Query 024373
Match_columns 268
No_of_seqs 128 out of 524
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 04:05:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024373.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024373hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF09778 Guanylate_cyc_2: Guan 100.0 1.8E-69 3.9E-74 479.1 20.3 204 57-262 1-212 (212)
2 KOG4621 Uncharacterized conser 100.0 5.2E-45 1.1E-49 299.9 13.4 158 108-265 1-167 (167)
3 PF11814 DUF3335: Peptidase_C3 99.9 9.1E-24 2E-28 186.7 17.2 172 57-256 1-198 (207)
4 PF03412 Peptidase_C39: Peptid 99.8 1.6E-20 3.4E-25 151.7 8.6 128 56-263 1-128 (131)
5 TIGR03796 NHPM_micro_ABC1 NHPM 99.8 4.8E-19 1E-23 180.2 13.0 121 56-251 1-121 (710)
6 cd02424 Peptidase_C39E A sub-f 99.8 2.7E-18 5.9E-23 139.5 13.7 122 57-250 1-123 (129)
7 cd02549 Peptidase_C39A A sub-f 99.7 4.8E-17 1E-21 132.2 14.7 133 63-254 2-135 (141)
8 cd02418 Peptidase_C39B A sub-f 99.7 6.4E-17 1.4E-21 130.7 13.9 134 57-264 1-134 (136)
9 TIGR01193 bacteriocin_ABC ABC- 99.7 6.6E-17 1.4E-21 164.7 13.6 121 62-251 1-123 (708)
10 cd02420 Peptidase_C39D A sub-f 99.7 2.5E-16 5.3E-21 126.2 12.7 118 58-250 2-119 (125)
11 cd02419 Peptidase_C39C A sub-f 99.7 1.1E-15 2.5E-20 122.5 12.9 119 57-250 1-119 (127)
12 PF13529 Peptidase_C39_2: Pept 99.6 9.8E-16 2.1E-20 122.7 10.4 139 55-232 1-144 (144)
13 cd02423 Peptidase_C39G A sub-f 99.6 4.2E-15 9.1E-20 119.0 13.5 119 60-250 4-123 (129)
14 COG2274 SunT ABC-type bacterio 99.6 8.9E-16 1.9E-20 157.5 11.3 119 57-250 2-120 (709)
15 cd02259 Peptidase_C39_like Pep 99.6 6.8E-15 1.5E-19 116.3 13.1 116 62-251 1-116 (122)
16 cd02425 Peptidase_C39F A sub-f 99.6 7.5E-15 1.6E-19 117.1 13.1 119 57-250 1-120 (126)
17 cd02417 Peptidase_C39_likeA A 99.5 1.5E-13 3.3E-18 109.2 12.0 112 65-250 4-115 (121)
18 cd02421 Peptidase_C39_likeD A 99.4 1E-12 2.2E-17 105.0 11.6 119 66-262 5-123 (124)
19 TIGR03375 type_I_sec_LssB type 99.4 6.1E-13 1.3E-17 135.5 12.6 109 70-251 2-111 (694)
20 TIGR01846 type_I_sec_HlyB type 99.4 1.1E-12 2.4E-17 133.7 12.1 108 69-251 1-108 (694)
21 TIGR03797 NHPM_micro_ABC2 NHPM 99.3 6.9E-12 1.5E-16 127.6 12.5 102 69-248 4-105 (686)
22 PF12385 Peptidase_C70: Papain 99.0 4.6E-09 9.9E-14 89.9 11.3 136 56-249 23-161 (166)
23 PF14399 Transpep_BrtH: NlpC/p 98.8 1.7E-07 3.7E-12 86.4 16.5 93 150-253 57-154 (317)
24 COG3271 Predicted double-glyci 98.8 4.2E-08 9E-13 87.2 11.1 124 60-254 36-159 (201)
25 COG4990 Uncharacterized protei 98.6 4E-07 8.6E-12 79.6 10.8 153 55-254 28-188 (195)
26 PF05023 Phytochelatin: Phytoc 98.4 3.6E-06 7.8E-11 75.5 11.5 142 58-250 40-196 (212)
27 KOG0632 Phytochelatin synthase 93.2 0.095 2.1E-06 49.6 3.8 26 209-234 158-183 (388)
28 PF07910 Peptidase_C78: Peptid 90.2 3.8 8.2E-05 37.0 10.6 65 56-120 10-111 (218)
29 PF05543 Peptidase_C47: Stapho 86.9 18 0.0004 31.8 12.2 74 146-235 69-147 (175)
30 PF15645 Tox-PLDMTX: Dermonecr 79.4 8.1 0.00017 32.6 6.8 24 208-234 41-64 (135)
31 cd02619 Peptidase_C1 C1 Peptid 78.2 9.8 0.00021 32.4 7.2 80 166-246 125-215 (223)
32 cd02248 Peptidase_C1A Peptidas 71.2 18 0.00039 31.0 7.1 61 166-232 117-182 (210)
33 PF00112 Peptidase_C1: Papain 67.8 7.3 0.00016 33.2 3.9 62 165-232 122-189 (219)
34 TIGR03590 PseG pseudaminic aci 55.7 46 0.001 30.4 7.2 70 102-194 21-96 (279)
35 COG2117 Predicted subunit of t 54.7 29 0.00064 30.6 5.3 46 105-167 17-62 (198)
36 PF01640 Peptidase_C10: Peptid 50.8 96 0.0021 27.0 8.0 23 61-83 16-38 (192)
37 cd02621 Peptidase_C1A_Cathepsi 47.7 71 0.0015 28.5 6.9 22 210-231 186-211 (243)
38 cd02698 Peptidase_C1A_Cathepsi 46.7 77 0.0017 28.3 7.0 88 165-258 137-233 (239)
39 PF13162 DUF3997: Protein of u 42.8 53 0.0012 27.0 4.8 39 225-263 74-112 (115)
40 KOG3040 Predicted sugar phosph 42.3 2E+02 0.0044 26.6 8.8 36 105-159 32-67 (262)
41 PF09671 Spore_GerQ: Spore coa 39.3 39 0.00084 26.1 3.2 24 213-236 36-61 (81)
42 cd00307 RuBisCO_small_like Rib 38.4 1.6E+02 0.0035 22.8 6.6 58 167-224 6-73 (84)
43 cd02620 Peptidase_C1A_Cathepsi 38.2 1E+02 0.0022 27.5 6.3 62 165-232 143-208 (236)
44 PF02677 DUF208: Uncharacteriz 36.2 73 0.0016 28.1 4.9 56 102-165 45-113 (176)
45 COG4451 RbcS Ribulose bisphosp 32.7 60 0.0013 27.1 3.6 27 208-234 79-109 (127)
46 TIGR02728 spore_gerQ spore coa 31.5 40 0.00086 26.1 2.2 23 214-236 35-59 (82)
47 PF13728 TraF: F plasmid trans 28.7 2.5E+02 0.0054 25.0 7.2 40 147-186 141-192 (215)
48 PF03421 YopJ: YopJ Serine/Thr 27.9 51 0.0011 28.8 2.6 42 49-91 130-171 (177)
49 PF02902 Peptidase_C48: Ulp1 p 27.5 49 0.0011 28.1 2.4 24 58-81 159-182 (216)
50 PF05563 SpvD: Salmonella plas 27.4 54 0.0012 28.3 2.5 40 213-254 166-205 (216)
51 PRK15250 virulence protein Spv 27.4 54 0.0012 28.3 2.5 40 213-254 166-205 (216)
52 PF13743 Thioredoxin_5: Thiore 27.1 54 0.0012 28.1 2.6 52 65-117 61-119 (176)
53 PRK10941 hypothetical protein; 26.7 1.2E+02 0.0027 28.1 5.0 68 153-254 93-162 (269)
54 PTZ00203 cathepsin L protease; 25.6 2.3E+02 0.005 27.3 6.8 61 165-232 247-310 (348)
55 TIGR02739 TraF type-F conjugat 24.8 2.2E+02 0.0047 26.4 6.3 41 146-186 170-222 (256)
56 PRK06552 keto-hydroxyglutarate 24.1 4.5E+02 0.0098 23.4 8.0 93 59-183 41-135 (213)
57 KOG0734 AAA+-type ATPase conta 24.0 69 0.0015 33.5 3.0 24 141-186 381-404 (752)
58 PF01081 Aldolase: KDPG and KH 23.4 4.2E+02 0.0091 23.5 7.6 90 63-185 40-129 (196)
59 KOG0852 Alkyl hydroperoxide re 23.2 1.4E+02 0.0031 26.7 4.4 47 208-264 30-76 (196)
60 KOG2433 Uncharacterized conser 22.9 8.1E+02 0.018 24.9 11.3 60 64-123 406-484 (577)
61 PF08671 SinI: Anti-repressor 22.8 1.4E+02 0.0029 18.9 3.1 22 146-174 6-27 (30)
62 PRK13703 conjugal pilus assemb 22.8 3.5E+02 0.0075 25.0 7.1 20 146-165 163-182 (248)
63 cd03527 RuBisCO_small Ribulose 21.8 1.2E+02 0.0026 24.3 3.4 17 208-224 72-88 (99)
64 cd01986 Alpha_ANH_like Adenine 21.4 3.7E+02 0.0079 20.4 6.1 64 104-172 14-77 (103)
No 1
>PF09778 Guanylate_cyc_2: Guanylylate cyclase; InterPro: IPR018616 Members of this family of proteins catalyse the conversion of guanosine triphosphate (GTP) to 3',5'-cyclic guanosine monophosphate (cGMP) and pyrophosphate.
Probab=100.00 E-value=1.8e-69 Score=479.10 Aligned_cols=204 Identities=54% Similarity=0.888 Sum_probs=194.8
Q ss_pred CceecccCcCcchHHHHHHHHHHhCCCCCChhHHHHHhc----ccccchhhHHHHHHHcCceeEEEEeecCCCCCCcchh
Q 024373 57 VPHINQLFSWDCGLACVLMVLRTIGINNCNIQGLAEQCC----TTSIWTVDLAYLLQKFNVGFSYFTITLGANPNYSVET 132 (268)
Q Consensus 57 vP~i~Q~~~~DCGlACl~MVL~y~g~~~~~~~~L~el~~----ttsiwtidLa~ll~~~gv~~~~~T~tlG~~p~y~~~~ 132 (268)
||||+|..+||||+||+.|||++.|+..++ ++++++|. |+|||||||+|||++||+++.|||+|+|+||+|+.++
T Consensus 1 vphi~Q~~~WDCGlACv~MvL~~~~~~~~~-~~~~~~c~~~~~t~SiWTIDLayLL~~f~v~~~f~T~TlGvnp~y~~~~ 79 (212)
T PF09778_consen 1 VPHIQQRYNWDCGLACVLMVLRYLGRNNFL-ANFEEICQEEGFTTSIWTIDLAYLLRRFGVRHSFYTVTLGVNPNYSVES 79 (212)
T ss_pred CCceeeeccccccHHHHHHHHHHcCccchH-HHHHHHHHHccCCcceehhHHHHHHHHcCCCeeEecCccccCcCccccc
Confidence 799999999999999999999999999855 89999997 9999999999999999999999999999999999999
Q ss_pred hhhhccCchHHHHHHHHHHHHHcCCeeeeeccCHHHHHHHHhcCCceEEEEEeCccccccc----ccccccCCccCCCCC
Q 024373 133 FYKEQLPTDLVRVDMLFQKARSAGIKIECGSISGVEISLMILSGNYIAIALVDQYKLSHSW----MEDVIVPGFYGSDSG 208 (268)
Q Consensus 133 FY~~~~~~D~~Rv~~lf~~A~~~Gi~~~~~~vs~~~L~~~l~~g~~PaIvLvn~~~L~~~~----~~~~~~~~~~~~~~~ 208 (268)
||+++++.|+.||++||++|++.|+.++++++++++|.++|++|+ |||||||+++|+|+. ..+.+.++.++++++
T Consensus 80 FY~~~~~~D~~RV~~lF~~A~~~gi~V~~rsvs~~ei~~hl~~g~-~aIvLVd~~~L~C~~Ck~~~~~~~~~~~~~~~~~ 158 (212)
T PF09778_consen 80 FYKKNFDEDENRVNRLFQKAKAAGINVEKRSVSIQEIIEHLSSGG-PAIVLVDASLLHCDLCKSNCFDPIGSKCFGRSPD 158 (212)
T ss_pred hHHHhhhhHHHHHHHHHHHHHHcCCceEEeeccHHHHHHHHhCCC-cEEEEEccccccChhhcccccccccccccCCCCC
Confidence 999999999999999999999999999999999999999999996 999999999999643 344556788999999
Q ss_pred cCCcEEEEEEEeCCCCEEEEecCCCCCceeEeCHHHHHHHhhcCCCCceEEEEe
Q 024373 209 YTGHYILICGYDANSDEFEIRDPASCRKREKVTLKCLEEARKSFGTDEDLLLIS 262 (268)
Q Consensus 209 y~gHYVVL~Gyd~~~~~f~I~DPa~g~~~~~is~~eFe~a~~s~GtD~dii~i~ 262 (268)
|+||||||||||.++++|+|+|||++++.+++|++.||+||+||||||||||||
T Consensus 159 Y~GHYVVlcGyd~~~~~~~yrdPa~~~~~c~~s~~~ld~AR~s~GTDeDii~Iy 212 (212)
T PF09778_consen 159 YQGHYVVLCGYDAATKEFEYRDPASSDRVCRVSPEALDEARKSFGTDEDIIFIY 212 (212)
T ss_pred ccEEEEEEEeecCCCCeEEEeCCccccceeecCHHHHHHHHhccCCCcceEEeC
Confidence 999999999999999999999999999999999999999999999999999997
No 2
>KOG4621 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=5.2e-45 Score=299.93 Aligned_cols=158 Identities=51% Similarity=0.841 Sum_probs=148.8
Q ss_pred HHHcCceeEEEEeecCCCCCCcchhhhhhccCchHHHHHHHHHHHHHcCCeeeeeccCHHHHHHHHhcCCceEEEEEeCc
Q 024373 108 LQKFNVGFSYFTITLGANPNYSVETFYKEQLPTDLVRVDMLFQKARSAGIKIECGSISGVEISLMILSGNYIAIALVDQY 187 (268)
Q Consensus 108 l~~~gv~~~~~T~tlG~~p~y~~~~FY~~~~~~D~~Rv~~lf~~A~~~Gi~~~~~~vs~~~L~~~l~~g~~PaIvLvn~~ 187 (268)
+++|+|.++|+|.|+|+||+|+.+.||+++|++|+.||+.||++|.+.|+.+++.++|+.+|+.+|++|+.+||||||+.
T Consensus 1 lhhF~V~~rfcT~T~GadkgYk~eeFYkehfd~detRVd~LFakA~ac~iiie~csVSi~dIqahLaqGnhiAIaLVdq~ 80 (167)
T KOG4621|consen 1 LHHFCVEFRFCTITFGADKGYKIEEFYKEHFDEDETRVDLLFAKAHACGIIIECCSVSIHDIQAHLAQGNHIAIALVDQD 80 (167)
T ss_pred CceeeEEEEEEEEEecCCCCcchHHHHHHhCChHHHHHHHHHHHhhhcceEEEEeeeeHHHHHHHHhcCCeEEEEEecCC
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccccccc-----C---CccCCCCCcCCcEEEEEEEeCCCCEEEEecCCCCC-ceeEeCHHHHHHHhhcCCCCceE
Q 024373 188 KLSHSWMEDVIV-----P---GFYGSDSGYTGHYILICGYDANSDEFEIRDPASCR-KREKVTLKCLEEARKSFGTDEDL 258 (268)
Q Consensus 188 ~L~~~~~~~~~~-----~---~~~~~~~~y~gHYVVL~Gyd~~~~~f~I~DPa~g~-~~~~is~~eFe~a~~s~GtD~di 258 (268)
+|+++|.++... | -.|++.+.|+||||||+|||+.+++|.|+|||+.+ .++++|.++||+||+||||||||
T Consensus 81 ~Lhcdlceeplk~ccfspnghhcfcrtp~YqGHfiVi~GYd~a~~c~~~ndPA~adpg~c~~Sik~fEeARkSfGTDEDi 160 (167)
T KOG4621|consen 81 KLHCDLCEEPLKSCCFSPNGHHCFCRTPCYQGHFIVICGYDAARDCFEINDPASADPGHCRISIKCFEEARKSFGTDEDI 160 (167)
T ss_pred ceehHHHHhHHHHhccCCCCccccccCCcccccEEEEeccccccCeEEEcCcccCCCcceeehhhHHHHHHhccCCCcce
Confidence 999999655432 2 36788899999999999999999999999999986 89999999999999999999999
Q ss_pred EEEecCC
Q 024373 259 LLISLEK 265 (268)
Q Consensus 259 i~i~~~~ 265 (268)
+||+|++
T Consensus 161 Lfi~Ldn 167 (167)
T KOG4621|consen 161 LFINLDN 167 (167)
T ss_pred EEEecCC
Confidence 9999984
No 3
>PF11814 DUF3335: Peptidase_C39 like family; InterPro: IPR021770 This family of proteins are functionally uncharacterised. This family is only found in bacteria. This presumed domain is typically between 226 to 230 amino acids in length.
Probab=99.92 E-value=9.1e-24 Score=186.75 Aligned_cols=172 Identities=20% Similarity=0.357 Sum_probs=145.8
Q ss_pred CceecccCcCcchHHHHHHHHHHhCCCCCChhHHHHHhc---ccccc---------hhhHHHHHHHcCceeEEEEeecCC
Q 024373 57 VPHINQLFSWDCGLACVLMVLRTIGINNCNIQGLAEQCC---TTSIW---------TVDLAYLLQKFNVGFSYFTITLGA 124 (268)
Q Consensus 57 vP~i~Q~~~~DCGlACl~MVL~y~g~~~~~~~~L~el~~---ttsiw---------tidLa~ll~~~gv~~~~~T~tlG~ 124 (268)
||+++|+.++.||+|||.|.+++++... .+++-.|+-. .|.|+ +.+||.++.+.|++++.+.++.|
T Consensus 1 vPyy~QTT~FTCGPa~lmMAm~~l~~~~-~~~r~~EL~lWREATTifmtsGhGGC~P~GLAlAA~rrG~~vev~~~~~~- 78 (207)
T PF11814_consen 1 VPYYRQTTEFTCGPACLMMAMAALDPEF-ELDRREELRLWREATTIFMTSGHGGCGPFGLALAAARRGFKVEVWVSTDG- 78 (207)
T ss_pred CCccccCCCCCcHHHHHHHHHHhcCCcC-CCCHHHHHHHHHHhceecccCCCCCcChHHHHHHHHHcCCceEEEECCCC-
Confidence 7999999999999999999999999876 6776666653 34443 68899999999999999998776
Q ss_pred CCCCcchhhhhhccCchHHHHHHHH-----HHHHHcCCeeeeeccCHHHHHHHHhcCCceEEEEEeCccccccccccccc
Q 024373 125 NPNYSVETFYKEQLPTDLVRVDMLF-----QKARSAGIKIECGSISGVEISLMILSGNYIAIALVDQYKLSHSWMEDVIV 199 (268)
Q Consensus 125 ~p~y~~~~FY~~~~~~D~~Rv~~lf-----~~A~~~Gi~~~~~~vs~~~L~~~l~~g~~PaIvLvn~~~L~~~~~~~~~~ 199 (268)
-.|..++.+++++.|.++. ++|++.|++++.+.+++++|.+.|++| ..+|+|++++.++..
T Consensus 79 ------plfld~vr~~~kk~v~~~v~~~f~~~a~~~gv~~~~~~~~~~~l~~~l~~G-~~~lvLIS~y~~~g~------- 144 (207)
T PF11814_consen 79 ------PLFLDSVRSEEKKEVMELVHEDFREEAEQAGVPVHYRPLSLADLRAALAAG-AIVLVLISTYRMDGK------- 144 (207)
T ss_pred ------CceeccCCCHHHHHHHHHHHHHHHHHHHHCCCceecCCCCHHHHHHHHHCC-CEEEEEEeecccCCC-------
Confidence 4688899999999888876 779999999999999999999999998 589999999888763
Q ss_pred CCccCCCCCcCCcEEEEEEEeCCCCEEEEecCCCCC---------ceeEeCHHHHHHHhhcCCCCc
Q 024373 200 PGFYGSDSGYTGHYILICGYDANSDEFEIRDPASCR---------KREKVTLKCLEEARKSFGTDE 256 (268)
Q Consensus 200 ~~~~~~~~~y~gHYVVL~Gyd~~~~~f~I~DPa~g~---------~~~~is~~eFe~a~~s~GtD~ 256 (268)
..+||||++|+|. +.+|||||..+. .+..++.++|++. .+||.+.
T Consensus 145 ---------k~PHWV~v~g~d~--~~vyihDP~~d~~~~~~~~d~~~lPi~~~~f~~m-~~~G~~~ 198 (207)
T PF11814_consen 145 ---------KVPHWVVVTGVDD--DFVYIHDPDVDAERGESWVDCQHLPIPRADFDRM-ARFGKSK 198 (207)
T ss_pred ---------CCCeEEEEEEecC--CEEEEeCCCCCcccCCCchhhccCCccHHHHHHH-Hhhcccc
Confidence 5799999999997 599999999872 3456788888876 3566554
No 4
>PF03412 Peptidase_C39: Peptidase C39 family This is family C39 in the peptidase classification. ; InterPro: IPR005074 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. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of sequences defined by this cysteine peptidase domain belong to the MEROPS peptidase family C39 (clan CA). It is found in a wide range of ABC transporters, which are maturation proteases for peptide bacteriocins, the proteolytic domain residing in the N-terminal region of the protein []. A number of the 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. Lantibiotic and non-lantibiotic bacteriocins are synthesised as precursor peptides containing N-terminal extensions (leader peptides) which are cleaved off during maturation. Most non-lantibiotics and also some lantibiotics have leader peptides of the so-called double-glycine type. These leader peptides share consensus sequences and also a common processing site with two conserved glycine residues in positions -1 and -2. The double- glycine-type leader peptides are unrelated to the N-terminal signal sequences which direct proteins across the cytoplasmic membrane via the sec pathway. Their processing sites are also different from typical signal peptidase cleavage sites, suggesting that a different processing enzyme is involved. ; GO: 0005524 ATP binding, 0008233 peptidase activity, 0006508 proteolysis, 0016021 integral to membrane; PDB: 3K8U_A 3B79_A.
Probab=99.83 E-value=1.6e-20 Score=151.72 Aligned_cols=128 Identities=30% Similarity=0.413 Sum_probs=84.9
Q ss_pred cCceecccCcCcchHHHHHHHHHHhCCCCCChhHHHHHhcccccchhhHHHHHHHcCceeEEEEeecCCCCCCcchhhhh
Q 024373 56 EVPHINQLFSWDCGLACVLMVLRTIGINNCNIQGLAEQCCTTSIWTVDLAYLLQKFNVGFSYFTITLGANPNYSVETFYK 135 (268)
Q Consensus 56 ~vP~i~Q~~~~DCGlACl~MVL~y~g~~~~~~~~L~el~~ttsiwtidLa~ll~~~gv~~~~~T~tlG~~p~y~~~~FY~ 135 (268)
++|+|+|.+..|||+||++|+++++|++. +.++|++.+.+.. . |.+
T Consensus 1 ~~~~v~Q~~~~dcg~acl~~l~~~~g~~~-s~~~l~~~~~~~~------------~-----------g~s---------- 46 (131)
T PF03412_consen 1 KYPVVKQSDSNDCGLACLAMLLKYYGIPV-SEEELRRQLGTSE------------E-----------GTS---------- 46 (131)
T ss_dssp -------SSTT-HHHHHHHHHHHHTT-----HHHHHCCTT-BT------------T-----------B------------
T ss_pred CcCeEEeCCCCCHHHHHHHHHHHHhCCCc-hHHHHHHHhcCCc------------c-----------CCC----------
Confidence 58999999999999999999999999998 8888887664221 0 111
Q ss_pred hccCchHHHHHHHHHHHHHcCCeeeeeccCHHHHHHHHhcCCceEEEEEeCcccccccccccccCCccCCCCCcCCcEEE
Q 024373 136 EQLPTDLVRVDMLFQKARSAGIKIECGSISGVEISLMILSGNYIAIALVDQYKLSHSWMEDVIVPGFYGSDSGYTGHYIL 215 (268)
Q Consensus 136 ~~~~~D~~Rv~~lf~~A~~~Gi~~~~~~vs~~~L~~~l~~g~~PaIvLvn~~~L~~~~~~~~~~~~~~~~~~~y~gHYVV 215 (268)
+..|.+.|++.|+.+...+++.++| .+.+.|+|+.++ .|||||
T Consensus 47 ---------~~~L~~~~~~~gl~~~~~~~~~~~l----~~~~~P~I~~~~------------------------~~h~vV 89 (131)
T PF03412_consen 47 ---------LADLKRAARKYGLKAKAVKLNFEKL----KRLPLPAIAHLK------------------------DGHFVV 89 (131)
T ss_dssp ---------CCCHHHHHHHTTEEEEEEE--GGGC----TCGGSSEEEEEC------------------------CCEEEE
T ss_pred ---------HHHHHHHHHhcccceeeeecchhhh----hhccccEEEEec------------------------CcceEE
Confidence 1234456666677766666776664 345689999986 499999
Q ss_pred EEEEeCCCCEEEEecCCCCCceeEeCHHHHHHHhhcCCCCceEEEEec
Q 024373 216 ICGYDANSDEFEIRDPASCRKREKVTLKCLEEARKSFGTDEDLLLISL 263 (268)
Q Consensus 216 L~Gyd~~~~~f~I~DPa~g~~~~~is~~eFe~a~~s~GtD~dii~i~~ 263 (268)
|.+++. +.+.|.||+.| ...++.++|++.|+ | .+|++.-
T Consensus 90 i~~~~~--~~~~i~dP~~g--~~~~~~~~f~~~w~--G---~~l~~~~ 128 (131)
T PF03412_consen 90 IYKIDD--GRVLIYDPKKG--KIKLSKEEFEEIWT--G---EVLLIKP 128 (131)
T ss_dssp EEEECC--CEEEECCTTTC--EEEEEHHHHHHHEE--E---EEEEEEE
T ss_pred EEeEcC--cEEEEEeCCCC--eEEEeHHHHHhhCC--C---EEEEEEe
Confidence 999965 69999999665 57899999999998 3 3566543
No 5
>TIGR03796 NHPM_micro_ABC1 NHPM bacteriocin system ABC transporter, peptidase/ATP-binding protein. This protein describes an multidomain ABC transporter subunit that is one of three protein families associated with some regularity with a distinctive family of putative bacteriocins. It includes a bacteriocin-processing peptidase domain at the N-terminus. Model TIGR03793 describes a conserved propeptide region for this bacteriocin family, unusual because it shows obvious homology a region of the enzyme nitrile hydratase up to the classic Gly-Gly cleavage motif. This family is therefore predicted to be a subunit of a bacteriocin processing and export system characteristic to this system that we designate NHPM, Nitrile Hydratase Propeptide Microcin.
Probab=99.79 E-value=4.8e-19 Score=180.24 Aligned_cols=121 Identities=21% Similarity=0.343 Sum_probs=99.7
Q ss_pred cCceecccCcCcchHHHHHHHHHHhCCCCCChhHHHHHhcccccchhhHHHHHHHcCceeEEEEeecCCCCCCcchhhhh
Q 024373 56 EVPHINQLFSWDCGLACVLMVLRTIGINNCNIQGLAEQCCTTSIWTVDLAYLLQKFNVGFSYFTITLGANPNYSVETFYK 135 (268)
Q Consensus 56 ~vP~i~Q~~~~DCGlACl~MVL~y~g~~~~~~~~L~el~~ttsiwtidLa~ll~~~gv~~~~~T~tlG~~p~y~~~~FY~ 135 (268)
++|++.|.++.|||+||++||++|||++. ++++|++.++.+. -|.+
T Consensus 1 ~~~~i~Q~~~~dCg~acl~mi~~~~g~~~-~~~~lr~~~~~~~-----------------------~g~s---------- 46 (710)
T TIGR03796 1 RTPTVLQMEAVECGAASLAMILAYYGRYV-PLEELREECGVSR-----------------------DGSK---------- 46 (710)
T ss_pred CCceEeecccccHHHHHHHHHHHHcCCCC-CHHHHHHHcCCCC-----------------------CCCC----------
Confidence 47999999999999999999999999998 9999998865331 0222
Q ss_pred hccCchHHHHHHHHHHHHHcCCeeeeeccCHHHHHHHHhcCCceEEEEEeCcccccccccccccCCccCCCCCcCCcEEE
Q 024373 136 EQLPTDLVRVDMLFQKARSAGIKIECGSISGVEISLMILSGNYIAIALVDQYKLSHSWMEDVIVPGFYGSDSGYTGHYIL 215 (268)
Q Consensus 136 ~~~~~D~~Rv~~lf~~A~~~Gi~~~~~~vs~~~L~~~l~~g~~PaIvLvn~~~L~~~~~~~~~~~~~~~~~~~y~gHYVV 215 (268)
+..+.+.|++.|+.++..+.+.++|. +.+.|||++|+ .+||||
T Consensus 47 ---------~~~l~~~~~~~g~~~~~~~~~~~~l~----~~~lP~i~~~~------------------------~~h~vv 89 (710)
T TIGR03796 47 ---------ASNLLKAARSYGLEAKGFRKELDALA----ELPLPYIVFWN------------------------FNHFVV 89 (710)
T ss_pred ---------HHHHHHHHHHCCCEeEEEecCHHHhc----cCCCCEEEEEc------------------------CCcEEE
Confidence 46677788888888888888777654 34589999998 489999
Q ss_pred EEEEeCCCCEEEEecCCCCCceeEeCHHHHHHHhhc
Q 024373 216 ICGYDANSDEFEIRDPASCRKREKVTLKCLEEARKS 251 (268)
Q Consensus 216 L~Gyd~~~~~f~I~DPa~g~~~~~is~~eFe~a~~s 251 (268)
|+++++ +.++|.||+.|+ .+++.+||++.|+.
T Consensus 90 l~~~~~--~~~~i~dP~~g~--~~~~~~e~~~~~~g 121 (710)
T TIGR03796 90 VEGFRG--GRVYLNDPALGP--RTVSLEEFDESFTG 121 (710)
T ss_pred EEEEeC--CEEEEECCCCCC--EEccHHHHHhhCCC
Confidence 999977 589999999984 48999999999963
No 6
>cd02424 Peptidase_C39E A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family, which contains Colicin V perocessing peptidase.
Probab=99.79 E-value=2.7e-18 Score=139.54 Aligned_cols=122 Identities=20% Similarity=0.258 Sum_probs=92.8
Q ss_pred CceecccCcCcchHHHHHHHHHH-hCCCCCChhHHHHHhcccccchhhHHHHHHHcCceeEEEEeecCCCCCCcchhhhh
Q 024373 57 VPHINQLFSWDCGLACVLMVLRT-IGINNCNIQGLAEQCCTTSIWTVDLAYLLQKFNVGFSYFTITLGANPNYSVETFYK 135 (268)
Q Consensus 57 vP~i~Q~~~~DCGlACl~MVL~y-~g~~~~~~~~L~el~~ttsiwtidLa~ll~~~gv~~~~~T~tlG~~p~y~~~~FY~ 135 (268)
+|.++|.+..|||+|||+|+++| ||++. ++++|+..++... -|
T Consensus 1 ~~~~~q~~~~dcgla~l~~i~~~~~g~~~-~~~~l~~~~~~~~-----------------------~g------------ 44 (129)
T cd02424 1 MKIIKQTDLNDCGIAVIQMLYNHYYKKKY-DLNELKIKANLKK-----------------------NG------------ 44 (129)
T ss_pred CceEEecCccchHHHHHHHHHHHhcCCCc-cHHHHHHHhCCCC-----------------------CC------------
Confidence 46799999999999999999999 89998 8888877644210 01
Q ss_pred hccCchHHHHHHHHHHHHHcCCeeeeeccCHHHHHHHHhcCCceEEEEEeCcccccccccccccCCccCCCCCcCCcEEE
Q 024373 136 EQLPTDLVRVDMLFQKARSAGIKIECGSISGVEISLMILSGNYIAIALVDQYKLSHSWMEDVIVPGFYGSDSGYTGHYIL 215 (268)
Q Consensus 136 ~~~~~D~~Rv~~lf~~A~~~Gi~~~~~~vs~~~L~~~l~~g~~PaIvLvn~~~L~~~~~~~~~~~~~~~~~~~y~gHYVV 215 (268)
..+..+.+.|++.|+.++..+++.++|.+. ..+.|+|++-+ ..+||||
T Consensus 45 -------~s~~~l~~~a~~~Gl~~k~~~~~~~~l~~~--~~p~P~i~~~~-----------------------~~~hfvV 92 (129)
T cd02424 45 -------LSIYDLENLAKKFGLETESYQGSFLEFLEL--KNKFIILLKSN-----------------------GLNHFVI 92 (129)
T ss_pred -------ccHHHHHHHHHHcCCceeEEEcCHHHHhhc--cCCEEEEEecC-----------------------CCCeEEE
Confidence 114667777888888888888888776543 23678887511 1369999
Q ss_pred EEEEeCCCCEEEEecCCCCCceeEeCHHHHHHHhh
Q 024373 216 ICGYDANSDEFEIRDPASCRKREKVTLKCLEEARK 250 (268)
Q Consensus 216 L~Gyd~~~~~f~I~DPa~g~~~~~is~~eFe~a~~ 250 (268)
+.+.++ +.++|.||+.+ ...++.++|++.|+
T Consensus 93 l~~~~~--~~v~I~DP~~g--~~~~s~~~f~~~ws 123 (129)
T cd02424 93 VKKIKK--NKFIVLDPKKG--KYKITYKEFEKIFN 123 (129)
T ss_pred EEEEEC--CEEEEECCCCC--CEEeCHHHHHHHhc
Confidence 999976 47999999766 44899999999995
No 7
>cd02549 Peptidase_C39A A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family of proteins with a single peptidase domain, which are
Probab=99.75 E-value=4.8e-17 Score=132.23 Aligned_cols=133 Identities=23% Similarity=0.297 Sum_probs=87.7
Q ss_pred cCcCcchHHHHHHHHHHhCCCCCChhHHHHHhcccccchhhHHHHHHHcCceeEEEEeecCCCCCCcchhhhhhccCchH
Q 024373 63 LFSWDCGLACVLMVLRTIGINNCNIQGLAEQCCTTSIWTVDLAYLLQKFNVGFSYFTITLGANPNYSVETFYKEQLPTDL 142 (268)
Q Consensus 63 ~~~~DCGlACl~MVL~y~g~~~~~~~~L~el~~ttsiwtidLa~ll~~~gv~~~~~T~tlG~~p~y~~~~FY~~~~~~D~ 142 (268)
....+||+|||+||++|+|.+. +..++...... ..+.+...|.+
T Consensus 2 ~~~~~C~~~slamvl~~~g~~~-~~~~l~~~~~~------------------~~~~~~~~g~~----------------- 45 (141)
T cd02549 2 QLENGCGPTSLAMVLSYLGVKV-TKPQLAAEGNT------------------YDFAKDGYGTY----------------- 45 (141)
T ss_pred CCCCccHHHHHHHHHHhcCCCC-CHHHHHhhccc------------------cccCCCCCCcC-----------------
Confidence 3467899999999999999997 76666632000 00000001111
Q ss_pred HHHHHHHHH-HHHcCCeeeeeccCHHHHHHHHhcCCceEEEEEeCcccccccccccccCCccCCCCCcCCcEEEEEEEeC
Q 024373 143 VRVDMLFQK-ARSAGIKIECGSISGVEISLMILSGNYIAIALVDQYKLSHSWMEDVIVPGFYGSDSGYTGHYILICGYDA 221 (268)
Q Consensus 143 ~Rv~~lf~~-A~~~Gi~~~~~~vs~~~L~~~l~~g~~PaIvLvn~~~L~~~~~~~~~~~~~~~~~~~y~gHYVVL~Gyd~ 221 (268)
...+.+. |++.|+.++..+.+.. +.++++++ .|+|++++.... ....||||||.|||.
T Consensus 46 --~~~l~~~~a~~~G~~~~~~~~~~~-~~~~l~~~-~Pvi~~~~~~~~-----------------~~~~gH~vVv~g~~~ 104 (141)
T cd02549 46 --PKPIVSAAARKYGLVVRPLTGLLA-LLRQLAAG-HPVIVSVNLGVS-----------------ITPSGHAMVVIGYDR 104 (141)
T ss_pred --HHHHHHHHHhhCCCcEEECCCHHH-HHHHHHCC-CeEEEEEecCcc-----------------cCCCCeEEEEEEEcC
Confidence 1334444 6666666555544433 55666666 699999984111 123689999999992
Q ss_pred CCCEEEEecCCCCCceeEeCHHHHHHHhhcCCC
Q 024373 222 NSDEFEIRDPASCRKREKVTLKCLEEARKSFGT 254 (268)
Q Consensus 222 ~~~~f~I~DPa~g~~~~~is~~eFe~a~~s~Gt 254 (268)
.+.++|+||+.+. ...++.++|+++|++.|.
T Consensus 105 -~~~~~i~DP~~~~-~~~~~~~~f~~~w~~~~~ 135 (141)
T cd02549 105 -KGNVYVNDPGGGR-RLVVSFDEFEKAWKRMGG 135 (141)
T ss_pred -CCCEEEECCCCCc-CEEEeHHHHHHHHHHcCC
Confidence 2579999999874 568999999999999883
No 8
>cd02418 Peptidase_C39B A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=99.73 E-value=6.4e-17 Score=130.74 Aligned_cols=134 Identities=22% Similarity=0.250 Sum_probs=98.8
Q ss_pred CceecccCcCcchHHHHHHHHHHhCCCCCChhHHHHHhcccccchhhHHHHHHHcCceeEEEEeecCCCCCCcchhhhhh
Q 024373 57 VPHINQLFSWDCGLACVLMVLRTIGINNCNIQGLAEQCCTTSIWTVDLAYLLQKFNVGFSYFTITLGANPNYSVETFYKE 136 (268)
Q Consensus 57 vP~i~Q~~~~DCGlACl~MVL~y~g~~~~~~~~L~el~~ttsiwtidLa~ll~~~gv~~~~~T~tlG~~p~y~~~~FY~~ 136 (268)
.|.++|.+..+||+||++|+++++|++. +.+.++..+..+. -|.+
T Consensus 1 ~~~~~q~~~~~~gl~~l~~~~~~~g~~~-~~~~l~~~~~~~~-----------------------~~~~----------- 45 (136)
T cd02418 1 YPYVLQVDEMDCGAACLAMIAKYYGKNY-SLAKLRELAGTDR-----------------------EGTS----------- 45 (136)
T ss_pred CCeEEecCcccHHHHHHHHHHHHhCCCC-CHHHHHHHcCCCC-----------------------CCcC-----------
Confidence 3789999999999999999999999998 8787776543210 0111
Q ss_pred ccCchHHHHHHHHHHHHHcCCeeeeeccCHHHHHHHHhcCCceEEEEEeCcccccccccccccCCccCCCCCcCCcEEEE
Q 024373 137 QLPTDLVRVDMLFQKARSAGIKIECGSISGVEISLMILSGNYIAIALVDQYKLSHSWMEDVIVPGFYGSDSGYTGHYILI 216 (268)
Q Consensus 137 ~~~~D~~Rv~~lf~~A~~~Gi~~~~~~vs~~~L~~~l~~g~~PaIvLvn~~~L~~~~~~~~~~~~~~~~~~~y~gHYVVL 216 (268)
...+.+.|++.|+.++...++.+++ . +.+.+.|+|++++.. ...|||+||
T Consensus 46 --------~~~l~~~a~~~Gl~~~~~~~~~~~~-~-l~~~~~P~I~~~~~~--------------------~~~~~~~Vl 95 (136)
T cd02418 46 --------LLGLVKAAEKLGFETRAVKADMDLF-E-LKDIPLPFIAHVIKE--------------------WKLNHYVVV 95 (136)
T ss_pred --------HHHHHHHHHHCCCeeEEEEcccchh-h-HhcCCCCEEEEEccC--------------------CCCCeEEEE
Confidence 3456677778888877777777621 1 234458999997631 125999999
Q ss_pred EEEeCCCCEEEEecCCCCCceeEeCHHHHHHHhhcCCCCceEEEEecC
Q 024373 217 CGYDANSDEFEIRDPASCRKREKVTLKCLEEARKSFGTDEDLLLISLE 264 (268)
Q Consensus 217 ~Gyd~~~~~f~I~DPa~g~~~~~is~~eFe~a~~s~GtD~dii~i~~~ 264 (268)
.|++. +.++|.||+.+ ...++.++|++.|. | .+++|+..
T Consensus 96 ~~~~~--~~~~i~dp~~~--~~~~~~~ef~~~w~--g---~~l~~~~~ 134 (136)
T cd02418 96 YKIKK--KKILIADPAVG--ITKISKEEFEKEWT--G---VALFLEPT 134 (136)
T ss_pred EEEcC--CEEEEECCCCC--CEEeeHHHHHhhCe--E---EEEEEecC
Confidence 99986 47999999554 55899999999997 3 57777654
No 9
>TIGR01193 bacteriocin_ABC ABC-type bacteriocin transporter. This model describes ABC-type bacteriocin transporter. The amino terminal domain (pfam03412) processes the N-terminal leader peptide from the bacteriocin while C-terminal domains resemble ABC transporter membrane protein and ATP-binding cassette domain. In general, bacteriocins are agents which are responsible for killing or inhibiting the closely related species or even different strains of the same species. Bacteriocins are usually encoded by bacterial plasmids. Bacteriocins are named after the species and hence in literature one encounters various names e.g., leucocin from Leuconostic geldium; pedicocin from Pedicoccus acidilactici; sakacin from Lactobacillus sake etc.
Probab=99.71 E-value=6.6e-17 Score=164.73 Aligned_cols=121 Identities=21% Similarity=0.213 Sum_probs=93.0
Q ss_pred ccCcCcchHHHHHHHHHHhCCCCCChhHHHHHhcccccchhhHHHHHHHcCceeEEEEeecCCCCCCcchhhhhhccCch
Q 024373 62 QLFSWDCGLACVLMVLRTIGINNCNIQGLAEQCCTTSIWTVDLAYLLQKFNVGFSYFTITLGANPNYSVETFYKEQLPTD 141 (268)
Q Consensus 62 Q~~~~DCGlACl~MVL~y~g~~~~~~~~L~el~~ttsiwtidLa~ll~~~gv~~~~~T~tlG~~p~y~~~~FY~~~~~~D 141 (268)
|.++.|||+||++||++|||++. ++++|++.++.++ . |.+
T Consensus 1 Q~~~~dCg~~cl~~i~~~~g~~~-~~~~lr~~~~~~~------------~-----------g~s---------------- 40 (708)
T TIGR01193 1 QVDEKDCGIAALSMILKKYGTEY-SLAKLRQLAKTDL------------E-----------GTT---------------- 40 (708)
T ss_pred CCCccchHHHHHHHHHHHcCCCC-CHHHHHHHhCCCC------------C-----------CCC----------------
Confidence 88899999999999999999999 9999998875431 0 222
Q ss_pred HHHHHHHHHHHHHcCCeeeeeccCHHHHHHHHhcCCceEEEEEeCcccccccccccccCCccCCCCCcCCcEEEEEEEeC
Q 024373 142 LVRVDMLFQKARSAGIKIECGSISGVEISLMILSGNYIAIALVDQYKLSHSWMEDVIVPGFYGSDSGYTGHYILICGYDA 221 (268)
Q Consensus 142 ~~Rv~~lf~~A~~~Gi~~~~~~vs~~~L~~~l~~g~~PaIvLvn~~~L~~~~~~~~~~~~~~~~~~~y~gHYVVL~Gyd~ 221 (268)
+..+.+.|++.|+.++..+.+.++|. +.+.+.|||++|-.+ +..+|||||+++++
T Consensus 41 ---~~~l~~~~~~~g~~~~~~~~~~~~l~--~~~~~~P~I~~~~~~--------------------~~~~H~vVl~~~~~ 95 (708)
T TIGR01193 41 ---VLGLVKAAEYLNFEAKAIQADMSLFE--DKNLPLPFIAHVIKN--------------------GKLPHYYVVYGVTK 95 (708)
T ss_pred ---HHHHHHHHHHCCCEEEEEecCHHHhc--cccCCCCEEEEEccC--------------------CCCCcEEEEEEEeC
Confidence 46677777888888878777776432 223457999998210 01479999999986
Q ss_pred CCCEEEEecC--CCCCceeEeCHHHHHHHhhc
Q 024373 222 NSDEFEIRDP--ASCRKREKVTLKCLEEARKS 251 (268)
Q Consensus 222 ~~~~f~I~DP--a~g~~~~~is~~eFe~a~~s 251 (268)
++++|.|| +.|+ .+++.+||++.|+.
T Consensus 96 --~~~~i~dP~~~~g~--~~~~~~ef~~~~~g 123 (708)
T TIGR01193 96 --NHLIIADPDPTVGI--TKISKEDFYEEWTG 123 (708)
T ss_pred --CEEEEEcCCcccCC--EEecHHHHHhhCCC
Confidence 58999999 7774 48999999999964
No 10
>cd02420 Peptidase_C39D A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=99.70 E-value=2.5e-16 Score=126.21 Aligned_cols=118 Identities=21% Similarity=0.353 Sum_probs=93.8
Q ss_pred ceecccCcCcchHHHHHHHHHHhCCCCCChhHHHHHhcccccchhhHHHHHHHcCceeEEEEeecCCCCCCcchhhhhhc
Q 024373 58 PHINQLFSWDCGLACVLMVLRTIGINNCNIQGLAEQCCTTSIWTVDLAYLLQKFNVGFSYFTITLGANPNYSVETFYKEQ 137 (268)
Q Consensus 58 P~i~Q~~~~DCGlACl~MVL~y~g~~~~~~~~L~el~~ttsiwtidLa~ll~~~gv~~~~~T~tlG~~p~y~~~~FY~~~ 137 (268)
|++.|....|||+||++|++++||... +.+.|+...+... -|
T Consensus 2 ~~~~q~~~~~~gl~~l~~i~~~~g~~~-~~~~l~~~~~~~~-----------------------~~-------------- 43 (125)
T cd02420 2 PTVLQMEATECGAASLAIILAYYGRYV-PLSELRIACGVSR-----------------------DG-------------- 43 (125)
T ss_pred CeeeeCcccCHHHHHHHHHHHHcCCCC-CHHHHHHHcCCCC-----------------------CC--------------
Confidence 678888889999999999999999998 8888876543210 01
Q ss_pred cCchHHHHHHHHHHHHHcCCeeeeeccCHHHHHHHHhcCCceEEEEEeCcccccccccccccCCccCCCCCcCCcEEEEE
Q 024373 138 LPTDLVRVDMLFQKARSAGIKIECGSISGVEISLMILSGNYIAIALVDQYKLSHSWMEDVIVPGFYGSDSGYTGHYILIC 217 (268)
Q Consensus 138 ~~~D~~Rv~~lf~~A~~~Gi~~~~~~vs~~~L~~~l~~g~~PaIvLvn~~~L~~~~~~~~~~~~~~~~~~~y~gHYVVL~ 217 (268)
.....+.+.|++.|+.++..+++.++|. +.+.|+|++++ .|||+||.
T Consensus 44 -----~~~~~l~~~a~~~Gl~~~~~~~~~~~L~----~~~lP~I~~~~------------------------~g~~~Vl~ 90 (125)
T cd02420 44 -----SNASNLLKAAREYGLTAKGYKKDLEALR----EVSLPAIVFWN------------------------FNHFLVVE 90 (125)
T ss_pred -----CCHHHHHHHHHHcCcccceEecCHHHHh----cCCCCEEEEeC------------------------CCEEEEEE
Confidence 1135677888888988888888887754 44589999887 49999999
Q ss_pred EEeCCCCEEEEecCCCCCceeEeCHHHHHHHhh
Q 024373 218 GYDANSDEFEIRDPASCRKREKVTLKCLEEARK 250 (268)
Q Consensus 218 Gyd~~~~~f~I~DPa~g~~~~~is~~eFe~a~~ 250 (268)
+++. +.++|.||+.+ ...++.++|++.|+
T Consensus 91 ~~~~--~~~~i~dp~~~--~~~~s~~el~~~~~ 119 (125)
T cd02420 91 GFDK--RKVFLNDPATG--RRTVSLEEFDQSFT 119 (125)
T ss_pred EEeC--CEEEEECCCcC--ceeecHHHHHhhCC
Confidence 9986 48999999875 45899999999996
No 11
>cd02419 Peptidase_C39C A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=99.67 E-value=1.1e-15 Score=122.47 Aligned_cols=119 Identities=20% Similarity=0.274 Sum_probs=93.9
Q ss_pred CceecccCcCcchHHHHHHHHHHhCCCCCChhHHHHHhcccccchhhHHHHHHHcCceeEEEEeecCCCCCCcchhhhhh
Q 024373 57 VPHINQLFSWDCGLACVLMVLRTIGINNCNIQGLAEQCCTTSIWTVDLAYLLQKFNVGFSYFTITLGANPNYSVETFYKE 136 (268)
Q Consensus 57 vP~i~Q~~~~DCGlACl~MVL~y~g~~~~~~~~L~el~~ttsiwtidLa~ll~~~gv~~~~~T~tlG~~p~y~~~~FY~~ 136 (268)
+|.+.|....|||++|+.|++++||+.. +.+.++......
T Consensus 1 ~~~~~q~~~~~~~l~~l~~~~~~~g~~~-~~~~l~~~~~~~--------------------------------------- 40 (127)
T cd02419 1 LPVILQTEAAECGLACLAMIASYHGHHV-DLASLRQRFPVS--------------------------------------- 40 (127)
T ss_pred CCeEeeCccccHHHHHHHHHHHHcCCCC-CHHHHHHHcCCC---------------------------------------
Confidence 3678899999999999999999999998 777777543211
Q ss_pred ccCchHHHHHHHHHHHHHcCCeeeeeccCHHHHHHHHhcCCceEEEEEeCcccccccccccccCCccCCCCCcCCcEEEE
Q 024373 137 QLPTDLVRVDMLFQKARSAGIKIECGSISGVEISLMILSGNYIAIALVDQYKLSHSWMEDVIVPGFYGSDSGYTGHYILI 216 (268)
Q Consensus 137 ~~~~D~~Rv~~lf~~A~~~Gi~~~~~~vs~~~L~~~l~~g~~PaIvLvn~~~L~~~~~~~~~~~~~~~~~~~y~gHYVVL 216 (268)
.+......+.+.|++.|+.++..+++.++|.. .+.|+|++++ .|||+||
T Consensus 41 ---~~~~~~~~l~~~a~~~Gl~~~~~~~~~~~l~~----~~lP~i~~~~------------------------~g~~~Vl 89 (127)
T cd02419 41 ---LKGATLADLIDIAQQLGLSTRALRLDLEELGQ----LKLPCILHWD------------------------MNHFVVL 89 (127)
T ss_pred ---CCCcCHHHHHHHHHHCCCceeEEEccHHHHhh----CCCCEEEEEC------------------------CCEEEEE
Confidence 00112456778888888888888888877544 3589999876 4999999
Q ss_pred EEEeCCCCEEEEecCCCCCceeEeCHHHHHHHhh
Q 024373 217 CGYDANSDEFEIRDPASCRKREKVTLKCLEEARK 250 (268)
Q Consensus 217 ~Gyd~~~~~f~I~DPa~g~~~~~is~~eFe~a~~ 250 (268)
.+++. +.+.|.||+.+ ...++.++|++.|+
T Consensus 90 ~~~~~--~~~~i~dp~~~--~~~~~~~el~~~~~ 119 (127)
T cd02419 90 KKVSR--RRIVIHDPALG--KRKLSLEEASRHFT 119 (127)
T ss_pred EEEcC--CEEEEECCccC--CEEEcHHHHHhhCC
Confidence 99965 58999999876 45899999999997
No 12
>PF13529 Peptidase_C39_2: Peptidase_C39 like family; PDB: 3ERV_A.
Probab=99.65 E-value=9.8e-16 Score=122.71 Aligned_cols=139 Identities=29% Similarity=0.349 Sum_probs=69.1
Q ss_pred ccCceecc--cCcCcchHHHHHHHHHHhCCCCCChhHHHHHhcccccchhhHHHHHHHcCceeEEEEeecCCCCCCcchh
Q 024373 55 VEVPHINQ--LFSWDCGLACVLMVLRTIGINNCNIQGLAEQCCTTSIWTVDLAYLLQKFNVGFSYFTITLGANPNYSVET 132 (268)
Q Consensus 55 ~~vP~i~Q--~~~~DCGlACl~MVL~y~g~~~~~~~~L~el~~ttsiwtidLa~ll~~~gv~~~~~T~tlG~~p~y~~~~ 132 (268)
++||.+.| .....||+||++|||+|+|+.. +..+|.+...+..- -|++ ..
T Consensus 1 l~vp~~~Q~~~~~~~Cg~as~~mvl~~~g~~~-~~~~l~~~~~~~~~------------------------~~~~---~~ 52 (144)
T PF13529_consen 1 LNVPYYSQYDETSYGCGPASAAMVLNYYGKNI-SQEDLADEAGTNPD------------------------GDPN---TG 52 (144)
T ss_dssp -TS-----TTT-TT-HHHHHHHHHHHHTT-----HHHHHHHS-EE-E--------------------------TT---TS
T ss_pred CCCCcEEeCCCCCCcCHHHHHHHHHHHcCCCC-CHHHHHHHhhhccC------------------------CCCC---cc
Confidence 47999999 7777899999999999999976 66677666543310 0000 00
Q ss_pred hhhhcc--CchHHHHHHHHHHHHHcCCe-eeeeccCHHHHHHHHhcCCceEEEEEeCcccccccccccccCCccCCCCCc
Q 024373 133 FYKEQL--PTDLVRVDMLFQKARSAGIK-IECGSISGVEISLMILSGNYIAIALVDQYKLSHSWMEDVIVPGFYGSDSGY 209 (268)
Q Consensus 133 FY~~~~--~~D~~Rv~~lf~~A~~~Gi~-~~~~~vs~~~L~~~l~~g~~PaIvLvn~~~L~~~~~~~~~~~~~~~~~~~y 209 (268)
|..+.. .........+.+.+++.|+. ......+.++|.+.|.+| .|+|+.++.+..... .. .....+
T Consensus 53 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~~G-~Pvi~~~~~~~~~~~---~~------~~~~~~ 122 (144)
T PF13529_consen 53 FVGNPYYDSGYGTSPDDLARYLEKYGYKATDTSDASFDDIKQEIDAG-RPVIVSVNSGWRPPN---GD------GYDGTY 122 (144)
T ss_dssp EEB-SSTS-B----HHHHHHHHHHH-TTEEE-TTS-HHHHHHHHHTT---EEEEEETTSS--T---TE------EEEE-T
T ss_pred cccCccccCCCccccHHHHHHHHHcCcceeeccCCcHHHHHHHHHCC-CcEEEEEEcccccCC---CC------CcCCCc
Confidence 000000 00011234445667777763 334566889999999988 599999974321110 00 000124
Q ss_pred CCcEEEEEEEeCCCCEEEEecCC
Q 024373 210 TGHYILICGYDANSDEFEIRDPA 232 (268)
Q Consensus 210 ~gHYVVL~Gyd~~~~~f~I~DPa 232 (268)
.||||||.||+.++ .|+|+||+
T Consensus 123 ~~H~vvi~Gy~~~~-~~~v~DP~ 144 (144)
T PF13529_consen 123 GGHYVVIIGYDEDG-YVYVNDPW 144 (144)
T ss_dssp TEEEEEEEEE-SSE--EEEE-TT
T ss_pred CCEEEEEEEEeCCC-EEEEeCCC
Confidence 69999999999854 59999996
No 13
>cd02423 Peptidase_C39G A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family of proteins with a single peptidase domain, which are
Probab=99.64 E-value=4.2e-15 Score=119.04 Aligned_cols=119 Identities=25% Similarity=0.330 Sum_probs=91.8
Q ss_pred ecccCcCcchHHHHHHHHHHhC-CCCCChhHHHHHhcccccchhhHHHHHHHcCceeEEEEeecCCCCCCcchhhhhhcc
Q 024373 60 INQLFSWDCGLACVLMVLRTIG-INNCNIQGLAEQCCTTSIWTVDLAYLLQKFNVGFSYFTITLGANPNYSVETFYKEQL 138 (268)
Q Consensus 60 i~Q~~~~DCGlACl~MVL~y~g-~~~~~~~~L~el~~ttsiwtidLa~ll~~~gv~~~~~T~tlG~~p~y~~~~FY~~~~ 138 (268)
+.|.+.++||+||++|++++|| ++. +...+++.+.... -|
T Consensus 4 ~~q~~~~~~~l~~l~~~~~~~g~~~~-~~~~l~~~~~~~~-----------------------~~--------------- 44 (129)
T cd02423 4 VRQSYDFSCGPAALATLLRYYGGINI-TEQEVLKLMLIRS-----------------------EG--------------- 44 (129)
T ss_pred eecCCCCChHHHHHHHHHHhcCCCCC-CHHHHHHHhCccc-----------------------CC---------------
Confidence 6888999999999999999999 887 7777776543110 01
Q ss_pred CchHHHHHHHHHHHHHcCCeeeeeccCHHHHHHHHhcCCceEEEEEeCcccccccccccccCCccCCCCCcCCcEEEEEE
Q 024373 139 PTDLVRVDMLFQKARSAGIKIECGSISGVEISLMILSGNYIAIALVDQYKLSHSWMEDVIVPGFYGSDSGYTGHYILICG 218 (268)
Q Consensus 139 ~~D~~Rv~~lf~~A~~~Gi~~~~~~vs~~~L~~~l~~g~~PaIvLvn~~~L~~~~~~~~~~~~~~~~~~~y~gHYVVL~G 218 (268)
.....+.+.|++.|+.++..+++.++|.. .+.|+|++++. +..+|||||.+
T Consensus 45 ----~s~~~l~~~a~~~Gl~~~~~~~~~~~L~~----~~lP~i~~~~~---------------------~~~~~~vvl~~ 95 (129)
T cd02423 45 ----FSMLDLKRYAEALGLKANGYRLNLDKLNA----LQIPVIVLVNN---------------------GGYGHFVVIKG 95 (129)
T ss_pred ----cCHHHHHHHHHHCCCcceEEEcCHHHHhh----CCCCEEEEEec---------------------CCCceEEEEEE
Confidence 11355667788888888888888877553 35899998742 12479999999
Q ss_pred EeCCCCEEEEecCCCCCceeEeCHHHHHHHhh
Q 024373 219 YDANSDEFEIRDPASCRKREKVTLKCLEEARK 250 (268)
Q Consensus 219 yd~~~~~f~I~DPa~g~~~~~is~~eFe~a~~ 250 (268)
++. +.+.|.||+.++ ..++.++|++.|+
T Consensus 96 ~~~--~~~~i~dp~~~~--~~~s~~el~~~w~ 123 (129)
T cd02423 96 IDG--DRVLVGDPALGN--ISMSREEFERIWT 123 (129)
T ss_pred EeC--CEEEEECCCCCC--cccCHHHHHHHhc
Confidence 986 589999999874 5899999999996
No 14
>COG2274 SunT ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]
Probab=99.64 E-value=8.9e-16 Score=157.48 Aligned_cols=119 Identities=24% Similarity=0.334 Sum_probs=99.7
Q ss_pred CceecccCcCcchHHHHHHHHHHhCCCCCChhHHHHHhcccccchhhHHHHHHHcCceeEEEEeecCCCCCCcchhhhhh
Q 024373 57 VPHINQLFSWDCGLACVLMVLRTIGINNCNIQGLAEQCCTTSIWTVDLAYLLQKFNVGFSYFTITLGANPNYSVETFYKE 136 (268)
Q Consensus 57 vP~i~Q~~~~DCGlACl~MVL~y~g~~~~~~~~L~el~~ttsiwtidLa~ll~~~gv~~~~~T~tlG~~p~y~~~~FY~~ 136 (268)
+|.+.|.+..|||+||++|+++|||++. +++.+++.++++. . |
T Consensus 2 ~~~~~q~~~~dcgla~l~mia~~~g~~~-~~~~lr~~~~~~~-----------------~------g------------- 44 (709)
T COG2274 2 MPIVLQQSANDCGLACLAMIANYHGKKI-SLNELRELVGLSR-----------------N------G------------- 44 (709)
T ss_pred CcccccCCccchHHHHHHHHHHHhCCCC-CHHHHHHHcCCCC-----------------C------C-------------
Confidence 6889999999999999999999999998 8899998876431 0 1
Q ss_pred ccCchHHHHHHHHHHHHHcCCeeeeeccCHHHHHHHHhcCCceEEEEEeCcccccccccccccCCccCCCCCcCCcEEEE
Q 024373 137 QLPTDLVRVDMLFQKARSAGIKIECGSISGVEISLMILSGNYIAIALVDQYKLSHSWMEDVIVPGFYGSDSGYTGHYILI 216 (268)
Q Consensus 137 ~~~~D~~Rv~~lf~~A~~~Gi~~~~~~vs~~~L~~~l~~g~~PaIvLvn~~~L~~~~~~~~~~~~~~~~~~~y~gHYVVL 216 (268)
.....+.+.|++.|+.++..+.+.+++. +-+.|+|++|+. +||||+
T Consensus 45 ------~sl~~l~~~a~~lGl~~~~~~~~~~~l~----~~~lP~ii~~~~------------------------~h~vVl 90 (709)
T COG2274 45 ------LSLLELKQAAEKLGLSARAVKLSLEELK----QLPLPAIIHWNG------------------------NHFVVL 90 (709)
T ss_pred ------CChHHHHHHHHHcCCccccccCCHHHhc----ccCCCEEEEEcC------------------------CcEEEE
Confidence 1146677889999999888888866654 445799999993 799999
Q ss_pred EEEeCCCCEEEEecCCCCCceeEeCHHHHHHHhh
Q 024373 217 CGYDANSDEFEIRDPASCRKREKVTLKCLEEARK 250 (268)
Q Consensus 217 ~Gyd~~~~~f~I~DPa~g~~~~~is~~eFe~a~~ 250 (268)
.|+++ +++++.||+.| ..+++.+||++.|+
T Consensus 91 ~~~~~--~~~~v~dp~~g--~~~l~~~e~~~~~t 120 (709)
T COG2274 91 YKIDK--NKVVVLDPAKG--IRRLSLEEFEKLWT 120 (709)
T ss_pred EEecC--CeEEEEeCCCC--cEEcCHHHHHHhhh
Confidence 99987 48999999766 56999999999999
No 15
>cd02259 Peptidase_C39_like Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in all sub-families.
Probab=99.63 E-value=6.8e-15 Score=116.33 Aligned_cols=116 Identities=25% Similarity=0.332 Sum_probs=86.9
Q ss_pred ccCcCcchHHHHHHHHHHhCCCCCChhHHHHHhcccccchhhHHHHHHHcCceeEEEEeecCCCCCCcchhhhhhccCch
Q 024373 62 QLFSWDCGLACVLMVLRTIGINNCNIQGLAEQCCTTSIWTVDLAYLLQKFNVGFSYFTITLGANPNYSVETFYKEQLPTD 141 (268)
Q Consensus 62 Q~~~~DCGlACl~MVL~y~g~~~~~~~~L~el~~ttsiwtidLa~ll~~~gv~~~~~T~tlG~~p~y~~~~FY~~~~~~D 141 (268)
|.+..+||++|++||++++|.+. +.+.+++...... -|
T Consensus 1 ~~~~~~~gl~~l~~i~~~~g~~~-~~~~l~~~~~~~~-----------------------~~------------------ 38 (122)
T cd02259 1 GGGPLDCGLACLQMLLRYFGIPV-RRDVLLNAQQRRQ-----------------------QG------------------ 38 (122)
T ss_pred CCCccchHHHHHHHHHHHcCCCC-CHHHHHHHHhhcc-----------------------CC------------------
Confidence 55667999999999999999998 7777765432110 01
Q ss_pred HHHHHHHHHHHHHcCCeeeeeccCHHHHHHHHhcCCceEEEEEeCcccccccccccccCCccCCCCCcCCcEEEEEEEeC
Q 024373 142 LVRVDMLFQKARSAGIKIECGSISGVEISLMILSGNYIAIALVDQYKLSHSWMEDVIVPGFYGSDSGYTGHYILICGYDA 221 (268)
Q Consensus 142 ~~Rv~~lf~~A~~~Gi~~~~~~vs~~~L~~~l~~g~~PaIvLvn~~~L~~~~~~~~~~~~~~~~~~~y~gHYVVL~Gyd~ 221 (268)
.....+.+.|++.|+.++..+.+.++|. +.+.|+|+++. .|||+||.|++.
T Consensus 39 -~~~~~l~~~a~~~gl~~~~~~~~~~~l~----~~~~P~i~~~~------------------------~~~~~Vl~~~~~ 89 (122)
T cd02259 39 -LSLADLVSLANKLGLTAQGVKLPLAALS----RLQLPALLLWK------------------------QGHFVILYGADK 89 (122)
T ss_pred -CCHHHHHHHHHHcCCeeeEEEcCHHHhc----cCCCCEEEEcC------------------------CCcEEEEEEEcC
Confidence 1134566778888888888888776643 44689998754 499999999985
Q ss_pred CCCEEEEecCCCCCceeEeCHHHHHHHhhc
Q 024373 222 NSDEFEIRDPASCRKREKVTLKCLEEARKS 251 (268)
Q Consensus 222 ~~~~f~I~DPa~g~~~~~is~~eFe~a~~s 251 (268)
+.++|.||+. .....++.++|++.|+.
T Consensus 90 --~~~~i~dp~~-~~~~~~~~~~l~~~w~g 116 (122)
T cd02259 90 --GQVLIADPLE-EGPVTLSESELEERWTG 116 (122)
T ss_pred --CEEEEECCcc-cCCEEeCHHHHHhhCCC
Confidence 5899999963 34568999999999973
No 16
>cd02425 Peptidase_C39F A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=99.62 E-value=7.5e-15 Score=117.15 Aligned_cols=119 Identities=24% Similarity=0.300 Sum_probs=93.3
Q ss_pred CceecccCcCcchHHHHHHHHHHhCCCCCChhHHHHHhcccccchhhHHHHHHHcCceeEEEEeecCCCCCCcchhhhhh
Q 024373 57 VPHINQLFSWDCGLACVLMVLRTIGINNCNIQGLAEQCCTTSIWTVDLAYLLQKFNVGFSYFTITLGANPNYSVETFYKE 136 (268)
Q Consensus 57 vP~i~Q~~~~DCGlACl~MVL~y~g~~~~~~~~L~el~~ttsiwtidLa~ll~~~gv~~~~~T~tlG~~p~y~~~~FY~~ 136 (268)
+|.+.|....+||++|+.|+++++|.+. +.+.+++.+.... -|
T Consensus 1 ~~~~~q~~~~~~~l~~l~~~~~~~~~~~-~~~~l~~~~~~~~-----------------------~~------------- 43 (126)
T cd02425 1 VKPILQNNQTECGLACYAMILNYFGYKV-SLNELREKYELGR-----------------------DG------------- 43 (126)
T ss_pred CCeEeecccccHHHHHHHHHHHHhCCCC-CHHHHHHhccCCC-----------------------CC-------------
Confidence 5789999999999999999999999998 7777776532110 01
Q ss_pred ccCchHHHHHHHHHHHHHcCCeeeeeccCH-HHHHHHHhcCCceEEEEEeCcccccccccccccCCccCCCCCcCCcEEE
Q 024373 137 QLPTDLVRVDMLFQKARSAGIKIECGSISG-VEISLMILSGNYIAIALVDQYKLSHSWMEDVIVPGFYGSDSGYTGHYIL 215 (268)
Q Consensus 137 ~~~~D~~Rv~~lf~~A~~~Gi~~~~~~vs~-~~L~~~l~~g~~PaIvLvn~~~L~~~~~~~~~~~~~~~~~~~y~gHYVV 215 (268)
.....+.+.|++.|+.++...++. +.|. ..+.|+|++++ .|||+|
T Consensus 44 ------~~~~~l~~~a~~~gl~~~~~~~~~~~~l~----~~~lP~I~~~~------------------------~~~~~V 89 (126)
T cd02425 44 ------LSLSYLKQLLEEYGFKCKVYKISFKKNLY----PLKLPVIIFWN------------------------NNHFVV 89 (126)
T ss_pred ------cCHHHHHHHHHHCCCcceEEEEchHHHHh----hCCCCEEEEEc------------------------CCcEEE
Confidence 113556677888888888888887 6544 44589999876 389999
Q ss_pred EEEEeCCCCEEEEecCCCCCceeEeCHHHHHHHhh
Q 024373 216 ICGYDANSDEFEIRDPASCRKREKVTLKCLEEARK 250 (268)
Q Consensus 216 L~Gyd~~~~~f~I~DPa~g~~~~~is~~eFe~a~~ 250 (268)
|.+++. +.++|.||..++ ..++.++|++.|+
T Consensus 90 l~~~~~--~~~~i~dp~~~~--~~~~~~~l~~~~~ 120 (126)
T cd02425 90 LEKIKK--NKVTIVDPAIGR--IKISIDEFLENFS 120 (126)
T ss_pred EEEEEC--CEEEEEcCCCCC--EEECHHHHHhhCC
Confidence 999976 479999999873 4899999999996
No 17
>cd02417 Peptidase_C39_likeA A sub-family of peptidase C39 which contains Cyclolysin and Hemolysin processing peptidases. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in this
Probab=99.52 E-value=1.5e-13 Score=109.20 Aligned_cols=112 Identities=21% Similarity=0.250 Sum_probs=87.2
Q ss_pred cCcchHHHHHHHHHHhCCCCCChhHHHHHhcccccchhhHHHHHHHcCceeEEEEeecCCCCCCcchhhhhhccCchHHH
Q 024373 65 SWDCGLACVLMVLRTIGINNCNIQGLAEQCCTTSIWTVDLAYLLQKFNVGFSYFTITLGANPNYSVETFYKEQLPTDLVR 144 (268)
Q Consensus 65 ~~DCGlACl~MVL~y~g~~~~~~~~L~el~~ttsiwtidLa~ll~~~gv~~~~~T~tlG~~p~y~~~~FY~~~~~~D~~R 144 (268)
..|||++|+.|++++||.+. +.+.|+..+.... -| ..
T Consensus 4 ~~~~~l~~l~~i~~~~g~~~-~~~~l~~~~~~~~-----------------------~~-------------------~~ 40 (121)
T cd02417 4 KPDSGLLALVLLARYHGIAA-DPEQLRHEFGLAG-----------------------EP-------------------FN 40 (121)
T ss_pred ccccHHHHHHHHHHHcCCCC-CHHHHHHHhcCCC-----------------------CC-------------------CC
Confidence 34899999999999999998 8888886643210 01 11
Q ss_pred HHHHHHHHHHcCCeeeeeccCHHHHHHHHhcCCceEEEEEeCcccccccccccccCCccCCCCCcCCcEEEEEEEeCCCC
Q 024373 145 VDMLFQKARSAGIKIECGSISGVEISLMILSGNYIAIALVDQYKLSHSWMEDVIVPGFYGSDSGYTGHYILICGYDANSD 224 (268)
Q Consensus 145 v~~lf~~A~~~Gi~~~~~~vs~~~L~~~l~~g~~PaIvLvn~~~L~~~~~~~~~~~~~~~~~~~y~gHYVVL~Gyd~~~~ 224 (268)
...+.+.|++.|+.++..+++.++|. +.+.|+|++++ .|||+||.+++. +
T Consensus 41 ~~~l~~~a~~~Gl~~~~~~~~~~~l~----~~~lP~I~~~~------------------------~g~~~Vl~~~~~--~ 90 (121)
T cd02417 41 STELLLAAKSLGLKAKAVRQPVERLA----RLPLPALAWDD------------------------DGGHFILAKLDG--Q 90 (121)
T ss_pred HHHHHHHHHHcCCeeEEEecCHHHhc----cCCCCEEEEcc------------------------CCCEEEEEEEcC--C
Confidence 35566778888888888888887754 44689999876 389999999985 4
Q ss_pred EEEEecCCCCCceeEeCHHHHHHHhh
Q 024373 225 EFEIRDPASCRKREKVTLKCLEEARK 250 (268)
Q Consensus 225 ~f~I~DPa~g~~~~~is~~eFe~a~~ 250 (268)
.++|.||+.+ ....++.++|++.|+
T Consensus 91 ~~~i~dp~~~-~~~~~~~~el~~~~~ 115 (121)
T cd02417 91 KYLIQDPISQ-RPEVLSREEFEARWS 115 (121)
T ss_pred CEEEECCCcC-CCeecCHHHHHhhcC
Confidence 7999999876 355899999999996
No 18
>cd02421 Peptidase_C39_likeD A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in this sub-family.
Probab=99.45 E-value=1e-12 Score=105.04 Aligned_cols=119 Identities=21% Similarity=0.233 Sum_probs=89.4
Q ss_pred CcchHHHHHHHHHHhCCCCCChhHHHHHhcccccchhhHHHHHHHcCceeEEEEeecCCCCCCcchhhhhhccCchHHHH
Q 024373 66 WDCGLACVLMVLRTIGINNCNIQGLAEQCCTTSIWTVDLAYLLQKFNVGFSYFTITLGANPNYSVETFYKEQLPTDLVRV 145 (268)
Q Consensus 66 ~DCGlACl~MVL~y~g~~~~~~~~L~el~~ttsiwtidLa~ll~~~gv~~~~~T~tlG~~p~y~~~~FY~~~~~~D~~Rv 145 (268)
.|||++|++|+++|||+.. +.+.++...+... +....
T Consensus 5 ~~~~l~~l~~i~~~~g~~~-~~~~l~~~~~~~~------------------------------------------~~~~~ 41 (124)
T cd02421 5 DDPLLDCLVLLARQFGKPA-SRDSLVAGLPLDD------------------------------------------GRLSP 41 (124)
T ss_pred CChHHHHHHHHHHHhCCCC-CHHHHHhcCCCCC------------------------------------------CCcCH
Confidence 3799999999999999998 7777775432110 01114
Q ss_pred HHHHHHHHHcCCeeeeeccCHHHHHHHHhcCCceEEEEEeCcccccccccccccCCccCCCCCcCCcEEEEEEEeCCCCE
Q 024373 146 DMLFQKARSAGIKIECGSISGVEISLMILSGNYIAIALVDQYKLSHSWMEDVIVPGFYGSDSGYTGHYILICGYDANSDE 225 (268)
Q Consensus 146 ~~lf~~A~~~Gi~~~~~~vs~~~L~~~l~~g~~PaIvLvn~~~L~~~~~~~~~~~~~~~~~~~y~gHYVVL~Gyd~~~~~ 225 (268)
..+.+.|+..|+.++..+++.+.|. +.+.|+|++++ .|||+||.+++. +.
T Consensus 42 ~~l~~~a~~~Gl~~~~~~~~~~~l~----~~~lP~i~~~~------------------------~g~~~Vl~~~~~--~~ 91 (124)
T cd02421 42 ALFPRAAARAGLSARVVRRPLDAIP----TLLLPAILLLK------------------------NGRACVLLGVDD--GH 91 (124)
T ss_pred HHHHHHHHHCCCcceeeeCCHHHCC----cccCCEEEEEc------------------------CCCEEEEEEecC--Ce
Confidence 5677888899998888888887643 44689999877 389999999986 57
Q ss_pred EEEecCCCCCceeEeCHHHHHHHhhcCCCCceEEEEe
Q 024373 226 FEIRDPASCRKREKVTLKCLEEARKSFGTDEDLLLIS 262 (268)
Q Consensus 226 f~I~DPa~g~~~~~is~~eFe~a~~s~GtD~dii~i~ 262 (268)
+.|.||........++.++|++.|+ | .+|++.
T Consensus 92 ~~i~dp~~~~~~~~~~~~el~~~~~--g---~~ll~~ 123 (124)
T cd02421 92 ARILDPESGGGEVEISLEELEEEYS--G---YAIFVK 123 (124)
T ss_pred EEEEccCCCCCcEEEcHHHHHhhCC--e---EEEEEe
Confidence 9999997222345899999999996 3 455553
No 19
>TIGR03375 type_I_sec_LssB type I secretion system ATPase, LssB family. Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion. This model is related to models TIGR01842 and TIGR01846, and to bacteriocin ABC transporters that cleave their substrates during export.
Probab=99.45 E-value=6.1e-13 Score=135.48 Aligned_cols=109 Identities=22% Similarity=0.246 Sum_probs=84.6
Q ss_pred HHHHHHHHHHhCCCCCChhHHHHHhcccccchhhHHHHHHHcCceeEEEEeecCCCCCCcchhhhhhccCchHHHHHHHH
Q 024373 70 LACVLMVLRTIGINNCNIQGLAEQCCTTSIWTVDLAYLLQKFNVGFSYFTITLGANPNYSVETFYKEQLPTDLVRVDMLF 149 (268)
Q Consensus 70 lACl~MVL~y~g~~~~~~~~L~el~~ttsiwtidLa~ll~~~gv~~~~~T~tlG~~p~y~~~~FY~~~~~~D~~Rv~~lf 149 (268)
+||++||++|||++. ++.+|++.++.+. -|.+ +.++.
T Consensus 2 laclami~~~~g~~~-~l~~lr~~~~~~~-----------------------~g~s-------------------l~~l~ 38 (694)
T TIGR03375 2 LDCLLLLARHYGRPV-SREALVAGLPLED-----------------------GRLT-------------------PELLP 38 (694)
T ss_pred HHHHHHHHHHcCCCC-CHHHHHhhCCCCC-----------------------CCCC-------------------HHHHH
Confidence 799999999999998 8899998865321 0222 46677
Q ss_pred HHHHHcCCeeeeeccCHHHHHHHHhcCCceEEEEEeCcccccccccccccCCccCCCCCcCCcEEEEEEEeCCCCE-EEE
Q 024373 150 QKARSAGIKIECGSISGVEISLMILSGNYIAIALVDQYKLSHSWMEDVIVPGFYGSDSGYTGHYILICGYDANSDE-FEI 228 (268)
Q Consensus 150 ~~A~~~Gi~~~~~~vs~~~L~~~l~~g~~PaIvLvn~~~L~~~~~~~~~~~~~~~~~~~y~gHYVVL~Gyd~~~~~-f~I 228 (268)
+.|++.|+.++..+++.+++. +.+.|+|++|+ .+||||+++++++ . ++|
T Consensus 39 ~~~~~~g~~~~~~~~~~~~l~----~~~~P~i~~~~------------------------~~h~vvl~~~~~~--~~~~i 88 (694)
T TIGR03375 39 RAARRAGLSARLVKRSLDDIS----PLLLPAILLLK------------------------DGRACVLLGIDED--GKARV 88 (694)
T ss_pred HHHHHCCCEEEEecCCHhhcC----cCCCCEEEEEc------------------------CCcEEEEEEEcCC--CcEEE
Confidence 777777777777777766643 44589999998 3899999999874 5 999
Q ss_pred ecCCCCCceeEeCHHHHHHHhhc
Q 024373 229 RDPASCRKREKVTLKCLEEARKS 251 (268)
Q Consensus 229 ~DPa~g~~~~~is~~eFe~a~~s 251 (268)
.||+.|....+++.+||++.|+.
T Consensus 89 ~DP~~g~~~~~~~~~e~~~~~~g 111 (694)
T TIGR03375 89 LLPETGDGEQELSLDALEALYSG 111 (694)
T ss_pred EccCCCCCceEecHHHHHhhcCC
Confidence 99999821348999999999963
No 20
>TIGR01846 type_I_sec_HlyB type I secretion system ABC transporter, HlyB family. Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion.
Probab=99.42 E-value=1.1e-12 Score=133.66 Aligned_cols=108 Identities=16% Similarity=0.158 Sum_probs=85.5
Q ss_pred hHHHHHHHHHHhCCCCCChhHHHHHhcccccchhhHHHHHHHcCceeEEEEeecCCCCCCcchhhhhhccCchHHHHHHH
Q 024373 69 GLACVLMVLRTIGINNCNIQGLAEQCCTTSIWTVDLAYLLQKFNVGFSYFTITLGANPNYSVETFYKEQLPTDLVRVDML 148 (268)
Q Consensus 69 GlACl~MVL~y~g~~~~~~~~L~el~~ttsiwtidLa~ll~~~gv~~~~~T~tlG~~p~y~~~~FY~~~~~~D~~Rv~~l 148 (268)
|+||++||++|||++. ++++|++.++... -|.+ +.++
T Consensus 1 g~acl~~i~~~~g~~~-~~~~lr~~~~~~~-----------------------~g~~-------------------~~~l 37 (694)
T TIGR01846 1 GLEALSLLAQVHNIAV-TPSQLRHMLGHAG-----------------------ASLD-------------------DLEI 37 (694)
T ss_pred CHHHHHHHHHHcCCCC-CHHHHHHhcCCCC-----------------------CCCC-------------------HHHH
Confidence 8999999999999999 9999998875331 0212 4566
Q ss_pred HHHHHHcCCeeeeeccCHHHHHHHHhcCCceEEEEEeCcccccccccccccCCccCCCCCcCCcEEEEEEEeCCCCEEEE
Q 024373 149 FQKARSAGIKIECGSISGVEISLMILSGNYIAIALVDQYKLSHSWMEDVIVPGFYGSDSGYTGHYILICGYDANSDEFEI 228 (268)
Q Consensus 149 f~~A~~~Gi~~~~~~vs~~~L~~~l~~g~~PaIvLvn~~~L~~~~~~~~~~~~~~~~~~~y~gHYVVL~Gyd~~~~~f~I 228 (268)
.+.|++.|+.++..+.+.+++. +.+.|+|++|+ +|||||+++++ ++++|
T Consensus 38 ~~~~~~~G~~~~~~~~~~~~l~----~~~lP~i~~~~-------------------------~~~vvl~~~~~--~~~~i 86 (694)
T TIGR01846 38 LLAAKQLGLKAKAVKVSIGRLN----KLPLPALIDGE-------------------------GGWFVLGKLTA--NGVTI 86 (694)
T ss_pred HHHHHHCCCEEEEEeCCHHHcc----CCCCCEEEEEC-------------------------CcEEEEEEEcC--CEEEE
Confidence 6777788888777777776643 44589999985 58999999987 58999
Q ss_pred ecCCCCCceeEeCHHHHHHHhhc
Q 024373 229 RDPASCRKREKVTLKCLEEARKS 251 (268)
Q Consensus 229 ~DPa~g~~~~~is~~eFe~a~~s 251 (268)
.||+.| ...+++.+||++.|+.
T Consensus 87 ~Dp~~g-~~~~i~~~e~~~~~~g 108 (694)
T TIGR01846 87 YDPPGD-APEVLSREVLEALWSG 108 (694)
T ss_pred EcCCCC-CceeeCHHHHHhhCCC
Confidence 999998 3568999999999963
No 21
>TIGR03797 NHPM_micro_ABC2 NHPM bacteriocin system ABC transporter, ATP-binding protein. Members of this protein family are ABC transporter ATP-binding subunits, part of a three-gene putative bacteriocin transport operon. The other subunits include another ATP-binding subunit (TIGR03796), which has an N-terminal propeptide cleavage domain, and an HlyD homolog (TIGR03794). In a number of genomes, a conserved propeptide sequence with a classic Gly-Gly motif
Probab=99.34 E-value=6.9e-12 Score=127.64 Aligned_cols=102 Identities=21% Similarity=0.191 Sum_probs=78.6
Q ss_pred hHHHHHHHHHHhCCCCCChhHHHHHhcccccchhhHHHHHHHcCceeEEEEeecCCCCCCcchhhhhhccCchHHHHHHH
Q 024373 69 GLACVLMVLRTIGINNCNIQGLAEQCCTTSIWTVDLAYLLQKFNVGFSYFTITLGANPNYSVETFYKEQLPTDLVRVDML 148 (268)
Q Consensus 69 GlACl~MVL~y~g~~~~~~~~L~el~~ttsiwtidLa~ll~~~gv~~~~~T~tlG~~p~y~~~~FY~~~~~~D~~Rv~~l 148 (268)
-+||++||++|||++. ++.+||+.+.+ + +..+
T Consensus 4 ~~~~l~~i~~~~~~~~-~~~~lr~~~~g-~----------------------------------------------~~~l 35 (686)
T TIGR03797 4 LLVACAAVGRAMGIEI-RPPARSENLSR-S----------------------------------------------PEPL 35 (686)
T ss_pred HHHHHHHHHHHhCCCC-ChHHHHHHcCC-C----------------------------------------------HHHH
Confidence 5899999999999998 99999987533 3 2345
Q ss_pred HHHHHHcCCeeeeeccCHHHHHHHHhcCCceEEEEEeCcccccccccccccCCccCCCCCcCCcEEEEEEEeCCCCEEEE
Q 024373 149 FQKARSAGIKIECGSISGVEISLMILSGNYIAIALVDQYKLSHSWMEDVIVPGFYGSDSGYTGHYILICGYDANSDEFEI 228 (268)
Q Consensus 149 f~~A~~~Gi~~~~~~vs~~~L~~~l~~g~~PaIvLvn~~~L~~~~~~~~~~~~~~~~~~~y~gHYVVL~Gyd~~~~~f~I 228 (268)
.+.|++.|+.++..+.+.+++. +.+.|||++|+. .+|||||+++++ ++++|
T Consensus 36 ~~~~~~~g~~~~~~~~~~~~l~----~~~lP~i~~~~~-----------------------~~h~vvl~~~~~--~~~~i 86 (686)
T TIGR03797 36 EAIARASRLRIRRVRLEGGWWR----QDSGPLLAYTAE-----------------------DGRPVALLPVSR--GGYEI 86 (686)
T ss_pred HHHHHHCCCceEEEecCHHHHh----hCCCCEEEEEcC-----------------------CCCEEEEEEEcC--CEEEE
Confidence 5556666666666666665543 335899999962 489999999976 58999
Q ss_pred ecCCCCCceeEeCHHHHHHH
Q 024373 229 RDPASCRKREKVTLKCLEEA 248 (268)
Q Consensus 229 ~DPa~g~~~~~is~~eFe~a 248 (268)
.||+.|+ ..+++.+||++.
T Consensus 87 ~dP~~g~-~~~~~~~e~~~~ 105 (686)
T TIGR03797 87 FDPATGT-RRRVDAAMAATL 105 (686)
T ss_pred ECCCCCC-CcccCHHHHHhc
Confidence 9999985 448999999887
No 22
>PF12385 Peptidase_C70: Papain-like cysteine protease AvrRpt2; InterPro: IPR022118 This is a family of cysteine proteases, found in actinobacteria, protobacteria and firmicutes. Papain-like cysteine proteases play a crucial role in plant-pathogen/pest interactions. On entering the host they act on non-self substrates, thereby manipulating the host to evade proteolysis []. AvrRpt2 from Pseudomonas syringae pv tomato DC3000 triggers resistance to P. syringae-2-dependent defence responses, including hypersensitive cell death, by cleaving the Arabidopsis RIN4 protein which is monitored by the cognate resistance protein RPS2 [].
Probab=99.00 E-value=4.6e-09 Score=89.86 Aligned_cols=136 Identities=15% Similarity=0.167 Sum_probs=94.0
Q ss_pred cCceecccCc-CcchHHHHHHHHHHhCCCCCChhHHHHHhcccccchhhHHHHHHH-cCceeEEEEeecCCCCCCcchhh
Q 024373 56 EVPHINQLFS-WDCGLACVLMVLRTIGINNCNIQGLAEQCCTTSIWTVDLAYLLQK-FNVGFSYFTITLGANPNYSVETF 133 (268)
Q Consensus 56 ~vP~i~Q~~~-~DCGlACl~MVL~y~g~~~~~~~~L~el~~ttsiwtidLa~ll~~-~gv~~~~~T~tlG~~p~y~~~~F 133 (268)
.||++.|..+ +-|=.||..||..|.+... . +++.+|.+. -|+..++
T Consensus 23 ~v~~v~Qq~~~mgCWaA~~~Mv~~w~~~~p-r---------------lg~~eLyra~~Glp~~l---------------- 70 (166)
T PF12385_consen 23 AVPYVPQQNTRMGCWAACACMVGGWRDQGP-R---------------LGPPELYRADEGLPSQL---------------- 70 (166)
T ss_pred EeeeeccCCCcccHHHHHHHHHHHHhcCCC-C---------------CCcHHHHHHhcCCchhh----------------
Confidence 3999999986 7999999999999997652 1 566666555 4433211
Q ss_pred hhhccCchHHHHHHHHHHHHHcCCeeee-eccCHHHHHHHHhcCCceEEEEEeCcccccccccccccCCccCCCCCcCCc
Q 024373 134 YKEQLPTDLVRVDMLFQKARSAGIKIEC-GSISGVEISLMILSGNYIAIALVDQYKLSHSWMEDVIVPGFYGSDSGYTGH 212 (268)
Q Consensus 134 Y~~~~~~D~~Rv~~lf~~A~~~Gi~~~~-~~vs~~~L~~~l~~g~~PaIvLvn~~~L~~~~~~~~~~~~~~~~~~~y~gH 212 (268)
+ |..++.++...+.-.++.... .+.+.+++..+|.+. .|.++=|..- . ....+|
T Consensus 71 -q-----~g~d~~~~~~~~gl~~v~~P~~~~~t~e~~~~LL~~y-GPLwv~~~~P--~----------------~~~~~H 125 (166)
T PF12385_consen 71 -Q-----DGLDPEDFIRNEGLKEVPEPANASYTAEGLANLLREY-GPLWVAWEAP--G----------------DSWVAH 125 (166)
T ss_pred -c-----ccccHHHHHHhcCccccCCCcccccCHHHHHHHHHHc-CCeEEEecCC--C----------------Ccceee
Confidence 0 111133333333333444433 466888999999775 5888776641 0 012369
Q ss_pred EEEEEEEeCCCCEEEEecCCCCCceeEeCHHHHHHHh
Q 024373 213 YILICGYDANSDEFEIRDPASCRKREKVTLKCLEEAR 249 (268)
Q Consensus 213 YVVL~Gyd~~~~~f~I~DPa~g~~~~~is~~eFe~a~ 249 (268)
-+||+|++.+.+.+.|+||..++ ..+|++++|..++
T Consensus 126 ~~ViTGI~~dg~~i~~~DP~~gP-~~~m~l~~fn~~~ 161 (166)
T PF12385_consen 126 ASVITGIDGDGDSIHVHDPEQGP-NLRMSLDMFNQAL 161 (166)
T ss_pred EEEEEeecCCCCeEEecCcccCC-CceecHHHHhhhh
Confidence 99999999988999999999995 5789999999874
No 23
>PF14399 Transpep_BrtH: NlpC/p60-like transpeptidase
Probab=98.83 E-value=1.7e-07 Score=86.35 Aligned_cols=93 Identities=30% Similarity=0.367 Sum_probs=70.0
Q ss_pred HHHHHcCCeeeeecc-CHH----HHHHHHhcCCceEEEEEeCcccccccccccccCCccCCCCCcCCcEEEEEEEeCCCC
Q 024373 150 QKARSAGIKIECGSI-SGV----EISLMILSGNYIAIALVDQYKLSHSWMEDVIVPGFYGSDSGYTGHYILICGYDANSD 224 (268)
Q Consensus 150 ~~A~~~Gi~~~~~~v-s~~----~L~~~l~~g~~PaIvLvn~~~L~~~~~~~~~~~~~~~~~~~y~gHYVVL~Gyd~~~~ 224 (268)
..++.+|+.++.... +.+ .|.+.|.+| .|+|+.+|.+.|.+.. . ..+....+|||||.|||.+++
T Consensus 57 ~~~~~lG~~~~~~~~~~~~~~~~~l~~~l~~g-~pv~~~~D~~~lpy~~-------~--~~~~~~~~H~i~v~G~d~~~~ 126 (317)
T PF14399_consen 57 NLLERLGIKYEWREFSSPDEAWEELKEALDAG-RPVIVWVDMYYLPYRP-------N--YYKKHHADHYIVVYGYDEEED 126 (317)
T ss_pred HHHHHCCceEEEEecCCHHHHHHHHHHHHhCC-CceEEEeccccCCCCc-------c--ccccccCCcEEEEEEEeCCCC
Confidence 567889999885444 344 577777777 6999999988775421 0 001223589999999997778
Q ss_pred EEEEecCCCCCceeEeCHHHHHHHhhcCC
Q 024373 225 EFEIRDPASCRKREKVTLKCLEEARKSFG 253 (268)
Q Consensus 225 ~f~I~DPa~g~~~~~is~~eFe~a~~s~G 253 (268)
.|+|.||.. .....++.++|.+||.+-+
T Consensus 127 ~~~v~D~~~-~~~~~~~~~~l~~A~~~~~ 154 (317)
T PF14399_consen 127 VFYVSDPPS-YEPGRLPYEDLAKARFSEG 154 (317)
T ss_pred EEEEEcCCC-CcceeecHHHHHHHHhccC
Confidence 999999944 4578999999999998766
No 24
>COG3271 Predicted double-glycine peptidase [General function prediction only]
Probab=98.81 E-value=4.2e-08 Score=87.17 Aligned_cols=124 Identities=15% Similarity=0.139 Sum_probs=93.9
Q ss_pred ecccCcCcchHHHHHHHHHHhCCCCCChhHHHHHhcccccchhhHHHHHHHcCceeEEEEeecCCCCCCcchhhhhhccC
Q 024373 60 INQLFSWDCGLACVLMVLRTIGINNCNIQGLAEQCCTTSIWTVDLAYLLQKFNVGFSYFTITLGANPNYSVETFYKEQLP 139 (268)
Q Consensus 60 i~Q~~~~DCGlACl~MVL~y~g~~~~~~~~L~el~~ttsiwtidLa~ll~~~gv~~~~~T~tlG~~p~y~~~~FY~~~~~ 139 (268)
|+|..++.||.|||+-+|.+++-+.-+.+...+ ...++++|+++
T Consensus 36 Irq~~d~ScGaaalatll~n~~gk~~~e~~~~~------------~m~~~~~~~s~------------------------ 79 (201)
T COG3271 36 IRQTTDFSCGAAALATLLNNDYGKLADESLVLI------------EMNLEEFGESF------------------------ 79 (201)
T ss_pred HHhhhccCchHHHHHHHHHhhccccCCHHHHHH------------HhhHHHhhhcH------------------------
Confidence 999999999999999999999666413222211 11255566544
Q ss_pred chHHHHHHHHHHHHHcCCeeeeeccCHHHHHHHHhcCCceEEEEEeCcccccccccccccCCccCCCCCcCCcEEEEEEE
Q 024373 140 TDLVRVDMLFQKARSAGIKIECGSISGVEISLMILSGNYIAIALVDQYKLSHSWMEDVIVPGFYGSDSGYTGHYILICGY 219 (268)
Q Consensus 140 ~D~~Rv~~lf~~A~~~Gi~~~~~~vs~~~L~~~l~~g~~PaIvLvn~~~L~~~~~~~~~~~~~~~~~~~y~gHYVVL~Gy 219 (268)
..+...+++.|.+++....+.+++.+. ..|+||++.-. -..||+|+.|.
T Consensus 80 ------~g~~~~~~~~g~~a~~~~~~~~~l~q~----~~p~iV~~~~~---------------------~~~hf~v~~~v 128 (201)
T COG3271 80 ------SGMARAIKSLGNRAQGYENEFESLAQL----KIPVIVTLKYP---------------------ANNHFDVVIGV 128 (201)
T ss_pred ------HHHHHHhhCCCCcccccccchhhhhhc----cCCeeEEeecC---------------------CCceeEEEEec
Confidence 345577889999988888888886543 35999988731 24799999999
Q ss_pred eCCCCEEEEecCCCCCceeEeCHHHHHHHhhcCCC
Q 024373 220 DANSDEFEIRDPASCRKREKVTLKCLEEARKSFGT 254 (268)
Q Consensus 220 d~~~~~f~I~DPa~g~~~~~is~~eFe~a~~s~Gt 254 (268)
+. +.+++.||+-+ ..+.+...|+..|...+.
T Consensus 129 ~~--~~v~l~Dp~~g--~i~~~~~~f~~~w~~~~~ 159 (201)
T COG3271 129 DG--DNVTLADPALG--NIRGKRAQFLSIWDGHVL 159 (201)
T ss_pred cC--CeeEEcChhhC--CccchhHHHHHHhhhcce
Confidence 87 47999999987 568999999999986654
No 25
>COG4990 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=98.61 E-value=4e-07 Score=79.59 Aligned_cols=153 Identities=24% Similarity=0.279 Sum_probs=96.1
Q ss_pred ccCceecccC---cCcchHHHHHHHHHHhCCCCCChhHHHHHhcccccchhhHHHHHHHcCceeEEEEeecCCCCCCcch
Q 024373 55 VEVPHINQLF---SWDCGLACVLMVLRTIGINNCNIQGLAEQCCTTSIWTVDLAYLLQKFNVGFSYFTITLGANPNYSVE 131 (268)
Q Consensus 55 ~~vP~i~Q~~---~~DCGlACl~MVL~y~g~~~~~~~~L~el~~ttsiwtidLa~ll~~~gv~~~~~T~tlG~~p~y~~~ 131 (268)
++||.|.|++ -.-|=+.+++|+|+|.|+.+ +-..+....-+. .++-- .|+. | ||..+.+
T Consensus 28 L~v~~InQm~i~ly~GCEvvslam~L~y~Gk~v-tk~~la~~~~t~---p~npn-----~Gy~--------G-nP~~~~v 89 (195)
T COG4990 28 LDVGLINQMTIGLYQGCEVVSLAMMLQYLGKTV-TKNILARNWPTH---PINPN-----SGYV--------G-NPWDAFV 89 (195)
T ss_pred ccccchhhcCcccccchHHHHHHHHHHHcCCCC-cHHHHhhccCCC---CCCCC-----cCcc--------C-CCchhhc
Confidence 6899999985 36799999999999999998 655554322111 00000 0000 0 0110000
Q ss_pred hhhhh----ccCchHHHHHHHHHHHHHcCCeeeeecc-CHHHHHHHHhcCCceEEEEEeCcccccccccccccCCccCCC
Q 024373 132 TFYKE----QLPTDLVRVDMLFQKARSAGIKIECGSI-SGVEISLMILSGNYIAIALVDQYKLSHSWMEDVIVPGFYGSD 206 (268)
Q Consensus 132 ~FY~~----~~~~D~~Rv~~lf~~A~~~Gi~~~~~~v-s~~~L~~~l~~g~~PaIvLvn~~~L~~~~~~~~~~~~~~~~~ 206 (268)
.|-.. ++. ..+...|++....+...+- |+.+|...|.+|+ |+.+.+-. ++.
T Consensus 90 g~~~n~g~tI~p------~al~~fakkY~~~a~d~tGksl~~ik~ql~kg~-PV~iw~T~--~~~--------------- 145 (195)
T COG4990 90 GFPYNYGLTIWP------TALVSFAKKYNGNAVDLTGKSLSDIKGQLLKGR-PVVIWVTN--FHS--------------- 145 (195)
T ss_pred cCccCCCceech------HHHHHHHHHhCCccccCcCCcHHHHHHHHhcCC-cEEEEEec--ccc---------------
Confidence 00000 111 2344555555555544443 7888988898885 65543332 322
Q ss_pred CCcCCcEEEEEEEeCCCCEEEEecCCCCCceeEeCHHHHHHHhhcCCC
Q 024373 207 SGYTGHYILICGYDANSDEFEIRDPASCRKREKVTLKCLEEARKSFGT 254 (268)
Q Consensus 207 ~~y~gHYVVL~Gyd~~~~~f~I~DPa~g~~~~~is~~eFe~a~~s~Gt 254 (268)
|.=|-|+|+|||+. .|++.||... +..+++.+.|+..|.+.|-
T Consensus 146 --~s~H~v~itgyDk~--n~yynDpyG~-kn~~~~~~~~e~g~n~~g~ 188 (195)
T COG4990 146 --YSIHSVLITGYDKY--NIYYNDPYGY-KNRKISHTYLEDGWNAQGN 188 (195)
T ss_pred --cceeeeEeeccccc--ceEecccccc-chhhhhHHHHHHHHhhhcc
Confidence 46799999999984 7999999954 6789999999999999886
No 26
>PF05023 Phytochelatin: Phytochelatin synthase; InterPro: IPR007719 This entry represents plant phytochelatin synthases (also known as glutathione gamma-glutamylcysteinyltransferase; 2.3.2.15 from EC), which is involved in the synthesis of phytochelatins (PC) and homophytochelatins (hPC), the heavy-metal-binding peptides of plants. This enzyme is required for detoxification of heavy metals such as cadmium and arsenate. The N-terminal region of phytochelatin synthase contains the active site, as well as four highly conserved cysteine residues that appear to play an important role in heavy-metal-induced phytochelatin catalysis. The C-terminal region is rich in cysteines, and may act as a metal sensor, whereby the Cys residues bind cadmium ions to bring them into closer proximity and transferring them to the activation site in the N-terminal catalytic domain []. The C-terminal region displays homology to the functional domains of metallothionein and metallochaperone.; GO: 0016756 glutathione gamma-glutamylcysteinyltransferase activity, 0046872 metal ion binding, 0010038 response to metal ion, 0046938 phytochelatin biosynthetic process; PDB: 2BTW_A 2BU3_B.
Probab=98.39 E-value=3.6e-06 Score=75.52 Aligned_cols=142 Identities=25% Similarity=0.263 Sum_probs=75.8
Q ss_pred ceecccCcCcchHHHHHHHHHHhCCCCCChhHHHHHhcccccchhh-------HHHHHHHcCceeEEEEeecCCCCCCcc
Q 024373 58 PHINQLFSWDCGLACVLMVLRTIGINNCNIQGLAEQCCTTSIWTVD-------LAYLLQKFNVGFSYFTITLGANPNYSV 130 (268)
Q Consensus 58 P~i~Q~~~~DCGlACl~MVL~y~g~~~~~~~~L~el~~ttsiwtid-------La~ll~~~gv~~~~~T~tlG~~p~y~~ 130 (268)
-|..|.+..-||+|+++|||+.++++. +. +. ..+....||-+ +.. -.+.|+
T Consensus 40 ~f~tQ~~~a~CGvASlamVLNAL~~d~-P~-~~--~~~~~~~~tq~~l~~~~~~~~-v~~~Gi----------------- 97 (212)
T PF05023_consen 40 QFVTQSNPAYCGVASLAMVLNALGIDA-PG-RV--WKGPWRWFTQEMLDCCIPLES-VKREGI----------------- 97 (212)
T ss_dssp H----SSCCGHHHHHHHHHHHHHT--------T--TTTT-----TTTCCHHS-HHH-HHHH-------------------
T ss_pred HhccCCCCCcchHHHHHHHHHHhcccC-Cc-cc--ccCCcceeehhhhhccccHHH-HhhcCC-----------------
Confidence 467788899999999999999999861 10 00 00111111111 111 111222
Q ss_pred hhhhhhccCchHHHHHHHHHHHHHcCCeeee---eccCHHHHHHHHhc----CCceEEEEEeCcccccccccccccCCcc
Q 024373 131 ETFYKEQLPTDLVRVDMLFQKARSAGIKIEC---GSISGVEISLMILS----GNYIAIALVDQYKLSHSWMEDVIVPGFY 203 (268)
Q Consensus 131 ~~FY~~~~~~D~~Rv~~lf~~A~~~Gi~~~~---~~vs~~~L~~~l~~----g~~PaIvLvn~~~L~~~~~~~~~~~~~~ 203 (268)
.+.++...|+..|+.++. ...+++++.+++.+ .+.-+||-.+...|..
T Consensus 98 -------------TL~e~~~la~~~g~~~~~~~~~~~s~~~FR~~l~~~~~~~~~~livnf~R~~lgq------------ 152 (212)
T PF05023_consen 98 -------------TLDEFACLAKCNGLRVEVYRADDSSLDEFRQHLKEALSDPNDFLIVNFDRKALGQ------------ 152 (212)
T ss_dssp --------------HHHHHHHHHTTT-EEEEEEGGGS-HHHHHHHHHHHCTSTTEEEEEEEEGGGGTS------------
T ss_pred -------------CHHHHHHHHHhcCCceEEEeCCcCCHHHHHHHHHHHhCCCCCEEEEECcccccCC------------
Confidence 246667778888876554 45677887777643 2234444344332221
Q ss_pred CCCCCcCCcEEEEEEEeCCCCEEEEecCCCC-CceeEeCHHHHHHHhh
Q 024373 204 GSDSGYTGHYILICGYDANSDEFEIRDPASC-RKREKVTLKCLEEARK 250 (268)
Q Consensus 204 ~~~~~y~gHYVVL~Gyd~~~~~f~I~DPa~g-~~~~~is~~eFe~a~~ 250 (268)
...|||-.|-|||.+++.|.|.|.+.. -....++.+.|-++=.
T Consensus 153 ----~G~GHfSPigaY~~~tD~vLilDVar~kYpp~WV~~~~L~~AM~ 196 (212)
T PF05023_consen 153 ----TGGGHFSPIGAYDAETDRVLILDVARFKYPPYWVPLERLYEAMN 196 (212)
T ss_dssp ----SSSEEEEEEEEEETTTTEEEE--S-TTT---EEEEHHHHHHHHS
T ss_pred ----CCCCcccccceecccCCeEEEEecccccCCCEEeEHHHHHHHHh
Confidence 125999999999999999999999954 3556788877766644
No 27
>KOG0632 consensus Phytochelatin synthase [Inorganic ion transport and metabolism]
Probab=93.21 E-value=0.095 Score=49.59 Aligned_cols=26 Identities=38% Similarity=0.451 Sum_probs=23.2
Q ss_pred cCCcEEEEEEEeCCCCEEEEecCCCC
Q 024373 209 YTGHYILICGYDANSDEFEIRDPASC 234 (268)
Q Consensus 209 y~gHYVVL~Gyd~~~~~f~I~DPa~g 234 (268)
-.|||--|-||+.+.+++.|.|=|.-
T Consensus 158 GtGHFSPiggy~e~~d~~LIlDVARF 183 (388)
T KOG0632|consen 158 GTGHFSPIGGYNEERDMALILDVARF 183 (388)
T ss_pred CCCccCcccccCcccCceEEeehhhc
Confidence 36999999999998899999998864
No 28
>PF07910 Peptidase_C78: Peptidase family C78; InterPro: IPR012462 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. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This entry contains UfSP1 and UfSP2, which are cysteine peptidases required for the processing and activation of Ubiquitin fold modifier 1 (Ufm1, IPR005375 from INTERPRO) and for its release from conjugated cellular proteins. UfSP1 and UfSP2 are 217 aa and 461 aa respectively [, ]. The peptidases belong to MEROPS peptidase family C78, clan CA. The UfSP2 family have an N-terminal extension with one or more zinc finger domains of the C2H2 type (IPR007087 from INTERPRO), which have been shown to be involved in protein:protein interaction. UfSP2 is present in most, if not all, multi-cellular organisms including plants, nematodes, flies, and mammals, whereas UfSP1 is not present in plants and nematodes []. ; PDB: 3OQC_B 2Z84_A.
Probab=90.22 E-value=3.8 Score=37.04 Aligned_cols=65 Identities=17% Similarity=0.282 Sum_probs=38.5
Q ss_pred cCceecc---cCcCcchHHHHHHHHHHhCC-------------CCCChhHHHHHhc-------------------ccccc
Q 024373 56 EVPHINQ---LFSWDCGLACVLMVLRTIGI-------------NNCNIQGLAEQCC-------------------TTSIW 100 (268)
Q Consensus 56 ~vP~i~Q---~~~~DCGlACl~MVL~y~g~-------------~~~~~~~L~el~~-------------------ttsiw 100 (268)
.+-|+.| ..-|-||-=-++|++.|+-. .+.++.+|.+... ++.-|
T Consensus 10 ~~~Hy~~~~~D~GWGCGYRniQml~S~l~~~~~~~~~~~~~~~~vPsi~~iQ~~le~awdkG~d~~G~~~~~~~~GsrkW 89 (218)
T PF07910_consen 10 DYYHYSQGFDDEGWGCGYRNIQMLCSWLLHQDQPGYEQFFGGSRVPSIREIQQWLEEAWDKGFDPQGAQLTGGFVGSRKW 89 (218)
T ss_dssp B---TTTT---TTT-HHHHHHHHHHCCCCC-------TTS--TT---HHHHHHHHHHCTSS---C-------CGTT----
T ss_pred CEEEEeecCCCCCccchhhHHHHHHHHHHhhhccccccccCCCCCCCHHHHHHHHHHHHhhcCCcccccccccccccccE
Confidence 4667777 55799999999999999855 1223444433321 34456
Q ss_pred --hhhHHHHHHHcCceeEEEEe
Q 024373 101 --TVDLAYLLQKFNVGFSYFTI 120 (268)
Q Consensus 101 --tidLa~ll~~~gv~~~~~T~ 120 (268)
|.+++.+|..+|++++....
T Consensus 90 IGt~E~~~~l~~~gi~~~i~~f 111 (218)
T PF07910_consen 90 IGTTEASALLRSLGIPCKIVDF 111 (218)
T ss_dssp --HHHHHHHHHHC-SEEEEEEE
T ss_pred EcHHHHHHHHhhCCceEEEEEE
Confidence 89999999999999876553
No 29
>PF05543 Peptidase_C47: Staphopain peptidase C47; InterPro: IPR008750 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. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the peptidase family C47 (staphopain family, clan CA). The type example are the staphopains, which are one of four major families of proteinases secreted by the Gram-positive Staphylococcus aureus. These staphylococcal cysteine proteases are secreted as preproenzymes that are proteolytically cleaved to generate the mature enzyme [, , ].; GO: 0008234 cysteine-type peptidase activity, 0006508 proteolysis; PDB: 1X9Y_D 1Y4H_B 1PXV_B 1CV8_A.
Probab=86.90 E-value=18 Score=31.83 Aligned_cols=74 Identities=18% Similarity=0.183 Sum_probs=43.7
Q ss_pred HHHHHHHHHcCCee--eeeccCHHHHHHHHhcCCceEEEEEeCcccccccccccccCCccCCCCCcCCcEEEEEEEeCCC
Q 024373 146 DMLFQKARSAGIKI--ECGSISGVEISLMILSGNYIAIALVDQYKLSHSWMEDVIVPGFYGSDSGYTGHYILICGYDANS 223 (268)
Q Consensus 146 ~~lf~~A~~~Gi~~--~~~~vs~~~L~~~l~~g~~PaIvLvn~~~L~~~~~~~~~~~~~~~~~~~y~gHYVVL~Gyd~~~ 223 (268)
+++++-++..|..+ ..+.++.+++.+++++. .|++++.+.- -.++....||=+||.||-...
T Consensus 69 ~~~i~y~ks~g~~~~~~n~~~s~~eV~~~~~~n-k~i~i~~~~v---------------~~~~~~~~gHAlavvGya~~~ 132 (175)
T PF05543_consen 69 NQMIKYAKSQGRNPQYNNRMPSFDEVKKLIDNN-KGIAILADRV---------------EQTNGPHAGHALAVVGYAKPN 132 (175)
T ss_dssp HHHHHHHHHTTEEEEEECS---HHHHHHHHHTT--EEEEEEEET---------------TSCTTB--EEEEEEEEEEEET
T ss_pred HHHHHHHHHcCcchhHhcCCCCHHHHHHHHHcC-CCeEEEeccc---------------ccCCCCccceeEEEEeeeecC
Confidence 45666677777544 44566899999888776 4666666631 011222479999999996422
Q ss_pred ---CEEEEecCCCCC
Q 024373 224 ---DEFEIRDPASCR 235 (268)
Q Consensus 224 ---~~f~I~DPa~g~ 235 (268)
..++|=+|--..
T Consensus 133 ~g~~~y~~WNPW~~~ 147 (175)
T PF05543_consen 133 NGQKTYYFWNPWWND 147 (175)
T ss_dssp TSEEEEEEE-TT-SS
T ss_pred CCCeEEEEeCCccCC
Confidence 378888998763
No 30
>PF15645 Tox-PLDMTX: Dermonecrotoxin of the Papain-like fold
Probab=79.36 E-value=8.1 Score=32.59 Aligned_cols=24 Identities=17% Similarity=0.369 Sum_probs=19.7
Q ss_pred CcCCcEEEEEEEeCCCCEEEEecCCCC
Q 024373 208 GYTGHYILICGYDANSDEFEIRDPASC 234 (268)
Q Consensus 208 ~y~gHYVVL~Gyd~~~~~f~I~DPa~g 234 (268)
.+++||||+-.++. +-|+.||...
T Consensus 41 ~p~NH~vv~~k~~g---~eyV~D~Ta~ 64 (135)
T PF15645_consen 41 SPTNHFVVVAKKNG---KEYVFDPTAH 64 (135)
T ss_pred CCcceEEEEEEECC---EEEEEeCcHH
Confidence 46899999988764 7899999865
No 31
>cd02619 Peptidase_C1 C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some exceptions like cathepsins B, C, H and X, which are exopeptidases. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage proteins in seeds while mammalian CPs are primarily lysosomal enzymes responsible for protein degradation in the lysosome. Papain-like CPs are synthesized as inactive proenzymes with N-terminal propeptide regions, which are removed upon activation. Bleomycin hydrolase (BH) is a CP that detoxifies bleomycin by hydrolysis of an amide group. It acts as a carboxypeptidase on its C-terminus to convert itself into an aminopeptidase and peptide ligase. BH is found in all tissues in mammals as well as in many other eukaryotes. It forms a hexameric ring barrel str
Probab=78.19 E-value=9.8 Score=32.43 Aligned_cols=80 Identities=20% Similarity=0.270 Sum_probs=45.4
Q ss_pred HHHHHHHHhcCCceEEEEEeCcccccccccccc---cCCccCCCCCcCCcEEEEEEEeCC----CCEEEEecCCCC----
Q 024373 166 GVEISLMILSGNYIAIALVDQYKLSHSWMEDVI---VPGFYGSDSGYTGHYILICGYDAN----SDEFEIRDPASC---- 234 (268)
Q Consensus 166 ~~~L~~~l~~g~~PaIvLvn~~~L~~~~~~~~~---~~~~~~~~~~y~gHYVVL~Gyd~~----~~~f~I~DPa~g---- 234 (268)
.++|++.|.++ .|+++=++.......+..... ............+|-|+|.||+.+ .+.++++|-...
T Consensus 125 ~~~ik~aL~~~-gPv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Hav~ivGy~~~~~~~~~~~i~~NSwG~~wg~ 203 (223)
T cd02619 125 IEDIKEALAKG-GPVVAGFDVYSGFDRLKEGIIYEEIVYLLYEDGDLGGHAVVIVGYDDNYVEGKGAFIVKNSWGTDWGD 203 (223)
T ss_pred HHHHHHHHHHC-CCEEEEEEcccchhcccCccccccccccccCCCccCCeEEEEEeecCCCCCCCCEEEEEeCCCCcccc
Confidence 57888888775 477775553221111111110 001111223346899999999864 367888886542
Q ss_pred CceeEeCHHHHH
Q 024373 235 RKREKVTLKCLE 246 (268)
Q Consensus 235 ~~~~~is~~eFe 246 (268)
.+..+++.+.+.
T Consensus 204 ~Gy~~i~~~~~~ 215 (223)
T cd02619 204 NGYGRISYEDVY 215 (223)
T ss_pred CCEEEEehhhhh
Confidence 246677777765
No 32
>cd02248 Peptidase_C1A Peptidase C1A subfamily (MEROPS database nomenclature); composed of cysteine peptidases (CPs) similar to papain, including the mammalian CPs (cathepsins B, C, F, H, L, K, O, S, V, X and W). Papain is an endopeptidase with specific substrate preferences, primarily for bulky hydrophobic or aromatic residues at the S2 subsite, a hydrophobic pocket in papain that accommodates the P2 sidechain of the substrate (the second residue away from the scissile bond). Most members of the papain subfamily are endopeptidases. Some exceptions to this rule can be explained by specific details of the catalytic domains like the occluding loop in cathepsin B which confers an additional carboxydipeptidyl activity and the mini-chain of cathepsin H resulting in an N-terminal exopeptidase activity. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage proteins in seeds. Parasitic CPs act extracellularly to help invade tissues and cells, to h
Probab=71.17 E-value=18 Score=30.95 Aligned_cols=61 Identities=15% Similarity=0.206 Sum_probs=35.7
Q ss_pred HHHHHHHHhcCCceEEEEEeCcccccccccccccCCccCCC---CCcCCcEEEEEEEeCC--CCEEEEecCC
Q 024373 166 GVEISLMILSGNYIAIALVDQYKLSHSWMEDVIVPGFYGSD---SGYTGHYILICGYDAN--SDEFEIRDPA 232 (268)
Q Consensus 166 ~~~L~~~l~~g~~PaIvLvn~~~L~~~~~~~~~~~~~~~~~---~~y~gHYVVL~Gyd~~--~~~f~I~DPa 232 (268)
.++|++.|.++ .|+++-++... +|+.. ..+.|... ....+|-|+|.||+.+ .+.++|++--
T Consensus 117 ~~~ik~~l~~~-gPV~~~~~~~~---~f~~y--~~Giy~~~~~~~~~~~Hav~iVGy~~~~~~~ywiv~NSW 182 (210)
T cd02248 117 EEALKAALANY-GPVSVAIDASS---SFQFY--KGGIYSGPCCSNTNLNHAVLLVGYGTENGVDYWIVKNSW 182 (210)
T ss_pred HHHHHHHHhhc-CCEEEEEecCc---ccccC--CCCceeCCCCCCCcCCEEEEEEEEeecCCceEEEEEcCC
Confidence 67888888774 47777665431 11101 11222211 2345799999999863 3467777755
No 33
>PF00112 Peptidase_C1: Papain family cysteine protease This is family C1 in the peptidase classification. ; InterPro: IPR000668 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. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of proteins belong to the peptidase family C1, sub-family C1A (papain family, clan CA). It includes proteins classed as non-peptidase homologs. These are have either been shown experimentally to lack peptidase activity or lack one or more of the active site residues. The papain family has a wide variety of activities, including broad-range (papain) and narrow-range endo-peptidases, aminopeptidases, dipeptidyl peptidases and enzymes with both exo- and endo-peptidase activity []. Members of the papain family are widespread, found in baculovirus [], eubacteria, yeast, and practically all protozoa, plants and mammals []. The proteins are typically lysosomal or secreted, and proteolytic cleavage of the propeptide is required for enzyme activation, although bleomycin hydrolase is cytosolic in fungi and mammals []. Papain-like cysteine proteinases are essentially synthesised as inactive proenzymes (zymogens) with N-terminal propeptide regions. The activation process of these enzymes includes the removal of propeptide regions. The propeptide regions serve a variety of functions in vivo and in vitro. The pro-region is required for the proper folding of the newly synthesised enzyme, the inactivation of the peptidase domain and stabilisation of the enzyme against denaturing at neutral to alkaline pH conditions. Amino acid residues within the pro-region mediate their membrane association, and play a role in the transport of the proenzyme to lysosomes. Among the most notable features of propeptides is their ability to inhibit the activity of their cognate enzymes and that certain propeptides exhibit high selectivity for inhibition of the peptidases from which they originate []. The catalytic residues of papain are Cys-25 and His-159, other important residues being Gln-19, which helps form the 'oxyanion hole', and Asn-175, which orientates the imidazole ring of His-159. ; GO: 0008234 cysteine-type peptidase activity, 0006508 proteolysis; PDB: 3MOR_B 3HHI_B 1S4V_A 3F75_A 1MEG_A 1PCI_C 1PPO_A 3HD3_B 1F29_A 1EWL_A ....
Probab=67.83 E-value=7.3 Score=33.21 Aligned_cols=62 Identities=19% Similarity=0.309 Sum_probs=35.0
Q ss_pred CHHHHHHHHhcCCceEEEEEeCccc-ccccccccccCCccCCC---CCcCCcEEEEEEEeCC--CCEEEEecCC
Q 024373 165 SGVEISLMILSGNYIAIALVDQYKL-SHSWMEDVIVPGFYGSD---SGYTGHYILICGYDAN--SDEFEIRDPA 232 (268)
Q Consensus 165 s~~~L~~~l~~g~~PaIvLvn~~~L-~~~~~~~~~~~~~~~~~---~~y~gHYVVL~Gyd~~--~~~f~I~DPa 232 (268)
..++|+++|.++ .|+++-++..-- ...+ ..+.+... ....+|-|+|.||+.+ .+.+++++--
T Consensus 122 ~~~~ik~~L~~~-gpV~~~~~~~~~~f~~~-----~~gi~~~~~~~~~~~~Hav~iVGy~~~~~~~~wiv~NSW 189 (219)
T PF00112_consen 122 DIEDIKKALMKY-GPVVASIDVSSEDFQNY-----KSGIYDPPDCSNESGGHAVLIVGYDDENGKGYWIVKNSW 189 (219)
T ss_dssp CHHHHHHHHHHH-SSEEEEEEEESHHHHTE-----ESSEECSTSSSSSSEEEEEEEEEEEEETTEEEEEEE-SB
T ss_pred chhHHHHHHhhC-ceeeeeeeccccccccc-----cceeeeccccccccccccccccccccccceeeEeeehhh
Confidence 478898888874 366665553220 0111 11222221 2356899999999865 4567777643
No 34
>TIGR03590 PseG pseudaminic acid biosynthesis-associated protein PseG. This protein is found in association with enzymes involved in the biosynthesis of pseudaminic acid, a component of polysaccharide in certain Pseudomonas strains as well as a modification of flagellin in Campylobacter and Hellicobacter. The role of this protein is unclear, although it may participate in N-acetylation in conjunction with, or in the absence of PseH (TIGR03585) as it often scores above the trusted cutoff to pfam00583 representing a family of acetyltransferases.
Probab=55.75 E-value=46 Score=30.44 Aligned_cols=70 Identities=21% Similarity=0.254 Sum_probs=49.1
Q ss_pred hhHHHHHHHcCceeEEEEeecCCCCCCcchhhhhhccCchHHHHHHHHHHHHHcCCeeeeecc------CHHHHHHHHhc
Q 024373 102 VDLAYLLQKFNVGFSYFTITLGANPNYSVETFYKEQLPTDLVRVDMLFQKARSAGIKIECGSI------SGVEISLMILS 175 (268)
Q Consensus 102 idLa~ll~~~gv~~~~~T~tlG~~p~y~~~~FY~~~~~~D~~Rv~~lf~~A~~~Gi~~~~~~v------s~~~L~~~l~~ 175 (268)
.-||..++..|..+.|.+...+ ..+.+..++.|+.+...+- +.+++.++|.+
T Consensus 21 l~LA~~l~~~g~~v~f~~~~~~----------------------~~~~~~i~~~g~~v~~~~~~~~~~~d~~~~~~~l~~ 78 (279)
T TIGR03590 21 LTLARALHAQGAEVAFACKPLP----------------------GDLIDLLLSAGFPVYELPDESSRYDDALELINLLEE 78 (279)
T ss_pred HHHHHHHHHCCCEEEEEeCCCC----------------------HHHHHHHHHcCCeEEEecCCCchhhhHHHHHHHHHh
Confidence 5689999889999999886433 2234666788887765543 24467777765
Q ss_pred CCceEEEEEeCcccccccc
Q 024373 176 GNYIAIALVDQYKLSHSWM 194 (268)
Q Consensus 176 g~~PaIvLvn~~~L~~~~~ 194 (268)
. .|-++.+|.+.+...|+
T Consensus 79 ~-~~d~vV~D~y~~~~~~~ 96 (279)
T TIGR03590 79 E-KFDILIVDHYGLDADWE 96 (279)
T ss_pred c-CCCEEEEcCCCCCHHHH
Confidence 4 37788899887776664
No 35
>COG2117 Predicted subunit of tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]
Probab=54.70 E-value=29 Score=30.65 Aligned_cols=46 Identities=17% Similarity=0.220 Sum_probs=36.8
Q ss_pred HHHHHHcCceeEEEEeecCCCCCCcchhhhhhccCchHHHHHHHHHHHHHcCCeeeeeccCHH
Q 024373 105 AYLLQKFNVGFSYFTITLGANPNYSVETFYKEQLPTDLVRVDMLFQKARSAGIKIECGSISGV 167 (268)
Q Consensus 105 a~ll~~~gv~~~~~T~tlG~~p~y~~~~FY~~~~~~D~~Rv~~lf~~A~~~Gi~~~~~~vs~~ 167 (268)
|-+|+++|+.++.-|.++|+-|+++. --++|..+|++-+..+++-+
T Consensus 17 A~iL~klgyev~LVTvnFGv~d~~k~-----------------A~~tA~~lgF~h~vl~Ldr~ 62 (198)
T COG2117 17 ALILDKLGYEVELVTVNFGVLDSWKY-----------------ARETAAILGFPHEVLQLDRE 62 (198)
T ss_pred HHHHHHhCCCcEEEEEEeccccchhh-----------------HHHHHHHhCCCcceeccCHH
Confidence 56789999999999999999987553 23778888888887777654
No 36
>PF01640 Peptidase_C10: Peptidase C10 family classification.; InterPro: IPR000200 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. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to MEROPS peptidase family C10 (streptopain family, clan CA). Streptopain is a cysteine protease found in Streptococcus pyogenes that shows some structural and functional similarity to papain (family C1) [, ]. The order of the catalytic cysteine/histidine dyad is the same and the surrounding sequences are similar. The two proteins also show similar specificities, both preferring a hydrophobic residue at the P2 site [, ]. Streptopain shows a high degree of sequence similarity to the S. pyogenes exotoxin B, and strong similarity to the prtT gene product of Porphyromonas gingivalis (Bacteroides gingivalis), both of which have been included in the family [].; GO: 0008234 cysteine-type peptidase activity, 0006508 proteolysis; PDB: 4D8I_A 4D8E_A 4D8B_A 3BBA_B 3BB7_A 2JTC_A 1PVJ_A 1DKI_D 2UZJ_A.
Probab=50.79 E-value=96 Score=27.00 Aligned_cols=23 Identities=4% Similarity=-0.061 Sum_probs=16.2
Q ss_pred cccCcCcchHHHHHHHHHHhCCC
Q 024373 61 NQLFSWDCGLACVLMVLRTIGIN 83 (268)
Q Consensus 61 ~Q~~~~DCGlACl~MVL~y~g~~ 83 (268)
.+....-|-+.+++.||+|+..+
T Consensus 16 ~~~~~tGCvatA~AQim~y~~~P 38 (192)
T PF01640_consen 16 GGRAPTGCVATAMAQIMYYHKWP 38 (192)
T ss_dssp TSB-B--HHHHHHHHHHHHHT--
T ss_pred CCccCccHHHHHHHHHHHHhcCC
Confidence 56667889999999999999843
No 37
>cd02621 Peptidase_C1A_CathepsinC Cathepsin C; also known as Dipeptidyl Peptidase I (DPPI), an atypical papain-like cysteine peptidase with chloride dependency and dipeptidyl aminopeptidase activity, resulting from its tetrameric structure which limits substrate access. Each subunit of the tetramer is composed of three peptides: the heavy and light chains, which together adopts the papain fold and forms the catalytic domain; and the residual propeptide region, which forms a beta barrel and points towards the substrate's N-terminus. The subunit composition is the result of the unique characteristic of procathepsin C maturation involving the cleavage of the catalytic domain and the non-autocatalytic excision of an activation peptide within its propeptide region. By removing N-terminal dipeptide extensions, cathepsin C activates granule serine peptidases (granzymes) involved in cell-mediated apoptosis, inflammation and tissue remodelling. Loss-of-function mutations in cathepsin C are assoc
Probab=47.73 E-value=71 Score=28.50 Aligned_cols=22 Identities=18% Similarity=0.560 Sum_probs=16.0
Q ss_pred CCcEEEEEEEeCCC----CEEEEecC
Q 024373 210 TGHYILICGYDANS----DEFEIRDP 231 (268)
Q Consensus 210 ~gHYVVL~Gyd~~~----~~f~I~DP 231 (268)
.+|-|+|.||+.+. +-++|++-
T Consensus 186 ~~HaV~iVGyg~~~~~g~~YWiirNS 211 (243)
T cd02621 186 TNHAVLLVGWGEDEIKGEKYWIVKNS 211 (243)
T ss_pred CCeEEEEEEeeccCCCCCcEEEEEcC
Confidence 57999999997532 45677763
No 38
>cd02698 Peptidase_C1A_CathepsinX Cathepsin X; the only papain-like lysosomal cysteine peptidase exhibiting carboxymonopeptidase activity. It can also act as a carboxydipeptidase, like cathepsin B, but has been shown to preferentially cleave substrates through a monopeptidyl carboxypeptidase pathway. The propeptide region of cathepsin X, the shortest among papain-like peptidases, is covalently attached to the active site cysteine in the inactive form of the enzyme. Little is known about the biological function of cathepsin X. Some studies point to a role in early tumorigenesis. A more recent study indicates that cathepsin X expression is restricted to immune cells suggesting a role in phagocytosis and the regulation of the immune response.
Probab=46.67 E-value=77 Score=28.31 Aligned_cols=88 Identities=14% Similarity=0.149 Sum_probs=49.5
Q ss_pred CHHHHHHHHhcCCceEEEEEeCcccccccccccccCCccCCC--CCcCCcEEEEEEEeCC---CCEEEEecCCCC----C
Q 024373 165 SGVEISLMILSGNYIAIALVDQYKLSHSWMEDVIVPGFYGSD--SGYTGHYILICGYDAN---SDEFEIRDPASC----R 235 (268)
Q Consensus 165 s~~~L~~~l~~g~~PaIvLvn~~~L~~~~~~~~~~~~~~~~~--~~y~gHYVVL~Gyd~~---~~~f~I~DPa~g----~ 235 (268)
+.++|+..|.+. .|+++-++.+. +|+.. ..+.|... ....+|-|+|.||+.+ .+-++|++--.. .
T Consensus 137 ~~~~i~~~l~~~-GPV~v~i~~~~---~f~~Y--~~GIy~~~~~~~~~~HaV~IVGyG~~~~g~~YWiikNSWG~~WGe~ 210 (239)
T cd02698 137 GRDKMMAEIYAR-GPISCGIMATE---ALENY--TGGVYKEYVQDPLINHIISVAGWGVDENGVEYWIVRNSWGEPWGER 210 (239)
T ss_pred CHHHHHHHHHHc-CCEEEEEEecc---ccccc--CCeEEccCCCCCcCCeEEEEEEEEecCCCCEEEEEEcCCCcccCcC
Confidence 356777777554 48888777532 11100 12223211 2345899999999643 245666664431 3
Q ss_pred ceeEeCHHHHHHHhhcCCCCceE
Q 024373 236 KREKVTLKCLEEARKSFGTDEDL 258 (268)
Q Consensus 236 ~~~~is~~eFe~a~~s~GtD~di 258 (268)
+..+|+...|.++....|+-.+.
T Consensus 211 Gy~~i~rg~~~~~~~~~~i~~~~ 233 (239)
T cd02698 211 GWFRIVTSSYKGARYNLAIEEDC 233 (239)
T ss_pred ceEEEEccCCcccccccccccce
Confidence 56777777766666666654443
No 39
>PF13162 DUF3997: Protein of unknown function (DUF3997)
Probab=42.79 E-value=53 Score=26.97 Aligned_cols=39 Identities=18% Similarity=0.259 Sum_probs=31.8
Q ss_pred EEEEecCCCCCceeEeCHHHHHHHhhcCCCCceEEEEec
Q 024373 225 EFEIRDPASCRKREKVTLKCLEEARKSFGTDEDLLLISL 263 (268)
Q Consensus 225 ~f~I~DPa~g~~~~~is~~eFe~a~~s~GtD~dii~i~~ 263 (268)
.++|.|=..+...-.++.++|.+.++.+|...++.++-.
T Consensus 74 ~Y~IId~~~~~v~GP~~k~~F~~k~k~l~I~~~l~~~~~ 112 (115)
T PF13162_consen 74 EYWIIDKKNDEVYGPFSKEQFQEKRKELNISDELKFVDT 112 (115)
T ss_pred eEEEEEcCCCcEECCCCHHHHHHHHHhcCCCcceeeccc
Confidence 477777666655558999999999999999999988754
No 40
>KOG3040 consensus Predicted sugar phosphatase (HAD superfamily) [General function prediction only]
Probab=42.31 E-value=2e+02 Score=26.59 Aligned_cols=36 Identities=17% Similarity=0.203 Sum_probs=24.3
Q ss_pred HHHHHHcCceeEEEEeecCCCCCCcchhhhhhccCchHHHHHHHHHHHHHcCCee
Q 024373 105 AYLLQKFNVGFSYFTITLGANPNYSVETFYKEQLPTDLVRVDMLFQKARSAGIKI 159 (268)
Q Consensus 105 a~ll~~~gv~~~~~T~tlG~~p~y~~~~FY~~~~~~D~~Rv~~lf~~A~~~Gi~~ 159 (268)
...|+.-+++++|.|+|-+-. =..|.+...++|+.+
T Consensus 32 l~rLr~~~~kVkFvTNttk~S-------------------k~~l~~rL~rlgf~v 67 (262)
T KOG3040|consen 32 LKRLRDQHVKVKFVTNTTKES-------------------KRNLHERLQRLGFDV 67 (262)
T ss_pred HHHHHhcCceEEEEecCcchh-------------------HHHHHHHHHHhCCCc
Confidence 344555788999999865511 245667778899864
No 41
>PF09671 Spore_GerQ: Spore coat protein (Spore_GerQ); InterPro: IPR014099 Members of this protein family are the spore coat protein GerQ of endospore-forming Firmicutes (low GC Gram-positive bacteria). This protein is cross-linked by a spore coat-associated transglutaminase.
Probab=39.34 E-value=39 Score=26.12 Aligned_cols=24 Identities=25% Similarity=0.391 Sum_probs=18.2
Q ss_pred EEEEEEE--eCCCCEEEEecCCCCCc
Q 024373 213 YILICGY--DANSDEFEIRDPASCRK 236 (268)
Q Consensus 213 YVVL~Gy--d~~~~~f~I~DPa~g~~ 236 (268)
==|..|+ ..+.+.|+|.||.+|++
T Consensus 36 akvf~GviE~aGRDhiiisDp~tg~r 61 (81)
T PF09671_consen 36 AKVFRGVIEAAGRDHIIISDPKTGKR 61 (81)
T ss_pred heeeEEEehhcCcceEEEeCCCCCcE
Confidence 3566776 35567999999999965
No 42
>cd00307 RuBisCO_small_like Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit and related proteins. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family of nuclear genes. After translation, the small subunits are translocated across the chloroplast membrane, where an N-terminal signal peptide is cleaved off. While the large subunits contain the catalytic activities, it has been shown that the small subunits are important for catalysis by enhancing the catalytic rate through inducing conformational changes in the large subunits. This superfamily also contains specific proteins from cyanobacteria. CcmM plays a role in a CO2 concentrating mechanism, which cyanobacteria need to to overcome t
Probab=38.38 E-value=1.6e+02 Score=22.78 Aligned_cols=58 Identities=14% Similarity=0.240 Sum_probs=35.8
Q ss_pred HHHHHHHhcCCceEEEEEeCcccccccc---ccc--ccC-Ccc----CCCCCcCCcEEEEEEEeCCCC
Q 024373 167 VEISLMILSGNYIAIALVDQYKLSHSWM---EDV--IVP-GFY----GSDSGYTGHYILICGYDANSD 224 (268)
Q Consensus 167 ~~L~~~l~~g~~PaIvLvn~~~L~~~~~---~~~--~~~-~~~----~~~~~y~gHYVVL~Gyd~~~~ 224 (268)
++|..+|++|-.|+|=+.|.+..+..|. -.. ..+ ... .-...|.||||=|.|||..++
T Consensus 6 ~QI~yll~qG~~~~iE~~d~~rywt~w~lp~f~~~~~~~~~Vl~el~~c~~~~p~~YVRlig~D~~~q 73 (84)
T cd00307 6 EQVRQLLAQGYKIGLEHADARRFRTSSWQSCGPIEGRSEAQVLAALEACLAEHPGEYVRLIGIDPKAK 73 (84)
T ss_pred HHHHHHHHCCCEeEEEECCCCccHhhhcCCCCCCCCCCHHHHHHHHHHHHHHCCCCeEEEEEEeCCcc
Confidence 4677778888889998998876655441 111 000 000 001346799999999997543
No 43
>cd02620 Peptidase_C1A_CathepsinB Cathepsin B group; composed of cathepsin B and similar proteins, including tubulointerstitial nephritis antigen (TIN-Ag). Cathepsin B is a lysosomal papain-like cysteine peptidase which is expressed in all tissues and functions primarily as an exopeptidase through its carboxydipeptidyl activity. Together with other cathepsins, it is involved in the degradation of proteins, proenzyme activation, Ag processing, metabolism and apoptosis. Cathepsin B has been implicated in a number of human diseases such as cancer, rheumatoid arthritis, osteoporosis and Alzheimer's disease. The unique carboxydipeptidyl activity of cathepsin B is attributed to the presence of an occluding loop in its active site which favors the binding of the C-termini of substrate proteins. Some members of this group do not possess the occluding loop. TIN-Ag is an extracellular matrix basement protein which was originally identified as a target Ag involved in anti-tubular basement membrane
Probab=38.23 E-value=1e+02 Score=27.52 Aligned_cols=62 Identities=16% Similarity=0.221 Sum_probs=33.2
Q ss_pred CHHHHHHHHhcCCceEEEEEeCcccccccccccccCCccCC--CCCcCCcEEEEEEEeCC--CCEEEEecCC
Q 024373 165 SGVEISLMILSGNYIAIALVDQYKLSHSWMEDVIVPGFYGS--DSGYTGHYILICGYDAN--SDEFEIRDPA 232 (268)
Q Consensus 165 s~~~L~~~l~~g~~PaIvLvn~~~L~~~~~~~~~~~~~~~~--~~~y~gHYVVL~Gyd~~--~~~f~I~DPa 232 (268)
+.++|+.+|.+. .|+++-++.+ .+|+.. ..+.|.. .....+|-|+|.||+.+ .+.++|++--
T Consensus 143 ~~~~ik~~l~~~-GPv~v~i~~~---~~f~~Y--~~Giy~~~~~~~~~~HaV~iVGyg~~~g~~YWivrNSW 208 (236)
T cd02620 143 DETDIMKEIMTN-GPVQAAFTVY---EDFLYY--KSGVYQHTSGKQLGGHAVKIIGWGVENGVPYWLAANSW 208 (236)
T ss_pred HHHHHHHHHHHC-CCeEEEEEec---hhhhhc--CCcEEeecCCCCcCCeEEEEEEEeccCCeeEEEEEeCC
Confidence 456788777654 3777777652 112110 1232321 11234799999999742 2235566543
No 44
>PF02677 DUF208: Uncharacterized BCR, COG1636; InterPro: IPR003828 This entry describes proteins of unknown function.
Probab=36.21 E-value=73 Score=28.06 Aligned_cols=56 Identities=14% Similarity=0.202 Sum_probs=43.5
Q ss_pred hhHHHHHHHcCceeEEEEeecCCCCCCcchhhhhhccCchH-------------HHHHHHHHHHHHcCCeeeeeccC
Q 024373 102 VDLAYLLQKFNVGFSYFTITLGANPNYSVETFYKEQLPTDL-------------VRVDMLFQKARSAGIKIECGSIS 165 (268)
Q Consensus 102 idLa~ll~~~gv~~~~~T~tlG~~p~y~~~~FY~~~~~~D~-------------~Rv~~lf~~A~~~Gi~~~~~~vs 165 (268)
-.+..+.+++|+++.. ..|..+.|++.+...+. .|+..-.+.|++.|+.....+++
T Consensus 45 ~~~~~~~~~~~i~~i~--------~~Y~~~~w~~~v~~~e~epE~g~RC~~Cy~~RL~~tA~~A~e~gfd~FtTTL~ 113 (176)
T PF02677_consen 45 EELKRFAEKLGIPLIE--------GDYDPEEWLRAVKGLEDEPEGGKRCRVCYDLRLEKTAQYAKELGFDYFTTTLL 113 (176)
T ss_pred HHHHHHHHHcCCCEEe--------cCCCHHHHHHHHhhCccCCccCchhHHHHHHHHHHHHHHHHHcCCCEEEcccc
Confidence 4567788888988752 24999999998766543 37888889999999998887774
No 45
>COG4451 RbcS Ribulose bisphosphate carboxylase small subunit [Energy production and conversion]
Probab=32.68 E-value=60 Score=27.08 Aligned_cols=27 Identities=26% Similarity=0.599 Sum_probs=21.8
Q ss_pred CcCCcEEEEEEEeCCCC----EEEEecCCCC
Q 024373 208 GYTGHYILICGYDANSD----EFEIRDPASC 234 (268)
Q Consensus 208 ~y~gHYVVL~Gyd~~~~----~f~I~DPa~g 234 (268)
++.||||=|.|+|..++ +|+|+-|.-.
T Consensus 79 dhp~eYIRliGfDp~gkrrv~sfIVhRPng~ 109 (127)
T COG4451 79 DHPGEYIRLIGFDPKGKRRVVSFIVHRPNGN 109 (127)
T ss_pred hCCCCeEEEEEecCCCceEEEEEEEECCCCC
Confidence 36799999999997655 5899999843
No 46
>TIGR02728 spore_gerQ spore coat protein GerQ. Members of this protein family are the spore coat protein GerQ of endospore-forming Firmicutes (low GC Gram-positive bacteria). This protein is cross-linked by a spore coat-associated transglutaminase.
Probab=31.55 E-value=40 Score=26.06 Aligned_cols=23 Identities=30% Similarity=0.424 Sum_probs=17.8
Q ss_pred EEEEEE--eCCCCEEEEecCCCCCc
Q 024373 214 ILICGY--DANSDEFEIRDPASCRK 236 (268)
Q Consensus 214 VVL~Gy--d~~~~~f~I~DPa~g~~ 236 (268)
=|..|+ +++.+.++|.||.+|++
T Consensus 35 kvf~G~iE~AGRDhiiisdp~tg~R 59 (82)
T TIGR02728 35 RVFRGQIENAGRDHIVISDPQSGMR 59 (82)
T ss_pred hheeeehhhcCcceEEEcCCCCCcE
Confidence 566776 45667999999999964
No 47
>PF13728 TraF: F plasmid transfer operon protein
Probab=28.66 E-value=2.5e+02 Score=25.02 Aligned_cols=40 Identities=23% Similarity=0.101 Sum_probs=26.7
Q ss_pred HHHHHHHHcCCeeeeeccCH------------HHHHHHHhcCCceEEEEEeC
Q 024373 147 MLFQKARSAGIKIECGSISG------------VEISLMILSGNYIAIALVDQ 186 (268)
Q Consensus 147 ~lf~~A~~~Gi~~~~~~vs~------------~~L~~~l~~g~~PaIvLvn~ 186 (268)
-+-.-|.+.|+.+...+++- ..+.+.+.=...|++.||+.
T Consensus 141 il~~~~~~yg~~v~~vs~DG~~~~~fp~~~~~~g~~~~l~v~~~Pal~Lv~~ 192 (215)
T PF13728_consen 141 ILQQFADKYGFSVIPVSLDGRPIPSFPNPRPDPGQAKRLGVKVTPALFLVNP 192 (215)
T ss_pred HHHHHHHHhCCEEEEEecCCCCCcCCCCCCCCHHHHHHcCCCcCCEEEEEEC
Confidence 34467899999999888861 23333332233799999995
No 48
>PF03421 YopJ: YopJ Serine/Threonine acetyltransferase; InterPro: IPR005083 The infection of mammalian host cells by Yersinia sp. causes a rapid induction of the mitogen-activated protein kinase (MAPK; including the ERK, JNK and p38 pathways) and nuclear factor kappaB (NF-kappaB) signalling pathways that would typically result in cytokine production and initiation of the innate immune response. However, these pathways are rapidly inhibited promoting apoptosis. YopJ has been shown to block phosphorylation of active site residues []. It has also been shown that YopJ acetyltransferase is activated by eukaryotic host cell inositol hexakisphosphate []. Serine and threonine acetylation is yet another complication to the control of signalling pathways and may be a may be a widespread mode of biochemical regulation of endogenous processes in eukaryotic cells. It has been shown that YopJ is a serine/threonine acetyltransferase []. It acetylates the serine and threonine residues in the phosphorylation sites of MAPK kinases and nuclear factor kappaB, preventing their activation by phosphorylation and the inhibition of these signalling pathways []. This entry contains YopJ and related proteins.
Probab=27.94 E-value=51 Score=28.76 Aligned_cols=42 Identities=21% Similarity=0.342 Sum_probs=30.4
Q ss_pred CCCCccccCceecccCcCcchHHHHHHHHHHhCCCCCChhHHH
Q 024373 49 LPSAHFVEVPHINQLFSWDCGLACVLMVLRTIGINNCNIQGLA 91 (268)
Q Consensus 49 l~~~~~~~vP~i~Q~~~~DCGlACl~MVL~y~g~~~~~~~~L~ 91 (268)
+|.-++.=+..=.|.+.+|||+=||.+.++.|-... .++.|-
T Consensus 130 ~~~~~~~~ie~diQkS~~dC~IFsLs~AkK~~~~~~-~~~~lH 171 (177)
T PF03421_consen 130 LPNAKFAVIEMDIQKSPSDCGIFSLSLAKKMYKEDD-KLDRLH 171 (177)
T ss_pred CCCcEEEEEecccccCcCcchhhHHHHHHHHhhcch-HHHHHH
Confidence 444444445666899999999999999999986553 444443
No 49
>PF02902 Peptidase_C48: Ulp1 protease family, C-terminal catalytic domain This family belongs to family C48 of the peptidase classification.; InterPro: IPR003653 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. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of proteins contain cysteine peptidases belonging to MEROPS peptidase family C48 (Ulp1 endopeptidase family, clan CE). The protein fold of the peptidase domain for members of this family resembles that of adenain, the type example for clan CE. This group of sequences also contains a number of hypothetical proteins, which have not yet been characterised, and non-peptidase homologues. These are proteins that have either been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity of the peptidases in the family. The Ulp1 endopeptidase family contain the deubiquitinating enzymes (DUB) that can de-conjugate ubiquitin or ubiquitin-like proteins from ubiquitin-conjugated proteins. They can be classified in 3 families according to sequence homology [, ]: Ubiquitin carboxyl-terminal hydrolase (UCH) (see PDOC00127 from PROSITEDOC), Ubiquitin-specific processing protease (UBP) (see PDOC00750 from PROSITEDOC), and ubiquitin-like protease (ULP) specific for de-conjugating ubiquitin-like proteins. In contrast to the UBP pathway, which is very redundant (16 UBP enzymes in yeast), there are few ubiquitin-like proteases (only one in yeast, Ulp1). Ulp1 catalyses two critical functions in the SUMO/Smt3 pathway via its cysteine protease activity. Ulp1 processes the Smt3 C-terminal sequence (-GGATY) to its mature form (-GG), and it de-conjugates Smt3 from the lysine epsilon-amino group of the target protein []. Crystal structure of yeast Ulp1 bound to Smt3 [] revealed that the catalytic and interaction interface is situated in a shallow and narrow cleft where conserved residues recognise the Gly-Gly motif at the C-terminal extremity of Smt3 protein. Ulp1 adopts a novel architecture despite some structural similarity with other cysteine protease. The secondary structure is composed of seven alpha helices and seven beta strands. The catalytic domain includes the central alpha helix, beta-strands 4 to 6, and the catalytic triad (Cys-His-Asp). This profile is directed against the C-terminal part of ULP proteins that displays full proteolytic activity [].; GO: 0008234 cysteine-type peptidase activity, 0006508 proteolysis; PDB: 1EUV_A 2HL8_A 2HKP_A 2HL9_A 1XT9_A 2BKQ_C 2BKR_A 2IO1_E 1TH0_B 1TGZ_A ....
Probab=27.50 E-value=49 Score=28.11 Aligned_cols=24 Identities=17% Similarity=0.252 Sum_probs=18.6
Q ss_pred ceecccCcCcchHHHHHHHHHHhC
Q 024373 58 PHINQLFSWDCGLACVLMVLRTIG 81 (268)
Q Consensus 58 P~i~Q~~~~DCGlACl~MVL~y~g 81 (268)
+.-+|...+|||+-++..+-.+..
T Consensus 159 ~~pqQ~n~~dCGv~vl~~~~~~~~ 182 (216)
T PF02902_consen 159 NVPQQPNGYDCGVYVLKFMECLLE 182 (216)
T ss_dssp TS-SSSSSSCHHHHHHHHHHHHHC
T ss_pred cccCCCCCCCcHHHHHHHHHHHHh
Confidence 334799999999999998866654
No 50
>PF05563 SpvD: Salmonella plasmid virulence protein SpvD; InterPro: IPR008834 This family consists of several SpvD plasmid virulence proteins from different Salmonella species.
Probab=27.35 E-value=54 Score=28.33 Aligned_cols=40 Identities=20% Similarity=0.287 Sum_probs=31.5
Q ss_pred EEEEEEEeCCCCEEEEecCCCCCceeEeCHHHHHHHhhcCCC
Q 024373 213 YILICGYDANSDEFEIRDPASCRKREKVTLKCLEEARKSFGT 254 (268)
Q Consensus 213 YVVL~Gyd~~~~~f~I~DPa~g~~~~~is~~eFe~a~~s~Gt 254 (268)
-||+|.||++. .+...|..... .+--++.|..++|.|.|-
T Consensus 166 avviceydkkp-yvqfidswkts-nilpslqeikkhfsssge 205 (216)
T PF05563_consen 166 AVVICEYDKKP-YVQFIDSWKTS-NILPSLQEIKKHFSSSGE 205 (216)
T ss_pred eEEEEecCCCc-hheeehhhhcc-ccchhHHHHHHhcccCce
Confidence 59999999864 67778877653 455688999999999885
No 51
>PRK15250 virulence protein SpvD; Provisional
Probab=27.35 E-value=54 Score=28.33 Aligned_cols=40 Identities=20% Similarity=0.287 Sum_probs=31.5
Q ss_pred EEEEEEEeCCCCEEEEecCCCCCceeEeCHHHHHHHhhcCCC
Q 024373 213 YILICGYDANSDEFEIRDPASCRKREKVTLKCLEEARKSFGT 254 (268)
Q Consensus 213 YVVL~Gyd~~~~~f~I~DPa~g~~~~~is~~eFe~a~~s~Gt 254 (268)
-||+|.||++. .+...|..... .+--++.|..++|.|.|-
T Consensus 166 avviceydkkp-yvqfidswkts-nilpslqeikkhfsssge 205 (216)
T PRK15250 166 AVVICEYDKKP-YVQFIDSWKTS-NILPSLQEIKKHFSSSGE 205 (216)
T ss_pred eEEEEecCCCc-hheeehhhhcc-ccchhHHHHHHhcccCce
Confidence 59999999864 67778877653 455688999999999885
No 52
>PF13743 Thioredoxin_5: Thioredoxin; PDB: 3KZQ_C.
Probab=27.07 E-value=54 Score=28.10 Aligned_cols=52 Identities=12% Similarity=0.123 Sum_probs=24.2
Q ss_pred cCcchHHHHHHHHHHh-CCCCCC---hhHHHHHhc--ccccch-hhHHHHHHHcCceeEE
Q 024373 65 SWDCGLACVLMVLRTI-GINNCN---IQGLAEQCC--TTSIWT-VDLAYLLQKFNVGFSY 117 (268)
Q Consensus 65 ~~DCGlACl~MVL~y~-g~~~~~---~~~L~el~~--ttsiwt-idLa~ll~~~gv~~~~ 117 (268)
.-.-=+||++..+.-+ |.+. . +..|++... ...+-. --|..++++.|++...
T Consensus 61 ~~~~y~a~la~kAA~~qg~k~-~~~fL~~lQ~a~~~~~~~~s~~~~l~~iA~~~gLD~~~ 119 (176)
T PF13743_consen 61 RSSSYPACLAYKAAQLQGKKK-ARRFLRALQEALFLEGKNYSDEELLLEIAEELGLDVEM 119 (176)
T ss_dssp BS--HHHHHHHHHHHTTT-H---HHHHHHHHHHHHTS---TTSHHHHHHHHHHTT--HHH
T ss_pred CCCchHHHHHHHHHHHhChhh-HHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHhCCCHHH
Confidence 3445678888877654 5443 2 334554432 222222 2267788888877643
No 53
>PRK10941 hypothetical protein; Provisional
Probab=26.67 E-value=1.2e+02 Score=28.14 Aligned_cols=68 Identities=19% Similarity=0.113 Sum_probs=43.1
Q ss_pred HHcCCeeeeeccCHHHHHHHHhc-CCceEEEEEeCcccccccccccccCCccCCCCCcCCcEEEEEEEeCCCCEEEEecC
Q 024373 153 RSAGIKIECGSISGVEISLMILS-GNYIAIALVDQYKLSHSWMEDVIVPGFYGSDSGYTGHYILICGYDANSDEFEIRDP 231 (268)
Q Consensus 153 ~~~Gi~~~~~~vs~~~L~~~l~~-g~~PaIvLvn~~~L~~~~~~~~~~~~~~~~~~~y~gHYVVL~Gyd~~~~~f~I~DP 231 (268)
++.|+ ++|+.-|.-++++ ...| +.-|+. -|||+|=..... +..++.||
T Consensus 93 ~R~G~-----PisL~il~l~iA~~lglp-~~gV~f-----------------------Pghfllr~~~~d--~~~~~IDP 141 (269)
T PRK10941 93 TRQGS-----AVSLGAILLWIANRLDLP-LMPVIF-----------------------PTQLILRADWLD--GEMWLINP 141 (269)
T ss_pred ccCCC-----cHHHHHHHHHHHHHcCCC-eeeeec-----------------------CchheeeeecCC--CceEEEeC
Confidence 55666 5677777666664 2233 333442 399998755433 35788999
Q ss_pred CCCCceeEeCHHHHHHHhh-cCCC
Q 024373 232 ASCRKREKVTLKCLEEARK-SFGT 254 (268)
Q Consensus 232 a~g~~~~~is~~eFe~a~~-s~Gt 254 (268)
-.|+ .++.+++++--. .+|.
T Consensus 142 f~G~---~L~~~~l~~~L~~~~g~ 162 (269)
T PRK10941 142 FNGE---TLDEHTLEVWLKGNISP 162 (269)
T ss_pred CCCC---CCCHHHHHHHHHhhcCC
Confidence 8875 588888876543 4443
No 54
>PTZ00203 cathepsin L protease; Provisional
Probab=25.57 E-value=2.3e+02 Score=27.30 Aligned_cols=61 Identities=20% Similarity=0.188 Sum_probs=34.5
Q ss_pred CHHHHHHHHhcCCceEEEEEeCcccccccccccccCCccCC-CCCcCCcEEEEEEEeCC--CCEEEEecCC
Q 024373 165 SGVEISLMILSGNYIAIALVDQYKLSHSWMEDVIVPGFYGS-DSGYTGHYILICGYDAN--SDEFEIRDPA 232 (268)
Q Consensus 165 s~~~L~~~l~~g~~PaIvLvn~~~L~~~~~~~~~~~~~~~~-~~~y~gHYVVL~Gyd~~--~~~f~I~DPa 232 (268)
..++|...|.+. .|+.+-++.. +|+.. ..+.|.. .....+|-|+|.||+.+ .+-++|++--
T Consensus 247 ~e~~~~~~l~~~-GPv~v~i~a~----~f~~Y--~~GIy~~c~~~~~nHaVliVGYG~~~g~~YWiikNSW 310 (348)
T PTZ00203 247 SERVMAAWLAKN-GPISIAVDAS----SFMSY--HSGVLTSCIGEQLNHGVLLVGYNMTGEVPYWVIKNSW 310 (348)
T ss_pred CHHHHHHHHHhC-CCEEEEEEhh----hhcCc--cCceeeccCCCCCCeEEEEEEEecCCCceEEEEEcCC
Confidence 456677777653 3777777753 22111 1233321 11235899999999753 2457777644
No 55
>TIGR02739 TraF type-F conjugative transfer system pilin assembly protein TraF. This protein is part of a large group of proteins involved in conjugative transfer of plasmid DNA, specifically the F-type system. This protein has been predicted to contain a thioredoxin fold and has been shown to be localized to the periplasm. Unlike the related protein TrbB (TIGR02738), TraF does not contain a conserved pair of cysteines and has been shown not to function as a thiol disulfide isomerase by complementation of an Ecoli DsbA defect. The protein is believed to be involved in pilin assembly. Even more closely related than TrbB is a clade of genes (TIGR02740) which do contain the CXXC motif, but it is unclear whether these genes are involved in type-F conjugation systems per se.
Probab=24.82 E-value=2.2e+02 Score=26.42 Aligned_cols=41 Identities=20% Similarity=0.164 Sum_probs=25.9
Q ss_pred HHHHHHHHHcCCeeeeeccCHHH------------HHHHHhcCCceEEEEEeC
Q 024373 146 DMLFQKARSAGIKIECGSISGVE------------ISLMILSGNYIAIALVDQ 186 (268)
Q Consensus 146 ~~lf~~A~~~Gi~~~~~~vs~~~------------L~~~l~~g~~PaIvLvn~ 186 (268)
--+-+-|.+.|+.+...+++-.- +.+.+.-...|++.|||.
T Consensus 170 pil~~fa~~ygi~v~~VS~DG~~~p~fp~~~~d~gqa~~l~v~~~Pal~Lv~~ 222 (256)
T TIGR02739 170 PVIQAFAKEYGISVIPISVDGTLIPGLPNSRSDSGQAQHLGVKYFPALYLVNP 222 (256)
T ss_pred HHHHHHHHHhCCeEEEEecCCCCCCCCCCccCChHHHHhcCCccCceEEEEEC
Confidence 33446789999999888876431 222222223689988884
No 56
>PRK06552 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=24.11 E-value=4.5e+02 Score=23.42 Aligned_cols=93 Identities=12% Similarity=-0.000 Sum_probs=64.8
Q ss_pred eecccCcCcchHHHHHHHHHHhCC--CCCChhHHHHHhcccccchhhHHHHHHHcCceeEEEEeecCCCCCCcchhhhhh
Q 024373 59 HINQLFSWDCGLACVLMVLRTIGI--NNCNIQGLAEQCCTTSIWTVDLAYLLQKFNVGFSYFTITLGANPNYSVETFYKE 136 (268)
Q Consensus 59 ~i~Q~~~~DCGlACl~MVL~y~g~--~~~~~~~L~el~~ttsiwtidLa~ll~~~gv~~~~~T~tlG~~p~y~~~~FY~~ 136 (268)
.+.=+....+++.++..+.+.++. +. ..|..+|-|.+-+..+..-|.+|-. +-|.|
T Consensus 41 ~iEit~~~~~a~~~i~~l~~~~~~~p~~--------~vGaGTV~~~~~~~~a~~aGA~Fiv---sP~~~----------- 98 (213)
T PRK06552 41 AIEVTYTNPFASEVIKELVELYKDDPEV--------LIGAGTVLDAVTARLAILAGAQFIV---SPSFN----------- 98 (213)
T ss_pred EEEEECCCccHHHHHHHHHHHcCCCCCe--------EEeeeeCCCHHHHHHHHHcCCCEEE---CCCCC-----------
Confidence 333344566788888888776643 12 2355667778888888888887752 22333
Q ss_pred ccCchHHHHHHHHHHHHHcCCeeeeeccCHHHHHHHHhcCCceEEEE
Q 024373 137 QLPTDLVRVDMLFQKARSAGIKIECGSISGVEISLMILSGNYIAIAL 183 (268)
Q Consensus 137 ~~~~D~~Rv~~lf~~A~~~Gi~~~~~~vs~~~L~~~l~~g~~PaIvL 183 (268)
.++.+.|++.|+.......+.+|+...+..| .-.|-+
T Consensus 99 ---------~~v~~~~~~~~i~~iPG~~T~~E~~~A~~~G-ad~vkl 135 (213)
T PRK06552 99 ---------RETAKICNLYQIPYLPGCMTVTEIVTALEAG-SEIVKL 135 (213)
T ss_pred ---------HHHHHHHHHcCCCEECCcCCHHHHHHHHHcC-CCEEEE
Confidence 4577899999999999999999999888666 334433
No 57
>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]
Probab=23.97 E-value=69 Score=33.49 Aligned_cols=24 Identities=29% Similarity=0.391 Sum_probs=19.5
Q ss_pred hHHHHHHHHHHHHHcCCeeeeeccCHHHHHHHHhcCCceEEEEEeC
Q 024373 141 DLVRVDMLFQKARSAGIKIECGSISGVEISLMILSGNYIAIALVDQ 186 (268)
Q Consensus 141 D~~Rv~~lf~~A~~~Gi~~~~~~vs~~~L~~~l~~g~~PaIvLvn~ 186 (268)
-.+||.+||++|++. .|||+++|.
T Consensus 381 GArRVRdLF~aAk~~----------------------APcIIFIDE 404 (752)
T KOG0734|consen 381 GARRVRDLFAAAKAR----------------------APCIIFIDE 404 (752)
T ss_pred cHHHHHHHHHHHHhc----------------------CCeEEEEec
Confidence 467999999888776 689999885
No 58
>PF01081 Aldolase: KDPG and KHG aldolase; InterPro: IPR000887 4-Hydroxy-2-oxoglutarate aldolase (4.1.3.16 from EC) (KHG-aldolase) catalyzes the interconversion of 4-hydroxy-2-oxoglutarate into pyruvate and glyoxylate. Phospho-2-dehydro-3-deoxygluconate aldolase (4.1.2.14 from EC) (KDPG-aldolase) catalyzes the interconversion of 6-phospho-2-dehydro-3-deoxy-D-gluconate into pyruvate and glyceraldehyde 3-phosphate. These two enzymes are structurally and functionally related []. They are both homotrimeric proteins of approximately 220 amino-acid residues. They are class I aldolases whose catalytic mechanism involves the formation of a Schiff-base intermediate between the substrate and the epsilon-amino group of a lysine residue. In both enzymes, an arginine is required for catalytic activity.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 3VCR_A 1FQ0_A 1EUN_A 1EUA_B 1FWR_A 2C0A_B 1WBH_A 1WAU_A 2YW3_B 2YW4_A ....
Probab=23.44 E-value=4.2e+02 Score=23.48 Aligned_cols=90 Identities=16% Similarity=0.123 Sum_probs=58.7
Q ss_pred cCcCcchHHHHHHHHHHhCCCCCChhHHHHHhcccccchhhHHHHHHHcCceeEEEEeecCCCCCCcchhhhhhccCchH
Q 024373 63 LFSWDCGLACVLMVLRTIGINNCNIQGLAEQCCTTSIWTVDLAYLLQKFNVGFSYFTITLGANPNYSVETFYKEQLPTDL 142 (268)
Q Consensus 63 ~~~~DCGlACl~MVL~y~g~~~~~~~~L~el~~ttsiwtidLa~ll~~~gv~~~~~T~tlG~~p~y~~~~FY~~~~~~D~ 142 (268)
+.....++.++..+.+.+. +. +.|..+|-|.+.+..+.+-|.+|-. +-+.|
T Consensus 40 T~~t~~a~~~I~~l~~~~p-~~--------~vGAGTV~~~e~a~~a~~aGA~Fiv---SP~~~----------------- 90 (196)
T PF01081_consen 40 TLRTPNALEAIEALRKEFP-DL--------LVGAGTVLTAEQAEAAIAAGAQFIV---SPGFD----------------- 90 (196)
T ss_dssp ETTSTTHHHHHHHHHHHHT-TS--------EEEEES--SHHHHHHHHHHT-SEEE---ESS-------------------
T ss_pred ecCCccHHHHHHHHHHHCC-CC--------eeEEEeccCHHHHHHHHHcCCCEEE---CCCCC-----------------
Confidence 3344566777776655552 22 2355667778888888889987742 22333
Q ss_pred HHHHHHHHHHHHcCCeeeeeccCHHHHHHHHhcCCceEEEEEe
Q 024373 143 VRVDMLFQKARSAGIKIECGSISGVEISLMILSGNYIAIALVD 185 (268)
Q Consensus 143 ~Rv~~lf~~A~~~Gi~~~~~~vs~~~L~~~l~~g~~PaIvLvn 185 (268)
.++.+.|++.|+.....-.|..|+...+..| .-++=+.=
T Consensus 91 ---~~v~~~~~~~~i~~iPG~~TptEi~~A~~~G-~~~vK~FP 129 (196)
T PF01081_consen 91 ---PEVIEYAREYGIPYIPGVMTPTEIMQALEAG-ADIVKLFP 129 (196)
T ss_dssp ---HHHHHHHHHHTSEEEEEESSHHHHHHHHHTT--SEEEETT
T ss_pred ---HHHHHHHHHcCCcccCCcCCHHHHHHHHHCC-CCEEEEec
Confidence 4678999999999999999999999888776 44443333
No 59
>KOG0852 consensus Alkyl hydroperoxide reductase, thiol specific antioxidant and related enzymes [Posttranslational modification, protein turnover, chaperones]
Probab=23.23 E-value=1.4e+02 Score=26.67 Aligned_cols=47 Identities=21% Similarity=0.415 Sum_probs=38.0
Q ss_pred CcCCcEEEEEEEeCCCCEEEEecCCCCCceeEeCHHHHHHHhhcCCCCceEEEEecC
Q 024373 208 GYTGHYILICGYDANSDEFEIRDPASCRKREKVTLKCLEEARKSFGTDEDLLLISLE 264 (268)
Q Consensus 208 ~y~gHYVVL~Gyd~~~~~f~I~DPa~g~~~~~is~~eFe~a~~s~GtD~dii~i~~~ 264 (268)
.|.|-|||+-=|.. .|-+.+|.- -+.+.++.+.+.+++| ++|.++.+
T Consensus 30 dy~gkyvvlfFypl---DftfVcPte-----IiafSd~~~eF~~~n~--eVig~S~D 76 (196)
T KOG0852|consen 30 DYKGKYVVLFFYPL---DFTFVCPTE-----IIAFSDRAPEFRKLNT--EVLGISTD 76 (196)
T ss_pred hhcccEEEEEecCC---ceeeECchh-----hhhhhhhHHHHHhcCC--eEEEEecc
Confidence 46789999987765 377788873 3567889999999999 89999876
No 60
>KOG2433 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.94 E-value=8.1e+02 Score=24.88 Aligned_cols=60 Identities=8% Similarity=0.313 Sum_probs=35.1
Q ss_pred CcCcchHHHHHHHHHHhC---C---CCCChhHHHHHh----------cccccc--hhhHHHHHHHc-CceeEEEEeecC
Q 024373 64 FSWDCGLACVLMVLRTIG---I---NNCNIQGLAEQC----------CTTSIW--TVDLAYLLQKF-NVGFSYFTITLG 123 (268)
Q Consensus 64 ~~~DCGlACl~MVL~y~g---~---~~~~~~~L~el~----------~ttsiw--tidLa~ll~~~-gv~~~~~T~tlG 123 (268)
.-|-|.--++..|++|+- - ++.+--++.+.. -+++-| ...+...|+.+ ++.+++.-+.-|
T Consensus 406 ~GWGCAYRSlQTIcSWFilqGYT~~pIPtHrEiQqaLvdi~DKpA~FVGSrQWIGStEis~vLn~ll~~~skil~v~sG 484 (577)
T KOG2433|consen 406 SGWGCAYRSLQTICSWFILQGYTDKPIPTHREIQQALVDIQDKPAKFVGSRQWIGSTEISFVLNELLKLESKILAVNSG 484 (577)
T ss_pred CCcchhhHhHHHHHHHHHHcCccCCCCCcHHHHHHHHHhccCcccceecccceecchhHHHHHHHHhccceEEEEeccc
Confidence 459999999999999883 2 222222333321 155666 35566666665 666665554444
No 61
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=22.84 E-value=1.4e+02 Score=18.88 Aligned_cols=22 Identities=27% Similarity=0.365 Sum_probs=16.0
Q ss_pred HHHHHHHHHcCCeeeeeccCHHHHHHHHh
Q 024373 146 DMLFQKARSAGIKIECGSISGVEISLMIL 174 (268)
Q Consensus 146 ~~lf~~A~~~Gi~~~~~~vs~~~L~~~l~ 174 (268)
..|.+.|++.|+ |.+++.++|.
T Consensus 6 ~~Li~eA~~~Gl-------s~eeir~FL~ 27 (30)
T PF08671_consen 6 VELIKEAKESGL-------SKEEIREFLE 27 (30)
T ss_dssp HHHHHHHHHTT---------HHHHHHHHH
T ss_pred HHHHHHHHHcCC-------CHHHHHHHHH
Confidence 467899999998 6778887764
No 62
>PRK13703 conjugal pilus assembly protein TraF; Provisional
Probab=22.82 E-value=3.5e+02 Score=25.01 Aligned_cols=20 Identities=10% Similarity=0.127 Sum_probs=14.7
Q ss_pred HHHHHHHHHcCCeeeeeccC
Q 024373 146 DMLFQKARSAGIKIECGSIS 165 (268)
Q Consensus 146 ~~lf~~A~~~Gi~~~~~~vs 165 (268)
--+-+-|++.|+.+...+++
T Consensus 163 Pil~~fa~~yg~~v~~VS~D 182 (248)
T PRK13703 163 QVINDFRDTYGLSVIPVSVD 182 (248)
T ss_pred HHHHHHHHHhCCeEEEEecC
Confidence 34456788999988887764
No 63
>cd03527 RuBisCO_small Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family of nuclear genes. After translation, the small subunits are translocated across the chloroplast membrane, where an N-terminal signal peptide is cleaved off. While the large subunits contain the catalytic activities, it has been shown that the small subunits are important for catalysis by enhancing the catalytic rate through inducing conformational changes in the large subunits.
Probab=21.77 E-value=1.2e+02 Score=24.29 Aligned_cols=17 Identities=29% Similarity=0.823 Sum_probs=13.9
Q ss_pred CcCCcEEEEEEEeCCCC
Q 024373 208 GYTGHYILICGYDANSD 224 (268)
Q Consensus 208 ~y~gHYVVL~Gyd~~~~ 224 (268)
.|.||||=|.|+|..++
T Consensus 72 ~~p~~YVRliG~D~~~q 88 (99)
T cd03527 72 AYPDHYVRVVGFDNYKQ 88 (99)
T ss_pred HCCCCeEEEEEEeCCcc
Confidence 36799999999997644
No 64
>cd01986 Alpha_ANH_like Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases and ATP sulphurylases. The domain forms a apha/beta/apha fold which binds to Adenosine group..
Probab=21.42 E-value=3.7e+02 Score=20.36 Aligned_cols=64 Identities=16% Similarity=0.118 Sum_probs=39.0
Q ss_pred HHHHHHHcCceeEEEEeecCCCCCCcchhhhhhccCchHHHHHHHHHHHHHcCCeeeeeccCHHHHHHH
Q 024373 104 LAYLLQKFNVGFSYFTITLGANPNYSVETFYKEQLPTDLVRVDMLFQKARSAGIKIECGSISGVEISLM 172 (268)
Q Consensus 104 La~ll~~~gv~~~~~T~tlG~~p~y~~~~FY~~~~~~D~~Rv~~lf~~A~~~Gi~~~~~~vs~~~L~~~ 172 (268)
+.+++.+.+.++..++...|..|......-+. +..|...+.+.|++.|..........+++.+.
T Consensus 14 ll~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~r~~~~~~~a~~~g~~~i~~g~~~~D~~~~ 77 (103)
T cd01986 14 AAALLKKLGYQVIAVTVDHGISPRLEDAKEIA-----KEAREEAAKRIAKEKGAETIATGTRRDDVANR 77 (103)
T ss_pred HHHHHHHhCCCEEEEEEcCCCcccHHHHHHHH-----HHHHHHHHHHHHHHcCCCEEEEcCCcchHHHH
Confidence 55666666666666666555554211111111 11667777788999998877777777776554
Done!