Query 021101
Match_columns 317
No_of_seqs 186 out of 681
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 07:37:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021101.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021101hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01434 Peptidase_M41: Peptid 99.9 2.4E-27 5.1E-32 215.7 12.0 140 164-308 22-207 (213)
2 CHL00176 ftsH cell division pr 99.9 2.7E-25 5.9E-30 230.8 14.4 147 165-315 433-625 (638)
3 KOG0734 AAA+-type ATPase conta 99.9 5.2E-26 1.1E-30 229.5 7.7 139 165-307 552-724 (752)
4 PRK10733 hflB ATP-dependent me 99.9 4.4E-25 9.5E-30 229.3 14.8 146 165-314 403-594 (644)
5 TIGR01241 FtsH_fam ATP-depende 99.9 3.6E-24 7.8E-29 215.5 14.6 141 164-308 305-487 (495)
6 COG0465 HflB ATP-dependent Zn 99.9 5.4E-24 1.2E-28 218.6 11.9 139 165-307 401-580 (596)
7 KOG0731 AAA+-type ATPase conta 99.9 3.7E-22 8E-27 209.0 11.2 147 164-315 563-748 (774)
8 CHL00206 ycf2 Ycf2; Provisiona 98.2 1.3E-06 2.9E-11 99.8 6.5 84 171-260 1891-1994(2281)
9 PRK10779 zinc metallopeptidase 97.8 1.3E-05 2.8E-10 80.8 4.0 69 172-240 17-109 (449)
10 cd06163 S2P-M50_PDZ_RseP-like 97.7 2.7E-05 5.8E-10 70.2 2.6 70 172-241 11-104 (182)
11 TIGR00054 RIP metalloprotease 97.5 7.8E-05 1.7E-09 74.7 4.2 69 172-240 16-109 (420)
12 cd06164 S2P-M50_SpoIVFB_CBS Sp 97.3 0.0023 4.9E-08 59.5 10.2 60 172-243 55-114 (227)
13 PF02163 Peptidase_M50: Peptid 96.8 0.0011 2.3E-08 58.7 3.2 26 173-198 10-35 (192)
14 cd06161 S2P-M50_SpoIVFB SpoIVF 96.8 0.0013 2.7E-08 60.1 3.8 60 172-243 40-99 (208)
15 cd05709 S2P-M50 Site-2 proteas 96.6 0.001 2.2E-08 58.5 2.1 64 173-243 11-91 (180)
16 cd06162 S2P-M50_PDZ_SREBP Ster 96.4 0.0031 6.8E-08 60.7 3.8 63 172-243 137-203 (277)
17 PF13398 Peptidase_M50B: Pepti 96.4 0.0039 8.4E-08 56.7 4.1 57 172-241 24-80 (200)
18 cd06159 S2P-M50_PDZ_Arch Uncha 96.0 0.0025 5.3E-08 60.8 1.0 62 173-243 121-186 (263)
19 cd06160 S2P-M50_like_2 Unchara 95.4 0.023 4.9E-07 51.4 4.8 58 172-241 43-106 (183)
20 cd06158 S2P-M50_like_1 Unchara 93.4 0.09 1.9E-06 47.3 3.9 26 173-198 12-41 (181)
21 KOG2921 Intramembrane metallop 89.0 0.42 9E-06 48.5 3.7 34 173-207 134-172 (484)
22 PF00413 Peptidase_M10: Matrix 80.3 0.86 1.9E-05 38.3 1.3 17 166-182 101-117 (154)
23 COG0750 Predicted membrane-ass 79.1 1.6 3.4E-05 42.4 2.8 26 172-197 15-40 (375)
24 PF14247 DUF4344: Domain of un 78.1 1.4 3.1E-05 41.2 2.1 61 124-193 53-114 (220)
25 cd04279 ZnMc_MMP_like_1 Zinc-d 76.3 1.6 3.5E-05 37.4 1.8 21 167-187 101-121 (156)
26 cd04786 HTH_MerR-like_sg7 Heli 75.6 15 0.00032 31.5 7.5 65 249-315 41-113 (131)
27 cd04268 ZnMc_MMP_like Zinc-dep 71.8 2.2 4.7E-05 36.4 1.5 18 167-184 91-108 (165)
28 PF02031 Peptidase_M7: Strepto 67.3 3.8 8.2E-05 35.7 2.0 14 169-182 76-89 (132)
29 PF04298 Zn_peptidase_2: Putat 67.3 2.9 6.2E-05 39.4 1.3 12 173-184 92-103 (222)
30 cd04278 ZnMc_MMP Zinc-dependen 67.3 2.6 5.6E-05 36.3 1.0 17 166-182 103-119 (157)
31 PF06114 DUF955: Domain of unk 66.8 6.1 0.00013 30.9 3.0 23 165-187 37-59 (122)
32 PF05572 Peptidase_M43: Pregna 65.9 2.7 5.9E-05 36.9 0.9 21 166-186 65-85 (154)
33 cd04769 HTH_MerR2 Helix-Turn-H 64.8 45 0.00098 27.5 7.9 66 249-316 40-115 (116)
34 PF09278 MerR-DNA-bind: MerR, 64.7 38 0.00082 24.6 6.7 49 259-309 10-65 (65)
35 cd04277 ZnMc_serralysin_like Z 63.1 4.8 0.0001 35.5 1.9 18 167-184 110-127 (186)
36 cd04327 ZnMc_MMP_like_3 Zinc-d 57.5 6.7 0.00014 35.3 1.9 19 169-187 91-109 (198)
37 smart00235 ZnMc Zinc-dependent 52.8 7 0.00015 32.7 1.1 10 173-182 89-98 (140)
38 cd04783 HTH_MerR1 Helix-Turn-H 50.5 94 0.002 25.9 7.6 60 249-310 41-107 (126)
39 PF08679 DsrD: Dissimilatory s 48.7 23 0.00049 27.6 3.2 44 30-73 14-57 (67)
40 cd01109 HTH_YyaN Helix-Turn-He 46.9 1.4E+02 0.0029 24.4 7.9 61 249-311 41-110 (113)
41 cd04784 HTH_CadR-PbrR Helix-Tu 46.1 1.4E+02 0.0031 24.8 8.1 52 249-302 41-100 (127)
42 TIGR02044 CueR Cu(I)-responsiv 45.8 1E+02 0.0022 25.8 7.1 60 249-310 41-109 (127)
43 PF11350 DUF3152: Protein of u 45.4 10 0.00023 35.3 1.1 18 167-185 136-153 (203)
44 cd00203 ZnMc Zinc-dependent me 45.3 11 0.00024 31.9 1.3 19 168-186 94-112 (167)
45 PF13485 Peptidase_MA_2: Pepti 43.6 24 0.00052 27.7 2.9 23 166-188 21-43 (128)
46 PF13812 PPR_3: Pentatricopept 43.4 32 0.0007 21.0 2.9 27 40-66 7-33 (34)
47 cd04768 HTH_BmrR-like Helix-Tu 43.3 77 0.0017 25.3 5.8 52 249-302 41-94 (96)
48 cd04777 HTH_MerR-like_sg1 Heli 42.8 1.1E+02 0.0024 24.6 6.7 52 249-302 39-102 (107)
49 TIGR01950 SoxR redox-sensitive 42.0 1.6E+02 0.0034 25.5 7.8 61 249-311 41-111 (142)
50 cd04787 HTH_HMRTR_unk Helix-Tu 41.8 1.7E+02 0.0037 24.6 8.0 52 249-302 41-100 (133)
51 PRK13267 archaemetzincin-like 41.6 7 0.00015 35.4 -0.6 11 172-182 127-137 (179)
52 COG0501 HtpX Zn-dependent prot 41.5 19 0.00041 33.6 2.2 24 164-187 151-174 (302)
53 PF13582 Reprolysin_3: Metallo 40.1 14 0.0003 29.9 1.0 12 171-182 108-119 (124)
54 cd01108 HTH_CueR Helix-Turn-He 38.7 2.3E+02 0.0049 23.7 8.2 52 249-302 41-100 (127)
55 TIGR02047 CadR-PbrR Cd(II)/Pb( 38.7 2.2E+02 0.0047 23.9 8.1 60 249-310 41-109 (127)
56 PF01435 Peptidase_M48: Peptid 37.1 24 0.00053 31.1 2.2 23 165-187 84-106 (226)
57 cd04788 HTH_NolA-AlbR Helix-Tu 37.1 99 0.0021 24.7 5.5 50 249-300 41-92 (96)
58 cd04770 HTH_HMRTR Helix-Turn-H 36.8 2.4E+02 0.0051 23.2 8.0 52 249-302 41-100 (123)
59 COG2856 Predicted Zn peptidase 36.1 29 0.00062 32.4 2.5 22 166-187 68-89 (213)
60 cd04776 HTH_GnyR Helix-Turn-He 35.1 2.6E+02 0.0057 23.2 8.7 61 249-311 39-111 (118)
61 PRK15002 redox-sensitivie tran 34.5 2.4E+02 0.0053 24.8 8.0 60 249-310 51-120 (154)
62 cd04773 HTH_TioE_rpt2 Second H 33.7 2.3E+02 0.0049 23.1 7.2 53 249-303 41-100 (108)
63 PF10819 DUF2564: Protein of u 33.7 2.3E+02 0.0051 22.8 6.9 68 248-316 1-77 (79)
64 cd01282 HTH_MerR-like_sg3 Heli 33.6 1.6E+02 0.0034 24.1 6.3 58 249-308 40-109 (112)
65 cd04782 HTH_BltR Helix-Turn-He 33.5 1.5E+02 0.0032 23.7 6.0 52 249-302 41-95 (97)
66 cd04785 HTH_CadR-PbrR-like Hel 33.4 2.8E+02 0.0061 23.1 7.9 52 249-302 41-100 (126)
67 TIGR02051 MerR Hg(II)-responsi 31.5 2.4E+02 0.0052 23.5 7.2 52 249-302 40-97 (124)
68 cd01106 HTH_TipAL-Mta Helix-Tu 31.3 1.6E+02 0.0034 23.6 5.9 50 249-300 41-92 (103)
69 PF12388 Peptidase_M57: Dual-a 31.2 32 0.00069 32.2 2.0 25 163-187 126-150 (211)
70 cd06258 Peptidase_M3_like The 31.1 27 0.00059 33.8 1.6 19 171-189 155-173 (365)
71 cd01204 IRS_PTB Insulin recept 30.8 26 0.00056 29.4 1.2 35 28-62 68-103 (104)
72 COG5549 Predicted Zn-dependent 29.7 28 0.00061 32.9 1.3 21 163-183 180-200 (236)
73 PRK05457 heat shock protein Ht 29.7 36 0.00077 32.8 2.1 19 164-182 128-146 (284)
74 PRK02391 heat shock protein Ht 29.6 35 0.00076 33.0 2.0 22 164-185 127-148 (296)
75 TIGR01675 plant-AP plant acid 29.6 55 0.0012 30.9 3.3 81 6-96 88-168 (229)
76 cd01107 HTH_BmrR Helix-Turn-He 29.1 2E+02 0.0042 23.4 6.1 52 249-302 42-96 (108)
77 cd04790 HTH_Cfa-like_unk Helix 29.0 2.5E+02 0.0053 25.0 7.2 18 249-266 42-61 (172)
78 PF07998 Peptidase_M54: Peptid 28.1 30 0.00065 31.9 1.2 11 172-182 147-157 (194)
79 PF09471 Peptidase_M64: IgA Pe 27.8 28 0.00061 33.4 1.0 20 166-185 212-231 (264)
80 PRK03982 heat shock protein Ht 27.6 44 0.00096 31.9 2.3 21 165-185 120-140 (288)
81 PF06969 HemN_C: HemN C-termin 27.5 71 0.0015 23.2 3.0 35 34-68 19-53 (66)
82 PRK04897 heat shock protein Ht 27.4 41 0.00088 32.5 2.0 19 164-182 131-149 (298)
83 COG2738 Predicted Zn-dependent 26.9 33 0.00072 32.2 1.3 14 172-185 94-107 (226)
84 PRK03001 M48 family peptidase; 26.6 49 0.0011 31.5 2.4 21 165-185 119-139 (283)
85 TIGR02043 ZntR Zn(II)-responsi 26.4 3.5E+02 0.0077 22.7 7.4 52 249-302 42-102 (131)
86 PF12994 DUF3878: Domain of un 26.0 13 0.00028 36.5 -1.6 17 168-184 92-108 (299)
87 cd04275 ZnMc_pappalysin_like Z 25.9 9.7 0.00021 35.6 -2.4 20 167-186 134-153 (225)
88 cd04280 ZnMc_astacin_like Zinc 25.6 35 0.00076 30.4 1.2 17 171-187 75-91 (180)
89 PF13583 Reprolysin_4: Metallo 24.6 38 0.00082 30.9 1.2 17 172-188 139-155 (206)
90 PF01400 Astacin: Astacin (Pep 24.6 48 0.001 29.8 1.9 17 171-187 80-96 (191)
91 cd04276 ZnMc_MMP_like_2 Zinc-d 23.9 51 0.0011 30.3 1.9 15 168-182 114-128 (197)
92 PRK09514 zntR zinc-responsive 23.8 4.6E+02 0.01 22.4 7.9 52 249-302 42-102 (140)
93 PF00901 Orbi_VP5: Orbivirus o 23.7 2.6E+02 0.0057 29.6 7.1 18 284-301 183-200 (508)
94 PRK03072 heat shock protein Ht 23.5 63 0.0014 31.1 2.5 23 164-186 121-143 (288)
95 KOG0058 Peptide exporter, ABC 23.4 48 0.001 36.3 1.9 87 219-309 535-650 (716)
96 PRK10227 DNA-binding transcrip 23.3 4.7E+02 0.01 22.3 7.9 18 249-266 41-60 (135)
97 cd06461 M2_ACE Peptidase famil 23.0 54 0.0012 34.1 2.1 20 286-305 422-441 (477)
98 COG4219 MecR1 Antirepressor re 22.6 50 0.0011 33.0 1.6 23 160-182 180-202 (337)
99 TIGR03455 HisG_C-term ATP phos 22.3 24 0.00052 29.0 -0.5 28 35-65 61-88 (100)
100 cd04283 ZnMc_hatching_enzyme Z 22.0 48 0.0011 30.1 1.4 17 172-188 79-95 (182)
101 PRK01345 heat shock protein Ht 21.8 60 0.0013 31.8 2.0 22 165-186 119-140 (317)
102 PF13688 Reprolysin_5: Metallo 20.6 59 0.0013 28.5 1.6 23 166-188 138-160 (196)
103 cd04281 ZnMc_BMP1_TLD Zinc-dep 20.5 53 0.0012 30.2 1.3 17 172-188 89-105 (200)
104 PF05569 Peptidase_M56: BlaR1 20.3 72 0.0016 30.2 2.2 18 164-181 190-207 (299)
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=99.95 E-value=2.4e-27 Score=215.74 Aligned_cols=140 Identities=26% Similarity=0.287 Sum_probs=110.5
Q ss_pred CCChhhhHHHHHHHhhHHHHHHHhC--CCCceEEeec-Cc--ccceecchHHHHhhhcCCCCHHHHHHHHHHHchHHHHH
Q 021101 164 SFFPDYQERVARHEAAHFLLAYLLG--LPILGYSLDI-GK--ENVNLIDERLEKLIYSGQLDAKELDRLAVVAMAGLAAE 238 (317)
Q Consensus 164 ~ls~~~r~RIA~HEAGHaLvAylLg--~PV~kvsI~p-G~--ggv~f~~~e~e~~~~~g~~s~~~L~r~~~VlLAGrAAE 238 (317)
.+++++|+++|||||||++|+++++ .||.++||.| |. |++.+.+++ +. ...+++++.+.++|+|||||||
T Consensus 22 ~~~~~~~~~~A~HEAGhAvva~~l~~~~~v~~vsi~prg~~~G~~~~~~~~-~~----~~~t~~~l~~~i~v~LaGraAE 96 (213)
T PF01434_consen 22 KLSEEEKRRIAYHEAGHAVVAYLLPPADPVSKVSIVPRGSALGFTQFTPDE-DR----YIRTRSYLEDRICVLLAGRAAE 96 (213)
T ss_dssp ---HHHHHHHHHHHHHHHHHHHHSSS---EEEEESSTTCCCCHCCEECHHT-T-----SS-BHHHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHhcccccEEEEEEecCCCcceeEEeccch-hc----ccccHHHHHhhHHHHHHHHHHH
Confidence 3589999999999999999999998 5999999998 32 345554432 21 1369999999999999999999
Q ss_pred HhhcC--C-ccchhhHHHHHHHHHHH----hCCCC---------------------------CH-------HHHHHHHHH
Q 021101 239 GLQYD--K-VVGQSADLFSLQRFINR----TKPPL---------------------------SQ-------DQQQNLTRW 277 (317)
Q Consensus 239 ~lvfG--~-atGa~~Dl~~lt~i~~~----lG~~~---------------------------s~-------~e~~~l~r~ 277 (317)
+++|| + ++|+++|+++++++++. +|++- ++ .+++++++.
T Consensus 97 e~~~g~~~~stGa~~DL~~At~iA~~mv~~~Gm~~~~g~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~i~~ev~~lL~~ 176 (213)
T PF01434_consen 97 ELFFGEDNVSTGASSDLQQATEIARKMVASYGMGDSLGLLSYSPNDDDEVFLGREWNSRRPMSEETRALIDREVRKLLEE 176 (213)
T ss_dssp HHHHSCCS-BGGGHHHHHHHHHHHHHHHHTST-TTTTTSS-SEEEE-S-SSS-E---EEESS-HHHHHHHHHHHHHHHHH
T ss_pred HhhcCcceecccchhHHHHHHHHHHHHHHHhCCCCCCceeeeeccccccccccccccccCCcchhhHHHHHHHHHHHHHH
Confidence 99999 5 58999999999888763 55530 11 246778899
Q ss_pred HHHHHHHHHHHcHHHHHHHHHHHHHhchHHH
Q 021101 278 AVLFAATLIKNNKAIHEALMAAMSKKATILE 308 (317)
Q Consensus 278 A~~~A~~LL~~~r~~leaLaeaLle~esl~e 308 (317)
||.+|+++|++||+.+++|+++|+++++|+.
T Consensus 177 a~~~a~~iL~~~r~~l~~la~~Lle~~~L~~ 207 (213)
T PF01434_consen 177 AYARAKEILEENREALEALAEALLEKETLSG 207 (213)
T ss_dssp HHHHHHHHHHHTHHHHHHHHHHHHHHSEEEH
T ss_pred HHHHHHHHHHHhHHHHHHHHHHHHHhCeeCH
Confidence 9999999999999999999999999997743
No 2
>CHL00176 ftsH cell division protein; Validated
Probab=99.93 E-value=2.7e-25 Score=230.83 Aligned_cols=147 Identities=20% Similarity=0.262 Sum_probs=121.8
Q ss_pred CChhhhHHHHHHHhhHHHHHHHhC--CCCceEEeec-Cc-ccceecchHHHHhhhcCCCCHHHHHHHHHHHchHHHHHHh
Q 021101 165 FFPDYQERVARHEAAHFLLAYLLG--LPILGYSLDI-GK-ENVNLIDERLEKLIYSGQLDAKELDRLAVVAMAGLAAEGL 240 (317)
Q Consensus 165 ls~~~r~RIA~HEAGHaLvAylLg--~PV~kvsI~p-G~-ggv~f~~~e~e~~~~~g~~s~~~L~r~~~VlLAGrAAE~l 240 (317)
.++++|++||||||||++++++++ .||+++||.| |+ .|+++..|+.++. .+++.++...++++|||||||++
T Consensus 433 ~~~~~~~~vA~hEaGhA~v~~~l~~~~~v~kvtI~prg~~~G~~~~~p~~~~~----~~t~~~l~~~i~~~LgGraAE~~ 508 (638)
T CHL00176 433 EDSKNKRLIAYHEVGHAIVGTLLPNHDPVQKVTLIPRGQAKGLTWFTPEEDQS----LVSRSQILARIVGALGGRAAEEV 508 (638)
T ss_pred ccHHHHHHHHHHhhhhHHHHhhccCCCceEEEEEeecCCCCCceEecCCcccc----cccHHHHHHHHHHHhhhHHHHHH
Confidence 468899999999999999999997 6999999998 43 3655555543332 47999999999999999999999
Q ss_pred hcCC---ccchhhHHHHHHHHHH----HhCCC--------------------------CCH-------HHHHHHHHHHHH
Q 021101 241 QYDK---VVGQSADLFSLQRFIN----RTKPP--------------------------LSQ-------DQQQNLTRWAVL 280 (317)
Q Consensus 241 vfG~---atGa~~Dl~~lt~i~~----~lG~~--------------------------~s~-------~e~~~l~r~A~~ 280 (317)
+||+ ++|++||++++|++++ ++||+ +++ .+++++++.||.
T Consensus 509 ~fg~~~~~~Ga~~Dl~~AT~iA~~mv~~~Gm~~~g~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~iD~ev~~~l~~~~~ 588 (638)
T CHL00176 509 VFGSTEVTTGASNDLQQVTNLARQMVTRFGMSSIGPISLESNNSTDPFLGRFMQRNSEYSEEIADKIDMEVRSILHTCYQ 588 (638)
T ss_pred hcCCCCcCCCchhHHHHHHHHHHHHHHHhCCCcCCceeecCCCCcccccccccccccCcCHHHHHHHHHHHHHHHHHHHH
Confidence 9994 4899999999987765 56664 111 367889999999
Q ss_pred HHHHHHHHcHHHHHHHHHHHHHhchHH--HHHHHHHh
Q 021101 281 FAATLIKNNKAIHEALMAAMSKKATIL--ECIEAIEN 315 (317)
Q Consensus 281 ~A~~LL~~~r~~leaLaeaLle~esl~--eC~~~Ie~ 315 (317)
+|+++|++||+.+++||++|+++|||+ |+.++++.
T Consensus 589 ~a~~iL~~~~~~l~~la~~Lle~Etl~~~ei~~il~~ 625 (638)
T CHL00176 589 YAYQILKDNRVLIDLLVELLLQKETIDGDEFREIVNS 625 (638)
T ss_pred HHHHHHHHhHHHHHHHHHHHHHhCccCHHHHHHHHhh
Confidence 999999999999999999999999774 56777764
No 3
>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]
Probab=99.92 E-value=5.2e-26 Score=229.48 Aligned_cols=139 Identities=21% Similarity=0.218 Sum_probs=119.0
Q ss_pred CChhhhHHHHHHHhhHHHHHHHhC--CCCceEEeec-Ccc-cceecchHHHHhhhcCCCCHHHHHHHHHHHchHHHHHHh
Q 021101 165 FFPDYQERVARHEAAHFLLAYLLG--LPILGYSLDI-GKE-NVNLIDERLEKLIYSGQLDAKELDRLAVVAMAGLAAEGL 240 (317)
Q Consensus 165 ls~~~r~RIA~HEAGHaLvAylLg--~PV~kvsI~p-G~g-gv~f~~~e~e~~~~~g~~s~~~L~r~~~VlLAGrAAE~l 240 (317)
++++-|+.+||||+||+|||++.. .|+||.||.| |.. |.+...|+.|+. .+|+.++..++-|+||||+||+|
T Consensus 552 i~~eak~~TAyHE~GHAivA~yTk~A~PlhKaTImPRG~sLG~t~~LPe~D~~----~~Tk~q~LA~lDV~MGGRvAEEL 627 (752)
T KOG0734|consen 552 IDEEAKKITAYHEGGHAIVALYTKGAMPLHKATIMPRGPSLGHTSQLPEKDRY----SITKAQLLARLDVCMGGRVAEEL 627 (752)
T ss_pred cChhhhhhhhhhccCceEEEeecCCCccccceeeccCCccccceeecCccchh----hHHHHHHHHHHHHhhcchHHHHH
Confidence 478889999999999999999998 5999999998 654 666666654443 47999999999999999999999
Q ss_pred hcCC---ccchhhHHHHHHHH----HHHhCCC-------C---------C-------HHHHHHHHHHHHHHHHHHHHHcH
Q 021101 241 QYDK---VVGQSADLFSLQRF----INRTKPP-------L---------S-------QDQQQNLTRWAVLFAATLIKNNK 290 (317)
Q Consensus 241 vfG~---atGa~~Dl~~lt~i----~~~lG~~-------~---------s-------~~e~~~l~r~A~~~A~~LL~~~r 290 (317)
+||. .+|+++|++|+|++ ++.+||+ + + +.|++++++.+|++|+.||+.|.
T Consensus 628 IfG~D~iTsGAssDl~qAT~lA~~MVt~fGMSd~vG~v~~~~~~~~~s~~~~t~~lidaEi~~lL~~sYeRak~iL~~h~ 707 (752)
T KOG0734|consen 628 IFGTDKITSGASSDLDQATKLARRMVTKFGMSDKVGPVTLSAEDNSSSLSPRTQELIDAEIKRLLRDSYERAKSILKTHK 707 (752)
T ss_pred hccCCcccccccchHHHHHHHHHHHHHHcCccccccceeeeccCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9995 47999999998765 5567876 1 0 24788999999999999999999
Q ss_pred HHHHHHHHHHHHhchHH
Q 021101 291 AIHEALMAAMSKKATIL 307 (317)
Q Consensus 291 ~~leaLaeaLle~esl~ 307 (317)
..+++||++|++.|||+
T Consensus 708 kEl~~LA~ALleYETL~ 724 (752)
T KOG0734|consen 708 KELHALAEALLEYETLD 724 (752)
T ss_pred HHHHHHHHHHHHhhcCC
Confidence 99999999999999885
No 4
>PRK10733 hflB ATP-dependent metalloprotease; Reviewed
Probab=99.92 E-value=4.4e-25 Score=229.33 Aligned_cols=146 Identities=20% Similarity=0.221 Sum_probs=120.0
Q ss_pred CChhhhHHHHHHHhhHHHHHHHhC--CCCceEEeec-Ccc-cceecchHHHHhhhcCCCCHHHHHHHHHHHchHHHHHHh
Q 021101 165 FFPDYQERVARHEAAHFLLAYLLG--LPILGYSLDI-GKE-NVNLIDERLEKLIYSGQLDAKELDRLAVVAMAGLAAEGL 240 (317)
Q Consensus 165 ls~~~r~RIA~HEAGHaLvAylLg--~PV~kvsI~p-G~g-gv~f~~~e~e~~~~~g~~s~~~L~r~~~VlLAGrAAE~l 240 (317)
+++++|+++||||+||++|+++++ .||+++||.| |.+ |+++..|+.+.. ..|++++.+.++|+|||||||++
T Consensus 403 ~~~~~~~~~a~he~gha~~~~~~~~~~~~~~v~i~prg~~~g~~~~~~~~~~~----~~~~~~l~~~i~~~lgGraAE~~ 478 (644)
T PRK10733 403 MTEAQKESTAYHEAGHAIIGRLVPEHDPVHKVTIIPRGRALGVTFFLPEGDAI----SASRQKLESQISTLYGGRLAEEI 478 (644)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHccCCCceeEEEEeccCCCcceeEECCCcccc----cccHHHHHHHHHHHHhhHHHHHH
Confidence 578899999999999999999997 6999999998 433 555554542222 36899999999999999999999
Q ss_pred hcCC---ccchhhHHHHHHHHHH----HhCCC--------------------------CC-------HHHHHHHHHHHHH
Q 021101 241 QYDK---VVGQSADLFSLQRFIN----RTKPP--------------------------LS-------QDQQQNLTRWAVL 280 (317)
Q Consensus 241 vfG~---atGa~~Dl~~lt~i~~----~lG~~--------------------------~s-------~~e~~~l~r~A~~ 280 (317)
+||. ++|++||++++|+|++ ++||+ ++ +.++++++++||.
T Consensus 479 ~~g~~~~ttGa~~Dl~~AT~lA~~mv~~~Gms~~lg~~~~~~~~~~~~lg~~~~~~~~~s~~~~~~id~ev~~il~~~~~ 558 (644)
T PRK10733 479 IYGPEHVSTGASNDIKVATNLARNMVTQWGFSEKLGPLLYAEEEGEVFLGRSVAKAKHMSDETARIIDQEVKALIERNYN 558 (644)
T ss_pred HhCCCCCCCCcHHHHHHHHHHHHHHHHHhCCCccccchhhcccccccccccccccccccCHHHHHHHHHHHHHHHHHHHH
Confidence 9984 4899999999988765 56665 11 1467889999999
Q ss_pred HHHHHHHHcHHHHHHHHHHHHHhchHH--HHHHHHH
Q 021101 281 FAATLIKNNKAIHEALMAAMSKKATIL--ECIEAIE 314 (317)
Q Consensus 281 ~A~~LL~~~r~~leaLaeaLle~esl~--eC~~~Ie 314 (317)
+|+++|++|++.+++||++|+++|||+ |..+++.
T Consensus 559 ~a~~iL~~~~~~l~~la~~Lle~etl~~~ei~~i~~ 594 (644)
T PRK10733 559 RARQLLTDNMDILHAMKDALMKYETIDAPQIDDLMA 594 (644)
T ss_pred HHHHHHHHhHHHHHHHHHHHHHhceeCHHHHHHHHh
Confidence 999999999999999999999999875 4555554
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=99.91 E-value=3.6e-24 Score=215.49 Aligned_cols=141 Identities=22% Similarity=0.199 Sum_probs=116.8
Q ss_pred CCChhhhHHHHHHHhhHHHHHHHhC--CCCceEEeec-Cc-ccceecchHHHHhhhcCCCCHHHHHHHHHHHchHHHHHH
Q 021101 164 SFFPDYQERVARHEAAHFLLAYLLG--LPILGYSLDI-GK-ENVNLIDERLEKLIYSGQLDAKELDRLAVVAMAGLAAEG 239 (317)
Q Consensus 164 ~ls~~~r~RIA~HEAGHaLvAylLg--~PV~kvsI~p-G~-ggv~f~~~e~e~~~~~g~~s~~~L~r~~~VlLAGrAAE~ 239 (317)
.+++++|+++|||||||++++++++ .||+++||.| |. +|+++..|..+ .+..++++++++++|+|||||||+
T Consensus 305 ~~~~~~~~~~A~hEaGhAlv~~~l~~~~~v~~vsi~prg~~~G~~~~~~~~~----~~~~t~~~l~~~i~v~LaGraAE~ 380 (495)
T TIGR01241 305 VISEKEKKLVAYHEAGHALVGLLLKDADPVHKVTIIPRGQALGYTQFLPEED----KYLYTKSQLLAQIAVLLGGRAAEE 380 (495)
T ss_pred cccHHHHHHHHHHHHhHHHHHHhcCCCCceEEEEEeecCCccceEEecCccc----cccCCHHHHHHHHHHHhhHHHHHH
Confidence 3578999999999999999999996 6999999998 43 34443333221 235799999999999999999999
Q ss_pred hhcCCc-cchhhHHHHHHHHHH----HhCCCC--------------------------C-------HHHHHHHHHHHHHH
Q 021101 240 LQYDKV-VGQSADLFSLQRFIN----RTKPPL--------------------------S-------QDQQQNLTRWAVLF 281 (317)
Q Consensus 240 lvfG~a-tGa~~Dl~~lt~i~~----~lG~~~--------------------------s-------~~e~~~l~r~A~~~ 281 (317)
++||++ +|+++|++++|++++ ++|+.- + +.++++++++||.+
T Consensus 381 ~~~G~~s~Ga~~Dl~~At~lA~~mv~~~Gm~~~~g~~~~~~~~~~~~l~~~~~~~~~~s~~~~~~id~~v~~lL~~a~~r 460 (495)
T TIGR01241 381 IIFGEVTTGASNDIKQATNIARAMVTEWGMSDKLGPVAYGSDGGDVFLGRGFAKAKEYSEETAREIDEEVKRIIEEAYKR 460 (495)
T ss_pred HHhcCCCCCchHHHHHHHHHHHHHHHHhCCCcccCceeeccCccccccccccccccccCHHHHHHHHHHHHHHHHHHHHH
Confidence 999986 799999999988865 456531 1 24577889999999
Q ss_pred HHHHHHHcHHHHHHHHHHHHHhchHHH
Q 021101 282 AATLIKNNKAIHEALMAAMSKKATILE 308 (317)
Q Consensus 282 A~~LL~~~r~~leaLaeaLle~esl~e 308 (317)
|+++|++|++++++||++|+++++|++
T Consensus 461 a~~lL~~~~~~l~~la~~Ll~~e~L~~ 487 (495)
T TIGR01241 461 AKQILTENRDELELLAKALLEKETITR 487 (495)
T ss_pred HHHHHHHhHHHHHHHHHHHHHcCeeCH
Confidence 999999999999999999999998763
No 6
>COG0465 HflB ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]
Probab=99.90 E-value=5.4e-24 Score=218.62 Aligned_cols=139 Identities=25% Similarity=0.244 Sum_probs=120.0
Q ss_pred CChhhhHHHHHHHhhHHHHHHHhCC--CCceEEeec-Ccc-cceecchHHHHhhhcCCCCHHHHHHHHHHHchHHHHHHh
Q 021101 165 FFPDYQERVARHEAAHFLLAYLLGL--PILGYSLDI-GKE-NVNLIDERLEKLIYSGQLDAKELDRLAVVAMAGLAAEGL 240 (317)
Q Consensus 165 ls~~~r~RIA~HEAGHaLvAylLg~--PV~kvsI~p-G~g-gv~f~~~e~e~~~~~g~~s~~~L~r~~~VlLAGrAAE~l 240 (317)
+++++|+.+|||||||++++++++. ||||+||+| |+. |+++..|+.|+ +.+|++++...++++||||+||++
T Consensus 401 ise~ek~~~AYhEaghalv~~~l~~~d~v~KvtIiPrG~alG~t~~~Pe~d~----~l~sk~~l~~~i~~~lgGRaAEel 476 (596)
T COG0465 401 ISEAEKKITAYHEAGHALVGLLLPDADPVHKVTIIPRGRALGYTLFLPEEDK----YLMSKEELLDRIDVLLGGRAAEEL 476 (596)
T ss_pred cChhhhcchHHHHHHHHHHHHhCCCCcccceeeeccCchhhcchhcCCcccc----ccccHHHHHHHHHHHhCCcHhhhh
Confidence 7889999999999999999999984 999999998 643 77777776433 458999999999999999999999
Q ss_pred hcC-Cc-cchhhHHHHHHHHHH----HhCCC------------------------CCH-------HHHHHHHHHHHHHHH
Q 021101 241 QYD-KV-VGQSADLFSLQRFIN----RTKPP------------------------LSQ-------DQQQNLTRWAVLFAA 283 (317)
Q Consensus 241 vfG-~a-tGa~~Dl~~lt~i~~----~lG~~------------------------~s~-------~e~~~l~r~A~~~A~ 283 (317)
+|| +. +|++||++++|.+++ ++|++ +++ .++++++..+|.+++
T Consensus 477 ~~g~e~ttGa~~D~~~at~~ar~mVt~~Gms~~lG~v~~~~~~~~flg~~~~~~~~Se~ta~~ID~evk~ii~~~y~~a~ 556 (596)
T COG0465 477 IFGYEITTGASNDLEKATDLARAMVTEYGMSAKLGPVAYEQVEGVFLGRYQKAKNYSEETAQEIDREVKDIIDEAYERAK 556 (596)
T ss_pred hhcccccccchhhHHHHHHHHHHhhhhcCcchhhCceehhhcccccccccccccCccHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999 75 899999999877654 56766 221 357889999999999
Q ss_pred HHHHHcHHHHHHHHHHHHHhchHH
Q 021101 284 TLIKNNKAIHEALMAAMSKKATIL 307 (317)
Q Consensus 284 ~LL~~~r~~leaLaeaLle~esl~ 307 (317)
.+|.+|++.++.++++|+++||++
T Consensus 557 ~il~~~~~~l~~~~~~Lle~Eti~ 580 (596)
T COG0465 557 ELLNENKDALETLAEMLLEKETID 580 (596)
T ss_pred HHHHHhHHHHHHHHHHHHHhhccC
Confidence 999999999999999999999965
No 7
>KOG0731 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]
Probab=99.87 E-value=3.7e-22 Score=209.05 Aligned_cols=147 Identities=22% Similarity=0.240 Sum_probs=123.2
Q ss_pred CCChhhhHHHHHHHhhHHHHHHHhC--CCCceEEeecCcc-cceecchHHHHhhhcCCCCHHHHHHHHHHHchHHHHHHh
Q 021101 164 SFFPDYQERVARHEAAHFLLAYLLG--LPILGYSLDIGKE-NVNLIDERLEKLIYSGQLDAKELDRLAVVAMAGLAAEGL 240 (317)
Q Consensus 164 ~ls~~~r~RIA~HEAGHaLvAylLg--~PV~kvsI~pG~g-gv~f~~~e~e~~~~~g~~s~~~L~r~~~VlLAGrAAE~l 240 (317)
.+++++++.+|||||||++++++++ +||.++||+||++ |+.+..|..+ +.+++++|..++||+|||||||++
T Consensus 563 ~~~~~~~~~~a~~eagha~~g~~l~~~dpl~kvsIiPGqalG~a~~~P~~~-----~l~sk~ql~~rm~m~LGGRaAEev 637 (774)
T KOG0731|consen 563 VLSLEEKKTVAYHEAGHAVVGWLLEHADPLLKVSIIPGQALGYAQYLPTDD-----YLLSKEQLFDRMVMALGGRAAEEV 637 (774)
T ss_pred hcCHhhhhhhhhhhccchhhhccccccCcceeEEeccCCccceEEECCccc-----ccccHHHHHHHHHHHhCcchhhhe
Confidence 4588999999999999999998888 5999999999865 5555555422 458999999999999999999999
Q ss_pred hcC-C-ccchhhHHHHHHHHHH----HhCCC---------------------CC-------HHHHHHHHHHHHHHHHHHH
Q 021101 241 QYD-K-VVGQSADLFSLQRFIN----RTKPP---------------------LS-------QDQQQNLTRWAVLFAATLI 286 (317)
Q Consensus 241 vfG-~-atGa~~Dl~~lt~i~~----~lG~~---------------------~s-------~~e~~~l~r~A~~~A~~LL 286 (317)
+|| + ++|++||++++|+|++ ++|++ ++ +.++++++..||++|.++|
T Consensus 638 ~fg~~iTtga~ddl~kvT~~A~~~V~~~Gms~kig~~~~~~~~~~~~~~~~p~s~~~~~~Id~ev~~lv~~ay~~~~~ll 717 (774)
T KOG0731|consen 638 VFGSEITTGAQDDLEKVTKIARAMVASFGMSEKIGPISFQMLLPGDESFRKPYSEKTAQLIDTEVRRLVQKAYERTKELL 717 (774)
T ss_pred ecCCccCchhhccHHHHHHHHHHHHHHcCcccccCceeccCcccccccccCccchhHHHHHHHHHHHHHhhHHHHHHHHH
Confidence 997 4 4899999999999876 45554 11 1357788999999999999
Q ss_pred HHcHHHHHHHHHHHHHhc--hHHHHHHHHHh
Q 021101 287 KNNKAIHEALMAAMSKKA--TILECIEAIEN 315 (317)
Q Consensus 287 ~~~r~~leaLaeaLle~e--sl~eC~~~Ie~ 315 (317)
++|++.++.+++.|+++| +-+|+++++..
T Consensus 718 ~~n~~~l~~ia~~LLeke~l~~ee~~~ll~~ 748 (774)
T KOG0731|consen 718 RTNRDKLDKIAEVLLEKEVLTGEEIIALLGE 748 (774)
T ss_pred HHhHHHHHHHHHHHHHhhhccHHHHHHHhcc
Confidence 999999999999999998 55788887753
No 8
>CHL00206 ycf2 Ycf2; Provisional
Probab=98.25 E-value=1.3e-06 Score=99.85 Aligned_cols=84 Identities=14% Similarity=0.004 Sum_probs=60.7
Q ss_pred HHHHHHHhhHHHHHHHhC--CCCceEEee--c-----Ccc-cceecchHHHHhhhcCCCCHHHHHHHHHHHchHHHHHHh
Q 021101 171 ERVARHEAAHFLLAYLLG--LPILGYSLD--I-----GKE-NVNLIDERLEKLIYSGQLDAKELDRLAVVAMAGLAAEGL 240 (317)
Q Consensus 171 ~RIA~HEAGHaLvAylLg--~PV~kvsI~--p-----G~g-gv~f~~~e~e~~~~~g~~s~~~L~r~~~VlLAGrAAE~l 240 (317)
++|++||+|||+|+.++. +||+++||. | |.+ |.++..|.. ..+++.++..++.++|||+|||.+
T Consensus 1891 ~~ia~yEiGhAvvq~~L~~~~pv~kISIy~~~~~~r~~~~yl~~wyle~~------~~mkk~tiL~~Il~cLAGraAedl 1964 (2281)
T CHL00206 1891 HGILFYQIGRAVAQNVLLSNCPIDPISIYMKKKSCKEGDSYLYKWYFELG------TSMKKLTILLYLLSCSAGSVAQDL 1964 (2281)
T ss_pred hhhhhhHHhHHHHHHhccCCCCcceEEEecCCccccCcccceeEeecCCc------ccCCHHHHHHHHHHHhhhhhhhhh
Confidence 358999999999999986 699999984 3 222 444444421 257899999999999999999999
Q ss_pred hcCCc---------cch-hhHHHHHHHHHH
Q 021101 241 QYDKV---------VGQ-SADLFSLQRFIN 260 (317)
Q Consensus 241 vfG~a---------tGa-~~Dl~~lt~i~~ 260 (317)
.|... -|- .+|..-+-.++.
T Consensus 1965 wf~~~~~~~n~It~yg~vEnD~~La~glLe 1994 (2281)
T CHL00206 1965 WSLPGPDEKNGITSYGLVENDSDLVHGLLE 1994 (2281)
T ss_pred ccCcchhhhcCcccccchhhhhHHhHhHHH
Confidence 99631 122 556555555544
No 9
>PRK10779 zinc metallopeptidase RseP; Provisional
Probab=97.84 E-value=1.3e-05 Score=80.80 Aligned_cols=69 Identities=25% Similarity=0.330 Sum_probs=47.1
Q ss_pred HHHHHHhhHHHHHHHhCCCCceEEee---------------------cCcccceecchHHHH---hhhcCCCCHHHHHHH
Q 021101 172 RVARHEAAHFLLAYLLGLPILGYSLD---------------------IGKENVNLIDERLEK---LIYSGQLDAKELDRL 227 (317)
Q Consensus 172 RIA~HEAGHaLvAylLg~PV~kvsI~---------------------pG~ggv~f~~~e~e~---~~~~g~~s~~~L~r~ 227 (317)
.|..||.||||+|.++|+.|.++||+ |-+|+|.+.+++.++ .-....+..+...++
T Consensus 17 li~vHElGHfl~Ar~~gv~V~~FsiGfGp~l~~~~~~~~Tey~i~~iPlGGyVk~~~e~~~~~~~~~~~~~f~~k~~~~R 96 (449)
T PRK10779 17 LITVHEFGHFWVARRCGVRVERFSIGFGKALWRRTDRQGTEYVIALIPLGGYVKMLDERVEPVAPELRHHAFNNKTVGQR 96 (449)
T ss_pred HHHHHHHHHHHHHHHcCCeeeEEEeecChhHeeEecCCCcEEEEEEEcCCCeeecCCCCCCcCChhhhhhhhccCCHHHh
Confidence 47899999999999999999999886 223456655432110 000112455556666
Q ss_pred HHHHchHHHHHHh
Q 021101 228 AVVAMAGLAAEGL 240 (317)
Q Consensus 228 ~~VlLAGrAAE~l 240 (317)
+.|++||..+.-+
T Consensus 97 ~~i~~AGp~~N~i 109 (449)
T PRK10779 97 AAIIAAGPIANFI 109 (449)
T ss_pred hhhhhhhHHHHHH
Confidence 7899999999853
No 10
>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=97.65 E-value=2.7e-05 Score=70.24 Aligned_cols=70 Identities=24% Similarity=0.284 Sum_probs=44.1
Q ss_pred HHHHHHhhHHHHHHHhCCCCceEEee--------------------cCcccceecchHHHHh----hhcCCCCHHHHHHH
Q 021101 172 RVARHEAAHFLLAYLLGLPILGYSLD--------------------IGKENVNLIDERLEKL----IYSGQLDAKELDRL 227 (317)
Q Consensus 172 RIA~HEAGHaLvAylLg~PV~kvsI~--------------------pG~ggv~f~~~e~e~~----~~~g~~s~~~L~r~ 227 (317)
-|..||.||+++|..+|.+|++++|+ |-+|++++.+++.++. .+...+.++.-.+.
T Consensus 11 ~v~iHElGH~~~Ar~~Gv~v~~f~iGfGp~l~~~~~~~t~~~i~~iPlGGyv~~~~~~~~~~~~~~~~~~~f~~~~~~~r 90 (182)
T cd06163 11 LIFVHELGHFLVAKLFGVKVEEFSIGFGPKLFSFKKGETEYSISAIPLGGYVKMLGEDPEEEADPEDDPRSFNSKPVWQR 90 (182)
T ss_pred HHHHHHHHHHHHHHHcCCeeeEeeeecCceeeeeecCCeEEEEEEEEeccEEEecCCCcccccccccchHHHccCCcchh
Confidence 37899999999999999999997653 4334566554321110 00001222123345
Q ss_pred HHHHchHHHHHHhh
Q 021101 228 AVVAMAGLAAEGLQ 241 (317)
Q Consensus 228 ~~VlLAGrAAE~lv 241 (317)
+.|.+||.+++-+.
T Consensus 91 i~V~lAGP~~Nlil 104 (182)
T cd06163 91 ILIVFAGPLANFLL 104 (182)
T ss_pred hhhhhhHHHHHHHH
Confidence 67999999999764
No 11
>TIGR00054 RIP metalloprotease RseP. A model that detects fragments as well matches a number of members of the PEPTIDASE FAMILY S2C. The region of match appears not to overlap the active site domain.
Probab=97.52 E-value=7.8e-05 Score=74.72 Aligned_cols=69 Identities=25% Similarity=0.295 Sum_probs=45.3
Q ss_pred HHHHHHhhHHHHHHHhCCCCceEEee--------------------cCcccceec--chHHHH---hhhcCCCCHHHHHH
Q 021101 172 RVARHEAAHFLLAYLLGLPILGYSLD--------------------IGKENVNLI--DERLEK---LIYSGQLDAKELDR 226 (317)
Q Consensus 172 RIA~HEAGHaLvAylLg~PV~kvsI~--------------------pG~ggv~f~--~~e~e~---~~~~g~~s~~~L~r 226 (317)
.|..||.||||+|.++|..|.++||+ |-+|++.+. +++.+. .-+...+..+...+
T Consensus 16 ~v~~HE~gH~~~a~~~g~~v~~FsiGfGp~l~~~~~~~tey~i~~~plGg~v~~~g~~~~~~~~~~~~~~~~f~~~~~~~ 95 (420)
T TIGR00054 16 LIFVHELGHFLAARLCGIKVERFSIGFGPKILKFKKNGTEYAISLIPLGGYVKMKGLDKEMEVKPPETDGDLFNNKSVFQ 95 (420)
T ss_pred HHHHHhHHHHHHHHHcCCEEEEEEEccCchheEEecCCeEEEEEEecCcceEeeccCCcccccCCcchhhhhhccCCHHH
Confidence 47899999999999999999987765 334566663 211110 00011244455566
Q ss_pred HHHHHchHHHHHHh
Q 021101 227 LAVVAMAGLAAEGL 240 (317)
Q Consensus 227 ~~~VlLAGrAAE~l 240 (317)
++.|.+||.++.-+
T Consensus 96 r~~i~~aGp~~N~~ 109 (420)
T TIGR00054 96 KAIIIFAGPLANFI 109 (420)
T ss_pred HHHhhhcccHHHHH
Confidence 66799999988854
No 12
>cd06164 S2P-M50_SpoIVFB_CBS SpoIVFB Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50B), regulates intramembrane proteolysis (RIP), and is involved in the pro-sigmaK pathway of bacterial spore formation. In this subgroup, SpoIVFB (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain. SpoIVFB is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA (bypass-of-forespore A), and SpoIVB (sporulation protein, stage IV cell wall formation, B locus). SpoIVFB is negatively regulated by SpoIVFA and BofA and activated by SpoIVB. It is thought that SpoIVFB, SpoIVFA, and BofA are located in the mother-cell membrane that surrounds the forespore and that SpoIVB is secreted from the forespore into the space between the two where it activates SpoIVFB. It has been proposed tha
Probab=97.26 E-value=0.0023 Score=59.49 Aligned_cols=60 Identities=25% Similarity=0.186 Sum_probs=43.9
Q ss_pred HHHHHHhhHHHHHHHhCCCCceEEeecCcccceecchHHHHhhhcCCCCHHHHHHHHHHHchHHHHHHhhcC
Q 021101 172 RVARHEAAHFLLAYLLGLPILGYSLDIGKENVNLIDERLEKLIYSGQLDAKELDRLAVVAMAGLAAEGLQYD 243 (317)
Q Consensus 172 RIA~HEAGHaLvAylLg~PV~kvsI~pG~ggv~f~~~e~e~~~~~g~~s~~~L~r~~~VlLAGrAAE~lvfG 243 (317)
-+..||.||+++|+.+|.||+++++.|-.|.+.+.+.. .++ .+...|.+||.++.-+...
T Consensus 55 ~v~iHElgH~~~A~~~G~~v~~i~l~p~Gg~~~~~~~~---------~~~---~~~~~IalAGPl~Nllla~ 114 (227)
T cd06164 55 SVLLHELGHSLVARRYGIPVRSITLFLFGGVARLEREP---------ETP---GQEFVIAIAGPLVSLVLAL 114 (227)
T ss_pred HHHHHHHHHHHHHHHcCCeECeEEEEeeeEEEEecCCC---------CCH---HHHhhhhhhHHHHHHHHHH
Confidence 47899999999999999999999999843334433221 122 2346799999999987644
No 13
>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=96.78 E-value=0.0011 Score=58.75 Aligned_cols=26 Identities=27% Similarity=0.319 Sum_probs=18.5
Q ss_pred HHHHHhhHHHHHHHhCCCCceEEeec
Q 021101 173 VARHEAAHFLLAYLLGLPILGYSLDI 198 (317)
Q Consensus 173 IA~HEAGHaLvAylLg~PV~kvsI~p 198 (317)
+..||.||+++|+..|+++.++++.+
T Consensus 10 i~~HE~gH~~~a~~~G~~~~~~~~~~ 35 (192)
T PF02163_consen 10 IVLHELGHALAARLYGDKVPRFEGGF 35 (192)
T ss_dssp HHHHHHHHHHHHHTTT--B--EEE--
T ss_pred cccccccccccccccccccccccccc
Confidence 67899999999999999999997653
No 14
>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=96.78 E-value=0.0013 Score=60.13 Aligned_cols=60 Identities=25% Similarity=0.184 Sum_probs=44.3
Q ss_pred HHHHHHhhHHHHHHHhCCCCceEEeecCcccceecchHHHHhhhcCCCCHHHHHHHHHHHchHHHHHHhhcC
Q 021101 172 RVARHEAAHFLLAYLLGLPILGYSLDIGKENVNLIDERLEKLIYSGQLDAKELDRLAVVAMAGLAAEGLQYD 243 (317)
Q Consensus 172 RIA~HEAGHaLvAylLg~PV~kvsI~pG~ggv~f~~~e~e~~~~~g~~s~~~L~r~~~VlLAGrAAE~lvfG 243 (317)
-+..||.||+++|+.+|.|++++++.|-+|.+...+.. . . -.+.+.|.+||..++-++..
T Consensus 40 ~v~iHElgH~~~A~~~G~~v~~i~l~p~Gg~~~~~~~~----------~-~-~~~~~lIalAGPl~n~~la~ 99 (208)
T cd06161 40 SVLLHELGHALVARRYGIRVRSITLLPFGGVAELEEEP----------E-T-PKEEFVIALAGPLVSLLLAG 99 (208)
T ss_pred HHHHHHHHHHHHHHHcCCCccceEEEeeeeeeeeccCC----------C-C-hhHheeeeeehHHHHHHHHH
Confidence 47899999999999999999999999854444442210 1 1 22345799999999987755
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=96.63 E-value=0.001 Score=58.51 Aligned_cols=64 Identities=27% Similarity=0.143 Sum_probs=41.3
Q ss_pred HHHHHhhHHHHHHHhCCCCceEEee-----------------cCcccceecchHHHHhhhcCCCCHHHHHHHHHHHchHH
Q 021101 173 VARHEAAHFLLAYLLGLPILGYSLD-----------------IGKENVNLIDERLEKLIYSGQLDAKELDRLAVVAMAGL 235 (317)
Q Consensus 173 IA~HEAGHaLvAylLg~PV~kvsI~-----------------pG~ggv~f~~~e~e~~~~~g~~s~~~L~r~~~VlLAGr 235 (317)
+..||.||+++|+..|+++.+.++. |-.|.+...+...+. .+..-.+...|.+||.
T Consensus 11 i~iHE~gH~~~A~~~G~~~~~~~~~~~~~~~~~~~~~~~~~ip~gG~~~~~~~~~~~-------~~~~~~~~~~i~laGP 83 (180)
T cd05709 11 VTVHELGHALVARRLGVKVARFSGGFTLNPLKHGDPYGIILIPLGGYAKPVGENPRA-------FKKPRWQRLLVALAGP 83 (180)
T ss_pred HHHHHHHHHHHHHHcCCCchheeeeEEECCcCCCCEehHHHHhccCeeccCCCChhh-------hccchhhhhhhhhhhH
Confidence 7889999999999999988766653 222233333322110 0112344567999999
Q ss_pred HHHHhhcC
Q 021101 236 AAEGLQYD 243 (317)
Q Consensus 236 AAE~lvfG 243 (317)
.++-+...
T Consensus 84 l~nllla~ 91 (180)
T cd05709 84 LANLLLAL 91 (180)
T ss_pred HHHHHHHH
Confidence 99987654
No 16
>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=96.39 E-value=0.0031 Score=60.66 Aligned_cols=63 Identities=16% Similarity=0.103 Sum_probs=43.0
Q ss_pred HHHHHHhhHHHHHHHhCCCCceEEeec----CcccceecchHHHHhhhcCCCCHHHHHHHHHHHchHHHHHHhhcC
Q 021101 172 RVARHEAAHFLLAYLLGLPILGYSLDI----GKENVNLIDERLEKLIYSGQLDAKELDRLAVVAMAGLAAEGLQYD 243 (317)
Q Consensus 172 RIA~HEAGHaLvAylLg~PV~kvsI~p----G~ggv~f~~~e~e~~~~~g~~s~~~L~r~~~VlLAGrAAE~lvfG 243 (317)
-+..||.||+++|...|++|+++.+.+ ..|.++.++++.+ ..++. +.+.|.+||.+++-+.-.
T Consensus 137 svvvHElgHal~A~~~gi~V~~iGl~l~~~~pGa~ve~~~e~~~------~~~~~---~~l~Ia~AGp~~NlvLa~ 203 (277)
T cd06162 137 SGVVHEMGHGVAAVREQVRVNGFGIFFFIIYPGAYVDLFTDHLN------LISPV---QQLRIFCAGVWHNFVLGL 203 (277)
T ss_pred HHHHHHHHHHHHHHHcCCeeceEEEeeeeccCeeEEeecccccc------cCChh---hhhheehhhHHHHHHHHH
Confidence 378999999999999999999998753 1234454333211 12222 345799999999987644
No 17
>PF13398 Peptidase_M50B: Peptidase M50B-like
Probab=96.36 E-value=0.0039 Score=56.75 Aligned_cols=57 Identities=26% Similarity=0.265 Sum_probs=41.1
Q ss_pred HHHHHHhhHHHHHHHhCCCCceEEeecCcccceecchHHHHhhhcCCCCHHHHHHHHHHHchHHHHHHhh
Q 021101 172 RVARHEAAHFLLAYLLGLPILGYSLDIGKENVNLIDERLEKLIYSGQLDAKELDRLAVVAMAGLAAEGLQ 241 (317)
Q Consensus 172 RIA~HEAGHaLvAylLg~PV~kvsI~pG~ggv~f~~~e~e~~~~~g~~s~~~L~r~~~VlLAGrAAE~lv 241 (317)
-+..||.||++++.+.|..|+++++.|..+|++..... ....+ ..+..||..+..+.
T Consensus 24 ~t~~HE~gHal~a~l~G~~v~~i~l~~~~~G~~~~~~~------------~~~~~-~~i~~aGyl~~~l~ 80 (200)
T PF13398_consen 24 VTFVHELGHALAALLTGGRVKGIVLFPDGSGVTVSSGP------------SGIGR-FLIALAGYLGPALF 80 (200)
T ss_pred HHHHHHHHHHHHHHHhCCCcceEEEEeCCCceEEEecC------------CCcch-hHHhcccchHHHHH
Confidence 38999999999999999999999999976665543220 01122 34677777777664
No 18
>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=96.00 E-value=0.0025 Score=60.79 Aligned_cols=62 Identities=23% Similarity=0.125 Sum_probs=41.4
Q ss_pred HHHHHhhHHHHHHHhCCCCceEEee----cCcccceecchHHHHhhhcCCCCHHHHHHHHHHHchHHHHHHhhcC
Q 021101 173 VARHEAAHFLLAYLLGLPILGYSLD----IGKENVNLIDERLEKLIYSGQLDAKELDRLAVVAMAGLAAEGLQYD 243 (317)
Q Consensus 173 IA~HEAGHaLvAylLg~PV~kvsI~----pG~ggv~f~~~e~e~~~~~g~~s~~~L~r~~~VlLAGrAAE~lvfG 243 (317)
+..||.||+++|+..|++|+++.+. |..|.++..+++ . .+..-.+...|.+||..++-+...
T Consensus 121 v~iHElgHa~~Ar~~G~~V~~iGl~l~~ip~Gg~v~~~~~~---~------~~~~~~~~~~Ia~AGP~~Nlvla~ 186 (263)
T cd06159 121 VVVHELSHGILARVEGIKVKSGGLLLLIIPPGAFVEPDEEE---L------NKADRRIRLRIFAAGVTANFVVAL 186 (263)
T ss_pred HHHHHHHHHHHHHHcCCEECchhHHHHhhhcEEEEEecchh---h------ccCChhheeeeeeehHHHHHHHHH
Confidence 7899999999999999999987542 333445543321 1 111223456799999999966543
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=95.42 E-value=0.023 Score=51.43 Aligned_cols=58 Identities=21% Similarity=0.052 Sum_probs=40.4
Q ss_pred HHHHHHhhHHHHHHHhCCCCceEEeecC-----cccc-eecchHHHHhhhcCCCCHHHHHHHHHHHchHHHHHHhh
Q 021101 172 RVARHEAAHFLLAYLLGLPILGYSLDIG-----KENV-NLIDERLEKLIYSGQLDAKELDRLAVVAMAGLAAEGLQ 241 (317)
Q Consensus 172 RIA~HEAGHaLvAylLg~PV~kvsI~pG-----~ggv-~f~~~e~e~~~~~g~~s~~~L~r~~~VlLAGrAAE~lv 241 (317)
.+..||.||+++|+..|+++.+..+.|. -|++ ...++. .++ .+.+.|.+||.++.-+.
T Consensus 43 ~l~iHElgH~~~A~~~G~~~~~~~l~P~~~~G~~G~~~~~~~~~---------~~~---~~~~~IalAGPl~nl~l 106 (183)
T cd06160 43 ILGIHEMGHYLAARRHGVKASLPYFIPFPFIGTFGAFIRMRSPI---------PNR---KALFDIALAGPLAGLLL 106 (183)
T ss_pred HHHHHHHHHHHHHHHCCCCccceeeeehHhcCcEEEEEEecCCC---------CCh---hHhehhhhhHHHHHHHH
Confidence 4678999999999999999999988872 2332 222111 122 24457889999988655
No 20
>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=93.39 E-value=0.09 Score=47.25 Aligned_cols=26 Identities=38% Similarity=0.529 Sum_probs=20.9
Q ss_pred HHHHHhhHHHHHHHhCCCCce----EEeec
Q 021101 173 VARHEAAHFLLAYLLGLPILG----YSLDI 198 (317)
Q Consensus 173 IA~HEAGHaLvAylLg~PV~k----vsI~p 198 (317)
+..||.||+++|+..|++..+ .|+.|
T Consensus 12 i~~HE~aHa~~A~~~Gd~t~~~~Grltlnp 41 (181)
T cd06158 12 ITLHEFAHAYVAYRLGDPTARRAGRLTLNP 41 (181)
T ss_pred HHHHHHHHHHHHHHcCCcHHHHcCceecCc
Confidence 678999999999999987654 45544
No 21
>KOG2921 consensus Intramembrane metalloprotease (sterol-regulatory element-binding protein (SREBP) protease) [Posttranslational modification, protein turnover, chaperones]
Probab=88.99 E-value=0.42 Score=48.55 Aligned_cols=34 Identities=32% Similarity=0.391 Sum_probs=26.6
Q ss_pred HHHHHhhHHHHHHHhCCCCceEEee-----cCcccceecc
Q 021101 173 VARHEAAHFLLAYLLGLPILGYSLD-----IGKENVNLID 207 (317)
Q Consensus 173 IA~HEAGHaLvAylLg~PV~kvsI~-----pG~ggv~f~~ 207 (317)
..+||-||+|+|..-|+||.++-|- || +.|.+..
T Consensus 134 ~vvHElGHalAA~segV~vngfgIfi~aiyPg-afvdl~~ 172 (484)
T KOG2921|consen 134 VVVHELGHALAAASEGVQVNGFGIFIAAIYPG-AFVDLDN 172 (484)
T ss_pred HHHHHhhHHHHHHhcCceeeeeEEEEEEEcCc-hhhhhhh
Confidence 4689999999999999999999763 54 3455443
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=80.34 E-value=0.86 Score=38.35 Aligned_cols=17 Identities=35% Similarity=0.302 Sum_probs=14.6
Q ss_pred ChhhhHHHHHHHhhHHH
Q 021101 166 FPDYQERVARHEAAHFL 182 (317)
Q Consensus 166 s~~~r~RIA~HEAGHaL 182 (317)
+..+...|+.||.||+|
T Consensus 101 ~~~~~~~v~~HEiGHaL 117 (154)
T PF00413_consen 101 SGNDLQSVAIHEIGHAL 117 (154)
T ss_dssp SSEEHHHHHHHHHHHHT
T ss_pred hhhhhhhhhhhcccccc
Confidence 56678899999999985
No 23
>COG0750 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]
Probab=79.09 E-value=1.6 Score=42.40 Aligned_cols=26 Identities=31% Similarity=0.438 Sum_probs=23.8
Q ss_pred HHHHHHhhHHHHHHHhCCCCceEEee
Q 021101 172 RVARHEAAHFLLAYLLGLPILGYSLD 197 (317)
Q Consensus 172 RIA~HEAGHaLvAylLg~PV~kvsI~ 197 (317)
.+..||.||+|+++.++..|.++++.
T Consensus 15 lv~~he~gh~~~a~~~~~~v~~f~ig 40 (375)
T COG0750 15 LVFVHELGHFWVARRCGVKVERFSIG 40 (375)
T ss_pred HHHHHHHhhHHHHHhcCceeEEEEec
Confidence 57899999999999999999999876
No 24
>PF14247 DUF4344: Domain of unknown function (DUF4344)
Probab=78.12 E-value=1.4 Score=41.22 Aligned_cols=61 Identities=28% Similarity=0.229 Sum_probs=38.5
Q ss_pred CCCCCcchhHHHHHHHHHHHHHHhccCC-chhHHHHHhhhcCCChhhhHHHHHHHhhHHHHHHHhCCCCce
Q 021101 124 QLPGDWGFFTPYLIGSISLVVLAVGSTS-PGLLQAAIQGFSSFFPDYQERVARHEAAHFLLAYLLGLPILG 193 (317)
Q Consensus 124 ~~p~~~g~~i~~~~~~~~l~~~~vg~~~-~gl~~~~~~~~~~ls~~~r~RIA~HEAGHaLvAylLg~PV~k 193 (317)
.+|.+--..+||-+..-.+-.++=.... +.+.+.+++.+ .-|.+||.||+|+..+ ++||.|
T Consensus 53 ydPe~~~I~iCYEf~~~~~~~f~~~~~~~~~~~~~~~~~~--------~~~l~HE~GHAlI~~~-~lPv~G 114 (220)
T PF14247_consen 53 YDPENRSITICYEFVDEILDRFAKANDPDEEYGQAAIGNV--------LFTLYHELGHALIDDL-DLPVLG 114 (220)
T ss_pred cCCCCCEEEECHHHHHHHHHHHHhCCcCcchHHHHHHHHH--------HHHHHHHHHHHHHHHh-cCCccc
Confidence 3454433378888777777666643444 44344444443 3699999999999865 466654
No 25
>cd04279 ZnMc_MMP_like_1 Zinc-dependent metalloprotease; MMP_like sub-family 1. A group of bacterial, archaeal, and fungal metalloproteinase domains similar to matrix metalloproteinases and astacin.
Probab=76.33 E-value=1.6 Score=37.41 Aligned_cols=21 Identities=24% Similarity=0.251 Sum_probs=16.0
Q ss_pred hhhhHHHHHHHhhHHHHHHHh
Q 021101 167 PDYQERVARHEAAHFLLAYLL 187 (317)
Q Consensus 167 ~~~r~RIA~HEAGHaLvAylL 187 (317)
..+.+.|+.||-||+|=-.-.
T Consensus 101 ~~~~~~~~~HEiGHaLGL~H~ 121 (156)
T cd04279 101 AENLQAIALHELGHALGLWHH 121 (156)
T ss_pred chHHHHHHHHHhhhhhcCCCC
Confidence 457789999999998754433
No 26
>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=75.62 E-value=15 Score=31.45 Aligned_cols=65 Identities=23% Similarity=0.209 Sum_probs=45.5
Q ss_pred hhHHHHHHHH--HHHhCCCCCHHHHHHHHHH-----HHHHHHHHHHHcHHHHHHHHHHHHH-hchHHHHHHHHHh
Q 021101 249 SADLFSLQRF--INRTKPPLSQDQQQNLTRW-----AVLFAATLIKNNKAIHEALMAAMSK-KATILECIEAIEN 315 (317)
Q Consensus 249 ~~Dl~~lt~i--~~~lG~~~s~~e~~~l~r~-----A~~~A~~LL~~~r~~leaLaeaLle-~esl~eC~~~Ie~ 315 (317)
.+|+.++..| ++.+||++ ++++.++.. ...+...+|+++.+.+++..+.|.+ ++.|.+++..+++
T Consensus 41 ~~~v~~l~~I~~lr~~GfsL--~eI~~ll~~~~~~~~~~~~~~~l~~k~~~i~~~i~~L~~~~~~L~~~i~~~~~ 113 (131)
T cd04786 41 PETVWVLEIISSAQQAGFSL--DEIRQLLPADASNWQHDELLAALERKVADIEALEARLAQNKAQLLVLIDLIES 113 (131)
T ss_pred HHHHHHHHHHHHHHHcCCCH--HHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 5677777655 55788876 455554431 2356677889999988888888877 4688888877764
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=71.81 E-value=2.2 Score=36.39 Aligned_cols=18 Identities=28% Similarity=0.172 Sum_probs=14.7
Q ss_pred hhhhHHHHHHHhhHHHHH
Q 021101 167 PDYQERVARHEAAHFLLA 184 (317)
Q Consensus 167 ~~~r~RIA~HEAGHaLvA 184 (317)
..+...++.||-||+|=-
T Consensus 91 ~~~~~~~~~HEiGHaLGL 108 (165)
T cd04268 91 GARLRNTAEHELGHALGL 108 (165)
T ss_pred HHHHHHHHHHHHHHHhcc
Confidence 457889999999999643
No 28
>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=67.29 E-value=3.8 Score=35.69 Aligned_cols=14 Identities=43% Similarity=0.672 Sum_probs=11.1
Q ss_pred hhHHHHHHHhhHHH
Q 021101 169 YQERVARHEAAHFL 182 (317)
Q Consensus 169 ~r~RIA~HEAGHaL 182 (317)
..-||+-||-||.|
T Consensus 76 ~~~RIaaHE~GHiL 89 (132)
T PF02031_consen 76 NSTRIAAHELGHIL 89 (132)
T ss_dssp -HHHHHHHHHHHHH
T ss_pred ccceeeeehhcccc
Confidence 45589999999975
No 29
>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=67.28 E-value=2.9 Score=39.40 Aligned_cols=12 Identities=42% Similarity=0.542 Sum_probs=10.3
Q ss_pred HHHHHhhHHHHH
Q 021101 173 VARHEAAHFLLA 184 (317)
Q Consensus 173 IA~HEAGHaLvA 184 (317)
||-||+||++=.
T Consensus 92 VAAHEvGHAiQ~ 103 (222)
T PF04298_consen 92 VAAHEVGHAIQH 103 (222)
T ss_pred HHHHHHhHHHhc
Confidence 789999999853
No 30
>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=67.25 E-value=2.6 Score=36.25 Aligned_cols=17 Identities=35% Similarity=0.137 Sum_probs=14.1
Q ss_pred ChhhhHHHHHHHhhHHH
Q 021101 166 FPDYQERVARHEAAHFL 182 (317)
Q Consensus 166 s~~~r~RIA~HEAGHaL 182 (317)
...+...|+.||-||+|
T Consensus 103 ~~~~~~~~~~HEiGHaL 119 (157)
T cd04278 103 GGTDLFSVAAHEIGHAL 119 (157)
T ss_pred ccchHHHHHHHHhcccc
Confidence 34567899999999995
No 31
>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=66.82 E-value=6.1 Score=30.88 Aligned_cols=23 Identities=30% Similarity=0.267 Sum_probs=18.0
Q ss_pred CChhhhHHHHHHHhhHHHHHHHh
Q 021101 165 FFPDYQERVARHEAAHFLLAYLL 187 (317)
Q Consensus 165 ls~~~r~RIA~HEAGHaLvAylL 187 (317)
.++..|+-++.||.||.+...-.
T Consensus 37 ~~~~~~~f~laHELgH~~~~~~~ 59 (122)
T PF06114_consen 37 LSPERQRFTLAHELGHILLHHGD 59 (122)
T ss_dssp S-HHHHHHHHHHHHHHHHHHH-H
T ss_pred CCHHHHHHHHHHHHHHHHhhhcc
Confidence 47788888999999999987654
No 32
>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=65.89 E-value=2.7 Score=36.91 Aligned_cols=21 Identities=24% Similarity=0.237 Sum_probs=14.2
Q ss_pred ChhhhHHHHHHHhhHHHHHHH
Q 021101 166 FPDYQERVARHEAAHFLLAYL 186 (317)
Q Consensus 166 s~~~r~RIA~HEAGHaLvAyl 186 (317)
++....+++.||.||+|==+-
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 456667999999999985443
No 33
>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=64.77 E-value=45 Score=27.47 Aligned_cols=66 Identities=9% Similarity=0.061 Sum_probs=46.0
Q ss_pred hhHHHHHHHH--HHHhCCCCCHHHHHHHHHH-------HHHHHHHHHHHcHHHHHHHHHHHHHh-chHHHHHHHHHhc
Q 021101 249 SADLFSLQRF--INRTKPPLSQDQQQNLTRW-------AVLFAATLIKNNKAIHEALMAAMSKK-ATILECIEAIENA 316 (317)
Q Consensus 249 ~~Dl~~lt~i--~~~lG~~~s~~e~~~l~r~-------A~~~A~~LL~~~r~~leaLaeaLle~-esl~eC~~~Ie~~ 316 (317)
.+|+..+..| ++.+|++++ +++.+++. .......+|+++++.++.--+.|.+. ..++.++..++++
T Consensus 40 ~~d~~~l~~I~~lr~~G~sl~--eI~~~l~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~~~~~l~~~~~~~~~~ 115 (116)
T cd04769 40 AQHVECLRFIKEARQLGFTLA--ELKAIFAGHEGRAVLPWPHLQQALEDKKQEIRAQITELQQLLARLDAFEASLKDA 115 (116)
T ss_pred HHHHHHHHHHHHHHHcCCCHH--HHHHHHhccccCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 5678777665 567998863 45444433 23456788888888888777777764 6888888887764
No 34
>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=64.66 E-value=38 Score=24.58 Aligned_cols=49 Identities=12% Similarity=0.099 Sum_probs=31.0
Q ss_pred HHHhCCCCCHHHHHHHH------HHHHHHHHHHHHHcHHHHHHHHHHHHH-hchHHHH
Q 021101 259 INRTKPPLSQDQQQNLT------RWAVLFAATLIKNNKAIHEALMAAMSK-KATILEC 309 (317)
Q Consensus 259 ~~~lG~~~s~~e~~~l~------r~A~~~A~~LL~~~r~~leaLaeaLle-~esl~eC 309 (317)
++.+||++ +|+++++ .........+++++++.+++--+.|.+ ...+.+|
T Consensus 10 ~r~lGfsL--~eI~~~l~l~~~~~~~~~~~~~~l~~~~~~i~~~i~~L~~~~~~L~~l 65 (65)
T PF09278_consen 10 LRELGFSL--EEIRELLELYDQGDPPCADRRALLEEKLEEIEEQIAELQALRAQLEHL 65 (65)
T ss_dssp HHHTT--H--HHHHHHHHHCCSHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHcCCCH--HHHHHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 45789886 5666665 335666778888888888877776665 3444443
No 35
>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=63.12 E-value=4.8 Score=35.53 Aligned_cols=18 Identities=28% Similarity=0.237 Sum_probs=14.9
Q ss_pred hhhhHHHHHHHhhHHHHH
Q 021101 167 PDYQERVARHEAAHFLLA 184 (317)
Q Consensus 167 ~~~r~RIA~HEAGHaLvA 184 (317)
..+...++.||.||+|==
T Consensus 110 g~~~~~t~~HEiGHaLGL 127 (186)
T cd04277 110 GSYGYQTIIHEIGHALGL 127 (186)
T ss_pred ChhhHHHHHHHHHHHhcC
Confidence 467789999999999753
No 36
>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=57.49 E-value=6.7 Score=35.31 Aligned_cols=19 Identities=32% Similarity=0.078 Sum_probs=14.4
Q ss_pred hhHHHHHHHhhHHHHHHHh
Q 021101 169 YQERVARHEAAHFLLAYLL 187 (317)
Q Consensus 169 ~r~RIA~HEAGHaLvAylL 187 (317)
+...++.||-||+|=-+-.
T Consensus 91 ~~~~~i~HElgHaLG~~HE 109 (198)
T cd04327 91 EFSRVVLHEFGHALGFIHE 109 (198)
T ss_pred hHHHHHHHHHHHHhcCccc
Confidence 4567999999999855443
No 37
>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=52.81 E-value=7 Score=32.66 Aligned_cols=10 Identities=60% Similarity=0.727 Sum_probs=9.6
Q ss_pred HHHHHhhHHH
Q 021101 173 VARHEAAHFL 182 (317)
Q Consensus 173 IA~HEAGHaL 182 (317)
|+.||-||+|
T Consensus 89 ~~~HEigHaL 98 (140)
T smart00235 89 VAAHELGHAL 98 (140)
T ss_pred cHHHHHHHHh
Confidence 9999999998
No 38
>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=50.48 E-value=94 Score=25.90 Aligned_cols=60 Identities=17% Similarity=0.143 Sum_probs=33.5
Q ss_pred hhHHHHHHHH--HHHhCCCCCHHHHHHHHHHH----HHHHHHHHHHcHHHHHHHHHHHHHh-chHHHHH
Q 021101 249 SADLFSLQRF--INRTKPPLSQDQQQNLTRWA----VLFAATLIKNNKAIHEALMAAMSKK-ATILECI 310 (317)
Q Consensus 249 ~~Dl~~lt~i--~~~lG~~~s~~e~~~l~r~A----~~~A~~LL~~~r~~leaLaeaLle~-esl~eC~ 310 (317)
.+|+.++..| ++.+||++ ++++.++... ......+|+++.+.++.=.+.|.+- +.|.+++
T Consensus 41 ~~~l~~l~~I~~lr~~G~sL--~eI~~~l~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~l~~~~ 107 (126)
T cd04783 41 EETVTRLRFIKRAQELGFTL--DEIAELLELDDGTDCSEARELAEQKLAEVDEKIADLQRMRASLQELV 107 (126)
T ss_pred HHHHHHHHHHHHHHHcCCCH--HHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5677776654 56788876 4555444422 2345666766666666555555442 3444443
No 39
>PF08679 DsrD: Dissimilatory sulfite reductase D (DsrD); InterPro: IPR014793 The structure of the dissimilatory sulphite reductase D (DsrD) protein has shown it to contain a winged-helix motif similar to those found in DNA binding proteins []. The structure suggests a possible role for DsrD in transcription or translation of genes, which catalyse dissimilatory sulphite reduction. ; PDB: 1WQ2_B 1UCR_B.
Probab=48.66 E-value=23 Score=27.61 Aligned_cols=44 Identities=23% Similarity=0.382 Sum_probs=36.2
Q ss_pred CccccccchHHHHHHHhhhchHHHHHHHHHHHhcccccccCCCC
Q 021101 30 SAATGRFDLKTLESAIAKKDSNAVKEALDQLSEVGWAKRWSSQP 73 (317)
Q Consensus 30 ~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~l~~~g~~~~~~~~~ 73 (317)
++.-+-+-++.+..++-..+...|+++.+.|-..|.|.-|++.+
T Consensus 14 ~~~KskfYfkD~~k~~pd~k~R~vKKi~~~LV~Eg~l~yWSSGS 57 (67)
T PF08679_consen 14 KKKKSKFYFKDFYKAFPDAKPREVKKIVNELVNEGKLEYWSSGS 57 (67)
T ss_dssp CCHSS-EEHHHHHHH-TTS-HHHHHHHHHHHHHTTSEEEEEETT
T ss_pred cCCCCceeHHHHHHHCCCcCHHHHHHHHHHHHhhCeEEEEcCCC
Confidence 34456678899999999999999999999999999999999875
No 40
>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=46.87 E-value=1.4e+02 Score=24.39 Aligned_cols=61 Identities=15% Similarity=0.156 Sum_probs=37.9
Q ss_pred hhHHHHHHHH--HHHhCCCCCHHHHHHHHHH------HHHHHHHHHHHcHHHHHHHHHHHHHh-chHHHHHH
Q 021101 249 SADLFSLQRF--INRTKPPLSQDQQQNLTRW------AVLFAATLIKNNKAIHEALMAAMSKK-ATILECIE 311 (317)
Q Consensus 249 ~~Dl~~lt~i--~~~lG~~~s~~e~~~l~r~------A~~~A~~LL~~~r~~leaLaeaLle~-esl~eC~~ 311 (317)
.+|+.++..| ++.+||++. +++.++.. ...+...+|+++...++.-.+.|... +.|+.+++
T Consensus 41 ~~~l~~l~~I~~lr~~G~sL~--eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~~~~~l~~~~~ 110 (113)
T cd01109 41 EEDLEWLEFIKCLRNTGMSIK--DIKEYAELRREGDSTIPERLELLEEHREELEEQIAELQETLAYLDYKID 110 (113)
T ss_pred HHHHHHHHHHHHHHHcCCCHH--HHHHHHHHHccCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5577777665 457888863 55544432 12455678888888777777666653 45555543
No 41
>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=46.12 E-value=1.4e+02 Score=24.76 Aligned_cols=52 Identities=19% Similarity=0.135 Sum_probs=30.8
Q ss_pred hhHHHHHHHH--HHHhCCCCCHHHHHHHHHHH------HHHHHHHHHHcHHHHHHHHHHHHH
Q 021101 249 SADLFSLQRF--INRTKPPLSQDQQQNLTRWA------VLFAATLIKNNKAIHEALMAAMSK 302 (317)
Q Consensus 249 ~~Dl~~lt~i--~~~lG~~~s~~e~~~l~r~A------~~~A~~LL~~~r~~leaLaeaLle 302 (317)
.+|+.++..| ++.+||++ .+++.++... ......+|+++...+++--+.|.+
T Consensus 41 ~~~l~~l~~I~~lr~~G~sL--~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 100 (127)
T cd04784 41 EEHLERLLFIRRCRSLDMSL--DEIRTLLQLQDDPEASCAEVNALIDEHLAHVRARIAELQA 100 (127)
T ss_pred HHHHHHHHHHHHHHHcCCCH--HHHHHHHHhhhcCCCcHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5677776655 55788776 4555555432 245566777777766655555443
No 42
>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=45.78 E-value=1e+02 Score=25.77 Aligned_cols=60 Identities=10% Similarity=0.036 Sum_probs=32.3
Q ss_pred hhHHHHHHHH--HHHhCCCCCHHHHHHHHHH------HHHHHHHHHHHcHHHHHHHHHHHHH-hchHHHHH
Q 021101 249 SADLFSLQRF--INRTKPPLSQDQQQNLTRW------AVLFAATLIKNNKAIHEALMAAMSK-KATILECI 310 (317)
Q Consensus 249 ~~Dl~~lt~i--~~~lG~~~s~~e~~~l~r~------A~~~A~~LL~~~r~~leaLaeaLle-~esl~eC~ 310 (317)
.+|+.++..| ++.+||++ +++++++.. .......+|.+++..+++-.+.|.+ +..|++++
T Consensus 41 ~~~l~~l~~I~~lr~~G~sL--~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~~~ 109 (127)
T TIGR02044 41 QQHLDELRLISRARQVGFSL--EECKELLNLWNDPNRTSADVKARTLEKVAEIERKISELQSMRDQLEALA 109 (127)
T ss_pred HHHHHHHHHHHHHHHCCCCH--HHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4577776654 45688775 345544432 1233455666666666555555544 34444443
No 43
>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=45.36 E-value=10 Score=35.27 Aligned_cols=18 Identities=33% Similarity=0.540 Sum_probs=15.9
Q ss_pred hhhhHHHHHHHhhHHHHHH
Q 021101 167 PDYQERVARHEAAHFLLAY 185 (317)
Q Consensus 167 ~~~r~RIA~HEAGHaLvAy 185 (317)
..||+-++-||.||+| +|
T Consensus 136 ~~YRqYvINHEVGH~L-Gh 153 (203)
T PF11350_consen 136 ASYRQYVINHEVGHAL-GH 153 (203)
T ss_pred HHHHHHhhhhhhhhhc-cc
Confidence 5799999999999999 44
No 44
>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=45.28 E-value=11 Score=31.87 Aligned_cols=19 Identities=26% Similarity=0.225 Sum_probs=14.8
Q ss_pred hhhHHHHHHHhhHHHHHHH
Q 021101 168 DYQERVARHEAAHFLLAYL 186 (317)
Q Consensus 168 ~~r~RIA~HEAGHaLvAyl 186 (317)
..-..++.||.||+|=-+-
T Consensus 94 ~~~~~~~~HElGH~LGl~H 112 (167)
T cd00203 94 KEGAQTIAHELGHALGFYH 112 (167)
T ss_pred ccchhhHHHHHHHHhCCCc
Confidence 4567899999999986443
No 45
>PF13485 Peptidase_MA_2: Peptidase MA superfamily
Probab=43.62 E-value=24 Score=27.66 Aligned_cols=23 Identities=35% Similarity=0.499 Sum_probs=19.0
Q ss_pred ChhhhHHHHHHHhhHHHHHHHhC
Q 021101 166 FPDYQERVARHEAAHFLLAYLLG 188 (317)
Q Consensus 166 s~~~r~RIA~HEAGHaLvAylLg 188 (317)
+++.-.+++.||-+|.+.....+
T Consensus 21 ~~~~~~~~l~HE~~H~~~~~~~~ 43 (128)
T PF13485_consen 21 DEDWLDRVLAHELAHQWFGNYFG 43 (128)
T ss_pred CHHHHHHHHHHHHHHHHHHHHcC
Confidence 45555699999999999988865
No 46
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=43.41 E-value=32 Score=20.97 Aligned_cols=27 Identities=22% Similarity=0.337 Sum_probs=23.4
Q ss_pred HHHHHHhhhchHHHHHHHHHHHhcccc
Q 021101 40 TLESAIAKKDSNAVKEALDQLSEVGWA 66 (317)
Q Consensus 40 ~~~~~~~~~~~~~v~~~~~~l~~~g~~ 66 (317)
.++++.+..+.+.+.+.++.|++.|.-
T Consensus 7 ll~a~~~~g~~~~a~~~~~~M~~~gv~ 33 (34)
T PF13812_consen 7 LLRACAKAGDPDAALQLFDEMKEQGVK 33 (34)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHhCCC
Confidence 467888999999999999999998853
No 47
>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=43.30 E-value=77 Score=25.27 Aligned_cols=52 Identities=13% Similarity=0.151 Sum_probs=34.7
Q ss_pred hhHHHHHHHH--HHHhCCCCCHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHH
Q 021101 249 SADLFSLQRF--INRTKPPLSQDQQQNLTRWAVLFAATLIKNNKAIHEALMAAMSK 302 (317)
Q Consensus 249 ~~Dl~~lt~i--~~~lG~~~s~~e~~~l~r~A~~~A~~LL~~~r~~leaLaeaLle 302 (317)
.+|+.++..| ++.+|+++ .+++.++...-.....+|++++..+++=.+.|.+
T Consensus 41 ~~~l~~l~~I~~lr~~G~~l--~~I~~~l~~~~~~~~~~l~~~~~~l~~~i~~l~~ 94 (96)
T cd04768 41 YAQLYQLQFILFLRELGFSL--AEIKELLDTEMEELTAMLLEKKQAIQQKIDRLQQ 94 (96)
T ss_pred HHHHHHHHHHHHHHHcCCCH--HHHHHHHhcCcHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4577777654 56788876 4566666544446778888888887776666543
No 48
>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=42.85 E-value=1.1e+02 Score=24.64 Aligned_cols=52 Identities=15% Similarity=0.111 Sum_probs=34.5
Q ss_pred hhHHHHHHHH--HHHhCCCCCHHHHHHHHHHH----------HHHHHHHHHHcHHHHHHHHHHHHH
Q 021101 249 SADLFSLQRF--INRTKPPLSQDQQQNLTRWA----------VLFAATLIKNNKAIHEALMAAMSK 302 (317)
Q Consensus 249 ~~Dl~~lt~i--~~~lG~~~s~~e~~~l~r~A----------~~~A~~LL~~~r~~leaLaeaLle 302 (317)
.+|+.++..| ++.+||++ ++++.++... ......+|+++++.+++-.+.|.+
T Consensus 39 ~~~~~~l~~I~~lr~~G~sL--~eI~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~ 102 (107)
T cd04777 39 EKCQDDLEFILELKGLGFSL--IEIQKIFSYKRLTKSRTHEDQDYYKSFLKNKKDELEKEIEDLKK 102 (107)
T ss_pred HHHHHHHHHHHHHHHCCCCH--HHHHHHHHhcccccccchhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4677777665 56789886 4565555431 233578888888888877766654
No 49
>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=41.99 E-value=1.6e+02 Score=25.54 Aligned_cols=61 Identities=13% Similarity=0.065 Sum_probs=34.9
Q ss_pred hhHHHHHHHH--HHHhCCCCCHHHHHHHHHH-------HHHHHHHHHHHcHHHHHHHHHHHHH-hchHHHHHH
Q 021101 249 SADLFSLQRF--INRTKPPLSQDQQQNLTRW-------AVLFAATLIKNNKAIHEALMAAMSK-KATILECIE 311 (317)
Q Consensus 249 ~~Dl~~lt~i--~~~lG~~~s~~e~~~l~r~-------A~~~A~~LL~~~r~~leaLaeaLle-~esl~eC~~ 311 (317)
.+|+.++..| ++.+||++ .+++.++.. .......+|.++...+++-.+.|.+ +..|++|+.
T Consensus 41 ~~di~~l~~I~~lr~~G~sL--~eI~~~l~~~~~~~~~~~~~~~~~l~~~~~~l~~ki~~L~~~~~~L~~~~~ 111 (142)
T TIGR01950 41 RDVLRRVAVIKAAQRVGIPL--ATIGEALAVLPEGRTPTADDWARLSSQWREELDERIDQLNALRDQLDGCIG 111 (142)
T ss_pred HHHHHHHHHHHHHHHcCCCH--HHHHHHHHhcccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 5688877655 45788876 345544432 1234456677766666655555444 455555543
No 50
>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=41.77 E-value=1.7e+02 Score=24.64 Aligned_cols=52 Identities=19% Similarity=0.148 Sum_probs=30.7
Q ss_pred hhHHHHHHHH--HHHhCCCCCHHHHHHHHHHHH------HHHHHHHHHcHHHHHHHHHHHHH
Q 021101 249 SADLFSLQRF--INRTKPPLSQDQQQNLTRWAV------LFAATLIKNNKAIHEALMAAMSK 302 (317)
Q Consensus 249 ~~Dl~~lt~i--~~~lG~~~s~~e~~~l~r~A~------~~A~~LL~~~r~~leaLaeaLle 302 (317)
.+|+.++..| ++.+||++ .+++.+++... .....+|+++...+++=.+.|.+
T Consensus 41 ~~~~~~l~~I~~lr~~G~sL--~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~ 100 (133)
T cd04787 41 EKDLSRLRFILSARQLGFSL--KDIKEILSHADQGESPCPMVRRLIEQRLAETERRIKELLK 100 (133)
T ss_pred HHHHHHHHHHHHHHHcCCCH--HHHHHHHhhhccCCCcHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5677776655 56788886 34555554321 23456777777766655555544
No 51
>PRK13267 archaemetzincin-like protein; Reviewed
Probab=41.57 E-value=7 Score=35.39 Aligned_cols=11 Identities=36% Similarity=0.528 Sum_probs=9.0
Q ss_pred HHHHHHhhHHH
Q 021101 172 RVARHEAAHFL 182 (317)
Q Consensus 172 RIA~HEAGHaL 182 (317)
+.+.||.||.|
T Consensus 127 k~~~HElGH~l 137 (179)
T PRK13267 127 KEVTHELGHTL 137 (179)
T ss_pred HHHHHHHHHHc
Confidence 45999999974
No 52
>COG0501 HtpX Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]
Probab=41.50 E-value=19 Score=33.61 Aligned_cols=24 Identities=29% Similarity=0.166 Sum_probs=20.2
Q ss_pred CCChhhhHHHHHHHhhHHHHHHHh
Q 021101 164 SFFPDYQERVARHEAAHFLLAYLL 187 (317)
Q Consensus 164 ~ls~~~r~RIA~HEAGHaLvAylL 187 (317)
.++++|-+-|.-||-||..-.+..
T Consensus 151 ~l~~dEl~aVlaHElgHi~~rd~~ 174 (302)
T COG0501 151 LLNDDELEAVLAHELGHIKNRHTL 174 (302)
T ss_pred hCCHHHHHHHHHHHHHHHhcccHH
Confidence 569999999999999998765554
No 53
>PF13582 Reprolysin_3: Metallo-peptidase family M12B Reprolysin-like; PDB: 3P24_C.
Probab=40.12 E-value=14 Score=29.94 Aligned_cols=12 Identities=33% Similarity=0.310 Sum_probs=10.4
Q ss_pred HHHHHHHhhHHH
Q 021101 171 ERVARHEAAHFL 182 (317)
Q Consensus 171 ~RIA~HEAGHaL 182 (317)
..+..||.||.|
T Consensus 108 ~~~~~HEiGH~l 119 (124)
T PF13582_consen 108 VDTFAHEIGHNL 119 (124)
T ss_dssp TTHHHHHHHHHT
T ss_pred ceEeeehhhHhc
Confidence 389999999986
No 54
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins 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 winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion 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=38.73 E-value=2.3e+02 Score=23.69 Aligned_cols=52 Identities=15% Similarity=0.052 Sum_probs=29.1
Q ss_pred hhHHHHHHHH--HHHhCCCCCHHHHHHHHHHH------HHHHHHHHHHcHHHHHHHHHHHHH
Q 021101 249 SADLFSLQRF--INRTKPPLSQDQQQNLTRWA------VLFAATLIKNNKAIHEALMAAMSK 302 (317)
Q Consensus 249 ~~Dl~~lt~i--~~~lG~~~s~~e~~~l~r~A------~~~A~~LL~~~r~~leaLaeaLle 302 (317)
.+|+.++..| ++.+||++ .+++.++... ..+...+|+++...++.--+.|.+
T Consensus 41 ~~~~~~l~~I~~lr~~G~sL--~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 100 (127)
T cd01108 41 QRDIEELRFIRRARDLGFSL--EEIRELLALWRDPSRASADVKALALEHIAELERKIAELQA 100 (127)
T ss_pred HHHHHHHHHHHHHHHcCCCH--HHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5677777655 45688775 3444444321 234456666666666655555544
No 55
>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=38.67 E-value=2.2e+02 Score=23.92 Aligned_cols=60 Identities=10% Similarity=0.099 Sum_probs=35.7
Q ss_pred hhHHHHHHHH--HHHhCCCCCHHHHHHHHHH------HHHHHHHHHHHcHHHHHHHHHHHHH-hchHHHHH
Q 021101 249 SADLFSLQRF--INRTKPPLSQDQQQNLTRW------AVLFAATLIKNNKAIHEALMAAMSK-KATILECI 310 (317)
Q Consensus 249 ~~Dl~~lt~i--~~~lG~~~s~~e~~~l~r~------A~~~A~~LL~~~r~~leaLaeaLle-~esl~eC~ 310 (317)
.+|+.++..| ++.+|+++ .+++.++.. ...+...+|+++.+.+++=.+.|.+ +..|+++.
T Consensus 41 ~~~l~~l~~I~~lr~lG~sL--~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~~~ 109 (127)
T TIGR02047 41 VGHVERLAFIRNCRTLDMSL--AEIRQLLRYQDKPEKSCSDVNALLDEHISHVRARIIKLQALIEQLVDLR 109 (127)
T ss_pred HHHHHHHHHHHHHHHcCCCH--HHHHHHHHhhhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5677777665 45788886 455555442 1245567777777777765555544 33444433
No 56
>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=37.10 E-value=24 Score=31.13 Aligned_cols=23 Identities=26% Similarity=0.234 Sum_probs=19.4
Q ss_pred CChhhhHHHHHHHhhHHHHHHHh
Q 021101 165 FFPDYQERVARHEAAHFLLAYLL 187 (317)
Q Consensus 165 ls~~~r~RIA~HEAGHaLvAylL 187 (317)
++++|..-|.-||.||..-.+..
T Consensus 84 ~~~~el~aVlaHElgH~~~~h~~ 106 (226)
T PF01435_consen 84 LSEDELAAVLAHELGHIKHRHIL 106 (226)
T ss_dssp SSHHHHHHHHHHHHHHHHTTHCC
T ss_pred ccHHHHHHHHHHHHHHHHcCCcc
Confidence 48999999999999999865554
No 57
>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=37.08 E-value=99 Score=24.65 Aligned_cols=50 Identities=16% Similarity=0.104 Sum_probs=30.8
Q ss_pred hhHHHHHHHH--HHHhCCCCCHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHH
Q 021101 249 SADLFSLQRF--INRTKPPLSQDQQQNLTRWAVLFAATLIKNNKAIHEALMAAM 300 (317)
Q Consensus 249 ~~Dl~~lt~i--~~~lG~~~s~~e~~~l~r~A~~~A~~LL~~~r~~leaLaeaL 300 (317)
.+|+.++..| ++.+|+++ .+++.++...-.....+|+++.+.+++=-+.|
T Consensus 41 ~~~l~~l~~I~~lr~~G~~l--~eI~~~l~~~~~~~~~~l~~~~~~l~~~i~~l 92 (96)
T cd04788 41 RADIRRLHQIIALRRLGFSL--REIGRALDGPDFDPLELLRRQLARLEEQLELA 92 (96)
T ss_pred HHHHHHHHHHHHHHHcCCCH--HHHHHHHhCCChhHHHHHHHHHHHHHHHHHHH
Confidence 5688877665 56788876 46655554433355666777766666544444
No 58
>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=36.85 E-value=2.4e+02 Score=23.16 Aligned_cols=52 Identities=21% Similarity=0.158 Sum_probs=30.5
Q ss_pred hhHHHHHHHH--HHHhCCCCCHHHHHHHHHHH------HHHHHHHHHHcHHHHHHHHHHHHH
Q 021101 249 SADLFSLQRF--INRTKPPLSQDQQQNLTRWA------VLFAATLIKNNKAIHEALMAAMSK 302 (317)
Q Consensus 249 ~~Dl~~lt~i--~~~lG~~~s~~e~~~l~r~A------~~~A~~LL~~~r~~leaLaeaLle 302 (317)
.+|+.++..| ++.+|+++ .+++.++... ......+|+++...+++=.+.|..
T Consensus 41 ~~~i~~l~~I~~lr~~G~sl--~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~ 100 (123)
T cd04770 41 EADLARLRFIRRAQALGFSL--AEIRELLSLRDDGAAPCAEVRALLEEKLAEVEAKIAELQA 100 (123)
T ss_pred HHHHHHHHHHHHHHHCCCCH--HHHHHHHHhhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4667666655 45788776 3455444432 234567777777776665555544
No 59
>COG2856 Predicted Zn peptidase [Amino acid transport and metabolism]
Probab=36.05 E-value=29 Score=32.43 Aligned_cols=22 Identities=27% Similarity=0.162 Sum_probs=16.9
Q ss_pred ChhhhHHHHHHHhhHHHHHHHh
Q 021101 166 FPDYQERVARHEAAHFLLAYLL 187 (317)
Q Consensus 166 s~~~r~RIA~HEAGHaLvAylL 187 (317)
+++.|+=++-||-||+|...-.
T Consensus 68 ~~~r~rFtlAHELGH~llH~~~ 89 (213)
T COG2856 68 SLERKRFTLAHELGHALLHTDL 89 (213)
T ss_pred CHHHHHHHHHHHHhHHHhcccc
Confidence 5555556999999999986554
No 60
>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=35.13 E-value=2.6e+02 Score=23.18 Aligned_cols=61 Identities=16% Similarity=0.051 Sum_probs=32.0
Q ss_pred hhHHHHHHHH--HHHhCCCCCHHHHHHHHHH---------HHHHHHHHHHHcHHHHHHHHHHHHHh-chHHHHHH
Q 021101 249 SADLFSLQRF--INRTKPPLSQDQQQNLTRW---------AVLFAATLIKNNKAIHEALMAAMSKK-ATILECIE 311 (317)
Q Consensus 249 ~~Dl~~lt~i--~~~lG~~~s~~e~~~l~r~---------A~~~A~~LL~~~r~~leaLaeaLle~-esl~eC~~ 311 (317)
.+|+.++..| ++.+||+++ +++++++. ...+...+|+++...++.--+.|.+. +.+++.+.
T Consensus 39 ~~~l~~l~~I~~lr~~G~~L~--~I~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~l~~~~~~L~~~~~ 111 (118)
T cd04776 39 RRDRARLKLILRGKRLGFSLE--EIRELLDLYDPPGGNRKQLEKMLEKIEKRRAELEQQRRDIDAALAELDAAEE 111 (118)
T ss_pred HHHHHHHHHHHHHHHCCCCHH--HHHHHHHhhccCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567776654 456787753 33333322 12344566777777666555555442 34444433
No 61
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=34.48 E-value=2.4e+02 Score=24.82 Aligned_cols=60 Identities=12% Similarity=0.038 Sum_probs=35.8
Q ss_pred hhHHHHHHHH--HHHhCCCCCHHHHHHHHHH-------HHHHHHHHHHHcHHHHHHHHHHHHH-hchHHHHH
Q 021101 249 SADLFSLQRF--INRTKPPLSQDQQQNLTRW-------AVLFAATLIKNNKAIHEALMAAMSK-KATILECI 310 (317)
Q Consensus 249 ~~Dl~~lt~i--~~~lG~~~s~~e~~~l~r~-------A~~~A~~LL~~~r~~leaLaeaLle-~esl~eC~ 310 (317)
.+|+.++.-| ++.+||++ +++++++.. .......+|.++...++.=.+.|.. ...|++|+
T Consensus 51 ~~~i~~L~~I~~lr~lG~sL--~eIk~ll~~~~~~~~~~~~~~~~ll~~k~~~l~~~I~~L~~~~~~L~~~i 120 (154)
T PRK15002 51 RDVLRYVAIIKIAQRIGIPL--ATIGEAFGVLPEGHTLSAKEWKQLSSQWREELDRRIHTLVALRDELDGCI 120 (154)
T ss_pred HHHHHHHHHHHHHHHcCCCH--HHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5677777654 56789886 456555542 2344566777776666665555554 34555554
No 62
>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=33.66 E-value=2.3e+02 Score=23.09 Aligned_cols=53 Identities=13% Similarity=0.061 Sum_probs=34.4
Q ss_pred hhHHHHHHHH--HHHhCCCCCHHHHHHHHHHH-----HHHHHHHHHHcHHHHHHHHHHHHHh
Q 021101 249 SADLFSLQRF--INRTKPPLSQDQQQNLTRWA-----VLFAATLIKNNKAIHEALMAAMSKK 303 (317)
Q Consensus 249 ~~Dl~~lt~i--~~~lG~~~s~~e~~~l~r~A-----~~~A~~LL~~~r~~leaLaeaLle~ 303 (317)
.+|+.++..+ ++..|+++ .+++.++... -.+...+|++++..+++=..+|..+
T Consensus 41 ~~dl~~l~~I~~lr~~G~~l--~~I~~~l~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~ 100 (108)
T cd04773 41 PSDVRDARLIHLLRRGGYLL--EQIATVVEQLRHAGGTEALAAALEQRRVALTQRGRAMLDA 100 (108)
T ss_pred HHHHHHHHHHHHHHHCCCCH--HHHHHHHHHhhcCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5688887665 45788876 3454444321 2456778888888887777776665
No 63
>PF10819 DUF2564: Protein of unknown function (DUF2564) ; InterPro: IPR020314 This entry contains proteins with no known function.
Probab=33.66 E-value=2.3e+02 Score=22.76 Aligned_cols=68 Identities=18% Similarity=0.245 Sum_probs=36.4
Q ss_pred hhhHHHHH-------HHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHh--chHHHHHHHHHhc
Q 021101 248 QSADLFSL-------QRFINRTKPPLSQDQQQNLTRWAVLFAATLIKNNKAIHEALMAAMSKK--ATILECIEAIENA 316 (317)
Q Consensus 248 a~~Dl~~l-------t~i~~~lG~~~s~~e~~~l~r~A~~~A~~LL~~~r~~leaLaeaLle~--esl~eC~~~Ie~~ 316 (317)
|-||++++ ++|+..--++.+.++.+. ...|+..|+.-|..-++.-.-+-+..+.. ..|++|..=+.++
T Consensus 1 g~nd~kQve~aVetAqkmvG~AT~smdp~~Le~-A~qAve~Ar~ql~~a~~~at~lD~~Fl~~~~~~L~~~eHQL~Ea 77 (79)
T PF10819_consen 1 GYNDLKQVEMAVETAQKMVGQATMSMDPDQLEH-ATQAVEDAREQLSQAKSHATGLDEPFLQQSEQLLDDCEHQLDEA 77 (79)
T ss_pred CccHHHHHHHHHHHHHHHHHHHHhcCCHHHHHH-HHHHHHHHHHHHHHHHHHHhCCcHHHHHHHHHHHHHHHHHHHHh
Confidence 35788876 345544445566555432 33466666655554443222234444443 4777777666553
No 64
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). 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=33.59 E-value=1.6e+02 Score=24.13 Aligned_cols=58 Identities=7% Similarity=0.093 Sum_probs=34.5
Q ss_pred hhHHHHHHHH--HHHhCCCCCHHHHHHHHHH---------HHHHHHHHHHHcHHHHHHHHHHHHHh-chHHH
Q 021101 249 SADLFSLQRF--INRTKPPLSQDQQQNLTRW---------AVLFAATLIKNNKAIHEALMAAMSKK-ATILE 308 (317)
Q Consensus 249 ~~Dl~~lt~i--~~~lG~~~s~~e~~~l~r~---------A~~~A~~LL~~~r~~leaLaeaLle~-esl~e 308 (317)
.+|+.++..| ++.+|+++ ++++.++.. ...+...+|+++...++.=.+.|... ..|++
T Consensus 40 ~~~~~~l~~I~~lr~~G~sl--~eI~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~ 109 (112)
T cd01282 40 EAAVDRVRQIRRLLAAGLTL--EEIREFLPCLRGGEPTFRPCPDLLAVLRRELARIDRQIADLTRSRDRLDA 109 (112)
T ss_pred HHHHHHHHHHHHHHHcCCCH--HHHHHHHHHhhCCCccCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5677777665 45688776 455544432 12345677777777777666666553 34443
No 65
>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=33.48 E-value=1.5e+02 Score=23.70 Aligned_cols=52 Identities=10% Similarity=0.049 Sum_probs=34.0
Q ss_pred hhHHHHHHHH--HHHhCCCCCHHHHHHHHH-HHHHHHHHHHHHcHHHHHHHHHHHHH
Q 021101 249 SADLFSLQRF--INRTKPPLSQDQQQNLTR-WAVLFAATLIKNNKAIHEALMAAMSK 302 (317)
Q Consensus 249 ~~Dl~~lt~i--~~~lG~~~s~~e~~~l~r-~A~~~A~~LL~~~r~~leaLaeaLle 302 (317)
.+|+..+..| ++.+|+++ .++++++. ....+...+|+++.+.+++=.+.|.+
T Consensus 41 ~~~~~~l~~I~~lr~~G~~l--~eI~~~l~~~~~~~~~~~l~~~~~~l~~~i~~l~~ 95 (97)
T cd04782 41 LEQFEQLDIILLLKELGISL--KEIKDYLDNRNPDELIELLKKQEKEIKEEIEELQK 95 (97)
T ss_pred HHHHHHHHHHHHHHHcCCCH--HHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 5677776654 56789887 45655543 23456677888888887776666654
No 66
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR 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 comprise 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=33.41 E-value=2.8e+02 Score=23.08 Aligned_cols=52 Identities=15% Similarity=0.109 Sum_probs=26.7
Q ss_pred hhHHHHHHHH--HHHhCCCCCHHHHHHHHHHH------HHHHHHHHHHcHHHHHHHHHHHHH
Q 021101 249 SADLFSLQRF--INRTKPPLSQDQQQNLTRWA------VLFAATLIKNNKAIHEALMAAMSK 302 (317)
Q Consensus 249 ~~Dl~~lt~i--~~~lG~~~s~~e~~~l~r~A------~~~A~~LL~~~r~~leaLaeaLle 302 (317)
.+|+.++..| ++.+||++ .+++.++... ......+|+++.+.++.-.+.|.+
T Consensus 41 ~~~l~~l~~I~~lr~~G~sL--~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 100 (126)
T cd04785 41 AAHVERLRFIRRARDLGFSL--EEIRALLALSDRPDRSCAEADAIARAHLADVRARIADLRR 100 (126)
T ss_pred HHHHHHHHHHHHHHHCCCCH--HHHHHHHhhhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566666554 45677765 3444443321 123455666666555554444443
No 67
>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=31.46 E-value=2.4e+02 Score=23.47 Aligned_cols=52 Identities=13% Similarity=0.029 Sum_probs=30.7
Q ss_pred hhHHHHHHHH--HHHhCCCCCHHHHHHHHHHH----HHHHHHHHHHcHHHHHHHHHHHHH
Q 021101 249 SADLFSLQRF--INRTKPPLSQDQQQNLTRWA----VLFAATLIKNNKAIHEALMAAMSK 302 (317)
Q Consensus 249 ~~Dl~~lt~i--~~~lG~~~s~~e~~~l~r~A----~~~A~~LL~~~r~~leaLaeaLle 302 (317)
.+|+.++..| ++.+||++ .++++++... ......+|+++.+.+++=.+.|..
T Consensus 40 ~~~l~~l~~I~~l~~~G~sl--~eI~~~l~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 97 (124)
T TIGR02051 40 EETVKRLRFIKRAQELGFSL--EEIGGLLGLVDGTHCREMYELASRKLKSVQAKMADLLR 97 (124)
T ss_pred HHHHHHHHHHHHHHHCCCCH--HHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5677777655 45788875 4555544421 244566777766666655555444
No 68
>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=31.28 E-value=1.6e+02 Score=23.57 Aligned_cols=50 Identities=16% Similarity=0.139 Sum_probs=30.9
Q ss_pred hhHHHHHHHH--HHHhCCCCCHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHH
Q 021101 249 SADLFSLQRF--INRTKPPLSQDQQQNLTRWAVLFAATLIKNNKAIHEALMAAM 300 (317)
Q Consensus 249 ~~Dl~~lt~i--~~~lG~~~s~~e~~~l~r~A~~~A~~LL~~~r~~leaLaeaL 300 (317)
.+|+..+..+ ++..|++++ +++.+++........+|++++..+++=-+.|
T Consensus 41 ~~di~~l~~i~~lr~~g~~l~--~i~~~~~~~~~~~~~~l~~~~~~l~~~i~~l 92 (103)
T cd01106 41 EEDLERLQQILFLKELGFSLK--EIKELLKDPSEDLLEALREQKELLEEKKERL 92 (103)
T ss_pred HHHHHHHHHHHHHHHcCCCHH--HHHHHHHcCcHHHHHHHHHHHHHHHHHHHHH
Confidence 5688887665 456888764 4544444333666777777777666544444
No 69
>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=31.19 E-value=32 Score=32.22 Aligned_cols=25 Identities=24% Similarity=0.202 Sum_probs=18.6
Q ss_pred cCCChhhhHHHHHHHhhHHHHHHHh
Q 021101 163 SSFFPDYQERVARHEAAHFLLAYLL 187 (317)
Q Consensus 163 ~~ls~~~r~RIA~HEAGHaLvAylL 187 (317)
+.-+....+.|+.||-||.+==+..
T Consensus 126 ~~~~~~~~~hvi~HEiGH~IGfRHT 150 (211)
T PF12388_consen 126 SNYSVNVIEHVITHEIGHCIGFRHT 150 (211)
T ss_pred CCCchhHHHHHHHHHhhhhcccccc
Confidence 3336677889999999998755544
No 70
>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=31.08 E-value=27 Score=33.84 Aligned_cols=19 Identities=21% Similarity=0.116 Sum_probs=15.7
Q ss_pred HHHHHHHhhHHHHHHHhCC
Q 021101 171 ERVARHEAAHFLLAYLLGL 189 (317)
Q Consensus 171 ~RIA~HEAGHaLvAylLg~ 189 (317)
=.+..||.||++=..+...
T Consensus 155 v~tl~HE~GHa~h~~l~~~ 173 (365)
T cd06258 155 INTLFHEFGHAVHFLLIQQ 173 (365)
T ss_pred HHHHHHHHhHHHHHHHhcC
Confidence 3789999999998887764
No 71
>cd01204 IRS_PTB Insulin receptor substrate (IRS) Phosphotyrosine-binding domain(PTB). Insulin receptor substrate (IRS) Phosphotyrosine-binding domain(PTB). This domain has a PH-like fold and is found in insulin receptor substrate molecules. IRS molecules have an N-terminal PH domain , which is followed by an IRS-like PTB domain. This PTBi domain is shorter than the PTB domain which is found in SHC, Numb and other proteins. The PTBi domain binds to phosphotyrosines which are in NPXpY motifs in the insulin receptor, IGF-I receptor and the IL-4 receptor.
Probab=30.82 E-value=26 Score=29.38 Aligned_cols=35 Identities=17% Similarity=0.194 Sum_probs=27.7
Q ss_pred CCCccccccchHHHHHHH-hhhchHHHHHHHHHHHh
Q 021101 28 SSSAATGRFDLKTLESAI-AKKDSNAVKEALDQLSE 62 (317)
Q Consensus 28 ~~~~~~~~~~~~~~~~~~-~~~~~~~v~~~~~~l~~ 62 (317)
.|+..-||--|+..|+++ ++.=-+.+.+||..|+|
T Consensus 68 Rsa~tG~GElWMq~dD~~vAqnmHe~iL~am~a~~e 103 (104)
T cd01204 68 RSAVTGPGELWMQVDDAVVAQNMHETILEAMKAMKE 103 (104)
T ss_pred ccccCCCCcEEEEcchHHHHHHHHHHHHHHHHhhcC
Confidence 667778999999999988 55555778888887765
No 72
>COG5549 Predicted Zn-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=29.72 E-value=28 Score=32.90 Aligned_cols=21 Identities=29% Similarity=0.272 Sum_probs=17.0
Q ss_pred cCCChhhhHHHHHHHhhHHHH
Q 021101 163 SSFFPDYQERVARHEAAHFLL 183 (317)
Q Consensus 163 ~~ls~~~r~RIA~HEAGHaLv 183 (317)
++.++++-.-+|.||-||+|-
T Consensus 180 pg~~~e~L~~tarhElGhaLg 200 (236)
T COG5549 180 PGELRENLNPTARHELGHALG 200 (236)
T ss_pred cccchhhhhHHHHHhhcchhe
Confidence 345677888899999999974
No 73
>PRK05457 heat shock protein HtpX; Provisional
Probab=29.65 E-value=36 Score=32.77 Aligned_cols=19 Identities=32% Similarity=0.345 Sum_probs=16.5
Q ss_pred CCChhhhHHHHHHHhhHHH
Q 021101 164 SFFPDYQERVARHEAAHFL 182 (317)
Q Consensus 164 ~ls~~~r~RIA~HEAGHaL 182 (317)
.++++|-+-|.-||.||.-
T Consensus 128 ~L~~~El~aVlAHElgHi~ 146 (284)
T PRK05457 128 NMSRDEVEAVLAHEISHIA 146 (284)
T ss_pred hCCHHHHHHHHHHHHHHHH
Confidence 3589999999999999973
No 74
>PRK02391 heat shock protein HtpX; Provisional
Probab=29.62 E-value=35 Score=33.05 Aligned_cols=22 Identities=32% Similarity=0.259 Sum_probs=17.7
Q ss_pred CCChhhhHHHHHHHhhHHHHHH
Q 021101 164 SFFPDYQERVARHEAAHFLLAY 185 (317)
Q Consensus 164 ~ls~~~r~RIA~HEAGHaLvAy 185 (317)
.++++|.+-|.-||.||.--.+
T Consensus 127 ~L~~~El~aVlaHElgHi~~~d 148 (296)
T PRK02391 127 RLDPDELEAVLAHELSHVKNRD 148 (296)
T ss_pred hCCHHHHHHHHHHHHHHHHcCC
Confidence 3489999999999999964433
No 75
>TIGR01675 plant-AP plant acid phosphatase. This model explicitly excludes the VSPs which lack the nucleophilc aspartate. The possibility exists, however, that some members of this family may, while containing all of the conserved HAD-superfamily catalytic residues, lack activity and have a function related to the function of the VSPs rather than the acid phosphatases.
Probab=29.61 E-value=55 Score=30.86 Aligned_cols=81 Identities=17% Similarity=0.132 Sum_probs=55.8
Q ss_pred hcccCcchhhhhhhhhhcccCCCCCccccccchHHHHHHHhhhchHHHHHHHHHHHhcccccccCCCCccccccccHHHH
Q 021101 6 ALTSFPYQSQKRFCFSRIRASSSSSAATGRFDLKTLESAIAKKDSNAVKEALDQLSEVGWAKRWSSQPYVSRRTTTLREL 85 (317)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~l~~~g~~~~~~~~~~v~~r~~~l~eL 85 (317)
.|.+.||+.++.+-- . .-....|......-+..-...+.+.++.|++.|+---|=+.|.-..|+.+.+.|
T Consensus 88 ~LsN~py~~~~~~g~-----~-----~~~~~~~~~wv~~~~apaip~al~l~~~l~~~G~~Vf~lTGR~e~~r~~T~~nL 157 (229)
T TIGR01675 88 LLSNIPYYKKHGYGT-----E-----KTDPTAFWLWLGKGAAPALPEGLKLYQKIIELGIKIFLLSGRWEELRNATLDNL 157 (229)
T ss_pred cccCHHHHHHhccCC-----C-----cCCHHHHHHHHHcCCCCCCHHHHHHHHHHHHCCCEEEEEcCCChHHHHHHHHHH
Confidence 456778887765410 0 011123555444445566777888999999999988887777777799999999
Q ss_pred HHcCCCCcccc
Q 021101 86 TLLGIKNAENL 96 (317)
Q Consensus 86 ~~~gi~~~~~l 96 (317)
+..|+..-+.|
T Consensus 158 ~~~G~~~~~~L 168 (229)
T TIGR01675 158 INAGFTGWKHL 168 (229)
T ss_pred HHcCCCCcCee
Confidence 99999864443
No 76
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares 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=29.12 E-value=2e+02 Score=23.39 Aligned_cols=52 Identities=17% Similarity=0.173 Sum_probs=29.4
Q ss_pred hhHHHHHHHH--HHHhCCCCCHHHHHHHHHHHH-HHHHHHHHHcHHHHHHHHHHHHH
Q 021101 249 SADLFSLQRF--INRTKPPLSQDQQQNLTRWAV-LFAATLIKNNKAIHEALMAAMSK 302 (317)
Q Consensus 249 ~~Dl~~lt~i--~~~lG~~~s~~e~~~l~r~A~-~~A~~LL~~~r~~leaLaeaLle 302 (317)
..|+.++..| ++.+|++++ +++.+.+... .....+|+++.+.+++=.+.|..
T Consensus 42 ~~~i~~l~~I~~lr~~G~sl~--~i~~l~~~~~~~~~~~~l~~~~~~l~~~i~~l~~ 96 (108)
T cd01107 42 AEQLERLNRIKYLRDLGFPLE--EIKEILDADNDDELRKLLREKLAELEAEIEELQR 96 (108)
T ss_pred HHHHHHHHHHHHHHHcCCCHH--HHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567776554 456888763 4444433222 45666677766666665555444
No 77
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, 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 domain
Probab=28.96 E-value=2.5e+02 Score=24.97 Aligned_cols=18 Identities=22% Similarity=0.259 Sum_probs=11.7
Q ss_pred hhHHHHHHHH--HHHhCCCC
Q 021101 249 SADLFSLQRF--INRTKPPL 266 (317)
Q Consensus 249 ~~Dl~~lt~i--~~~lG~~~ 266 (317)
.+|+.++..| ++.+|+++
T Consensus 42 ~~dl~rL~~I~~lr~~G~sL 61 (172)
T cd04790 42 ERDLERLEQICAYRSAGVSL 61 (172)
T ss_pred HHHHHHHHHHHHHHHcCCCH
Confidence 4577777554 45678775
No 78
>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=28.06 E-value=30 Score=31.91 Aligned_cols=11 Identities=36% Similarity=0.610 Sum_probs=9.6
Q ss_pred HHHHHHhhHHH
Q 021101 172 RVARHEAAHFL 182 (317)
Q Consensus 172 RIA~HEAGHaL 182 (317)
+.+.||.||.+
T Consensus 147 Kea~HElGH~~ 157 (194)
T PF07998_consen 147 KEAVHELGHLF 157 (194)
T ss_dssp HHHHHHHHHHT
T ss_pred HHHHHHHHHHc
Confidence 58999999975
No 79
>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=27.77 E-value=28 Score=33.39 Aligned_cols=20 Identities=20% Similarity=0.047 Sum_probs=14.2
Q ss_pred ChhhhHHHHHHHhhHHHHHH
Q 021101 166 FPDYQERVARHEAAHFLLAY 185 (317)
Q Consensus 166 s~~~r~RIA~HEAGHaLvAy 185 (317)
+...=+-|++||.||.+..-
T Consensus 212 ~~~~~~~v~vHE~GHsf~~L 231 (264)
T PF09471_consen 212 DNPSFKQVVVHEFGHSFGGL 231 (264)
T ss_dssp TSTTHHHHHHHHHHHHTT--
T ss_pred Ccccccceeeeecccccccc
Confidence 34456789999999987653
No 80
>PRK03982 heat shock protein HtpX; Provisional
Probab=27.63 E-value=44 Score=31.89 Aligned_cols=21 Identities=29% Similarity=0.175 Sum_probs=17.7
Q ss_pred CChhhhHHHHHHHhhHHHHHH
Q 021101 165 FFPDYQERVARHEAAHFLLAY 185 (317)
Q Consensus 165 ls~~~r~RIA~HEAGHaLvAy 185 (317)
++++|-+-|.-||.||.--.+
T Consensus 120 l~~~El~AVlAHElgHi~~~h 140 (288)
T PRK03982 120 LNEDELEGVIAHELTHIKNRD 140 (288)
T ss_pred CCHHHHHHHHHHHHHHHHcCC
Confidence 489999999999999986444
No 81
>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.
Probab=27.51 E-value=71 Score=23.17 Aligned_cols=35 Identities=20% Similarity=0.288 Sum_probs=28.0
Q ss_pred cccchHHHHHHHhhhchHHHHHHHHHHHhcccccc
Q 021101 34 GRFDLKTLESAIAKKDSNAVKEALDQLSEVGWAKR 68 (317)
Q Consensus 34 ~~~~~~~~~~~~~~~~~~~v~~~~~~l~~~g~~~~ 68 (317)
-|+||..++.....+-.+.+.+.+..+.++|++..
T Consensus 19 ~Gi~~~~~~~~~g~~~~~~~~~~l~~l~~~Gll~~ 53 (66)
T PF06969_consen 19 EGIDLSEFEQRFGIDFAEEFQKELEELQEDGLLEI 53 (66)
T ss_dssp SEEEHHHHHHHTT--THHH-HHHHHHHHHTTSEEE
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHHHCCCEEE
Confidence 58899999988887777788889999999999965
No 82
>PRK04897 heat shock protein HtpX; Provisional
Probab=27.40 E-value=41 Score=32.48 Aligned_cols=19 Identities=26% Similarity=0.232 Sum_probs=16.6
Q ss_pred CCChhhhHHHHHHHhhHHH
Q 021101 164 SFFPDYQERVARHEAAHFL 182 (317)
Q Consensus 164 ~ls~~~r~RIA~HEAGHaL 182 (317)
.++++|-+-|.-||-||.-
T Consensus 131 ~l~~~El~aVlAHElgHi~ 149 (298)
T PRK04897 131 IMNREELEGVIGHEISHIR 149 (298)
T ss_pred hCCHHHHHHHHHHHHHHHh
Confidence 4588999999999999965
No 83
>COG2738 Predicted Zn-dependent protease [General function prediction only]
Probab=26.92 E-value=33 Score=32.16 Aligned_cols=14 Identities=36% Similarity=0.422 Sum_probs=11.0
Q ss_pred HHHHHHhhHHHHHH
Q 021101 172 RVARHEAAHFLLAY 185 (317)
Q Consensus 172 RIA~HEAGHaLvAy 185 (317)
-||-||.||++=-.
T Consensus 94 aVAAHEVGHAiQd~ 107 (226)
T COG2738 94 AVAAHEVGHAIQDQ 107 (226)
T ss_pred HHHHHHhhHHHhhh
Confidence 37889999998543
No 84
>PRK03001 M48 family peptidase; Provisional
Probab=26.56 E-value=49 Score=31.49 Aligned_cols=21 Identities=24% Similarity=0.078 Sum_probs=17.5
Q ss_pred CChhhhHHHHHHHhhHHHHHH
Q 021101 165 FFPDYQERVARHEAAHFLLAY 185 (317)
Q Consensus 165 ls~~~r~RIA~HEAGHaLvAy 185 (317)
++++|-+-|.-||-||.--.+
T Consensus 119 l~~~El~aVlAHElgHi~~~h 139 (283)
T PRK03001 119 LSEREIRGVMAHELAHVKHRD 139 (283)
T ss_pred CCHHHHHHHHHHHHHHHhCCC
Confidence 489999999999999975443
No 85
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator. This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc 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-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=26.40 E-value=3.5e+02 Score=22.73 Aligned_cols=52 Identities=12% Similarity=0.140 Sum_probs=31.4
Q ss_pred hhHHHHHHHH--HHHhCCCCCHHHHHHHHHH-------HHHHHHHHHHHcHHHHHHHHHHHHH
Q 021101 249 SADLFSLQRF--INRTKPPLSQDQQQNLTRW-------AVLFAATLIKNNKAIHEALMAAMSK 302 (317)
Q Consensus 249 ~~Dl~~lt~i--~~~lG~~~s~~e~~~l~r~-------A~~~A~~LL~~~r~~leaLaeaLle 302 (317)
.+|+.++..| ++.+||++ .+++.++.. .......+|+++.+.+++-.+.|.+
T Consensus 42 ~~~l~~l~~I~~lr~~G~sl--~eI~~~l~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 102 (131)
T TIGR02043 42 DEDQKRLRFILKAKELGFTL--DEIKELLSIKLDATEHSCAEVKAIVDAKLELVDEKINELTK 102 (131)
T ss_pred HHHHHHHHHHHHHHHcCCCH--HHHHHHHHhhccCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5688887765 45688776 344444431 2245566777777766666555554
No 86
>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=25.97 E-value=13 Score=36.46 Aligned_cols=17 Identities=18% Similarity=0.210 Sum_probs=13.4
Q ss_pred hhhHHHHHHHhhHHHHH
Q 021101 168 DYQERVARHEAAHFLLA 184 (317)
Q Consensus 168 ~~r~RIA~HEAGHaLvA 184 (317)
.+..--=|||-|||||-
T Consensus 92 ~~~~lY~Y~~iGHFWVk 108 (299)
T PF12994_consen 92 EETHLYNYGEIGHFWVK 108 (299)
T ss_pred HHHHHhhccccceeeec
Confidence 45556779999999984
No 87
>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=25.88 E-value=9.7 Score=35.59 Aligned_cols=20 Identities=35% Similarity=0.451 Sum_probs=15.4
Q ss_pred hhhhHHHHHHHhhHHHHHHH
Q 021101 167 PDYQERVARHEAAHFLLAYL 186 (317)
Q Consensus 167 ~~~r~RIA~HEAGHaLvAyl 186 (317)
+-..-+++.||.||+|--+-
T Consensus 134 ~~n~g~t~~HEvGH~lGL~H 153 (225)
T cd04275 134 PYNLGDTATHEVGHWLGLYH 153 (225)
T ss_pred cccccceeEEeccceeeeee
Confidence 45667899999999985443
No 88
>cd04280 ZnMc_astacin_like Zinc-dependent metalloprotease, astacin_like subfamily or peptidase family M12A, a group of zinc-dependent proteolytic enzymes with a HExxH zinc-binding site/active site. Members of this family may have an amino terminal propeptide, which is cleaved to yield the active protease domain, which is consequently always found at the N-terminus in multi-domain architectures. This family includes: astacin, a digestive enzyme from Crayfish; meprin, a multiple domain membrane component that is constructed from a homologous alpha and beta chain, proteins involved in (bone) morphogenesis, tolloid from drosophila, and the sea urchin SPAN protein, which may also play a role in development.
Probab=25.64 E-value=35 Score=30.37 Aligned_cols=17 Identities=29% Similarity=0.104 Sum_probs=13.1
Q ss_pred HHHHHHHhhHHHHHHHh
Q 021101 171 ERVARHEAAHFLLAYLL 187 (317)
Q Consensus 171 ~RIA~HEAGHaLvAylL 187 (317)
..++.||-||+|=-+-.
T Consensus 75 ~g~v~HE~~HalG~~HE 91 (180)
T cd04280 75 LGTIVHELMHALGFYHE 91 (180)
T ss_pred CchhHHHHHHHhcCcch
Confidence 57999999999755443
No 89
>PF13583 Reprolysin_4: Metallo-peptidase family M12B Reprolysin-like
Probab=24.61 E-value=38 Score=30.86 Aligned_cols=17 Identities=24% Similarity=-0.070 Sum_probs=13.8
Q ss_pred HHHHHHhhHHHHHHHhC
Q 021101 172 RVARHEAAHFLLAYLLG 188 (317)
Q Consensus 172 RIA~HEAGHaLvAylLg 188 (317)
.+.-||.||.|=+.--+
T Consensus 139 ~~~aHEiGH~lGl~H~~ 155 (206)
T PF13583_consen 139 QTFAHEIGHNLGLRHDF 155 (206)
T ss_pred hHHHHHHHHHhcCCCCc
Confidence 56889999998777655
No 90
>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=24.59 E-value=48 Score=29.78 Aligned_cols=17 Identities=24% Similarity=0.069 Sum_probs=12.0
Q ss_pred HHHHHHHhhHHHHHHHh
Q 021101 171 ERVARHEAAHFLLAYLL 187 (317)
Q Consensus 171 ~RIA~HEAGHaLvAylL 187 (317)
..++.||.||+|=-+-.
T Consensus 80 ~~~i~HEl~HaLG~~HE 96 (191)
T PF01400_consen 80 VGTILHELGHALGFWHE 96 (191)
T ss_dssp HHHHHHHHHHHHTB--G
T ss_pred ccchHHHHHHHHhhhhh
Confidence 46899999999855443
No 91
>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=23.87 E-value=51 Score=30.27 Aligned_cols=15 Identities=27% Similarity=0.286 Sum_probs=12.3
Q ss_pred hhhHHHHHHHhhHHH
Q 021101 168 DYQERVARHEAAHFL 182 (317)
Q Consensus 168 ~~r~RIA~HEAGHaL 182 (317)
+.-+.++.||.||+|
T Consensus 114 ~~~~~~~~he~gh~l 128 (197)
T cd04276 114 ASLRYLLAHEVGHTL 128 (197)
T ss_pred HHHHHHHHHHHHHHh
Confidence 556679999999986
No 92
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=23.75 E-value=4.6e+02 Score=22.37 Aligned_cols=52 Identities=17% Similarity=0.140 Sum_probs=29.4
Q ss_pred hhHHHHHHHH--HHHhCCCCCHHHHHHHHHH-------HHHHHHHHHHHcHHHHHHHHHHHHH
Q 021101 249 SADLFSLQRF--INRTKPPLSQDQQQNLTRW-------AVLFAATLIKNNKAIHEALMAAMSK 302 (317)
Q Consensus 249 ~~Dl~~lt~i--~~~lG~~~s~~e~~~l~r~-------A~~~A~~LL~~~r~~leaLaeaLle 302 (317)
.+|+.++..| ++.+||+++ +++.++.. .......+|+++.+.+++-.+.|.+
T Consensus 42 ~~~l~~l~~I~~lr~~G~sL~--eI~~~l~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 102 (140)
T PRK09514 42 EQDLQRLRFIRRAKQLGFTLE--EIRELLSIRLDPEHHTCQEVKGIVDEKLAEVEAKIAELQH 102 (140)
T ss_pred HHHHHHHHHHHHHHHcCCCHH--HHHHHHHhcccCCcCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5577777655 456787753 44444331 2344556666666666665555554
No 93
>PF00901 Orbi_VP5: Orbivirus outer capsid protein VP5; InterPro: IPR000145 The orbivirus VP5 protein is one of the two proteins (with VP2) which make up the virus particle outer capsid. Cryoelectron microscopy indicates that VP5 is a trimer suggesting that there are 360 copies of VP5 per virion [].; GO: 0005198 structural molecule activity, 0019028 viral capsid
Probab=23.73 E-value=2.6e+02 Score=29.55 Aligned_cols=18 Identities=17% Similarity=0.324 Sum_probs=10.0
Q ss_pred HHHHHcHHHHHHHHHHHH
Q 021101 284 TLIKNNKAIHEALMAAMS 301 (317)
Q Consensus 284 ~LL~~~r~~leaLaeaLl 301 (317)
.++++.|..+++|.++..
T Consensus 183 ~mv~~yr~ki~aL~~aIe 200 (508)
T PF00901_consen 183 KMVEEYRQKIDALKNAIE 200 (508)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 355555555555555544
No 94
>PRK03072 heat shock protein HtpX; Provisional
Probab=23.49 E-value=63 Score=31.07 Aligned_cols=23 Identities=17% Similarity=0.069 Sum_probs=18.2
Q ss_pred CCChhhhHHHHHHHhhHHHHHHH
Q 021101 164 SFFPDYQERVARHEAAHFLLAYL 186 (317)
Q Consensus 164 ~ls~~~r~RIA~HEAGHaLvAyl 186 (317)
.++++|-+-|.-||.||.--.+.
T Consensus 121 ~l~~~El~aVlAHElgHi~~~d~ 143 (288)
T PRK03072 121 ILNERELRGVLGHELSHVYNRDI 143 (288)
T ss_pred hCCHHHHHHHHHHHHHHHhcCCH
Confidence 34899999999999999754433
No 95
>KOG0058 consensus Peptide exporter, ABC superfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=23.44 E-value=48 Score=36.31 Aligned_cols=87 Identities=18% Similarity=0.215 Sum_probs=58.6
Q ss_pred CCHHHHHHHHH------HHchHHHHHHhhcCCccchhhHHHHHHHHHHHh----CCC-------------CCHHHHHHHH
Q 021101 219 LDAKELDRLAV------VAMAGLAAEGLQYDKVVGQSADLFSLQRFINRT----KPP-------------LSQDQQQNLT 275 (317)
Q Consensus 219 ~s~~~L~r~~~------VlLAGrAAE~lvfG~atGa~~Dl~~lt~i~~~l----G~~-------------~s~~e~~~l~ 275 (317)
++.+++++.+. |+++|-..|.|.||.-....+|+..+.++++.- +++ +|-. || +
T Consensus 535 ~~~~~lr~~Ig~V~QEPvLFs~sI~eNI~YG~~~~t~e~i~~AAk~ANah~FI~~~p~gY~T~VGEkG~qLSGG-QK--Q 611 (716)
T KOG0058|consen 535 INHKYLRRKIGLVGQEPVLFSGSIRENIAYGLDNATDEEIEAAAKMANAHEFITNFPDGYNTVVGEKGSQLSGG-QK--Q 611 (716)
T ss_pred cCHHHHHHHeeeeeccceeecccHHHHHhcCCCCCCHHHHHHHHHHhChHHHHHhCccccccccCCccccccch-HH--H
Confidence 56777776642 578999999999998877788999888887632 222 2222 33 3
Q ss_pred HHHHHHHH------HHHHHcHHHHHHHHHHHHHhchHHHH
Q 021101 276 RWAVLFAA------TLIKNNKAIHEALMAAMSKKATILEC 309 (317)
Q Consensus 276 r~A~~~A~------~LL~~~r~~leaLaeaLle~esl~eC 309 (317)
|-|..||. -||.|--.+||+-.|.|.++ .++.|
T Consensus 612 RIAIARALlr~P~VLILDEATSALDaeSE~lVq~-aL~~~ 650 (716)
T KOG0058|consen 612 RIAIARALLRNPRVLILDEATSALDAESEYLVQE-ALDRL 650 (716)
T ss_pred HHHHHHHHhcCCCEEEEechhhhcchhhHHHHHH-HHHHh
Confidence 44444442 35667778999999888764 34444
No 96
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=23.34 E-value=4.7e+02 Score=22.30 Aligned_cols=18 Identities=17% Similarity=0.086 Sum_probs=9.6
Q ss_pred hhHHHHHHHH--HHHhCCCC
Q 021101 249 SADLFSLQRF--INRTKPPL 266 (317)
Q Consensus 249 ~~Dl~~lt~i--~~~lG~~~ 266 (317)
..|+.++..| ++.+||++
T Consensus 41 ~~~l~~l~~I~~lr~~G~sl 60 (135)
T PRK10227 41 QQHLNELTLLRQARQVGFNL 60 (135)
T ss_pred HHHHHHHHHHHHHHHCCCCH
Confidence 3455555443 34566664
No 97
>cd06461 M2_ACE Peptidase family M2 Angiotensin converting enzyme (ACE, EC 3.4.15.1) is a membrane-bound, zinc dependent dipeptidase that catalyzes the conversion of the decapeptide angiotensin I to the potent vasopressor ocatapeptide angiotensin II, by removing two C-terminal amino acids. There are two forms of the enzyme in humans, the ubiquitous somatic ACE and the sperm-specific germinal ACE, both encoded by the same gene through transcription from alternative promoters. Somatic ACE has two tandem active sites with distinct catalytic properties, whereas germinal ACE, the function of which is largely unknown, has just a single active site. Recently, an ACE homolog, ACE2, has been identified in humans that differs from ACE; it preferentially removes carboxy-terminal hydrophobic or basic amino acids and appears to be important in cardiac function. ACE homologs (also known as members of the M2 gluzincin family) have been found in a wide variety of species, including those that neither h
Probab=22.96 E-value=54 Score=34.12 Aligned_cols=20 Identities=25% Similarity=0.225 Sum_probs=15.3
Q ss_pred HHHcHHHHHHHHHHHHHhch
Q 021101 286 IKNNKAIHEALMAAMSKKAT 305 (317)
Q Consensus 286 L~~~r~~leaLaeaLle~es 305 (317)
+...+++.+.+.+.|.-+.|
T Consensus 422 ~~~s~~Ag~~l~~~l~lG~S 441 (477)
T cd06461 422 IYGSKEAGKKLRAMLSLGSS 441 (477)
T ss_pred ccChHHHHHHHHHHHhCcCC
Confidence 35688899999988877753
No 98
>COG4219 MecR1 Antirepressor regulating drug resistance, predicted signal transduction N-terminal membrane component [Transcription / Signal transduction mechanisms]
Probab=22.60 E-value=50 Score=33.04 Aligned_cols=23 Identities=13% Similarity=0.121 Sum_probs=19.0
Q ss_pred hhhcCCChhhhHHHHHHHhhHHH
Q 021101 160 QGFSSFFPDYQERVARHEAAHFL 182 (317)
Q Consensus 160 ~~~~~ls~~~r~RIA~HEAGHaL 182 (317)
|-+.++++||++-|+.||-+|+=
T Consensus 180 d~~~r~~~ee~~yIilHEl~Hlk 202 (337)
T COG4219 180 DFVERLTDEELKYIILHELSHLK 202 (337)
T ss_pred HHHhhcCHHhhhhhHhHHHhhhh
Confidence 33456799999999999999973
No 99
>TIGR03455 HisG_C-term ATP phosphoribosyltransferase, C-terminal domain. This domain corresponds to the C-terminal third of the HisG protein. It is absent in many lineages.
Probab=22.28 E-value=24 Score=29.02 Aligned_cols=28 Identities=18% Similarity=0.235 Sum_probs=22.6
Q ss_pred ccchHHHHHHHhhhchHHHHHHHHHHHhccc
Q 021101 35 RFDLKTLESAIAKKDSNAVKEALDQLSEVGW 65 (317)
Q Consensus 35 ~~~~~~~~~~~~~~~~~~v~~~~~~l~~~g~ 65 (317)
..+|-++.+.|.+++... .+++||+.|-
T Consensus 61 ~~~w~AV~~vv~~~~v~~---~~~~Lk~~GA 88 (100)
T TIGR03455 61 DEGWVAVHAVVDEKVVNE---LIDKLKAAGA 88 (100)
T ss_pred CCCeEEEEEEEcHHHHHH---HHHHHHHcCC
Confidence 468999999998887666 8888888873
No 100
>cd04283 ZnMc_hatching_enzyme Zinc-dependent metalloprotease, hatching enzyme-like subfamily. Hatching enzymes are secreted by teleost embryos to digest the egg envelope or chorion. In some teleosts, the hatching enzyme may be a system consisting of two evolutionary related metalloproteases, high choriolytic enzyme and low choriolytic enzyme (HCE and LCE), which may have different substrate specificities and cooperatively digest the chorion.
Probab=22.00 E-value=48 Score=30.05 Aligned_cols=17 Identities=29% Similarity=0.258 Sum_probs=13.3
Q ss_pred HHHHHHhhHHHHHHHhC
Q 021101 172 RVARHEAAHFLLAYLLG 188 (317)
Q Consensus 172 RIA~HEAGHaLvAylLg 188 (317)
-++.||-||+|--+-.-
T Consensus 79 G~i~HEl~HaLG~~HEh 95 (182)
T cd04283 79 GIIQHELLHALGFYHEQ 95 (182)
T ss_pred chHHHHHHHHhCCcccc
Confidence 48999999998666543
No 101
>PRK01345 heat shock protein HtpX; Provisional
Probab=21.78 E-value=60 Score=31.77 Aligned_cols=22 Identities=27% Similarity=0.206 Sum_probs=18.2
Q ss_pred CChhhhHHHHHHHhhHHHHHHH
Q 021101 165 FFPDYQERVARHEAAHFLLAYL 186 (317)
Q Consensus 165 ls~~~r~RIA~HEAGHaLvAyl 186 (317)
++++|-+-|.-||.||.--.+.
T Consensus 119 L~~dEL~aVlAHElgHi~~~d~ 140 (317)
T PRK01345 119 LSPEEVAGVMAHELAHVKNRDT 140 (317)
T ss_pred CCHHHHHHHHHHHHHHHHcCCH
Confidence 4789999999999999865544
No 102
>PF13688 Reprolysin_5: Metallo-peptidase family M12; PDB: 2FV5_B 3EWJ_A 3KME_A 3L0T_B 1BKC_E 3G42_D 2I47_D 2FV9_B 3LEA_A 1ZXC_B ....
Probab=20.63 E-value=59 Score=28.49 Aligned_cols=23 Identities=26% Similarity=-0.032 Sum_probs=15.0
Q ss_pred ChhhhHHHHHHHhhHHHHHHHhC
Q 021101 166 FPDYQERVARHEAAHFLLAYLLG 188 (317)
Q Consensus 166 s~~~r~RIA~HEAGHaLvAylLg 188 (317)
++.....+.-||.||-|=+.--+
T Consensus 138 ~~~~~~~~~AHEiGH~lGa~HD~ 160 (196)
T PF13688_consen 138 PTYNGAITFAHEIGHNLGAPHDG 160 (196)
T ss_dssp -HHHHHHHHHHHHHHHTT-----
T ss_pred CCCceehhhHHhHHHhcCCCCCC
Confidence 46777889999999998777644
No 103
>cd04281 ZnMc_BMP1_TLD Zinc-dependent metalloprotease; BMP1/TLD-like subfamily. BMP1 (Bone morphogenetic protein 1) and TLD (tolloid)-like metalloproteases play vital roles in extracellular matrix formation, by cleaving precursor proteins such as enzymes, structural proteins, and proteins involved in the mineralization of the extracellular matrix. The drosophila protein tolloid and its Xenopus homologue xolloid cleave and inactivate Sog and chordin, respectively, which are inhibitors of Dpp (the Drosophila decapentaplegic gene product) and its homologue BMP4, involved in dorso-ventral patterning.
Probab=20.47 E-value=53 Score=30.19 Aligned_cols=17 Identities=18% Similarity=0.184 Sum_probs=13.0
Q ss_pred HHHHHHhhHHHHHHHhC
Q 021101 172 RVARHEAAHFLLAYLLG 188 (317)
Q Consensus 172 RIA~HEAGHaLvAylLg 188 (317)
=++.||-||+|=-+-.-
T Consensus 89 Gti~HEl~HaLGf~HEh 105 (200)
T cd04281 89 GIVVHELGHVIGFWHEH 105 (200)
T ss_pred chHHHHHHHHhcCcchh
Confidence 38999999998665543
No 104
>PF05569 Peptidase_M56: BlaR1 peptidase M56; InterPro: IPR008756 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M56 (clan M-). The predicted active site residues for members of this family occur in the motif HEXXH. The type example is BlaR1 peptidase from Bacillus licheniformis. Production of beta-Lactamase and penicillin-binding protein 2a (which mediate staphylococcal resistance to beta-lactam antibiotics) is regulated by a signal-transducing integral membrane protein and a transcriptional repressor. The signal transducer is a fusion protein with penicillin-binding and zinc metalloprotease domains. The signal for protein expression is transmitted by site-specific proteolytic cleavage of both the transducer, which auto-activates, and the repressor, which is inactivated, unblocking gene transcription.
Probab=20.32 E-value=72 Score=30.15 Aligned_cols=18 Identities=22% Similarity=0.278 Sum_probs=16.0
Q ss_pred CCChhhhHHHHHHHhhHH
Q 021101 164 SFFPDYQERVARHEAAHF 181 (317)
Q Consensus 164 ~ls~~~r~RIA~HEAGHa 181 (317)
.+++++.+-|..||-.|.
T Consensus 190 ~~~~~el~~il~HEl~Hi 207 (299)
T PF05569_consen 190 DLSEEELRAILLHELAHI 207 (299)
T ss_pred ccCHHHHHHHHHHHHHHH
Confidence 568999999999999995
Done!