~~~Gm~~~g~~~~~~~~~~~~ 555 (638)
T CHL00176 480 PEE----DQSLVSRSQILARIVGALGGRAAEEVVFGSTEVTTGASNDLQQVTNLARQMVTRFGMSSIGPISLESNNSTDP 555 (638)
T ss_pred CCc----ccccccHHHHHHHHHHHhhhHHHHHHhcCCCCcCCCchhHHHHHHHHHHHHHHHhCCCcCCceeecCCCCccc
Confidence 543 346789999999999999999999999994 36999999999999875 46631
Q ss_pred -----------------HHHHHHHH----HHHHHHHHHHHHcHHHHHHHHHHHHcccch--HHHHHHHHhh
Q 019841 282 -----------------KKADSQVR----WSLLNTVLLLRRHKGARAKLAEAMTMGKSL--GSCIDIIEDN 329 (335)
Q Consensus 282 -----------------~~~d~evR----~A~~~A~~LLr~hr~aleaLaeaLle~esl--~~Ci~~Ie~~ 329 (335)
..+|.+++ .||.+|++||++||+.+++||++|+++||| +++.++++..
T Consensus 556 ~~~~~~~~~~~~s~~~~~~iD~ev~~~l~~~~~~a~~iL~~~~~~l~~la~~Lle~Etl~~~ei~~il~~~ 626 (638)
T CHL00176 556 FLGRFMQRNSEYSEEIADKIDMEVRSILHTCYQYAYQILKDNRVLIDLLVELLLQKETIDGDEFREIVNSY 626 (638)
T ss_pred ccccccccccCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhCccCHHHHHHHHhhc
Confidence 13556655 799999999999999999999999999999 6777887653
No 4
>PRK10733 hflB ATP-dependent metalloprotease; Reviewed
Probab=99.94 E-value=8.5e-26 Score=236.71 Aligned_cols=163 Identities=21% Similarity=0.237 Sum_probs=132.3
Q ss_pred HHHHHhhhcCCCCccccccccCCCCHhHHHHHHHHHHhHHHHHHHhC--CCCceeEecchhHHhhhCccccccceeeecc
Q 019841 146 WTVDSVSYNGGVGSLVLDTIGHTFSQKYHNRVIQHEAGHFLIAYLVG--ILPKGYTLTSLEALKKEGSLNVQAGTAFVDF 223 (335)
Q Consensus 146 ~aiD~v~lgg~~~~llld~l~r~~s~~~r~RIA~HEAGHaLVAylLg--~PV~~~TI~p~eal~~~G~~~~~gG~~f~~~ 223 (335)
-++|++.+|..... ..+++++|+++||||||||+|+++++ .||+++||+|| | ..+|+++..|
T Consensus 387 ~a~~~v~~g~~~~~-------~~~~~~~~~~~a~he~gha~~~~~~~~~~~~~~v~i~pr------g---~~~g~~~~~~ 450 (644)
T PRK10733 387 KAKDKIMMGAERRS-------MVMTEAQKESTAYHEAGHAIIGRLVPEHDPVHKVTIIPR------G---RALGVTFFLP 450 (644)
T ss_pred HHHHHHhccccccc-------ccccHHHHHHHHHHHHHHHHHHHHccCCCceeEEEEecc------C---CCcceeEECC
Confidence 46777777765332 23578999999999999999999997 69999999998 5 3567776655
Q ss_pred hhhhhhccccCCHHHHHHHHHHHhhHHHHHHHHhCC---ccchhhHHHHHHHHHHh----cCCCHH--------------
Q 019841 224 EFLEEVNSGKVSATTLNRFSCIALAGVATEYLLYGY---AEGGLADINKLDALLKG----LGFTQK-------------- 282 (335)
Q Consensus 224 ~~~~~l~~g~~s~~~L~r~~~VlLAGrAAE~LvyG~---a~Gg~~Dl~~at~i~~~----lG~s~~-------------- 282 (335)
+. +....|+++|++.++|+|||||||+++||. .+|+++|++++|++++. +|||.+
T Consensus 451 ~~----~~~~~~~~~l~~~i~~~lgGraAE~~~~g~~~~ttGa~~Dl~~AT~lA~~mv~~~Gms~~lg~~~~~~~~~~~~ 526 (644)
T PRK10733 451 EG----DAISASRQKLESQISTLYGGRLAEEIIYGPEHVSTGASNDIKVATNLARNMVTQWGFSEKLGPLLYAEEEGEVF 526 (644)
T ss_pred Cc----ccccccHHHHHHHHHHHHhhHHHHHHHhCCCCCCCCcHHHHHHHHHHHHHHHHHhCCCccccchhhcccccccc
Confidence 42 234579999999999999999999999994 36999999999999864 576531
Q ss_pred -----------------HHHHHHH----HHHHHHHHHHHHcHHHHHHHHHHHHcccch--HHHHHHHHh
Q 019841 283 -----------------KADSQVR----WSLLNTVLLLRRHKGARAKLAEAMTMGKSL--GSCIDIIED 328 (335)
Q Consensus 283 -----------------~~d~evR----~A~~~A~~LLr~hr~aleaLaeaLle~esl--~~Ci~~Ie~ 328 (335)
.+|+++| .||.+|++||++|++.+++||++|+++||| ++..+++..
T Consensus 527 lg~~~~~~~~~s~~~~~~id~ev~~il~~~~~~a~~iL~~~~~~l~~la~~Lle~etl~~~ei~~i~~~ 595 (644)
T PRK10733 527 LGRSVAKAKHMSDETARIIDQEVKALIERNYNRARQLLTDNMDILHAMKDALMKYETIDAPQIDDLMAR 595 (644)
T ss_pred cccccccccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhceeCHHHHHHHHhc
Confidence 3566655 799999999999999999999999999999 556677764
No 5
>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH. HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.
Probab=99.93 E-value=2.9e-25 Score=225.48 Aligned_cols=162 Identities=20% Similarity=0.236 Sum_probs=129.2
Q ss_pred HHHHHHhhhcCCCCccccccccCCCCHhHHHHHHHHHHhHHHHHHHhC--CCCceeEecchhHHhhhCccccccceeeec
Q 019841 145 LWTVDSVSYNGGVGSLVLDTIGHTFSQKYHNRVIQHEAGHFLIAYLVG--ILPKGYTLTSLEALKKEGSLNVQAGTAFVD 222 (335)
Q Consensus 145 l~aiD~v~lgg~~~~llld~l~r~~s~~~r~RIA~HEAGHaLVAylLg--~PV~~~TI~p~eal~~~G~~~~~gG~~f~~ 222 (335)
..+++++.+|..... ..+++++|+|+||||||||||+|+++ .|+.++||.|| | ..+|+++..
T Consensus 289 ~~a~~~~~~~~~~~~-------~~~~~~~~~~~A~hEaGhAlv~~~l~~~~~v~~vsi~pr------g---~~~G~~~~~ 352 (495)
T TIGR01241 289 EEAIDRVIAGPEKKS-------RVISEKEKKLVAYHEAGHALVGLLLKDADPVHKVTIIPR------G---QALGYTQFL 352 (495)
T ss_pred HHHHHHHhccccccc-------ccccHHHHHHHHHHHHhHHHHHHhcCCCCceEEEEEeec------C---CccceEEec
Confidence 446777777765432 34589999999999999999999995 68999999997 4 255665543
Q ss_pred chhhhhhccccCCHHHHHHHHHHHhhHHHHHHHHhCCcc-chhhHHHHHHHHHHh----cCCCH----------------
Q 019841 223 FEFLEEVNSGKVSATTLNRFSCIALAGVATEYLLYGYAE-GGLADINKLDALLKG----LGFTQ---------------- 281 (335)
Q Consensus 223 ~~~~~~l~~g~~s~~~L~r~~~VlLAGrAAE~LvyG~a~-Gg~~Dl~~at~i~~~----lG~s~---------------- 281 (335)
+.. +.+..|+++++++++|+|||||||+++||+++ |+++|++++|+++.. +||+.
T Consensus 353 ~~~----~~~~~t~~~l~~~i~v~LaGraAE~~~~G~~s~Ga~~Dl~~At~lA~~mv~~~Gm~~~~g~~~~~~~~~~~~l 428 (495)
T TIGR01241 353 PEE----DKYLYTKSQLLAQIAVLLGGRAAEEIIFGEVTTGASNDIKQATNIARAMVTEWGMSDKLGPVAYGSDGGDVFL 428 (495)
T ss_pred Ccc----ccccCCHHHHHHHHHHHhhHHHHHHHHhcCCCCCchHHHHHHHHHHHHHHHHhCCCcccCceeeccCcccccc
Confidence 321 34678999999999999999999999999975 999999999999763 56643
Q ss_pred ---------------HHHHHHH----HHHHHHHHHHHHHcHHHHHHHHHHHHcccchH--HHHHHH
Q 019841 282 ---------------KKADSQV----RWSLLNTVLLLRRHKGARAKLAEAMTMGKSLG--SCIDII 326 (335)
Q Consensus 282 ---------------~~~d~ev----R~A~~~A~~LLr~hr~aleaLaeaLle~esl~--~Ci~~I 326 (335)
..+|.++ ++||.+|+++|++||+++++||++|+++++|+ |..++|
T Consensus 429 ~~~~~~~~~~s~~~~~~id~~v~~lL~~a~~ra~~lL~~~~~~l~~la~~Ll~~e~L~~~ei~~il 494 (495)
T TIGR01241 429 GRGFAKAKEYSEETAREIDEEVKRIIEEAYKRAKQILTENRDELELLAKALLEKETITREEIKELL 494 (495)
T ss_pred ccccccccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcCeeCHHHHHHHh
Confidence 1234444 49999999999999999999999999999993 444443
No 6
>COG0465 HflB ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]
Probab=99.93 E-value=3.4e-25 Score=229.15 Aligned_cols=155 Identities=24% Similarity=0.238 Sum_probs=136.3
Q ss_pred HHHHHHhhhcCCCCccccccccCCCCHhHHHHHHHHHHhHHHHHHHhC--CCCceeEecchhHHhhhCccccccceeeec
Q 019841 145 LWTVDSVSYNGGVGSLVLDTIGHTFSQKYHNRVIQHEAGHFLIAYLVG--ILPKGYTLTSLEALKKEGSLNVQAGTAFVD 222 (335)
Q Consensus 145 l~aiD~v~lgg~~~~llld~l~r~~s~~~r~RIA~HEAGHaLVAylLg--~PV~~~TI~p~eal~~~G~~~~~gG~~f~~ 222 (335)
-.++|+|.+|.+..+ +++++++|+.+|||||||++++++++ +||+|+||+|+ | ..+|+++..
T Consensus 384 ~ea~drv~~G~erks-------~vise~ek~~~AYhEaghalv~~~l~~~d~v~KvtIiPr------G---~alG~t~~~ 447 (596)
T COG0465 384 EEAIDRVIAGPERKS-------RVISEAEKKITAYHEAGHALVGLLLPDADPVHKVTIIPR------G---RALGYTLFL 447 (596)
T ss_pred HHHHHHHhcCcCcCC-------cccChhhhcchHHHHHHHHHHHHhCCCCcccceeeeccC------c---hhhcchhcC
Confidence 468999999999765 35689999999999999999999997 59999999998 5 467888887
Q ss_pred chhhhhhccccCCHHHHHHHHHHHhhHHHHHHHHhC-Cc-cchhhHHHHHHHHHHh----cCCCH---------------
Q 019841 223 FEFLEEVNSGKVSATTLNRFSCIALAGVATEYLLYG-YA-EGGLADINKLDALLKG----LGFTQ--------------- 281 (335)
Q Consensus 223 ~~~~~~l~~g~~s~~~L~r~~~VlLAGrAAE~LvyG-~a-~Gg~~Dl~~at~i~~~----lG~s~--------------- 281 (335)
|+. |++.+|++++...++++|||||||+++|| ++ +|+++|++++|.+++. +|||.
T Consensus 448 Pe~----d~~l~sk~~l~~~i~~~lgGRaAEel~~g~e~ttGa~~D~~~at~~ar~mVt~~Gms~~lG~v~~~~~~~~fl 523 (596)
T COG0465 448 PEE----DKYLMSKEELLDRIDVLLGGRAAEELIFGYEITTGASNDLEKATDLARAMVTEYGMSAKLGPVAYEQVEGVFL 523 (596)
T ss_pred Ccc----ccccccHHHHHHHHHHHhCCcHhhhhhhcccccccchhhHHHHHHHHHHhhhhcCcchhhCceehhhcccccc
Confidence 764 57889999999999999999999999999 76 5999999999999874 56653
Q ss_pred --------------HHHHHHHH----HHHHHHHHHHHHcHHHHHHHHHHHHcccch
Q 019841 282 --------------KKADSQVR----WSLLNTVLLLRRHKGARAKLAEAMTMGKSL 319 (335)
Q Consensus 282 --------------~~~d~evR----~A~~~A~~LLr~hr~aleaLaeaLle~esl 319 (335)
+.+|.++| .+|.+++.||.+|++.++.++++|+++||+
T Consensus 524 g~~~~~~~~Se~ta~~ID~evk~ii~~~y~~a~~il~~~~~~l~~~~~~Lle~Eti 579 (596)
T COG0465 524 GRYQKAKNYSEETAQEIDREVKDIIDEAYERAKELLNENKDALETLAEMLLEKETI 579 (596)
T ss_pred cccccccCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhhcc
Confidence 24667766 699999999999999999999999999998
No 7
>KOG0731 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]
Probab=99.88 E-value=1.3e-22 Score=213.99 Aligned_cols=164 Identities=23% Similarity=0.279 Sum_probs=137.5
Q ss_pred HHHHHHHhhhcCCCCccccccccCCCCHhHHHHHHHHHHhHHHHHHHhC--CCCceeEecchhHHhhhCccccccceeee
Q 019841 144 FLWTVDSVSYNGGVGSLVLDTIGHTFSQKYHNRVIQHEAGHFLIAYLVG--ILPKGYTLTSLEALKKEGSLNVQAGTAFV 221 (335)
Q Consensus 144 ~l~aiD~v~lgg~~~~llld~l~r~~s~~~r~RIA~HEAGHaLVAylLg--~PV~~~TI~p~eal~~~G~~~~~gG~~f~ 221 (335)
+..++|++..|-...+ +.+++++++.+|||||||++++++++ +|+.++||+| | + ..|+++.
T Consensus 546 ~~~a~~Rvi~G~~~~~-------~~~~~~~~~~~a~~eagha~~g~~l~~~dpl~kvsIiP-------G-q--alG~a~~ 608 (774)
T KOG0731|consen 546 LEYAIERVIAGMEKKS-------RVLSLEEKKTVAYHEAGHAVVGWLLEHADPLLKVSIIP-------G-Q--ALGYAQY 608 (774)
T ss_pred HHHHHHHHhccccccc-------hhcCHhhhhhhhhhhccchhhhccccccCcceeEEecc-------C-C--ccceEEE
Confidence 4568998888866443 34589999999999999999998887 6999999999 5 2 4567666
Q ss_pred cchhhhhhccccCCHHHHHHHHHHHhhHHHHHHHHhC-Cc-cchhhHHHHHHHHHHh----cCCCH--------------
Q 019841 222 DFEFLEEVNSGKVSATTLNRFSCIALAGVATEYLLYG-YA-EGGLADINKLDALLKG----LGFTQ-------------- 281 (335)
Q Consensus 222 ~~~~~~~l~~g~~s~~~L~r~~~VlLAGrAAE~LvyG-~a-~Gg~~Dl~~at~i~~~----lG~s~-------------- 281 (335)
.|.. .+.+|+++|...+|++|||||||+++|| ++ +|+.+|++++|++++. +||++
T Consensus 609 ~P~~-----~~l~sk~ql~~rm~m~LGGRaAEev~fg~~iTtga~ddl~kvT~~A~~~V~~~Gms~kig~~~~~~~~~~~ 683 (774)
T KOG0731|consen 609 LPTD-----DYLLSKEQLFDRMVMALGGRAAEEVVFGSEITTGAQDDLEKVTKIARAMVASFGMSEKIGPISFQMLLPGD 683 (774)
T ss_pred CCcc-----cccccHHHHHHHHHHHhCcchhhheecCCccCchhhccHHHHHHHHHHHHHHcCcccccCceeccCccccc
Confidence 6653 3889999999999999999999999997 55 5999999999999875 56642
Q ss_pred ------------HHHHHHHH----HHHHHHHHHHHHcHHHHHHHHHHHHcccch--HHHHHHHHhh
Q 019841 282 ------------KKADSQVR----WSLLNTVLLLRRHKGARAKLAEAMTMGKSL--GSCIDIIEDN 329 (335)
Q Consensus 282 ------------~~~d~evR----~A~~~A~~LLr~hr~aleaLaeaLle~esl--~~Ci~~Ie~~ 329 (335)
+.+|.++| .||.+|.++|++|++.++.+++.|+++|++ +++++++..-
T Consensus 684 ~~~~~p~s~~~~~~Id~ev~~lv~~ay~~~~~ll~~n~~~l~~ia~~LLeke~l~~ee~~~ll~~~ 749 (774)
T KOG0731|consen 684 ESFRKPYSEKTAQLIDTEVRRLVQKAYERTKELLRTNRDKLDKIAEVLLEKEVLTGEEIIALLGER 749 (774)
T ss_pred ccccCccchhHHHHHHHHHHHHHhhHHHHHHHHHHHhHHHHHHHHHHHHHhhhccHHHHHHHhccC
Confidence 25777777 499999999999999999999999999998 8888887653
No 8
>CHL00206 ycf2 Ycf2; Provisional
Probab=98.71 E-value=1.9e-08 Score=115.14 Aligned_cols=112 Identities=12% Similarity=0.005 Sum_probs=78.4
Q ss_pred HHHHHHHhhhcCCCCccccccccCCCCHhHHHHHHHHHHhHHHHHHHhC--CCCceeEecch-hHHhhhCccccccceee
Q 019841 144 FLWTVDSVSYNGGVGSLVLDTIGHTFSQKYHNRVIQHEAGHFLIAYLVG--ILPKGYTLTSL-EALKKEGSLNVQAGTAF 220 (335)
Q Consensus 144 ~l~aiD~v~lgg~~~~llld~l~r~~s~~~r~RIA~HEAGHaLVAylLg--~PV~~~TI~p~-eal~~~G~~~~~gG~~f 220 (335)
+-.|+|++++|-+.. ..+.+++ +|++||+|||+|+.++. +||+++||.|. +.+++ | ...|+++
T Consensus 1870 I~~Al~Rq~~g~~~~---------~~~~~~~-~ia~yEiGhAvvq~~L~~~~pv~kISIy~~~~~~r~-~---~~yl~~w 1935 (2281)
T CHL00206 1870 IRSALHRQTWDLRSQ---------VRSVQDH-GILFYQIGRAVAQNVLLSNCPIDPISIYMKKKSCKE-G---DSYLYKW 1935 (2281)
T ss_pred HHHHHHHHHhhhhhc---------ccCcchh-hhhhhHHhHHHHHHhccCCCCcceEEEecCCccccC-c---ccceeEe
Confidence 345789999886532 1234444 48999999999999985 79999999642 22222 1 2335666
Q ss_pred ecchhhhhhccccCCHHHHHHHHHHHhhHHHHHHHHhCCc-------c--c-hhhHHHHHHHHHH
Q 019841 221 VDFEFLEEVNSGKVSATTLNRFSCIALAGVATEYLLYGYA-------E--G-GLADINKLDALLK 275 (335)
Q Consensus 221 ~~~~~~~~l~~g~~s~~~L~r~~~VlLAGrAAE~LvyG~a-------~--G-g~~Dl~~at~i~~ 275 (335)
..+. +..+++.++..+++++|||+|||++.|... + | ..+|...+-.++.
T Consensus 1936 yle~------~~~mkk~tiL~~Il~cLAGraAedlwf~~~~~~~n~It~yg~vEnD~~La~glLe 1994 (2281)
T CHL00206 1936 YFEL------GTSMKKLTILLYLLSCSAGSVAQDLWSLPGPDEKNGITSYGLVENDSDLVHGLLE 1994 (2281)
T ss_pred ecCC------cccCCHHHHHHHHHHHhhhhhhhhhccCcchhhhcCcccccchhhhhHHhHhHHH
Confidence 5432 257889999999999999999999999632 1 2 2567777766655
No 9
>cd06163 S2P-M50_PDZ_RseP-like RseP-like Site-2 proteases (S2P), zinc metalloproteases (MEROPS family M50A), cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. In Escherichia coli, the S2P homolog RseP is involved in the sigmaE pathway of extracytoplasmic stress responses. Also included in this group are such homologs as Bacillus subtilis YluC, Mycobacterium tuberculosis Rv2869c S2P, and Bordetella bronchiseptica HurP. Rv2869c S2P appears to have a role in the regulation of prokaryotic lipid biosynthesis and membrane composition and YluC of Bacillus has a role in transducing membrane stress. This group includes bacterial and eukaryotic S2P/M50s homologs with either one or two PDZ domains present. PDZ domains are believed to have a regulatory role. The RseP PDZ domain is required for the inhibitory reaction that prevents cleavage of its substrate, RseA.
Probab=96.95 E-value=0.0015 Score=59.40 Aligned_cols=24 Identities=38% Similarity=0.801 Sum_probs=21.3
Q ss_pred HHHHHHhHHHHHHHhCCCCceeEe
Q 019841 177 VIQHEAGHFLIAYLVGILPKGYTL 200 (335)
Q Consensus 177 IA~HEAGHaLVAylLg~PV~~~TI 200 (335)
|..||.||+++|...|.+|.+++|
T Consensus 12 v~iHElGH~~~Ar~~Gv~v~~f~i 35 (182)
T cd06163 12 IFVHELGHFLVAKLFGVKVEEFSI 35 (182)
T ss_pred HHHHHHHHHHHHHHcCCeeeEeee
Confidence 789999999999999999988443
No 10
>cd06164 S2P-M50_SpoIVFB_CBS SpoIVFB Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50B), regulates intramembrane proteolysis (RIP), and is involved in the pro-sigmaK pathway of bacterial spore formation. In this subgroup, SpoIVFB (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain. SpoIVFB is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA (bypass-of-forespore A), and SpoIVB (sporulation protein, stage IV cell wall formation, B locus). SpoIVFB is negatively regulated by SpoIVFA and BofA and activated by SpoIVB. It is thought that SpoIVFB, SpoIVFA, and BofA are located in the mother-cell membrane that surrounds the forespore and that SpoIVB is secreted from the forespore into the space between the two where it activates SpoIVFB. It has been proposed tha
Probab=96.50 E-value=0.004 Score=58.36 Aligned_cols=60 Identities=33% Similarity=0.353 Sum_probs=44.9
Q ss_pred HHHHHHHhHHHHHHHhCCCCceeEecchhHHhhhCccccccceeeecchhhhhhccccCCHHHHHHHHHHHhhHHHHHHH
Q 019841 176 RVIQHEAGHFLIAYLVGILPKGYTLTSLEALKKEGSLNVQAGTAFVDFEFLEEVNSGKVSATTLNRFSCIALAGVATEYL 255 (335)
Q Consensus 176 RIA~HEAGHaLVAylLg~PV~~~TI~p~eal~~~G~~~~~gG~~f~~~~~~~~l~~g~~s~~~L~r~~~VlLAGrAAE~L 255 (335)
-+..||-||+++|..+|.|++++++.|. | |++..++.. .++ .+...|.+||-++.-+
T Consensus 55 ~v~iHElgH~~~A~~~G~~v~~i~l~p~------G------g~~~~~~~~--------~~~---~~~~~IalAGPl~Nll 111 (227)
T cd06164 55 SVLLHELGHSLVARRYGIPVRSITLFLF------G------GVARLEREP--------ETP---GQEFVIAIAGPLVSLV 111 (227)
T ss_pred HHHHHHHHHHHHHHHcCCeECeEEEEee------e------EEEEecCCC--------CCH---HHHhhhhhhHHHHHHH
Confidence 4789999999999999999999999986 4 444332211 132 4567899999999877
Q ss_pred HhC
Q 019841 256 LYG 258 (335)
Q Consensus 256 vyG 258 (335)
...
T Consensus 112 la~ 114 (227)
T cd06164 112 LAL 114 (227)
T ss_pred HHH
Confidence 654
No 11
>cd06161 S2P-M50_SpoIVFB SpoIVFB Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50B), regulates intramembrane proteolysis (RIP), and is involved in the pro-sigmaK pathway of bacterial spore formation. SpoIVFB (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA (bypass-of-forespore A), and SpoIVB (sporulation protein, stage IV cell wall formation, B locus). SpoIVFB is negatively regulated by SpoIVFA and BofA and activated by SpoIVB. It is thought that SpoIVFB, SpoIVFA, and BofA are located in the mother-cell membrane that surrounds the forespore and that SpoIVB is secreted from the forespore into the space between the two where it activates SpoIVFB.
Probab=96.21 E-value=0.0054 Score=56.49 Aligned_cols=60 Identities=38% Similarity=0.458 Sum_probs=43.8
Q ss_pred HHHHHHHhHHHHHHHhCCCCceeEecchhHHhhhCccccccceeeecchhhhhhccccCCHHHHHHHHHHHhhHHHHHHH
Q 019841 176 RVIQHEAGHFLIAYLVGILPKGYTLTSLEALKKEGSLNVQAGTAFVDFEFLEEVNSGKVSATTLNRFSCIALAGVATEYL 255 (335)
Q Consensus 176 RIA~HEAGHaLVAylLg~PV~~~TI~p~eal~~~G~~~~~gG~~f~~~~~~~~l~~g~~s~~~L~r~~~VlLAGrAAE~L 255 (335)
-+..||-||+++|..+|.|++++++.|. | |....+.. .. + -.+...|.+||-.+.-+
T Consensus 40 ~v~iHElgH~~~A~~~G~~v~~i~l~p~------G------g~~~~~~~-------~~-~---~~~~~lIalAGPl~n~~ 96 (208)
T cd06161 40 SVLLHELGHALVARRYGIRVRSITLLPF------G------GVAELEEE-------PE-T---PKEEFVIALAGPLVSLL 96 (208)
T ss_pred HHHHHHHHHHHHHHHcCCCccceEEEee------e------eeeeeccC-------CC-C---hhHheeeeeehHHHHHH
Confidence 4789999999999999999999999986 4 32222211 11 2 24566788999999877
Q ss_pred HhC
Q 019841 256 LYG 258 (335)
Q Consensus 256 vyG 258 (335)
+..
T Consensus 97 la~ 99 (208)
T cd06161 97 LAG 99 (208)
T ss_pred HHH
Confidence 654
No 12
>TIGR00054 RIP metalloprotease RseP. A model that detects fragments as well matches a number of members of the PEPTIDASE FAMILY S2C. The region of match appears not to overlap the active site domain.
Probab=95.94 E-value=0.0066 Score=61.52 Aligned_cols=22 Identities=45% Similarity=0.653 Sum_probs=19.9
Q ss_pred HHHHHHHhHHHHHHHhCCCCce
Q 019841 176 RVIQHEAGHFLIAYLVGILPKG 197 (335)
Q Consensus 176 RIA~HEAGHaLVAylLg~PV~~ 197 (335)
-|..||.||+|+|...|..|.+
T Consensus 16 ~v~~HE~gH~~~a~~~g~~v~~ 37 (420)
T TIGR00054 16 LIFVHELGHFLAARLCGIKVER 37 (420)
T ss_pred HHHHHhHHHHHHHHHcCCEEEE
Confidence 3889999999999999988875
No 13
>PRK10779 zinc metallopeptidase RseP; Provisional
Probab=95.81 E-value=0.01 Score=60.63 Aligned_cols=26 Identities=27% Similarity=0.523 Sum_probs=23.4
Q ss_pred HHHHHHHhHHHHHHHhCCCCceeEec
Q 019841 176 RVIQHEAGHFLIAYLVGILPKGYTLT 201 (335)
Q Consensus 176 RIA~HEAGHaLVAylLg~PV~~~TI~ 201 (335)
-|.+||-||||+|.+.|+.|.+++|.
T Consensus 17 li~vHElGHfl~Ar~~gv~V~~FsiG 42 (449)
T PRK10779 17 LITVHEFGHFWVARRCGVRVERFSIG 42 (449)
T ss_pred HHHHHHHHHHHHHHHcCCeeeEEEee
Confidence 38899999999999999999887775
No 14
>PF02163 Peptidase_M50: Peptidase family M50; InterPro: IPR008915 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This entry contains metallopeptidases belonging to MEROPS peptidase family M50 (S2P protease family, clan MM). Members of the M50 metallopeptidase family include: mammalian sterol-regulatory element binding protein (SREBP) site 2 protease, Escherichia coli protease EcfE, stage IV sporulation protein FB and various hypothetical bacterial and eukaryotic homologues. A number of proteins are classified as non-peptidase homologues as they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity.; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 3B4R_A 3ID4_A 3ID2_A 2ZPL_B 3ID1_A 2ZPM_A 3ID3_B 2HGA_A.
Probab=95.57 E-value=0.012 Score=52.42 Aligned_cols=25 Identities=32% Similarity=0.359 Sum_probs=18.0
Q ss_pred HHHHHHhHHHHHHHhCCCCceeEec
Q 019841 177 VIQHEAGHFLIAYLVGILPKGYTLT 201 (335)
Q Consensus 177 IA~HEAGHaLVAylLg~PV~~~TI~ 201 (335)
+..||.||+++|+..|+++.++++.
T Consensus 10 i~~HE~gH~~~a~~~G~~~~~~~~~ 34 (192)
T PF02163_consen 10 IVLHELGHALAARLYGDKVPRFEGG 34 (192)
T ss_dssp HHHHHHHHHHHHHTTT--B--EEE-
T ss_pred ccccccccccccccccccccccccc
Confidence 6899999999999999988888543
No 15
>cd05709 S2P-M50 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. The domain core structure appears to contain at least three transmembrane helices with a catalytic zinc atom coordinated by three conserved residues contained within the consensus sequence HExxH, together with a conserved aspartate residue. The S2P/M50 family of RIP proteases is widely distributed; in eukaryotic cells, they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum (ER) stress responses. In sterol-depleted mammalian cells, a two-step proteolytic process releases the N-terminal domains of sterol regulatory element-bindin
Probab=95.46 E-value=0.011 Score=52.42 Aligned_cols=24 Identities=33% Similarity=0.472 Sum_probs=20.2
Q ss_pred HHHHHHhHHHHHHHhCCCCceeEe
Q 019841 177 VIQHEAGHFLIAYLVGILPKGYTL 200 (335)
Q Consensus 177 IA~HEAGHaLVAylLg~PV~~~TI 200 (335)
+..||.||+++|+..|+++.+.++
T Consensus 11 i~iHE~gH~~~A~~~G~~~~~~~~ 34 (180)
T cd05709 11 VTVHELGHALVARRLGVKVARFSG 34 (180)
T ss_pred HHHHHHHHHHHHHHcCCCchheee
Confidence 789999999999999997755443
No 16
>PF13398 Peptidase_M50B: Peptidase M50B-like
Probab=95.32 E-value=0.02 Score=52.58 Aligned_cols=27 Identities=41% Similarity=0.411 Sum_probs=25.3
Q ss_pred HHHHHHhHHHHHHHhCCCCceeEecch
Q 019841 177 VIQHEAGHFLIAYLVGILPKGYTLTSL 203 (335)
Q Consensus 177 IA~HEAGHaLVAylLg~PV~~~TI~p~ 203 (335)
+..||.||++++.+.|-.++++++.|.
T Consensus 25 t~~HE~gHal~a~l~G~~v~~i~l~~~ 51 (200)
T PF13398_consen 25 TFVHELGHALAALLTGGRVKGIVLFPD 51 (200)
T ss_pred HHHHHHHHHHHHHHhCCCcceEEEEeC
Confidence 799999999999999999999999873
No 17
>cd06162 S2P-M50_PDZ_SREBP Sterol regulatory element-binding protein (SREBP) Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50A), regulates intramembrane proteolysis (RIP) of SREBP and is part of a signal transduction mechanism involved in sterol and lipid metabolism. In sterol-depleted mammalian cells, a two-step proteolytic process releases the N-terminal domains of SREBPs from membranes of the endoplasmic reticulum (ER). These domains translocate into the nucleus, where they activate genes of cholesterol and fatty acid biosynthesis. The first cleavage occurs at Site-1 within the ER lumen to generate an intermediate that is subsequently released from the membrane by cleavage at Site-2, which lies within the first transmembrane domain. It is the second proteolytic step that is carried out by the SREBP Site-2 protease (S2P) which is present in this CD family. This group appears to be limited to eumetazoan proteins and contains one PDZ domain.
Probab=94.37 E-value=0.072 Score=51.77 Aligned_cols=66 Identities=21% Similarity=0.164 Sum_probs=44.3
Q ss_pred HHHHHHhHHHHHHHhCCCCceeEecchhHHhhhCccccccceeeecchhhhhhccccCCHHHHHHHHHHHhhHHHHHHHH
Q 019841 177 VIQHEAGHFLIAYLVGILPKGYTLTSLEALKKEGSLNVQAGTAFVDFEFLEEVNSGKVSATTLNRFSCIALAGVATEYLL 256 (335)
Q Consensus 177 IA~HEAGHaLVAylLg~PV~~~TI~p~eal~~~G~~~~~gG~~f~~~~~~~~l~~g~~s~~~L~r~~~VlLAGrAAE~Lv 256 (335)
+..||-||+++|...|++|+++.+.+.- -..+| |.++.+++ + ...++ .+++.|.+||.++.-+.
T Consensus 138 vvvHElgHal~A~~~gi~V~~iGl~l~~--------~~pGa--~ve~~~e~-~--~~~~~---~~~l~Ia~AGp~~NlvL 201 (277)
T cd06162 138 GVVHEMGHGVAAVREQVRVNGFGIFFFI--------IYPGA--YVDLFTDH-L--NLISP---VQQLRIFCAGVWHNFVL 201 (277)
T ss_pred HHHHHHHHHHHHHHcCCeeceEEEeeee--------ccCee--EEeecccc-c--ccCCh---hhhhheehhhHHHHHHH
Confidence 5699999999999999999999877540 01133 44443211 1 12333 34778999999988766
Q ss_pred hC
Q 019841 257 YG 258 (335)
Q Consensus 257 yG 258 (335)
-.
T Consensus 202 a~ 203 (277)
T cd06162 202 GL 203 (277)
T ss_pred HH
Confidence 54
No 18
>cd06158 S2P-M50_like_1 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the S2P/M50 family of RIP proteases use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. In eukaryotic cells they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum stress responses. In prokaryotes they regulate such processes as sporulation, cell division, stress response, and cell differentiation. This group includes bacterial, eukaryotic, and Archaeal S2P/M50s homologs with a minimal core protein and no PDZ domains.
Probab=93.84 E-value=0.071 Score=48.30 Aligned_cols=77 Identities=19% Similarity=0.222 Sum_probs=42.7
Q ss_pred HHHHHHhHHHHHHHhCCCCc----eeEecchhHHhhhCcccc----ccceeeecchhhhhhccccCCHHHHHHHHHHHhh
Q 019841 177 VIQHEAGHFLIAYLVGILPK----GYTLTSLEALKKEGSLNV----QAGTAFVDFEFLEEVNSGKVSATTLNRFSCIALA 248 (335)
Q Consensus 177 IA~HEAGHaLVAylLg~PV~----~~TI~p~eal~~~G~~~~----~gG~~f~~~~~~~~l~~g~~s~~~L~r~~~VlLA 248 (335)
+..||-||+++|+..|++.. ..|+.|..-+---|+.-. ..|.++..|.+... ... +..-.+...|.+|
T Consensus 12 i~~HE~aHa~~A~~~Gd~t~~~~Grltlnp~~hid~~g~l~~~~~~~~~~G~a~p~~~~~---~~~-~~~r~~~~~valA 87 (181)
T cd06158 12 ITLHEFAHAYVAYRLGDPTARRAGRLTLNPLAHIDPIGTIILPLLLPFLFGWAKPVPVNP---RNF-KNPRRGMLLVSLA 87 (181)
T ss_pred HHHHHHHHHHHHHHcCCcHHHHcCceecCcHHhcCcchHHHHHHHHHhCeEEecccccCh---Hhh-cccHhhHhhhhhh
Confidence 67999999999999998643 467777521111111100 00333443332111 111 1122456679999
Q ss_pred HHHHHHHHh
Q 019841 249 GVATEYLLY 257 (335)
Q Consensus 249 GrAAE~Lvy 257 (335)
|-++.-+..
T Consensus 88 GP~~n~~la 96 (181)
T cd06158 88 GPLSNLLLA 96 (181)
T ss_pred hHHHHHHHH
Confidence 999987554
No 19
>cd06160 S2P-M50_like_2 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the S2P/M50 family of RIP proteases use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. In eukaryotic cells they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum stress responses. In prokaryotes they regulate such processes as sporulation, cell division, stress response, and cell differentiation. This group includes bacterial, eukaryotic, and Archaeal S2P/M50s homologs with additional putative N- and C-terminal transmembrane spanning regions, relative to the core protein, and no PDZ domains.
Probab=92.58 E-value=0.11 Score=47.45 Aligned_cols=27 Identities=26% Similarity=0.244 Sum_probs=24.9
Q ss_pred HHHHHHHhHHHHHHHhCCCCceeEecc
Q 019841 176 RVIQHEAGHFLIAYLVGILPKGYTLTS 202 (335)
Q Consensus 176 RIA~HEAGHaLVAylLg~PV~~~TI~p 202 (335)
-+..||.||+++|...|+++.+..+.|
T Consensus 43 ~l~iHElgH~~~A~~~G~~~~~~~l~P 69 (183)
T cd06160 43 ILGIHEMGHYLAARRHGVKASLPYFIP 69 (183)
T ss_pred HHHHHHHHHHHHHHHCCCCccceeeee
Confidence 478999999999999999999988888
No 20
>cd06159 S2P-M50_PDZ_Arch Uncharacterized Archaeal homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the S2P/M50 family of RIP proteases use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. In eukaryotic cells they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum stress responses. In prokaryotes they regulate such processes as sporulation, cell division, stress response, and cell differentiation. This group appears to be limited to Archaeal S2P/M50s homologs with additional putative N-terminal transmembrane spanning regions, relative to the core protein, and either one or two PDZ domains present.
Probab=87.32 E-value=0.28 Score=47.20 Aligned_cols=66 Identities=26% Similarity=0.211 Sum_probs=39.7
Q ss_pred HHHHHHhHHHHHHHhCCCCceeEecchhHHhhhCccccccceeeecchhhhhhccccCCHHHHHHHHHHHhhHHHHHHHH
Q 019841 177 VIQHEAGHFLIAYLVGILPKGYTLTSLEALKKEGSLNVQAGTAFVDFEFLEEVNSGKVSATTLNRFSCIALAGVATEYLL 256 (335)
Q Consensus 177 IA~HEAGHaLVAylLg~PV~~~TI~p~eal~~~G~~~~~gG~~f~~~~~~~~l~~g~~s~~~L~r~~~VlLAGrAAE~Lv 256 (335)
+..||-||+++|...|++|+++.+.-. . . --|| |..++.. +..+.+ -.++..|.+||-.+.-+.
T Consensus 121 v~iHElgHa~~Ar~~G~~V~~iGl~l~------~-i-p~Gg--~v~~~~~---~~~~~~---~~~~~~Ia~AGP~~Nlvl 184 (263)
T cd06159 121 VVVHELSHGILARVEGIKVKSGGLLLL------I-I-PPGA--FVEPDEE---ELNKAD---RRIRLRIFAAGVTANFVV 184 (263)
T ss_pred HHHHHHHHHHHHHHcCCEECchhHHHH------h-h-hcEE--EEEecch---hhccCC---hhheeeeeeehHHHHHHH
Confidence 779999999999999999887654200 0 0 0123 4443221 111122 235667888998888655
Q ss_pred hC
Q 019841 257 YG 258 (335)
Q Consensus 257 yG 258 (335)
..
T Consensus 185 a~ 186 (263)
T cd06159 185 AL 186 (263)
T ss_pred HH
Confidence 43
No 21
>PF14247 DUF4344: Domain of unknown function (DUF4344)
Probab=78.65 E-value=1.5 Score=41.39 Aligned_cols=22 Identities=36% Similarity=0.410 Sum_probs=17.3
Q ss_pred HHHHHHHhHHHHHHHhCCCCcee
Q 019841 176 RVIQHEAGHFLIAYLVGILPKGY 198 (335)
Q Consensus 176 RIA~HEAGHaLVAylLg~PV~~~ 198 (335)
-|.+||.||+|+..+ ++||.|-
T Consensus 94 ~~l~HE~GHAlI~~~-~lPv~Gr 115 (220)
T PF14247_consen 94 FTLYHELGHALIDDL-DLPVLGR 115 (220)
T ss_pred HHHHHHHHHHHHHHh-cCCcccc
Confidence 478999999999865 4577663
No 22
>PF00413 Peptidase_M10: Matrixin This Prosite motif covers only the active site.; InterPro: IPR001818 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M10 (clan MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA. Sequences having this domain are extracellular metalloproteases, such as collagenase and stromelysin, which degrade the extracellular matrix, are known as matrixins. They are zinc-dependent, calcium-activated proteases synthesised as inactive precursors (zymogens), which are proteolytically cleaved to yield the active enzyme [, ]. All matrixins and related proteins possess 2 domains: an N-terminal domain, and a zinc-binding active site domain. The N-terminal domain peptide, cleaved during the activation step, includes a conserved PRCGVPDV octapeptide, known as the cysteine switch, whose Cys residue chelates the active site zinc atom, rendering the enzyme inactive [, ]. The active enzyme degrades components of the extracellular matrix, playing a role in the initial steps of tissue remodelling during morphogenesis, wound healing, angiogenesis and tumour invasion [, ].; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis, 0031012 extracellular matrix; PDB: 1Q3A_C 3V96_B 1HV5_D 1CXV_A 1SRP_A 1FBL_A 1ZVX_A 1JH1_A 1I76_A 2OY4_A ....
Probab=76.53 E-value=1.1 Score=38.14 Aligned_cols=17 Identities=41% Similarity=0.425 Sum_probs=14.0
Q ss_pred CHhHHHHHHHHHHhHHH
Q 019841 170 SQKYHNRVIQHEAGHFL 186 (335)
Q Consensus 170 s~~~r~RIA~HEAGHaL 186 (335)
+..+...|+.||-||+|
T Consensus 101 ~~~~~~~v~~HEiGHaL 117 (154)
T PF00413_consen 101 SGNDLQSVAIHEIGHAL 117 (154)
T ss_dssp SSEEHHHHHHHHHHHHT
T ss_pred hhhhhhhhhhhcccccc
Confidence 34567789999999985
No 23
>cd04279 ZnMc_MMP_like_1 Zinc-dependent metalloprotease; MMP_like sub-family 1. A group of bacterial, archaeal, and fungal metalloproteinase domains similar to matrix metalloproteinases and astacin.
Probab=71.44 E-value=2.6 Score=36.45 Aligned_cols=21 Identities=24% Similarity=0.251 Sum_probs=16.1
Q ss_pred HhHHHHHHHHHHhHHHHHHHh
Q 019841 171 QKYHNRVIQHEAGHFLIAYLV 191 (335)
Q Consensus 171 ~~~r~RIA~HEAGHaLVAylL 191 (335)
..+.+.|+.||-||+|--.-.
T Consensus 101 ~~~~~~~~~HEiGHaLGL~H~ 121 (156)
T cd04279 101 AENLQAIALHELGHALGLWHH 121 (156)
T ss_pred chHHHHHHHHHhhhhhcCCCC
Confidence 457789999999999754443
No 24
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic su
Probab=69.16 E-value=26 Score=30.16 Aligned_cols=68 Identities=19% Similarity=0.268 Sum_probs=44.6
Q ss_pred hhHHHHHHHH--HHhcCCCHHHHHHHHH-----HHHHHHHHHHHHcHHHHHHHHHHHHcc-cchHHHHHHHHhhhc
Q 019841 264 LADINKLDAL--LKGLGFTQKKADSQVR-----WSLLNTVLLLRRHKGARAKLAEAMTMG-KSLGSCIDIIEDNID 331 (335)
Q Consensus 264 ~~Dl~~at~i--~~~lG~s~~~~d~evR-----~A~~~A~~LLr~hr~aleaLaeaLle~-esl~~Ci~~Ie~~~~ 331 (335)
.+|+..+..| ++.+|||-+++..-+. +.......+|+++.+.++...+.|.+. +.|.++++.+++...
T Consensus 41 ~~~v~~l~~I~~lr~~GfsL~eI~~ll~~~~~~~~~~~~~~~l~~k~~~i~~~i~~L~~~~~~L~~~i~~~~~~~~ 116 (131)
T cd04786 41 PETVWVLEIISSAQQAGFSLDEIRQLLPADASNWQHDELLAALERKVADIEALEARLAQNKAQLLVLIDLIESKPD 116 (131)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 3566666655 5668888776554332 123455678888888887777777774 667888777776543
No 25
>KOG2921 consensus Intramembrane metalloprotease (sterol-regulatory element-binding protein (SREBP) protease) [Posttranslational modification, protein turnover, chaperones]
Probab=68.58 E-value=3.8 Score=42.07 Aligned_cols=25 Identities=36% Similarity=0.553 Sum_probs=21.4
Q ss_pred HHHHHHhHHHHHHHhCCCCceeEec
Q 019841 177 VIQHEAGHFLIAYLVGILPKGYTLT 201 (335)
Q Consensus 177 IA~HEAGHaLVAylLg~PV~~~TI~ 201 (335)
..+||-||+|+|..-|.||.++-|-
T Consensus 134 ~vvHElGHalAA~segV~vngfgIf 158 (484)
T KOG2921|consen 134 VVVHELGHALAAASEGVQVNGFGIF 158 (484)
T ss_pred HHHHHhhHHHHHHhcCceeeeeEEE
Confidence 3589999999999999998887654
No 26
>PF04298 Zn_peptidase_2: Putative neutral zinc metallopeptidase; InterPro: IPR007395 Members of this family of bacterial proteins are described as hypothetical proteins or zinc-dependent proteases. The majority have a HExxH zinc-binding motif characteristic of neutral zinc metallopeptidases, however there is no evidence to support their function as metallopeptidases.
Probab=68.26 E-value=2.7 Score=39.85 Aligned_cols=13 Identities=38% Similarity=0.562 Sum_probs=10.9
Q ss_pred HHHHHHHhHHHHH
Q 019841 176 RVIQHEAGHFLIA 188 (335)
Q Consensus 176 RIA~HEAGHaLVA 188 (335)
-||-||+|||+=-
T Consensus 91 aVAAHEvGHAiQ~ 103 (222)
T PF04298_consen 91 AVAAHEVGHAIQH 103 (222)
T ss_pred HHHHHHHhHHHhc
Confidence 4899999999853
No 27
>cd04268 ZnMc_MMP_like Zinc-dependent metalloprotease, MMP_like subfamily. This group contains matrix metalloproteinases (MMPs), serralysins, and the astacin_like family of proteases.
Probab=67.87 E-value=3.4 Score=35.54 Aligned_cols=20 Identities=25% Similarity=0.164 Sum_probs=15.4
Q ss_pred HhHHHHHHHHHHhHHHHHHH
Q 019841 171 QKYHNRVIQHEAGHFLIAYL 190 (335)
Q Consensus 171 ~~~r~RIA~HEAGHaLVAyl 190 (335)
..+...++.||-||+|--.-
T Consensus 91 ~~~~~~~~~HEiGHaLGL~H 110 (165)
T cd04268 91 GARLRNTAEHELGHALGLRH 110 (165)
T ss_pred HHHHHHHHHHHHHHHhcccc
Confidence 35678999999999975433
No 28
>COG0750 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]
Probab=64.90 E-value=4.8 Score=39.39 Aligned_cols=26 Identities=31% Similarity=0.562 Sum_probs=22.5
Q ss_pred HHHHHHHhHHHHHHHhCCCCceeEec
Q 019841 176 RVIQHEAGHFLIAYLVGILPKGYTLT 201 (335)
Q Consensus 176 RIA~HEAGHaLVAylLg~PV~~~TI~ 201 (335)
.|..||-||+|+++..+..|+++++.
T Consensus 15 lv~~he~gh~~~a~~~~~~v~~f~ig 40 (375)
T COG0750 15 LVFVHELGHFWVARRCGVKVERFSIG 40 (375)
T ss_pred HHHHHHHhhHHHHHhcCceeEEEEec
Confidence 58899999999999999877777765
No 29
>PF02031 Peptidase_M7: Streptomyces extracellular neutral proteinase (M7) family; InterPro: IPR000013 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M7 (snapalysin family, clan MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA. With a molecular weight of around 16kDa, Streptomyces extracellular neutral protease is one of the smallest known proteases []; it is capable of hydrolysing milk proteins []. The enzyme is synthesised as a proenzyme with a signal peptide, a propeptide and an active domain that contains the conserved HEXXH motif characteristic of metalloproteases. Although family M7 shows active site sequence similarity to other members, it differs in one major respect: the third zinc ligand appears to be an aspartate residue rather than the usual histidine.; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis, 0005576 extracellular region; PDB: 1C7K_A 1KUH_A.
Probab=64.68 E-value=4.7 Score=35.30 Aligned_cols=31 Identities=32% Similarity=0.464 Sum_probs=17.3
Q ss_pred cCCCCccccccccCCCCHhHHHHHHHHHHhHHH
Q 019841 154 NGGVGSLVLDTIGHTFSQKYHNRVIQHEAGHFL 186 (335)
Q Consensus 154 gg~~~~llld~l~r~~s~~~r~RIA~HEAGHaL 186 (335)
|.+.+.+.+|.-.. -.-..-||+.||-||.|
T Consensus 59 g~G~G~I~l~~~~~--qgy~~~RIaaHE~GHiL 89 (132)
T PF02031_consen 59 GLGSGYIFLDYQQN--QGYNSTRIAAHELGHIL 89 (132)
T ss_dssp SSS-EEEEEEHHHH--HHS-HHHHHHHHHHHHH
T ss_pred CCCcEEEEechHHh--hCCccceeeeehhcccc
Confidence 33444566664210 12345599999999975
No 30
>cd08316 Death_FAS_TNFRSF6 Death domain of FAS or TNF receptor superfamily member 6. Death Domain (DD) found in the FS7-associated cell surface antigen (FAS). FAS, also known as TNFRSF6 (TNF receptor superfamily member 6), APT1, CD95, FAS1, or APO-1, together with FADD (Fas-associating via Death Domain) and caspase 8, is an integral part of the death inducing signalling complex (DISC), which plays an important role in the induction of apoptosis and is activated by binding of the ligand FasL to FAS. FAS also plays a critical role in self-tolerance by eliminating cell types (autoreactive T and B cells) that contribute to autoimmunity. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in sign
Probab=63.69 E-value=42 Score=27.73 Aligned_cols=62 Identities=23% Similarity=0.250 Sum_probs=42.5
Q ss_pred HHHHHHHHhcCCCHHHHHHHH----HHHHHHHHHHHHHcHH------HHHHHHHHHHcccchHHHHHHHHhhh
Q 019841 268 NKLDALLKGLGFTQKKADSQV----RWSLLNTVLLLRRHKG------ARAKLAEAMTMGKSLGSCIDIIEDNI 330 (335)
Q Consensus 268 ~~at~i~~~lG~s~~~~d~ev----R~A~~~A~~LLr~hr~------aleaLaeaLle~esl~~Ci~~Ie~~~ 330 (335)
.+..++++.+|+|+.+||.-. +...++.+++|+..+. +++.|.++|.. --+..|-+.|++.+
T Consensus 21 ~~wK~faR~lglse~~Id~I~~~~~~d~~Eq~~qmL~~W~~~~G~~a~~~~Li~aLr~-~~l~~~Ad~I~~~l 92 (97)
T cd08316 21 KDVKKFVRKSGLSEPKIDEIKLDNPQDTAEQKVQLLRAWYQSHGKTGAYRTLIKTLRK-AKLCTKADKIQDII 92 (97)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHcCCCChHHHHHHHHHHHHHHhCCCchHHHHHHHHHH-ccchhHHHHHHHHH
Confidence 457778899999998887532 2457788888876544 57888877766 44555555566554
No 31
>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=60.21 E-value=4.1 Score=35.34 Aligned_cols=17 Identities=35% Similarity=0.239 Sum_probs=13.9
Q ss_pred HhHHHHHHHHHHhHHHH
Q 019841 171 QKYHNRVIQHEAGHFLI 187 (335)
Q Consensus 171 ~~~r~RIA~HEAGHaLV 187 (335)
..+...|+.||-||+|-
T Consensus 104 ~~~~~~~~~HEiGHaLG 120 (157)
T cd04278 104 GTDLFSVAAHEIGHALG 120 (157)
T ss_pred cchHHHHHHHHhccccc
Confidence 45678899999999953
No 32
>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=59.38 E-value=6 Score=35.21 Aligned_cols=19 Identities=37% Similarity=0.394 Sum_probs=15.2
Q ss_pred HhHHHHHHHHHHhHHHHHH
Q 019841 171 QKYHNRVIQHEAGHFLIAY 189 (335)
Q Consensus 171 ~~~r~RIA~HEAGHaLVAy 189 (335)
..+...++.||-||+|-=.
T Consensus 110 g~~~~~t~~HEiGHaLGL~ 128 (186)
T cd04277 110 GSYGYQTIIHEIGHALGLE 128 (186)
T ss_pred ChhhHHHHHHHHHHHhcCC
Confidence 4667889999999998543
No 33
>PF05572 Peptidase_M43: Pregnancy-associated plasma protein-A; InterPro: IPR008754 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase M43 (cytophagalysin family, clan MA(M)), subfamily M43. The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH. The type example of this family is the pregnancy-associated plasma protein A (PAPP-A), which cleaves insulin-like growth factor (IGF) binding protein-4 (IGFBP-4), causing a dramatic reduction in its affinity for IGF-I and -II. Through this mechanism, PAPP-A is a regulator of IGF bioactivity in several systems, including the Homo sapiens ovary and the cardiovascular system [, , , ].; PDB: 3LUN_A 3LUM_B 2J83_A 2CKI_A.
Probab=59.06 E-value=4.9 Score=35.56 Aligned_cols=21 Identities=38% Similarity=0.593 Sum_probs=14.0
Q ss_pred CHhHHHHHHHHHHhHHHHHHH
Q 019841 170 SQKYHNRVIQHEAGHFLIAYL 190 (335)
Q Consensus 170 s~~~r~RIA~HEAGHaLVAyl 190 (335)
++....+++.||.||+|-=+-
T Consensus 65 ~~~~~g~TltHEvGH~LGL~H 85 (154)
T PF05572_consen 65 SQYNFGKTLTHEVGHWLGLYH 85 (154)
T ss_dssp TTS-SSHHHHHHHHHHTT---
T ss_pred Cccccccchhhhhhhhhcccc
Confidence 355667999999999985444
No 34
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=57.16 E-value=61 Score=26.89 Aligned_cols=66 Identities=14% Similarity=0.088 Sum_probs=44.6
Q ss_pred hhHHHHHHHH--HHhcCCCHHHHHHHHHH-------HHHHHHHHHHHcHHHHHHHHHHHHcc-cchHHHHHHHHhh
Q 019841 264 LADINKLDAL--LKGLGFTQKKADSQVRW-------SLLNTVLLLRRHKGARAKLAEAMTMG-KSLGSCIDIIEDN 329 (335)
Q Consensus 264 ~~Dl~~at~i--~~~lG~s~~~~d~evR~-------A~~~A~~LLr~hr~aleaLaeaLle~-esl~~Ci~~Ie~~ 329 (335)
.+|+..+..| ++.+|||-+++..-... .......+|++++..++.=-+.|.+. ..+..++..++++
T Consensus 40 ~~d~~~l~~I~~lr~~G~sl~eI~~~l~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~~~~~l~~~~~~~~~~ 115 (116)
T cd04769 40 AQHVECLRFIKEARQLGFTLAELKAIFAGHEGRAVLPWPHLQQALEDKKQEIRAQITELQQLLARLDAFEASLKDA 115 (116)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHhccccCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 4677777766 57799998877654432 22455678888888877777776664 5577777766654
No 35
>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=54.07 E-value=12 Score=33.84 Aligned_cols=26 Identities=27% Similarity=0.158 Sum_probs=18.2
Q ss_pred hHHHHHHHHHHhHHHHHHHhC-CCCce
Q 019841 172 KYHNRVIQHEAGHFLIAYLVG-ILPKG 197 (335)
Q Consensus 172 ~~r~RIA~HEAGHaLVAylLg-~PV~~ 197 (335)
.+...++.||-||+|--+-.- -|-+.
T Consensus 90 ~~~~~~i~HElgHaLG~~HEh~rpdrd 116 (198)
T cd04327 90 PEFSRVVLHEFGHALGFIHEHQSPAAN 116 (198)
T ss_pred hhHHHHHHHHHHHHhcCcccccCCCCC
Confidence 345679999999998766553 24444
No 36
>COG0501 HtpX Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]
Probab=53.62 E-value=8.2 Score=36.35 Aligned_cols=32 Identities=19% Similarity=0.222 Sum_probs=24.5
Q ss_pred cccccccCCCCHhHHHHHHHHHHhHHHHHHHh
Q 019841 160 LVLDTIGHTFSQKYHNRVIQHEAGHFLIAYLV 191 (335)
Q Consensus 160 llld~l~r~~s~~~r~RIA~HEAGHaLVAylL 191 (335)
.+-+.+-+.++++|-+-|.-||-||..-.+..
T Consensus 143 ~vt~gLl~~l~~dEl~aVlaHElgHi~~rd~~ 174 (302)
T COG0501 143 VVTTGLLDLLNDDELEAVLAHELGHIKNRHTL 174 (302)
T ss_pred EecHHHHhhCCHHHHHHHHHHHHHHHhcccHH
Confidence 34445555678999999999999998766654
No 37
>smart00005 DEATH DEATH domain, found in proteins involved in cell death (apoptosis). Alpha-helical domain present in a variety of proteins with apoptotic functions. Some (but not all) of these domains form homotypic and heterotypic dimers.
Probab=49.93 E-value=96 Score=23.79 Aligned_cols=58 Identities=19% Similarity=0.223 Sum_probs=37.3
Q ss_pred HHHHHHHhcCCCHHHHHHHHHH----HHHHHHHHHHHcHH------HHHHHHHHHHcccchHHHHHHHH
Q 019841 269 KLDALLKGLGFTQKKADSQVRW----SLLNTVLLLRRHKG------ARAKLAEAMTMGKSLGSCIDIIE 327 (335)
Q Consensus 269 ~at~i~~~lG~s~~~~d~evR~----A~~~A~~LLr~hr~------aleaLaeaLle~esl~~Ci~~Ie 327 (335)
.-..+++.+||+...++.-... ...+++.+|+.-+. .++.|.++|.+-. ..++.+.|+
T Consensus 19 ~W~~la~~Lg~~~~~i~~i~~~~~~~~~~~~~~lL~~W~~~~g~~at~~~L~~aL~~~~-~~d~a~~i~ 86 (88)
T smart00005 19 DWRELARKLGLSEADIDQIRTEAPRDLAEQSVQLLRLWEQREGKNATLGTLLEALRKMG-RDDAVELLR 86 (88)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHccchhhHHHHHHHHHHHcC-hHHHHHHHh
Confidence 3566788899998877752222 34788999876654 6677777776632 334444443
No 38
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=45.48 E-value=1e+02 Score=22.37 Aligned_cols=42 Identities=14% Similarity=0.177 Sum_probs=27.5
Q ss_pred HHhcCCCHHHHHHHHH------HHHHHHHHHHHHcHHHHHHHHHHHHc
Q 019841 274 LKGLGFTQKKADSQVR------WSLLNTVLLLRRHKGARAKLAEAMTM 315 (335)
Q Consensus 274 ~~~lG~s~~~~d~evR------~A~~~A~~LLr~hr~aleaLaeaLle 315 (335)
++.+|||-+++..-.. ........+++++.+.+++=-+.|.+
T Consensus 10 ~r~lGfsL~eI~~~l~l~~~~~~~~~~~~~~l~~~~~~i~~~i~~L~~ 57 (65)
T PF09278_consen 10 LRELGFSLEEIRELLELYDQGDPPCADRRALLEEKLEEIEEQIAELQA 57 (65)
T ss_dssp HHHTT--HHHHHHHHHHCCSHCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHcCCCHHHHHHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5679999887776541 34556667888888887776666654
No 39
>smart00235 ZnMc Zinc-dependent metalloprotease. Neutral zinc metallopeptidases. This alignment represents a subset of known subfamilies. Highest similarity occurs in the HExxH zinc-binding site/ active site.
Probab=44.50 E-value=11 Score=31.63 Aligned_cols=17 Identities=41% Similarity=0.421 Sum_probs=12.6
Q ss_pred HHHHHHHhHHHHHHHhC
Q 019841 176 RVIQHEAGHFLIAYLVG 192 (335)
Q Consensus 176 RIA~HEAGHaLVAylLg 192 (335)
.++.||-||+|-..-..
T Consensus 88 ~~~~HEigHaLGl~H~~ 104 (140)
T smart00235 88 GVAAHELGHALGLYHEQ 104 (140)
T ss_pred ccHHHHHHHHhcCCcCC
Confidence 49999999998444333
No 40
>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=43.84 E-value=27 Score=27.35 Aligned_cols=25 Identities=24% Similarity=0.301 Sum_probs=18.6
Q ss_pred CCCHhHHHHHHHHHHhHHHHHHHhC
Q 019841 168 TFSQKYHNRVIQHEAGHFLIAYLVG 192 (335)
Q Consensus 168 ~~s~~~r~RIA~HEAGHaLVAylLg 192 (335)
..++..++=++.||-||.+...--.
T Consensus 36 ~~~~~~~~f~laHELgH~~~~~~~~ 60 (122)
T PF06114_consen 36 NLSPERQRFTLAHELGHILLHHGDE 60 (122)
T ss_dssp SS-HHHHHHHHHHHHHHHHHHH-HH
T ss_pred CCCHHHHHHHHHHHHHHHHhhhccc
Confidence 3467888888999999999877654
No 41
>cd00203 ZnMc Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease.
Probab=40.81 E-value=15 Score=31.45 Aligned_cols=20 Identities=40% Similarity=0.384 Sum_probs=15.2
Q ss_pred hHHHHHHHHHHhHHHHHHHh
Q 019841 172 KYHNRVIQHEAGHFLIAYLV 191 (335)
Q Consensus 172 ~~r~RIA~HEAGHaLVAylL 191 (335)
.+-..++.||-||+|-.+--
T Consensus 94 ~~~~~~~~HElGH~LGl~H~ 113 (167)
T cd00203 94 KEGAQTIAHELGHALGFYHD 113 (167)
T ss_pred ccchhhHHHHHHHHhCCCcc
Confidence 35678999999999865443
No 42
>PF13485 Peptidase_MA_2: Peptidase MA superfamily
Probab=40.01 E-value=32 Score=27.21 Aligned_cols=23 Identities=26% Similarity=0.525 Sum_probs=19.4
Q ss_pred CHhHHHHHHHHHHhHHHHHHHhC
Q 019841 170 SQKYHNRVIQHEAGHFLIAYLVG 192 (335)
Q Consensus 170 s~~~r~RIA~HEAGHaLVAylLg 192 (335)
+++.-.+++.||-+|.+.....+
T Consensus 21 ~~~~~~~~l~HE~~H~~~~~~~~ 43 (128)
T PF13485_consen 21 DEDWLDRVLAHELAHQWFGNYFG 43 (128)
T ss_pred CHHHHHHHHHHHHHHHHHHHHcC
Confidence 45656799999999999998876
No 43
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=39.59 E-value=1.3e+02 Score=24.17 Aligned_cols=51 Identities=20% Similarity=0.294 Sum_probs=33.3
Q ss_pred hHHHHHHHH--HHhcCCCHHHHHHHHH-HHHHHHHHHHHHcHHHHHHHHHHHHc
Q 019841 265 ADINKLDAL--LKGLGFTQKKADSQVR-WSLLNTVLLLRRHKGARAKLAEAMTM 315 (335)
Q Consensus 265 ~Dl~~at~i--~~~lG~s~~~~d~evR-~A~~~A~~LLr~hr~aleaLaeaLle 315 (335)
+|+..+..| ++.+|||-+++..-.. ....+...+|+++.+.+++=.+.|.+
T Consensus 42 ~~~~~l~~I~~lr~~G~~l~eI~~~l~~~~~~~~~~~l~~~~~~l~~~i~~l~~ 95 (97)
T cd04782 42 EQFEQLDIILLLKELGISLKEIKDYLDNRNPDELIELLKKQEKEIKEEIEELQK 95 (97)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 555555544 5778999877665433 23345677888888887776666654
No 44
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain),
Probab=39.53 E-value=1.9e+02 Score=22.93 Aligned_cols=58 Identities=22% Similarity=0.232 Sum_probs=36.8
Q ss_pred HHHHHHhcCCCHHHHHHHH----HHHHHHHHHHHHHc------HHHHHHHHHHHHcccchHHHHHHHHh
Q 019841 270 LDALLKGLGFTQKKADSQV----RWSLLNTVLLLRRH------KGARAKLAEAMTMGKSLGSCIDIIED 328 (335)
Q Consensus 270 at~i~~~lG~s~~~~d~ev----R~A~~~A~~LLr~h------r~aleaLaeaLle~esl~~Ci~~Ie~ 328 (335)
-.++++.+|||+..++.-. +...++++++|+.- ...++.|.++|.+-.- ...-+.|++
T Consensus 16 Wk~laR~LGlse~~Id~i~~~~~~~~~eq~~~mL~~W~~~~g~~At~~~L~~aL~~~~l-~~~ad~i~~ 83 (86)
T cd08306 16 WRKLARKLGLSETKIESIEEAHPRNLREQVRQSLREWKKIKKKEAKVADLIKALRDCQL-NLVADLVEE 83 (86)
T ss_pred HHHHHHHcCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHhHCcchHHHHHHHHHHHcCc-HHHHHHHHH
Confidence 4567788999998887521 13457888888643 3466788888877433 333344444
No 45
>PRK02391 heat shock protein HtpX; Provisional
Probab=38.37 E-value=22 Score=34.72 Aligned_cols=28 Identities=14% Similarity=0.139 Sum_probs=22.1
Q ss_pred ccccCCCCHhHHHHHHHHHHhHHHHHHH
Q 019841 163 DTIGHTFSQKYHNRVIQHEAGHFLIAYL 190 (335)
Q Consensus 163 d~l~r~~s~~~r~RIA~HEAGHaLVAyl 190 (335)
|.+-+.++++|.+-|.-||-||.--.+.
T Consensus 122 ~gLl~~L~~~El~aVlaHElgHi~~~di 149 (296)
T PRK02391 122 TGLMRRLDPDELEAVLAHELSHVKNRDV 149 (296)
T ss_pred HHHHhhCCHHHHHHHHHHHHHHHHcCCH
Confidence 5566667899999999999999754443
No 46
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=38.25 E-value=1.3e+02 Score=24.09 Aligned_cols=51 Identities=18% Similarity=0.268 Sum_probs=33.1
Q ss_pred hHHHHHHHH--HHhcCCCHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHc
Q 019841 265 ADINKLDAL--LKGLGFTQKKADSQVRWSLLNTVLLLRRHKGARAKLAEAMTM 315 (335)
Q Consensus 265 ~Dl~~at~i--~~~lG~s~~~~d~evR~A~~~A~~LLr~hr~aleaLaeaLle 315 (335)
+|+..+..| ++.+|||-+++..-....-.....+|++++..++.=.+.|.+
T Consensus 42 ~~l~~l~~I~~lr~~G~~l~~I~~~l~~~~~~~~~~l~~~~~~l~~~i~~l~~ 94 (96)
T cd04768 42 AQLYQLQFILFLRELGFSLAEIKELLDTEMEELTAMLLEKKQAIQQKIDRLQQ 94 (96)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHhcCcHHHHHHHHHHHHHHHHHHHHHHh
Confidence 466666554 567899988776544432236677788888777776665543
No 47
>PF13582 Reprolysin_3: Metallo-peptidase family M12B Reprolysin-like; PDB: 3P24_C.
Probab=37.39 E-value=17 Score=29.76 Aligned_cols=12 Identities=42% Similarity=0.509 Sum_probs=10.5
Q ss_pred HHHHHHHhHHHH
Q 019841 176 RVIQHEAGHFLI 187 (335)
Q Consensus 176 RIA~HEAGHaLV 187 (335)
.+..||.||.|-
T Consensus 109 ~~~~HEiGH~lG 120 (124)
T PF13582_consen 109 DTFAHEIGHNLG 120 (124)
T ss_dssp THHHHHHHHHTT
T ss_pred eEeeehhhHhcC
Confidence 799999999863
No 48
>PRK05457 heat shock protein HtpX; Provisional
Probab=37.13 E-value=26 Score=34.01 Aligned_cols=22 Identities=23% Similarity=0.342 Sum_probs=18.3
Q ss_pred ccCCCCHhHHHHHHHHHHhHHH
Q 019841 165 IGHTFSQKYHNRVIQHEAGHFL 186 (335)
Q Consensus 165 l~r~~s~~~r~RIA~HEAGHaL 186 (335)
+-+.++++|.+-|.-||-||.-
T Consensus 125 Ll~~L~~~El~aVlAHElgHi~ 146 (284)
T PRK05457 125 LLQNMSRDEVEAVLAHEISHIA 146 (284)
T ss_pred HhhhCCHHHHHHHHHHHHHHHH
Confidence 4445689999999999999973
No 49
>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=37.04 E-value=1.2e+02 Score=24.06 Aligned_cols=46 Identities=15% Similarity=0.129 Sum_probs=31.2
Q ss_pred HHHHHHhcCCCHHHHHH---HHHHHHHHHHHHHHHcHH------HHHHHHHHHHc
Q 019841 270 LDALLKGLGFTQKKADS---QVRWSLLNTVLLLRRHKG------ARAKLAEAMTM 315 (335)
Q Consensus 270 at~i~~~lG~s~~~~d~---evR~A~~~A~~LLr~hr~------aleaLaeaLle 315 (335)
-.++++.+||+...|+. +-+....++.++|+.-++ .++.|.++|.+
T Consensus 21 Wk~Lar~LGls~~dI~~i~~~~~~~~eq~~~mL~~W~~r~g~~AT~~~L~~aL~~ 75 (86)
T cd08318 21 WKTLAPHLEMKDKEIRAIESDSEDIKMQAKQLLVAWQDREGSQATPETLITALNA 75 (86)
T ss_pred HHHHHHHcCCCHHHHHHHHhcCCCHHHHHHHHHHHHHHhcCccccHHHHHHHHHH
Confidence 45567789999987764 112346788888876554 45677777765
No 50
>PRK03982 heat shock protein HtpX; Provisional
Probab=35.63 E-value=27 Score=33.65 Aligned_cols=30 Identities=23% Similarity=0.174 Sum_probs=23.1
Q ss_pred ccccccCCCCHhHHHHHHHHHHhHHHHHHH
Q 019841 161 VLDTIGHTFSQKYHNRVIQHEAGHFLIAYL 190 (335)
Q Consensus 161 lld~l~r~~s~~~r~RIA~HEAGHaLVAyl 190 (335)
+-|.+-+.++++|-+-|.-||-||.--.+.
T Consensus 112 vt~gLl~~l~~~El~AVlAHElgHi~~~h~ 141 (288)
T PRK03982 112 VTEGILNLLNEDELEGVIAHELTHIKNRDT 141 (288)
T ss_pred eehHHHhhCCHHHHHHHHHHHHHHHHcCCH
Confidence 445555566899999999999999875554
No 51
>PF00531 Death: Death domain; InterPro: IPR000488 The death domain (DD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. DD is related in sequence and structure to the death effector domain (DED, see IPR001875 from INTERPRO) and the caspase recruitment domain (CARD, see IPR001315 from INTERPRO), which work in similar pathways and show similar interaction properties []. DD bind each other forming oligomers. Mammals have numerous and diverse DD-containing proteins []. Within these proteins, the DD domains can be found in combination with other domains, including: CARDs, DEDs, ankyrin repeats (IPR002110 from INTERPRO), caspase-like folds, kinase domains, leucine zippers (IPR002158 from INTERPRO), leucine-rich repeats (LRR) (IPR001611 from INTERPRO), TIR domains (IPR000157 from INTERPRO), and ZU5 domains (IPR000906 from INTERPRO) []. Some DD-containing proteins are involved in the regulation of apoptosis and inflammation through their activation of caspases and NF-kappaB, which typically involves interactions with TNF (tumour necrosis factor) cytokine receptors [, ]. In humans, eight of the over 30 known TNF receptors contain DD in their cytoplasmic tails; several of these TNF receptors use caspase activation as a signalling mechanism. The DD mediates self-association of these receptors, thus giving the signal to downstream events that lead to apoptosis. Other DD-containing proteins, such as ankyrin, MyD88 and pelle, are probably not directly involved in cell death signalling. DD-containing proteins also have links to innate immunity, communicating with Toll family receptors through bipartite adapter proteins such as MyD88 [].; GO: 0005515 protein binding, 0007165 signal transduction; PDB: 3OQ9_L 3EZQ_F 1E41_A 1E3Y_A 2GF5_A 2OF5_L 3EWV_E 3G5B_A 3MOP_L 2A9I_A ....
Probab=35.57 E-value=1.9e+02 Score=21.63 Aligned_cols=57 Identities=18% Similarity=0.202 Sum_probs=35.5
Q ss_pred HHHHHHhcCCCHHHHHHHHHH----HHHHHHHHHHHcHHH------HHHHHHHHHcccchHHHHHHHHh
Q 019841 270 LDALLKGLGFTQKKADSQVRW----SLLNTVLLLRRHKGA------RAKLAEAMTMGKSLGSCIDIIED 328 (335)
Q Consensus 270 at~i~~~lG~s~~~~d~evR~----A~~~A~~LLr~hr~a------leaLaeaLle~esl~~Ci~~Ie~ 328 (335)
-..+++.+||+...++. ++. ...++.++|..-+.. ++.|.++|.+-+ ..++.+.|++
T Consensus 15 Wk~La~~Lg~~~~~i~~-i~~~~~~~~~~~~~~L~~W~~~~~~~at~~~L~~aL~~~~-~~d~~~~i~~ 81 (83)
T PF00531_consen 15 WKRLARKLGLSESEIEN-IEEENPDLREQTYEMLQRWRQREGPNATVDQLIQALRDIG-RNDLAEKIEQ 81 (83)
T ss_dssp HHHHHHHTTS-HHHHHH-HHHHSTSHHHHHHHHHHHHHHHHGSTSSHHHHHHHHHHTT-HHHHHHHHHH
T ss_pred HHHHHHHhCcCHHHHHH-HHHhCCChHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHCC-cHHHHHHHHh
Confidence 44566778999887774 322 347888888655444 778888876533 3455555554
No 52
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=35.02 E-value=2.7e+02 Score=23.28 Aligned_cols=63 Identities=13% Similarity=0.194 Sum_probs=32.9
Q ss_pred hHHHHHHHH--HHhcCCCHHHHHHHHHH---------HHHHHHHHHHHcHHHHHHHHHHHHcc-cchHHHHHHHH
Q 019841 265 ADINKLDAL--LKGLGFTQKKADSQVRW---------SLLNTVLLLRRHKGARAKLAEAMTMG-KSLGSCIDIIE 327 (335)
Q Consensus 265 ~Dl~~at~i--~~~lG~s~~~~d~evR~---------A~~~A~~LLr~hr~aleaLaeaLle~-esl~~Ci~~Ie 327 (335)
+|+..+..| ++.+|||-+++..-+.. ...+..++|++|...++.--+.|.+. +.+.+.+.-.+
T Consensus 40 ~~l~~l~~I~~lr~~G~~L~~I~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~l~~~~~~L~~~~~~~~ 114 (118)
T cd04776 40 RDRARLKLILRGKRLGFSLEEIRELLDLYDPPGGNRKQLEKMLEKIEKRRAELEQQRRDIDAALAELDAAEERCR 114 (118)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHhhccCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 555665544 45678876655442221 12344566777776666555554442 34444444333
No 53
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=34.22 E-value=2.4e+02 Score=23.09 Aligned_cols=52 Identities=15% Similarity=0.261 Sum_probs=30.5
Q ss_pred hhHHHHHHHH--HHhcCCCHHHHHHHHHH------HHHHHHHHHHHcHHHHHHHHHHHHc
Q 019841 264 LADINKLDAL--LKGLGFTQKKADSQVRW------SLLNTVLLLRRHKGARAKLAEAMTM 315 (335)
Q Consensus 264 ~~Dl~~at~i--~~~lG~s~~~~d~evR~------A~~~A~~LLr~hr~aleaLaeaLle 315 (335)
.+|+.++..| ++.+|||-+++..-... ...+...+|+++...++.-.+.|..
T Consensus 41 ~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~ 100 (113)
T cd01109 41 EEDLEWLEFIKCLRNTGMSIKDIKEYAELRREGDSTIPERLELLEEHREELEEQIAELQE 100 (113)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHccCCccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3566666655 45688887766543321 1234456777777766666555554
No 54
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=33.88 E-value=1.4e+02 Score=23.98 Aligned_cols=50 Identities=26% Similarity=0.377 Sum_probs=30.1
Q ss_pred hhHHHHHHHH--HHhcCCCHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHH
Q 019841 264 LADINKLDAL--LKGLGFTQKKADSQVRWSLLNTVLLLRRHKGARAKLAEAM 313 (335)
Q Consensus 264 ~~Dl~~at~i--~~~lG~s~~~~d~evR~A~~~A~~LLr~hr~aleaLaeaL 313 (335)
.+|+..+..| ++.+|||-+++..-+........++|+++.+.++.=-+.|
T Consensus 41 ~~~l~~l~~I~~lr~~G~~l~eI~~~l~~~~~~~~~~l~~~~~~l~~~i~~l 92 (96)
T cd04788 41 RADIRRLHQIIALRRLGFSLREIGRALDGPDFDPLELLRRQLARLEEQLELA 92 (96)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHhCCChhHHHHHHHHHHHHHHHHHHH
Confidence 3566666655 5678999877765443222245666777766666544444
No 55
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=31.64 E-value=2.2e+02 Score=23.88 Aligned_cols=51 Identities=12% Similarity=0.154 Sum_probs=26.7
Q ss_pred hHHHHHHHH--HHhcCCCHHHHHHHHHHH----HHHHHHHHHHcHHHHHHHHHHHHc
Q 019841 265 ADINKLDAL--LKGLGFTQKKADSQVRWS----LLNTVLLLRRHKGARAKLAEAMTM 315 (335)
Q Consensus 265 ~Dl~~at~i--~~~lG~s~~~~d~evR~A----~~~A~~LLr~hr~aleaLaeaLle 315 (335)
+|+.++..| ++.+|||-+++..-+... ......+|+++...++.=.+.|.+
T Consensus 42 ~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 98 (126)
T cd04783 42 ETVTRLRFIKRAQELGFTLDEIAELLELDDGTDCSEARELAEQKLAEVDEKIADLQR 98 (126)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444444444 567888877665433311 234456666665555544444433
No 56
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=31.50 E-value=2.3e+02 Score=23.01 Aligned_cols=51 Identities=22% Similarity=0.263 Sum_probs=33.7
Q ss_pred hHHHHHHHH--HHhcCCCHHHHHHHHHH----------HHHHHHHHHHHcHHHHHHHHHHHHc
Q 019841 265 ADINKLDAL--LKGLGFTQKKADSQVRW----------SLLNTVLLLRRHKGARAKLAEAMTM 315 (335)
Q Consensus 265 ~Dl~~at~i--~~~lG~s~~~~d~evR~----------A~~~A~~LLr~hr~aleaLaeaLle 315 (335)
+|+..+..| ++.+|||-+++..-+.. .......+|+++...+++-.+.|.+
T Consensus 40 ~~~~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~ 102 (107)
T cd04777 40 KCQDDLEFILELKGLGFSLIEIQKIFSYKRLTKSRTHEDQDYYKSFLKNKKDELEKEIEDLKK 102 (107)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHhcccccccchhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 566666665 56799998876653331 1233578888888888776666654
No 57
>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR. SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.
Probab=31.27 E-value=2.4e+02 Score=24.49 Aligned_cols=60 Identities=8% Similarity=0.154 Sum_probs=32.4
Q ss_pred hhHHHHHHHH--HHhcCCCHHHHHHHHHH-------HHHHHHHHHHHcHHHHHHHHHHHHc-ccchHHHH
Q 019841 264 LADINKLDAL--LKGLGFTQKKADSQVRW-------SLLNTVLLLRRHKGARAKLAEAMTM-GKSLGSCI 323 (335)
Q Consensus 264 ~~Dl~~at~i--~~~lG~s~~~~d~evR~-------A~~~A~~LLr~hr~aleaLaeaLle-~esl~~Ci 323 (335)
.+|+.++..| ++.+|||-+++..-+.. .......++.++...++.-.+.|.+ +..|.+++
T Consensus 41 ~~di~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~~l~~~~~~l~~ki~~L~~~~~~L~~~~ 110 (142)
T TIGR01950 41 RDVLRRVAVIKAAQRVGIPLATIGEALAVLPEGRTPTADDWARLSSQWREELDERIDQLNALRDQLDGCI 110 (142)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHhcccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3566666655 46688887766653321 1233445666666555554444444 34455544
No 58
>cd08313 Death_TNFR1 Death domain of Tumor Necrosis Factor Receptor 1. Death Domain (DD) found in tumor necrosis factor receptor-1 (TNFR-1). TNFR-1 has many names including TNFRSF1A, CD120a, p55, p60, and TNFR60. It activates two major intracellular signaling pathways that lead to the activation of the transcription factor NF-kB and the induction of cell death. Upon binding of its ligand TNF, TNFR-1 trimerizes which leads to the recruitment of an adaptor protein named TNFR-associated death domain protein (TRADD) through a DD/DD interaction. Mutations in the TNFRSF1A gene causes TNFR-associated periodic syndrome (TRAPS), a rare disorder characterized recurrent fever, myalgia, abdominal pain, conjunctivitis and skin eruptions. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation a
Probab=31.20 E-value=1.7e+02 Score=23.29 Aligned_cols=49 Identities=10% Similarity=0.148 Sum_probs=32.8
Q ss_pred HHHHHHHHHhcCCCHHHHHHH---HHHHHHHHHHHHHHc-------HHHHHHHHHHHHc
Q 019841 267 INKLDALLKGLGFTQKKADSQ---VRWSLLNTVLLLRRH-------KGARAKLAEAMTM 315 (335)
Q Consensus 267 l~~at~i~~~lG~s~~~~d~e---vR~A~~~A~~LLr~h-------r~aleaLaeaLle 315 (335)
..+..+++|.+|+|+.+||.- -+...++.+++|+.- +..++.|.++|..
T Consensus 11 ~~~wk~~~R~LGlse~~Id~ie~~~~~~~Eq~yqmL~~W~~~~g~~~At~~~L~~aLr~ 69 (80)
T cd08313 11 PRRWKEFVRRLGLSDNEIERVELDHRRCRDAQYQMLKVWKERGPRPYATLQHLLSVLRD 69 (80)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCCcchHHHHHHHHHH
Confidence 456788999999999887752 124556667777542 4466777777654
No 59
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=30.89 E-value=1.7e+02 Score=23.93 Aligned_cols=62 Identities=18% Similarity=0.254 Sum_probs=39.3
Q ss_pred HHHHHHHHhcCCCHHHHHHH---HHHHHHHHHHHHHHcH------HHHHHHHHHHHcccchHHHHHHHHhhh
Q 019841 268 NKLDALLKGLGFTQKKADSQ---VRWSLLNTVLLLRRHK------GARAKLAEAMTMGKSLGSCIDIIEDNI 330 (335)
Q Consensus 268 ~~at~i~~~lG~s~~~~d~e---vR~A~~~A~~LLr~hr------~aleaLaeaLle~esl~~Ci~~Ie~~~ 330 (335)
.+..++++.+|+|+.+|+.- -+.-.++.+++|+.-+ ..++.|.++|..- -+..|-+-|++.+
T Consensus 20 ~~Wk~laR~LGLse~~I~~i~~~~~~~~eq~~qmL~~W~~~~G~~At~~~L~~aL~~~-~~~~~Ae~I~~~l 90 (96)
T cd08315 20 DSWNRLMRQLGLSENEIDVAKANERVTREQLYQMLLTWVNKTGRKASVNTLLDALEAI-GLRLAKESIQDEL 90 (96)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHhhCCCcHHHHHHHHHHHc-ccccHHHHHHHHH
Confidence 35677889999999887741 1122677778876544 4678888888762 2333444455444
No 60
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=30.87 E-value=1.9e+02 Score=23.33 Aligned_cols=47 Identities=26% Similarity=0.358 Sum_probs=25.8
Q ss_pred hHHHHHHHH--HHhcCCCHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHH
Q 019841 265 ADINKLDAL--LKGLGFTQKKADSQVRWSLLNTVLLLRRHKGARAKLAE 311 (335)
Q Consensus 265 ~Dl~~at~i--~~~lG~s~~~~d~evR~A~~~A~~LLr~hr~aleaLae 311 (335)
+|+..+..+ ++..|||-+.+..-.+.......++|++++..++.=-+
T Consensus 42 ~di~~l~~i~~lr~~g~~l~~i~~~~~~~~~~~~~~l~~~~~~l~~~i~ 90 (103)
T cd01106 42 EDLERLQQILFLKELGFSLKEIKELLKDPSEDLLEALREQKELLEEKKE 90 (103)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHH
Confidence 456555554 35678887766654332224555666666655554333
No 61
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=30.86 E-value=2.8e+02 Score=22.73 Aligned_cols=52 Identities=15% Similarity=0.161 Sum_probs=28.9
Q ss_pred hHHHHHHHH--HHhcCCCHHHHHHHHHH-----HHHHHHHHHHHcHHHHHHHHHHHHcc
Q 019841 265 ADINKLDAL--LKGLGFTQKKADSQVRW-----SLLNTVLLLRRHKGARAKLAEAMTMG 316 (335)
Q Consensus 265 ~Dl~~at~i--~~~lG~s~~~~d~evR~-----A~~~A~~LLr~hr~aleaLaeaLle~ 316 (335)
+|+..+..+ ++.+|||-+++..-+.. .......+|++++..++.=..+|..+
T Consensus 42 ~dl~~l~~I~~lr~~G~~l~~I~~~l~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~ 100 (108)
T cd04773 42 SDVRDARLIHLLRRGGYLLEQIATVVEQLRHAGGTEALAAALEQRRVALTQRGRAMLDA 100 (108)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455555554 45677777665543321 02345666777776666655555543
No 62
>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=30.73 E-value=41 Score=30.01 Aligned_cols=24 Identities=25% Similarity=0.353 Sum_probs=20.3
Q ss_pred CCHhHHHHHHHHHHhHHHHHHHhC
Q 019841 169 FSQKYHNRVIQHEAGHFLIAYLVG 192 (335)
Q Consensus 169 ~s~~~r~RIA~HEAGHaLVAylLg 192 (335)
+++++..-|..||-||..-.+..-
T Consensus 84 ~~~~el~aVlaHElgH~~~~h~~~ 107 (226)
T PF01435_consen 84 LSEDELAAVLAHELGHIKHRHILK 107 (226)
T ss_dssp SSHHHHHHHHHHHHHHHHTTHCCC
T ss_pred ccHHHHHHHHHHHHHHHHcCCcch
Confidence 479999999999999998766654
No 63
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=30.12 E-value=2.7e+02 Score=23.25 Aligned_cols=51 Identities=10% Similarity=0.127 Sum_probs=27.5
Q ss_pred hhHHHHHHHH--HHhcCCCHHHHHHHHHH------HHHHHHHHHHHcHHHHHHHHHHHH
Q 019841 264 LADINKLDAL--LKGLGFTQKKADSQVRW------SLLNTVLLLRRHKGARAKLAEAMT 314 (335)
Q Consensus 264 ~~Dl~~at~i--~~~lG~s~~~~d~evR~------A~~~A~~LLr~hr~aleaLaeaLl 314 (335)
.+|+..+..| ++.+|||-+++..-+.. .......+|+++...+++--+.|.
T Consensus 41 ~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~ 99 (127)
T cd04784 41 EEHLERLLFIRRCRSLDMSLDEIRTLLQLQDDPEASCAEVNALIDEHLAHVRARIAELQ 99 (127)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHhhhcCCCcHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3566655544 46678877666543332 123445666666666654444443
No 64
>cd06258 Peptidase_M3_like The peptidase M3-like family, also called neurolysin-like family, is part of the "zincins" metallopeptidases, and includes M3, M2 and M32 families of metallopeptidases. The M3 family is subdivided into two subfamilies: the widespread M3A, which comprises a number of high-molecular mass endo- and exopeptidases from bacteria, archaea, protozoa, fungi, plants and animals, and the small M3B, whose members are enzymes primarily from bacteria. Well-known mammalian/eukaryotic M3A endopeptidases are the thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (alias endopeptidase 3.4.24.16), and the mitochondrial intermediate peptidase. The first two are intracellular oligopeptidases, which act only on relatively short substrates of less than 20 amino acid residues, while the latter cleaves N-terminal octapeptides from proteins during their import into the mitochondria. The M3A subfamily also contains several bacterial endopeptidases, collectively called olig
Probab=28.70 E-value=32 Score=33.69 Aligned_cols=17 Identities=29% Similarity=0.423 Sum_probs=14.7
Q ss_pred HHHHHHHhHHHHHHHhC
Q 019841 176 RVIQHEAGHFLIAYLVG 192 (335)
Q Consensus 176 RIA~HEAGHaLVAylLg 192 (335)
.+..||.||++=..+..
T Consensus 156 ~tl~HE~GHa~h~~l~~ 172 (365)
T cd06258 156 NTLFHEFGHAVHFLLIQ 172 (365)
T ss_pred HHHHHHHhHHHHHHHhc
Confidence 57999999999887775
No 65
>PF14362 DUF4407: Domain of unknown function (DUF4407)
Probab=28.68 E-value=1.1e+02 Score=29.51 Aligned_cols=43 Identities=21% Similarity=0.263 Sum_probs=26.5
Q ss_pred HHHHHHhhhhhhhhcCCCh-HHHHHHHHHHHHHHHHHHhhhcCC
Q 019841 114 QLAAIAGGVSAWNVFSFNP-QQILYLSLALLFLWTVDSVSYNGG 156 (335)
Q Consensus 114 ~~~a~~g~~~~~~~~~ls~-~~~~~~~~~~l~l~aiD~v~lgg~ 156 (335)
.++++.|+++++-.++.++ ..+++.++-.++++.+|+.....-
T Consensus 27 ~la~~s~~~a~~~~~~~~~~~ai~~glvwgl~I~~lDR~ivss~ 70 (301)
T PF14362_consen 27 LLAGLSGGYALYTVFGGPVWAAIPFGLVWGLVIFNLDRFIVSSI 70 (301)
T ss_pred HHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 3455666666677777774 333333444457789999877644
No 66
>PRK04897 heat shock protein HtpX; Provisional
Probab=28.08 E-value=43 Score=32.57 Aligned_cols=25 Identities=20% Similarity=0.137 Sum_probs=19.5
Q ss_pred ccCCCCHhHHHHHHHHHHhHHHHHH
Q 019841 165 IGHTFSQKYHNRVIQHEAGHFLIAY 189 (335)
Q Consensus 165 l~r~~s~~~r~RIA~HEAGHaLVAy 189 (335)
+-+.++++|.+-|.-||-||.--.+
T Consensus 128 Ll~~l~~~El~aVlAHElgHi~~~d 152 (298)
T PRK04897 128 LLAIMNREELEGVIGHEISHIRNYD 152 (298)
T ss_pred HHhhCCHHHHHHHHHHHHHHHhcCC
Confidence 4445689999999999999975433
No 67
>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator. Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.
Probab=27.73 E-value=2.5e+02 Score=24.27 Aligned_cols=59 Identities=12% Similarity=0.164 Sum_probs=27.0
Q ss_pred hHHHHHHHH--HHhcCCCHHHHHHHHHHH-------HHHHHHHHHHcHHHHHHHHHHHHc-ccchHHHH
Q 019841 265 ADINKLDAL--LKGLGFTQKKADSQVRWS-------LLNTVLLLRRHKGARAKLAEAMTM-GKSLGSCI 323 (335)
Q Consensus 265 ~Dl~~at~i--~~~lG~s~~~~d~evR~A-------~~~A~~LLr~hr~aleaLaeaLle-~esl~~Ci 323 (335)
+|+.++..| ++.+|||-+++.+-+... ...-..++++++..++.-.+.|.+ ...|.+|+
T Consensus 42 ~dl~~l~~I~~lr~~G~sl~eI~~~l~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~~i 110 (139)
T cd01110 42 DVLRRIAFIKVAQRLGLSLAEIAEALATLPEDRTPTKADWERLSRAWRDRLDERIAELQQLRDQLDGCI 110 (139)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455555544 345677766555433211 112234455544444444444443 23344443
No 68
>PF12388 Peptidase_M57: Dual-action HEIGH metallo-peptidase; InterPro: IPR024653 This entry represents the metallopeptidases M10, M27 and M57. The catalytic triad for proteases in this entry is HE-H-H, which in many members is in the sequence motif HEIGH [].
Probab=27.63 E-value=39 Score=31.84 Aligned_cols=22 Identities=32% Similarity=0.305 Sum_probs=17.4
Q ss_pred CHhHHHHHHHHHHhHHHHHHHh
Q 019841 170 SQKYHNRVIQHEAGHFLIAYLV 191 (335)
Q Consensus 170 s~~~r~RIA~HEAGHaLVAylL 191 (335)
+....+.|+.||-||.+--.-.
T Consensus 129 ~~~~~~hvi~HEiGH~IGfRHT 150 (211)
T PF12388_consen 129 SVNVIEHVITHEIGHCIGFRHT 150 (211)
T ss_pred chhHHHHHHHHHhhhhcccccc
Confidence 5677889999999998755443
No 69
>PF10728 DUF2520: Domain of unknown function (DUF2520); InterPro: IPR018931 This presumed domain is found C-terminal to a Rossmann-like domain suggesting that these proteins are oxidoreductases. ; PDB: 3D1L_A 2I76_A 3DFU_A.
Probab=27.46 E-value=1.2e+02 Score=26.16 Aligned_cols=62 Identities=21% Similarity=0.137 Sum_probs=47.8
Q ss_pred ccchhhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHcccchHH
Q 019841 260 AEGGLADINKLDALLKGLGFTQKKADSQVRWSLLNTVLLLRRHKGARAKLAEAMTMGKSLGS 321 (335)
Q Consensus 260 a~Gg~~Dl~~at~i~~~lG~s~~~~d~evR~A~~~A~~LLr~hr~aleaLaeaLle~esl~~ 321 (335)
++|...+++.+.+++..+|-..-.++.+.|..|.-|.-+-.++-..+-..+..|+++.-++.
T Consensus 6 iEgd~~~~~~l~~l~~~lg~~~~~i~~~~r~~yHaAav~asNf~~~L~~~a~~ll~~~gi~~ 67 (132)
T PF10728_consen 6 IEGDEEALEVLQELAKELGGRPFEIDSEQRALYHAAAVFASNFLVALYALAAELLEQAGIDF 67 (132)
T ss_dssp EEESHHHHHHHHHHHHHTTSEEEE--GGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SH
T ss_pred EecCHHHHHHHHHHHHHhCCceEEeCHHhHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCCc
Confidence 35767788889999999997777777778888888888888888888888888888777655
No 70
>PF11350 DUF3152: Protein of unknown function (DUF3152); InterPro: IPR022603 This entry represents Actinobacteria proteins of unknown function. Some are annotated as membrane proteins, however this cannot be confirmed.
Probab=27.46 E-value=32 Score=32.27 Aligned_cols=24 Identities=33% Similarity=0.296 Sum_probs=18.3
Q ss_pred HhHHHHHHHHHHhHHHHHHHhCCC
Q 019841 171 QKYHNRVIQHEAGHFLIAYLVGIL 194 (335)
Q Consensus 171 ~~~r~RIA~HEAGHaLVAylLg~P 194 (335)
..||+-++=||-||+|----.+||
T Consensus 136 ~~YRqYvINHEVGH~LGh~H~~Cp 159 (203)
T PF11350_consen 136 ASYRQYVINHEVGHALGHGHEPCP 159 (203)
T ss_pred HHHHHHhhhhhhhhhcccCCCcCC
Confidence 689999999999999943223344
No 71
>PRK03001 M48 family peptidase; Provisional
Probab=27.38 E-value=39 Score=32.47 Aligned_cols=29 Identities=21% Similarity=0.193 Sum_probs=21.9
Q ss_pred cccccCCCCHhHHHHHHHHHHhHHHHHHH
Q 019841 162 LDTIGHTFSQKYHNRVIQHEAGHFLIAYL 190 (335)
Q Consensus 162 ld~l~r~~s~~~r~RIA~HEAGHaLVAyl 190 (335)
-|.+-+.++++|-+-|.-||-||.--.+.
T Consensus 112 t~gLl~~l~~~El~aVlAHElgHi~~~h~ 140 (283)
T PRK03001 112 TTGILRVLSEREIRGVMAHELAHVKHRDI 140 (283)
T ss_pred cHHHHhhCCHHHHHHHHHHHHHHHhCCCh
Confidence 34444556899999999999999865544
No 72
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=26.77 E-value=2.7e+02 Score=23.34 Aligned_cols=51 Identities=6% Similarity=0.143 Sum_probs=24.6
Q ss_pred hHHHHHHHH--HHhcCCCHHHHHHHHHH------HHHHHHHHHHHcHHHHHHHHHHHHc
Q 019841 265 ADINKLDAL--LKGLGFTQKKADSQVRW------SLLNTVLLLRRHKGARAKLAEAMTM 315 (335)
Q Consensus 265 ~Dl~~at~i--~~~lG~s~~~~d~evR~------A~~~A~~LLr~hr~aleaLaeaLle 315 (335)
+|+.++..| ++.+|||-+++.+-+.. .......+|.+++..+++-.+.|.+
T Consensus 42 ~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 100 (127)
T TIGR02044 42 QHLDELRLISRARQVGFSLEECKELLNLWNDPNRTSADVKARTLEKVAEIERKISELQS 100 (127)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455555544 45677776655543321 1223344555555555444444433
No 73
>PF08858 IDEAL: IDEAL domain; InterPro: IPR014957 This entry represents the C-terminal domain of Bacteriophage SPP1, p90. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. his domain may also be referred to as the IDEAL domain, after the sequence of the most conserved region of the domain.; PDB: 3DO9_A.
Probab=26.52 E-value=1.3e+02 Score=20.47 Aligned_cols=26 Identities=31% Similarity=0.438 Sum_probs=19.9
Q ss_pred hhhHHHHHHHHHHHHccCcHHHHHHH
Q 019841 33 EVSKRRVLKQVDEELSKGDERAALAL 58 (335)
Q Consensus 33 ~~~~~~~~~~~d~~l~~~~~~~al~~ 58 (335)
.-++...+++||..|-++|.+.=+.+
T Consensus 8 ~~~~~~L~~~ID~ALd~~D~e~F~~L 33 (37)
T PF08858_consen 8 EFRKEQLLELIDEALDNRDKEWFYEL 33 (37)
T ss_dssp HHHHHHHHHHHHHHHHTT-HHHHHHH
T ss_pred HHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence 46788899999999999998744443
No 74
>PRK03072 heat shock protein HtpX; Provisional
Probab=25.80 E-value=42 Score=32.56 Aligned_cols=25 Identities=16% Similarity=0.200 Sum_probs=19.6
Q ss_pred cCCCCHhHHHHHHHHHHhHHHHHHH
Q 019841 166 GHTFSQKYHNRVIQHEAGHFLIAYL 190 (335)
Q Consensus 166 ~r~~s~~~r~RIA~HEAGHaLVAyl 190 (335)
-+.++++|-+-|.-||-||.-=.+.
T Consensus 119 l~~l~~~El~aVlAHElgHi~~~d~ 143 (288)
T PRK03072 119 LQILNERELRGVLGHELSHVYNRDI 143 (288)
T ss_pred HHhCCHHHHHHHHHHHHHHHhcCCH
Confidence 3456899999999999999765444
No 75
>COG2738 Predicted Zn-dependent protease [General function prediction only]
Probab=25.56 E-value=37 Score=32.05 Aligned_cols=13 Identities=38% Similarity=0.575 Sum_probs=10.9
Q ss_pred HHHHHHHhHHHHH
Q 019841 176 RVIQHEAGHFLIA 188 (335)
Q Consensus 176 RIA~HEAGHaLVA 188 (335)
-||-||-|||+=-
T Consensus 94 aVAAHEVGHAiQd 106 (226)
T COG2738 94 AVAAHEVGHAIQD 106 (226)
T ss_pred HHHHHHhhHHHhh
Confidence 4899999999854
No 76
>COG1913 Predicted Zn-dependent proteases [General function prediction only]
Probab=24.63 E-value=47 Score=30.69 Aligned_cols=16 Identities=44% Similarity=0.891 Sum_probs=12.3
Q ss_pred HhHHHHH---HHHHHhHHH
Q 019841 171 QKYHNRV---IQHEAGHFL 186 (335)
Q Consensus 171 ~~~r~RI---A~HEAGHaL 186 (335)
+-.++|+ +.||+||.+
T Consensus 118 ~lf~ERv~KEv~HElGH~~ 136 (181)
T COG1913 118 ELFKERVVKEVLHELGHLL 136 (181)
T ss_pred HHHHHHHHHHHHHHhhhhc
Confidence 5566777 799999965
No 77
>PF07998 Peptidase_M54: Peptidase family M54; InterPro: IPR012962 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This entry represents zinc-dependent peptidases belonging to the MEROPS peptidase family M54, more commonly known as the archaemetzincins. The family has a wide taxonomic distribution, being found in archaea, bacteria and eukaryotes. Two human homologues have been characterised []. ; GO: 0008237 metallopeptidase activity, 0008270 zinc ion binding; PDB: 3LMC_A 2XHQ_A 2X7M_A.
Probab=24.58 E-value=48 Score=30.82 Aligned_cols=11 Identities=36% Similarity=0.712 Sum_probs=9.1
Q ss_pred HHHHHHHhHHH
Q 019841 176 RVIQHEAGHFL 186 (335)
Q Consensus 176 RIA~HEAGHaL 186 (335)
..+.||.||.+
T Consensus 147 Kea~HElGH~~ 157 (194)
T PF07998_consen 147 KEAVHELGHLF 157 (194)
T ss_dssp HHHHHHHHHHT
T ss_pred HHHHHHHHHHc
Confidence 45899999975
No 78
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=24.48 E-value=4e+02 Score=21.94 Aligned_cols=51 Identities=16% Similarity=0.220 Sum_probs=28.0
Q ss_pred hHHHHHHHH--HHhcCCCHHHHHHHHHHH------HHHHHHHHHHcHHHHHHHHHHHHc
Q 019841 265 ADINKLDAL--LKGLGFTQKKADSQVRWS------LLNTVLLLRRHKGARAKLAEAMTM 315 (335)
Q Consensus 265 ~Dl~~at~i--~~~lG~s~~~~d~evR~A------~~~A~~LLr~hr~aleaLaeaLle 315 (335)
+|+..+..| ++.+|||-+++..-.... ......+|+++...++.=.+.|..
T Consensus 42 ~~i~~l~~I~~lr~~G~sl~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~ 100 (123)
T cd04770 42 ADLARLRFIRRAQALGFSLAEIRELLSLRDDGAAPCAEVRALLEEKLAEVEAKIAELQA 100 (123)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHhhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444444444 566788877665433321 234456677776666655555444
No 79
>cd08311 Death_p75NR Death domain of p75 Neurotophin Receptor. Death Domain (DD) found in p75 neurotrophin receptor (p75NTR, NGFR, TNFRSF16). p75NTR binds members of the neurotrophin (NT) family including nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and NT3, among others. It contains an NT-binding extracellular region that bears four cysteine-rich repeats, a transmembrane domain, and an intracellular DD. p75NTR plays roles in the immune, vascular, and nervous systems, and has been shown to promote cell death or survival, and to induce neurite outgrowth or collapse depending on its ligands and co-receptors. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptor
Probab=24.44 E-value=2e+02 Score=22.66 Aligned_cols=33 Identities=18% Similarity=0.191 Sum_probs=24.3
Q ss_pred HHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHcH
Q 019841 270 LDALLKGLGFTQKKADSQVRWSLLNTVLLLRRHK 303 (335)
Q Consensus 270 at~i~~~lG~s~~~~d~evR~A~~~A~~LLr~hr 303 (335)
-+.+++.+||+...|+. ++.-+.++.++|+.-.
T Consensus 18 W~~LA~~LG~~~~~I~~-i~~~~~p~~~lL~~W~ 50 (77)
T cd08311 18 WRSLAGELGYEDEAIDT-FGREESPVRTLLADWS 50 (77)
T ss_pred HHHHHHHcCCCHHHHHH-HHcChhHHHHHHHHHH
Confidence 77788899999988875 3444577777776544
No 80
>COG3402 Uncharacterized conserved protein [Function unknown]
Probab=24.32 E-value=1.7e+02 Score=26.55 Aligned_cols=36 Identities=17% Similarity=0.166 Sum_probs=21.7
Q ss_pred HHHHHHHhhhhhhhhcCCChHHHHHHHHHHHHHHHH
Q 019841 113 LQLAAIAGGVSAWNVFSFNPQQILYLSLALLFLWTV 148 (335)
Q Consensus 113 ~~~~a~~g~~~~~~~~~ls~~~~~~~~~~~l~l~ai 148 (335)
+.+...++....++.+|.+|.|+......+..++++
T Consensus 27 l~Ll~av~~~~~~~~~~~~~~w~~~a~~av~l~~~v 62 (161)
T COG3402 27 LVLLIAVAAGVLLYFVGLDPNWSSVAAVAVILLAAV 62 (161)
T ss_pred HHHHHHHHHHHHHheeccCCccHHHHHHHHHHHHHH
Confidence 333334444455677899998888765555544444
No 81
>PF12994 DUF3878: Domain of unknown function, E. rectale Gene description (DUF3878); InterPro: IPR024538 This entry represents proteins of unknown function found primarily in Firmicutes. The Eubacterium rectale gene appears to be upregulated in the presence of Bacteroides thetaiotaomicron compared to growth in pure culture [].
Probab=24.15 E-value=15 Score=36.33 Aligned_cols=17 Identities=24% Similarity=0.288 Sum_probs=12.4
Q ss_pred hHHHHHHHHHHhHHHHH
Q 019841 172 KYHNRVIQHEAGHFLIA 188 (335)
Q Consensus 172 ~~r~RIA~HEAGHaLVA 188 (335)
.+..--=|||-|||||-
T Consensus 92 ~~~~lY~Y~~iGHFWVk 108 (299)
T PF12994_consen 92 EETHLYNYGEIGHFWVK 108 (299)
T ss_pred HHHHHhhccccceeeec
Confidence 34444569999999984
No 82
>cd08779 Death_PIDD Death Domain of p53-induced protein with a death domain. Death domain (DD) found in PIDD (p53-induced protein with a death domain) and similar proteins. PIDD is a component of the PIDDosome complex, which is an oligomeric caspase-activating complex involved in caspase-2 activation and plays a role in mediating stress-induced apoptosis. The PIDDosome complex is composed of three components, PIDD, RAIDD and caspase-2, which interact through their DDs and DD-like domains. The DD of PIDD interacts with the DD of RAIDD, which also contains a Caspase Activation and Recruitment Domain (CARD) that interacts with the caspase-2 CARD. Autoproteolysis of PIDD determines the downstream signaling event, between pro-survival NF-kB or pro-death caspase-2 activation. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members
Probab=23.74 E-value=3.8e+02 Score=21.31 Aligned_cols=57 Identities=16% Similarity=0.044 Sum_probs=36.3
Q ss_pred HHHHhcCCCHHHHHH-HH---HHHHHHHHHHHHHc-------HHHHHHHHHHHHcccchHHHHHHHHhh
Q 019841 272 ALLKGLGFTQKKADS-QV---RWSLLNTVLLLRRH-------KGARAKLAEAMTMGKSLGSCIDIIEDN 329 (335)
Q Consensus 272 ~i~~~lG~s~~~~d~-ev---R~A~~~A~~LLr~h-------r~aleaLaeaLle~esl~~Ci~~Ie~~ 329 (335)
.+++.+|+|...++. +. +-...++..+|+.- ...++.|.+||.+ --..+|.+-|++.
T Consensus 18 ~lar~LGlse~~Id~Ie~~~~~dl~eq~~~mL~~W~~~~~~~~atv~~L~~AL~~-~gr~dlae~l~~~ 85 (86)
T cd08779 18 AIGLHLGLSYRELQRIKYNNRDDLDEQIFDMLFSWAQRQAGDPDAVGKLVTALEE-SGRQDLADEVRAV 85 (86)
T ss_pred HHHHHcCCCHHHHHHHHHHCccCHHHHHHHHHHHHHHhcCCCchHHHHHHHHHHH-cCHHHHHHHHHhh
Confidence 445668999987774 11 12456777777322 2456788888876 4456777767654
No 83
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=23.46 E-value=3.1e+02 Score=23.11 Aligned_cols=52 Identities=13% Similarity=0.195 Sum_probs=30.5
Q ss_pred hhHHHHHHHH--HHhcCCCHHHHHHHHHH------HHHHHHHHHHHcHHHHHHHHHHHHc
Q 019841 264 LADINKLDAL--LKGLGFTQKKADSQVRW------SLLNTVLLLRRHKGARAKLAEAMTM 315 (335)
Q Consensus 264 ~~Dl~~at~i--~~~lG~s~~~~d~evR~------A~~~A~~LLr~hr~aleaLaeaLle 315 (335)
.+|+.++..| ++.+|||-++|..-+.. .......+|+++...+++=.+.|.+
T Consensus 41 ~~~l~~l~~I~~lr~lG~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 100 (127)
T TIGR02047 41 VGHVERLAFIRNCRTLDMSLAEIRQLLRYQDKPEKSCSDVNALLDEHISHVRARIIKLQA 100 (127)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3566666655 56688887766653331 1234566777777766655555544
No 84
>PF13583 Reprolysin_4: Metallo-peptidase family M12B Reprolysin-like
Probab=23.27 E-value=42 Score=30.80 Aligned_cols=17 Identities=29% Similarity=0.141 Sum_probs=13.8
Q ss_pred HHHHHHHhHHHHHHHhC
Q 019841 176 RVIQHEAGHFLIAYLVG 192 (335)
Q Consensus 176 RIA~HEAGHaLVAylLg 192 (335)
.+..||.||.|-+.--+
T Consensus 139 ~~~aHEiGH~lGl~H~~ 155 (206)
T PF13583_consen 139 QTFAHEIGHNLGLRHDF 155 (206)
T ss_pred hHHHHHHHHHhcCCCCc
Confidence 56889999998876654
No 85
>cd08784 Death_DRs Death Domain of Death Receptors. Death domain (DD) found in death receptor proteins. Death receptors are members of the tumor necrosis factor (TNF) receptor superfamily, characterized by having a cytoplasmic DD. Known members of the family are Fas (CD95/APO-1), TNF-receptor 1 (TNFR1/TNFRSF1A/p55/CD120a), TNF-related apoptosis-inducing ligand receptor 1 (TRAIL-R1 /DR4), and receptor 2 (TRAIL-R2/DR5/APO-2/KILLER), as well as Death Receptor 3 (DR3/APO-3/TRAMP/WSL-1/LARD). They are involved in apoptosis signaling pathways. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=22.99 E-value=2.5e+02 Score=21.90 Aligned_cols=48 Identities=15% Similarity=0.173 Sum_probs=31.9
Q ss_pred HHHHHHHHhcCCCHHHHHHH---HHHHHHHHHHHHHHcH------HHHHHHHHHHHc
Q 019841 268 NKLDALLKGLGFTQKKADSQ---VRWSLLNTVLLLRRHK------GARAKLAEAMTM 315 (335)
Q Consensus 268 ~~at~i~~~lG~s~~~~d~e---vR~A~~~A~~LLr~hr------~aleaLaeaLle 315 (335)
.+-..+++.+||+..+|+.- -+...++++++|+.-+ ..++.|.++|..
T Consensus 12 ~~Wk~laR~LGls~~~I~~ie~~~~~~~eq~~~mL~~W~~k~G~~At~~~L~~aL~~ 68 (79)
T cd08784 12 DQHKRFFRKLGLSDNEIKVAELDNPQHRDRVYELLRIWRNKEGRKATLNTLIKALKD 68 (79)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHcCCchHHHHHHHHHHHHhccCcCcHHHHHHHHHHH
Confidence 34667889999999877752 1135677888886543 356666666655
No 86
>PRK01265 heat shock protein HtpX; Provisional
Probab=22.76 E-value=54 Score=32.66 Aligned_cols=29 Identities=17% Similarity=0.156 Sum_probs=22.1
Q ss_pred ccccccCCCCHhHHHHHHHHHHhHHHHHH
Q 019841 161 VLDTIGHTFSQKYHNRVIQHEAGHFLIAY 189 (335)
Q Consensus 161 lld~l~r~~s~~~r~RIA~HEAGHaLVAy 189 (335)
+-|.+-+.++++|.+-|.-||-||.--.+
T Consensus 127 vt~gLl~~l~~~El~aVlAHElgHik~~d 155 (324)
T PRK01265 127 ITLPLLKILNRDEIKAVAGHELGHLKHRD 155 (324)
T ss_pred EehHHHhhCCHHHHHHHHHHHHHHHHccc
Confidence 44555566789999999999999964333
No 87
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c
Probab=22.62 E-value=3.5e+02 Score=22.90 Aligned_cols=51 Identities=14% Similarity=0.229 Sum_probs=28.8
Q ss_pred hHHHHHHHH--HHhcCCCHHHHHHHHHHH------HHHHHHHHHHcHHHHHHHHHHHHc
Q 019841 265 ADINKLDAL--LKGLGFTQKKADSQVRWS------LLNTVLLLRRHKGARAKLAEAMTM 315 (335)
Q Consensus 265 ~Dl~~at~i--~~~lG~s~~~~d~evR~A------~~~A~~LLr~hr~aleaLaeaLle 315 (335)
+|+..+..| ++.+|||-+++..-+... .....++|+++...+++=.+.|.+
T Consensus 42 ~~~~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~ 100 (133)
T cd04787 42 KDLSRLRFILSARQLGFSLKDIKEILSHADQGESPCPMVRRLIEQRLAETERRIKELLK 100 (133)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHhhhccCCCcHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455554444 567888887666543321 123456677776666655555544
No 88
>PF09471 Peptidase_M64: IgA Peptidase M64; InterPro: IPR019026 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This is a family of highly selective metallo-endopeptidases belonging to the MEROPS peptidase family M64 (IgA peptidase, clan MA). The primary structure of the Clostridium ramosum IgA peptidase shows no significant overall similarity to any other known metallo-endopeptidase []. ; PDB: 3P1V_A 4DF9_D.
Probab=22.48 E-value=37 Score=32.84 Aligned_cols=20 Identities=25% Similarity=0.323 Sum_probs=13.7
Q ss_pred HhHHHHHHHHHHhHHHHHHH
Q 019841 171 QKYHNRVIQHEAGHFLIAYL 190 (335)
Q Consensus 171 ~~~r~RIA~HEAGHaLVAyl 190 (335)
..+-+-|++||.||.+....
T Consensus 213 ~~~~~~v~vHE~GHsf~~La 232 (264)
T PF09471_consen 213 NPSFKQVVVHEFGHSFGGLA 232 (264)
T ss_dssp STTHHHHHHHHHHHHTT---
T ss_pred cccccceeeeeccccccccc
Confidence 34566799999999887643
No 89
>cd04276 ZnMc_MMP_like_2 Zinc-dependent metalloprotease; MMP_like sub-family 2. A group of bacterial metalloproteinase domains similar to matrix metalloproteinases and astacin.
Probab=22.20 E-value=62 Score=29.92 Aligned_cols=15 Identities=33% Similarity=0.507 Sum_probs=12.0
Q ss_pred hHHHHHHHHHHhHHH
Q 019841 172 KYHNRVIQHEAGHFL 186 (335)
Q Consensus 172 ~~r~RIA~HEAGHaL 186 (335)
+..+-++.||.||+|
T Consensus 114 ~~~~~~~~he~gh~l 128 (197)
T cd04276 114 ASLRYLLAHEVGHTL 128 (197)
T ss_pred HHHHHHHHHHHHHHh
Confidence 445568999999986
No 90
>PLN02598 omega-6 fatty acid desaturase
Probab=22.00 E-value=1.3e+02 Score=31.05 Aligned_cols=19 Identities=16% Similarity=0.302 Sum_probs=11.2
Q ss_pred cCCccccChhHHhhhcccccc
Q 019841 77 QIPQRLYTLDELKLNGIETRS 97 (335)
Q Consensus 77 ~vp~r~~~~~elk~~gi~~~~ 97 (335)
++| -.+|+.|+| .-|.++-
T Consensus 73 ~~~-~~~tl~~i~-~aiP~~~ 91 (421)
T PLN02598 73 PLP-DNVTLKDVV-KTLPKEV 91 (421)
T ss_pred cCC-CCcCHHHHH-HhCCHHH
Confidence 344 467888887 3354443
No 91
>cd08777 Death_RIP1 Death Domain of Receptor-Interacting Protein 1. Death domain (DD) found in Receptor-Interacting Protein 1 (RIP1) and related proteins. RIP kinases serve as essential sensors of cellular stress. Vertebrates contain several types containing a homologous N-terminal kinase domain and varying C-terminal domains. RIP1 harbors a C-terminal DD, which binds death receptors (DRs) including TNF receptor 1, Fas, TNF-related apoptosis-inducing ligand receptor 1 (TRAILR1), and TRAILR2. It also interacts with other DD-containing adaptor proteins such as TRADD and FADD. RIP1 plays a crucial role in determining a cell's fate, between survival or death, following exposure to stress signals. It is important in the signaling of NF-kappaB and MAPKs, and it links DR-associated signaling to reactive oxygen species (ROS) production. Abnormal RIP1 function may result in ROS accumulation affecting inflammatory responses, innate immunity, stress responses, and cell survival. In general, DDs ar
Probab=21.94 E-value=4.2e+02 Score=21.16 Aligned_cols=47 Identities=21% Similarity=0.194 Sum_probs=30.6
Q ss_pred HHHHHHhcCCCHHHHHHHHHH-----HHHHHHHHHHHcH-------HHHHHHHHHHHcc
Q 019841 270 LDALLKGLGFTQKKADSQVRW-----SLLNTVLLLRRHK-------GARAKLAEAMTMG 316 (335)
Q Consensus 270 at~i~~~lG~s~~~~d~evR~-----A~~~A~~LLr~hr-------~aleaLaeaLle~ 316 (335)
-.++++.||||..+|+.-... -.++++++|+.-+ ..++.|.+||..-
T Consensus 16 Wk~lar~LG~s~~eI~~ie~~~~r~~~~eq~~~mL~~W~~r~g~~~ATv~~L~~aL~~~ 74 (86)
T cd08777 16 WKRCARKLGFTESEIEEIDHDYERDGLKEKVHQMLHKWKMKEGSKGATVGKLAQALEGC 74 (86)
T ss_pred HHHHHHHcCCCHHHHHHHHHhcccCCHHHHHHHHHHHHHHccCCCCcHHHHHHHHHHHc
Confidence 445677899999888752221 2567888886544 4456777777654
No 92
>COG4317 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.81 E-value=1.5e+02 Score=24.33 Aligned_cols=32 Identities=13% Similarity=-0.012 Sum_probs=20.6
Q ss_pred HHhhhhhhhhcCCChHHHHHHHHHHHHHHHHH
Q 019841 118 IAGGVSAWNVFSFNPQQILYLSLALLFLWTVD 149 (335)
Q Consensus 118 ~~g~~~~~~~~~ls~~~~~~~~~~~l~l~aiD 149 (335)
++.|+.+..+---||+.|+++.+|++++..=+
T Consensus 12 llVGiiyaLl~vrsPAPP~iAlvGllGilvGe 43 (93)
T COG4317 12 LLVGIIYALLKVRSPAPPAIALVGLLGILVGE 43 (93)
T ss_pred HHHHHHHHHHhCCCCCCcHHHHHHHHHHHHHH
Confidence 34455544444468899998888888765333
No 93
>PRK01345 heat shock protein HtpX; Provisional
Probab=21.54 E-value=58 Score=32.12 Aligned_cols=28 Identities=18% Similarity=0.126 Sum_probs=21.3
Q ss_pred cccCCCCHhHHHHHHHHHHhHHHHHHHh
Q 019841 164 TIGHTFSQKYHNRVIQHEAGHFLIAYLV 191 (335)
Q Consensus 164 ~l~r~~s~~~r~RIA~HEAGHaLVAylL 191 (335)
.+-+.++++|.+-|.-||-||.--.+.+
T Consensus 114 gLL~~L~~dEL~aVlAHElgHi~~~d~~ 141 (317)
T PRK01345 114 GLLQRLSPEEVAGVMAHELAHVKNRDTL 141 (317)
T ss_pred HHHhhCCHHHHHHHHHHHHHHHHcCCHH
Confidence 3334458899999999999998765544
No 94
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=21.46 E-value=3.7e+02 Score=22.51 Aligned_cols=51 Identities=12% Similarity=0.138 Sum_probs=27.6
Q ss_pred hHHHHHHHH--HHhcCCCHHHHHHHHHH----HHHHHHHHHHHcHHHHHHHHHHHHc
Q 019841 265 ADINKLDAL--LKGLGFTQKKADSQVRW----SLLNTVLLLRRHKGARAKLAEAMTM 315 (335)
Q Consensus 265 ~Dl~~at~i--~~~lG~s~~~~d~evR~----A~~~A~~LLr~hr~aleaLaeaLle 315 (335)
+|+.++.-| ++.+|||-+++..-+.. .......+|+++...+++=.+.|..
T Consensus 41 ~~l~~l~~I~~l~~~G~sl~eI~~~l~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 97 (124)
T TIGR02051 41 ETVKRLRFIKRAQELGFSLEEIGGLLGLVDGTHCREMYELASRKLKSVQAKMADLLR 97 (124)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444444433 56788887766654331 1234556666666665554444443
No 95
>PRK13267 archaemetzincin-like protein; Reviewed
Probab=21.43 E-value=62 Score=29.50 Aligned_cols=11 Identities=45% Similarity=0.809 Sum_probs=8.8
Q ss_pred HHHHHHHhHHH
Q 019841 176 RVIQHEAGHFL 186 (335)
Q Consensus 176 RIA~HEAGHaL 186 (335)
+.+.||.||.|
T Consensus 127 k~~~HElGH~l 137 (179)
T PRK13267 127 KEVTHELGHTL 137 (179)
T ss_pred HHHHHHHHHHc
Confidence 34899999974
No 96
>COG2317 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]
Probab=21.32 E-value=44 Score=35.21 Aligned_cols=10 Identities=50% Similarity=0.710 Sum_probs=8.7
Q ss_pred HHHHHhHHHH
Q 019841 178 IQHEAGHFLI 187 (335)
Q Consensus 178 A~HEAGHaLV 187 (335)
.+||+|||+=
T Consensus 263 ~iHE~GHAlY 272 (497)
T COG2317 263 TIHETGHALY 272 (497)
T ss_pred HHHhhhhHHH
Confidence 5899999984
No 97
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=21.13 E-value=4.7e+02 Score=22.57 Aligned_cols=9 Identities=33% Similarity=0.571 Sum_probs=4.1
Q ss_pred CCHHHHHHH
Q 019841 234 VSATTLNRF 242 (335)
Q Consensus 234 ~s~~~L~r~ 242 (335)
++.+++++.
T Consensus 38 Y~~~~l~~l 46 (134)
T cd04779 38 YDETALDRL 46 (134)
T ss_pred ECHHHHHHH
Confidence 344444444
No 98
>cd04275 ZnMc_pappalysin_like Zinc-dependent metalloprotease, pappalysin_like subfamily. The pregnancy-associated plasma protein A (PAPP-A or pappalysin-1) cleaves insulin-like growth factor-binding proteins 4 and 5, thereby promoting cell growth by releasing bound growth factor. This model includes pappalysins and related metalloprotease domains from all three kingdoms of life. The three-dimensional structure of an archaeal representative, ulilysin, has been solved.
Probab=21.08 E-value=13 Score=34.91 Aligned_cols=20 Identities=30% Similarity=0.398 Sum_probs=15.5
Q ss_pred HhHHHHHHHHHHhHHHHHHH
Q 019841 171 QKYHNRVIQHEAGHFLIAYL 190 (335)
Q Consensus 171 ~~~r~RIA~HEAGHaLVAyl 190 (335)
+...-+++.||.||+|--|-
T Consensus 134 ~~n~g~t~~HEvGH~lGL~H 153 (225)
T cd04275 134 PYNLGDTATHEVGHWLGLYH 153 (225)
T ss_pred cccccceeEEeccceeeeee
Confidence 45566899999999986554
No 99
>PF02074 Peptidase_M32: Carboxypeptidase Taq (M32) metallopeptidase; InterPro: IPR001333 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 M32 (carboxypeptidase Taq 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. Carboxypeptidase Taq is a zinc-containing thermostable metallopeptidase. It was originally discovered and purified from Thermus aquaticus; optimal enzymatic activity occurs at 80 celcius. Although very little is known about this enzyme, it is thought either to be associated with a membrane or to be particle bound.; GO: 0004181 metallocarboxypeptidase activity, 0006508 proteolysis; PDB: 1K9X_A 1KA4_A 1KA2_A 3DWC_A 1WGZ_A 3HQ2_A 3HOA_B.
Probab=20.92 E-value=51 Score=34.78 Aligned_cols=15 Identities=47% Similarity=0.724 Sum_probs=11.2
Q ss_pred HHHHHhHHHHHHHhCCC
Q 019841 178 IQHEAGHFLIAYLVGIL 194 (335)
Q Consensus 178 A~HEAGHaLVAylLg~P 194 (335)
.+||+||+| |-.|+|
T Consensus 263 ~iHE~GHal--YEq~~~ 277 (494)
T PF02074_consen 263 TIHETGHAL--YEQGLP 277 (494)
T ss_dssp HHHHHHHHH--HHHTS-
T ss_pred HHHHHHHHH--HHcCCC
Confidence 579999998 556755
No 100
>PF01400 Astacin: Astacin (Peptidase family M12A) This Prosite motif covers only the active site.; InterPro: IPR001506 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M12, subfamily M12A (astacin family, clan MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA and the predicted active site residues for members of this family and thermolysin occur in the motif HEXXH []. The astacin () family of metalloendopeptidases encompasses a range of proteins found in hydra to humans, in mature and developmental systems []. Their functions include activation of growth factors, degradation of polypeptides, and processing of extracellular proteins []. The proteins are synthesised with N-terminal signal and pro-enzyme sequences, and many contain multiple domains C-terminal to the protease domain. They are either secreted from cells, or are associated with the plasma membrane. The astacin molecule adopts a kidney shape, with a deep active-site cleft between its N- and C-terminal domains []. The zinc ion, which lies at the bottom of the cleft, exhibits a unique penta-coordinated mode of binding, involving 3 histidine residues, a tyrosine and a water molecule (which is also bound to the carboxylate side chain of Glu93) []. The N-terminal domain comprises 2 alpha-helices and a 5-stranded beta-sheet. The overall topology of this domain is shared by the archetypal zinc-endopeptidase thermolysin. Astacin protease domains also share common features with serralysins, matrix metalloendopeptidases, and snake venom proteases; they cleave peptide bonds in polypeptides such as insulin B chain and bradykinin, and in proteins such as casein and gelatin; and they have arylamidase activity [].; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 3LQB_A 3EDH_A 3EDG_A 3EDI_A 1IAE_A 1IAB_A 1IAA_A 1AST_A 1IAC_A 1QJJ_A ....
Probab=20.21 E-value=64 Score=29.22 Aligned_cols=18 Identities=33% Similarity=0.283 Sum_probs=13.0
Q ss_pred HHHHHHHHHhHHHHHHHh
Q 019841 174 HNRVIQHEAGHFLIAYLV 191 (335)
Q Consensus 174 r~RIA~HEAGHaLVAylL 191 (335)
...++.||-||+|--+--
T Consensus 79 ~~~~i~HEl~HaLG~~HE 96 (191)
T PF01400_consen 79 SVGTILHELGHALGFWHE 96 (191)
T ss_dssp SHHHHHHHHHHHHTB--G
T ss_pred CccchHHHHHHHHhhhhh
Confidence 346999999999866554
No 101
>PF01890 CbiG_C: Cobalamin synthesis G C-terminus; InterPro: IPR002750 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. CbiG proteins are specific for anaerobic cobalamin biosynthesis. CbiG, which shows homology with CobE of the aerobic pathway, participates in the conversion of cobalt-precorrin 5 into cobalt-precorrin 6 []. CbiG is responsible for the opening of the delta-lactone ring and extrusion of the C2-unit []. The aerobic pathway uses molecular oxygen to trigger the events at C-20 leading to contraction and expulsion of the C2-unit as acetic acid from a metal-free intermediate, whereas the anaerobic route involves the internal delivery of oxygen from a carboxylic acid terminus to C-20 followed by extrusion of the C2-unit as acetaldehyde, using cobalt complexes as substrates []. This entry represents the core domain of CibG.; GO: 0009236 cobalamin biosynthetic process; PDB: 3BY5_A 2W6K_A 2W6L_A 3EEQ_B.
Probab=20.19 E-value=12 Score=31.81 Aligned_cols=85 Identities=19% Similarity=0.289 Sum_probs=42.1
Q ss_pred hhhHHHHHHHHHHHHccCcH-HHHHHHHHhhcCCC--CccccccccccCCccccChhHHhhhccccccCCCCccccchhh
Q 019841 33 EVSKRRVLKQVDEELSKGDE-RAALALVKDLQGKP--GGLRCFGAARQIPQRLYTLDELKLNGIETRSLLSPVDETLGSI 109 (335)
Q Consensus 33 ~~~~~~~~~~~d~~l~~~~~-~~al~~~~~l~~~~--g~l~~~g~~~~vp~r~~~~~elk~~gi~~~~~lsp~d~~l~~v 109 (335)
+.......+.+++.+.+.+. ...++.+-+...|. =+|..+....++|-+.|+++||+....-+.+-.+-+..+.+||
T Consensus 11 ~~~~~~i~~ai~~~l~~~~~~~~~i~~iasi~~K~~E~~l~~~A~~l~~~~~~~~~eeL~~~~~~~~S~~v~~~~Gv~sV 90 (121)
T PF01890_consen 11 GAPAEEIEEAIEQALAEAGLSPRSIAAIASIDIKADEPGLLELAEELGIPLRFFSAEELNAVEVPTPSEFVKKTTGVGSV 90 (121)
T ss_dssp S--HHHHHHHHHHHHHHCT--GGGEEEEEESSSSS--HHHHHHHHHCTSEEEEE-HHHHHCHHCSCT-CHHHCCCSSS-H
T ss_pred CCCHHHHHHHHHHHHHHcCCChhhccEEEeccccCCCHHHHHHHHHhCCCeEEECHHHHhcCCCCCCCHHHHHHcCCchH
Confidence 45666777777777776553 11222222222222 2455555556799999999999843221111122233456677
Q ss_pred hHHHHHHH
Q 019841 110 ERNLQLAA 117 (335)
Q Consensus 110 ~~~~~~~a 117 (335)
-...++++
T Consensus 91 aEaaAl~a 98 (121)
T PF01890_consen 91 AEAAALLA 98 (121)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHh
Confidence 66555433
No 102
>PLN02498 omega-3 fatty acid desaturase
Probab=20.10 E-value=1.5e+02 Score=31.12 Aligned_cols=15 Identities=13% Similarity=0.439 Sum_probs=8.6
Q ss_pred ccChhHHhhhcccccc
Q 019841 82 LYTLDELKLNGIETRS 97 (335)
Q Consensus 82 ~~~~~elk~~gi~~~~ 97 (335)
.+|+.|+| .-|.+..
T Consensus 101 ~~tl~dir-~aIP~hc 115 (450)
T PLN02498 101 PFNLADIR-AAIPKHC 115 (450)
T ss_pred CCCHHHHH-HhCCHHH
Confidence 35677776 3355544
Done!