Query 045385
Match_columns 188
No_of_seqs 109 out of 205
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 12:42:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045385.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045385hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02099 Josephin: Josephin; 100.0 5.1E-65 1.1E-69 411.5 11.5 157 14-173 1-157 (157)
2 KOG2935 Ataxin 3/Josephin [Gen 100.0 4.7E-62 1E-66 416.8 7.7 164 8-177 2-165 (315)
3 KOG2934 Uncharacterized conser 100.0 2.6E-42 5.6E-47 281.7 5.7 148 7-173 23-188 (204)
4 cd02424 Peptidase_C39E A sub-f 92.0 1.6 3.4E-05 32.9 8.6 102 17-152 9-116 (129)
5 cd02420 Peptidase_C39D A sub-f 87.8 2.6 5.7E-05 31.1 6.7 101 17-152 9-112 (125)
6 cd02549 Peptidase_C39A A sub-f 87.2 5.3 0.00012 29.8 8.2 125 15-170 2-139 (141)
7 cd02419 Peptidase_C39C A sub-f 86.2 5 0.00011 29.6 7.4 82 81-171 44-126 (127)
8 PF03412 Peptidase_C39: Peptid 84.5 4 8.7E-05 30.3 6.2 120 14-172 6-128 (131)
9 cd02418 Peptidase_C39B A sub-f 82.5 9.8 0.00021 28.2 7.7 105 14-152 5-118 (136)
10 PF01088 Peptidase_C12: Ubiqui 82.2 2.9 6.4E-05 35.3 5.1 110 5-151 75-193 (214)
11 cd02259 Peptidase_C39_like Pep 80.9 15 0.00033 26.4 8.0 69 81-152 39-108 (122)
12 cd02425 Peptidase_C39F A sub-f 78.8 18 0.00039 26.3 7.9 100 18-152 10-113 (126)
13 COG2274 SunT ABC-type bacterio 76.1 25 0.00055 35.0 10.2 117 17-173 10-129 (709)
14 TIGR02616 tnaC_leader tryptoph 73.2 1.4 3.1E-05 25.7 0.4 11 134-144 8-18 (26)
15 cd02423 Peptidase_C39G A sub-f 71.7 29 0.00063 25.3 7.5 70 81-152 45-116 (129)
16 cd02674 Peptidase_C19R A subfa 63.3 8.1 0.00018 31.3 3.2 34 115-148 176-215 (230)
17 cd02417 Peptidase_C39_likeA A 61.2 60 0.0013 23.4 7.8 70 80-152 38-108 (121)
18 TIGR01684 viral_ppase viral ph 60.2 16 0.00034 33.0 4.6 40 135-174 129-171 (301)
19 KOG1415 Ubiquitin C-terminal h 59.5 15 0.00033 31.6 4.2 104 7-152 76-188 (222)
20 cd02257 Peptidase_C19 Peptidas 58.4 12 0.00026 29.4 3.3 36 115-150 195-237 (255)
21 KOG2778 Ubiquitin C-terminal h 58.2 36 0.00078 30.9 6.5 109 8-151 69-187 (328)
22 cd02673 Peptidase_C19Q A subfa 55.8 15 0.00032 31.5 3.6 33 115-147 186-226 (245)
23 PHA03398 viral phosphatase sup 52.2 24 0.00051 31.9 4.4 40 135-174 131-173 (303)
24 cd02661 Peptidase_C19E A subfa 51.1 17 0.00036 30.6 3.2 34 115-148 250-289 (304)
25 cd01427 HAD_like Haloacid deha 50.4 23 0.0005 24.9 3.4 25 152-176 27-51 (139)
26 PF13529 Peptidase_C39_2: Pept 49.7 27 0.00058 25.4 3.8 29 16-44 12-42 (144)
27 COG1654 BirA Biotin operon rep 49.6 20 0.00042 26.1 2.9 25 149-173 31-55 (79)
28 cd02657 Peptidase_C19A A subfa 48.1 23 0.00049 30.3 3.6 34 115-148 243-283 (305)
29 PF02251 PA28_alpha: Proteasom 46.2 2.6 5.6E-05 29.5 -2.1 25 23-47 33-57 (64)
30 cd02659 peptidase_C19C A subfa 45.8 23 0.00051 30.6 3.3 34 115-148 254-293 (334)
31 cd02667 Peptidase_C19K A subfa 45.3 25 0.00054 30.0 3.4 34 115-148 204-264 (279)
32 cd02658 Peptidase_C19B A subfa 42.5 29 0.00062 29.8 3.4 33 115-147 254-295 (311)
33 cd02668 Peptidase_C19L A subfa 40.0 34 0.00073 29.8 3.4 33 115-147 248-287 (324)
34 TIGR03796 NHPM_micro_ABC1 NHPM 38.9 3.8E+02 0.0082 26.1 11.0 114 17-171 10-127 (710)
35 PF05152 DUF705: Protein of un 37.4 48 0.001 29.9 4.0 37 135-171 125-164 (297)
36 PF00288 GHMP_kinases_N: GHMP 36.8 50 0.0011 22.0 3.2 29 18-47 21-49 (67)
37 cd02663 Peptidase_C19G A subfa 35.3 41 0.00089 29.0 3.2 32 116-147 240-276 (300)
38 PF01473 CW_binding_1: Putativ 34.8 41 0.00088 17.4 2.0 12 131-142 5-16 (19)
39 cd08324 CARD_NOD1_CARD4 Caspas 33.9 46 0.001 24.7 2.8 30 24-53 20-49 (85)
40 PF00443 UCH: Ubiquitin carbox 33.3 50 0.0011 26.4 3.3 34 115-148 213-252 (269)
41 cd02660 Peptidase_C19D A subfa 31.6 53 0.0011 28.3 3.3 34 115-148 275-313 (328)
42 PF04473 DUF553: Transglutamin 27.6 1.2E+02 0.0026 24.5 4.5 39 124-168 109-147 (153)
43 cd02672 Peptidase_C19P A subfa 27.1 59 0.0013 28.2 2.8 33 115-147 215-258 (268)
44 smart00460 TGc Transglutaminas 25.9 1.9E+02 0.0041 18.6 5.8 53 83-142 13-67 (68)
45 cd02665 Peptidase_C19I A subfa 25.2 96 0.0021 26.5 3.7 34 115-148 166-205 (228)
46 COG3012 Uncharacterized protei 25.2 61 0.0013 26.5 2.3 16 129-144 115-130 (151)
47 cd02421 Peptidase_C39_likeD A 24.2 2.8E+02 0.006 20.0 7.9 72 79-153 37-110 (124)
48 TIGR01670 YrbI-phosphatas 3-de 24.0 97 0.0021 24.1 3.3 21 157-177 36-56 (154)
49 cd02662 Peptidase_C19F A subfa 22.8 91 0.002 26.0 3.1 35 115-149 165-225 (240)
50 PF01624 MutS_I: MutS domain I 22.7 1.2E+02 0.0026 22.5 3.5 24 150-173 62-85 (113)
51 COG1105 FruK Fructose-1-phosph 22.6 1.2E+02 0.0027 27.4 4.0 43 135-180 100-144 (310)
52 cd00086 homeodomain Homeodomai 22.5 1.2E+02 0.0025 19.1 3.0 30 22-51 12-42 (59)
53 PF02902 Peptidase_C48: Ulp1 p 22.1 1.5E+02 0.0033 23.4 4.2 32 116-147 86-120 (216)
54 PF13443 HTH_26: Cro/C1-type H 21.4 1.3E+02 0.0028 19.4 3.0 30 20-49 22-53 (63)
55 TIGR01846 type_I_sec_HlyB type 20.9 6.3E+02 0.014 24.5 8.8 84 81-173 32-116 (694)
56 PRK03669 mannosyl-3-phosphogly 20.8 1.3E+02 0.0028 25.4 3.7 49 129-177 4-52 (271)
57 PF08645 PNK3P: Polynucleotide 20.5 1.3E+02 0.0029 23.9 3.5 21 153-173 33-53 (159)
No 1
>PF02099 Josephin: Josephin; InterPro: IPR006155 Human genes containing triplet repeats can markedly expand in length, leading to neuropsychiatric disease. Expansion of triplet repeats explains the phenomenon of anticipation, i.e. the increasing severity or earlier age of onset in successive generations in a pedigree []. A novel gene containing CAG repeats has been identified and mapped to chromosome 14q32.1, the genetic locus for Machado-Joseph disease (MJD). Normally, the gene contains 13-36 CAG repeats, but most clinically diagnosed patients and all affected members of a family with the clinical and pathological diagnosis of MJD show expansion of the repeat number, from 68-79 []. Similar abnormalities in related genes may give rise to diseases similar to MJD. MJD is a neurodegenerative disorder characterised by cerebellar ataxia, pyramidal and extra-pyramidal signs, peripheral nerve palsy, external ophtalmoplegia, facial and lingual fasciculation and bulging. The disease is autosomal dominant, with late onset of symptoms, generally after the fourth decade.; GO: 0008242 omega peptidase activity; PDB: 3O65_G 1YZB_A 2JRI_A 2DOS_A 2AGA_A.
Probab=100.00 E-value=5.1e-65 Score=411.51 Aligned_cols=157 Identities=48% Similarity=0.869 Sum_probs=141.7
Q ss_pred eccchhhHHHHHHhhhCCCCCCHHHHHHHHhhhCHHHHHHhhhCCCCCCCCCccccccccccCCCCCchHHHHHHHHhhC
Q 045385 14 VQESKLCAVHCVNTVLQGPFFSEFDLAALASDLDRSERQVMLEGRVPAASSGDFLTEESHNVSLDGDFSIQVLQKALEVW 93 (188)
Q Consensus 14 kQ~~~lCalHaLNnLlQ~~~ft~~dL~~Ia~~Ld~~er~~~~~~~~~~~~~~~~~~~~s~n~~~~GNydinVL~~AL~~~ 93 (188)
||+++|||+||||||||||+||+.||++||++||+.||..|.+ ++.++.+++.++|+||+++||||||||++||++|
T Consensus 1 kQ~~~lCalHaLNnLlQ~~~ft~~dL~~Ia~~Ld~~E~~~~~~---~~~~~~~~~~~~s~n~~~~GnysinVL~~AL~~~ 77 (157)
T PF02099_consen 1 KQELQLCALHALNNLLQGPYFTAVDLDEIAQELDEEERSLMAE---DSWTPLSFLFNPSRNVDGTGNYSINVLMAALQVW 77 (157)
T ss_dssp S-STTSHHHHHHHHHCTSS-S-HHHHHHHHHHHHHHHHHHHHC---TSHHHHHHHTSTSSTCSTTSTCECHHHHHHHHCC
T ss_pred CcHHHHHHHHHHHHHhhhhhcCHHHHHHHHHHhChhhhhhhhc---cCccchhhccccccCccccCCcCHHHHHHHHHHc
Confidence 8999999999999999999999999999999999999999987 4556777888899999999999999999999999
Q ss_pred CceeEEcCCCCCCCCCCCcccceeeeeccCCceEEEEeeCCEEEEeeCCCCCceEcchhhHHHHHHHHHhCCeEEEEEEC
Q 045385 94 DLQVIPLNCPIAEPAQIDPELENAFICHLHDHWFCIRKVNGEWYNFDSLYAAPEHLSKFYLSAYLDSLKGFGWSIFIVRG 173 (188)
Q Consensus 94 ~~~~~~~d~~~~~~~~~~~~~~~gFI~N~~rHWfaIRki~g~wyNLDS~l~~P~~i~~~~L~~~L~~l~~~g~sIFvV~g 173 (188)
|++++||..++.....++|+.+.|||||.+|||||||||+|+||||||++++|+.|+++||.+||++++++||+||||+|
T Consensus 78 g~~~~~~~~~~~~~~~~~~~~~~gfI~N~~~HWf~iRki~~~wyNLDS~l~~P~~i~~~~l~~fL~~l~~~g~~ifvV~~ 157 (157)
T PF02099_consen 78 GLELVPWFDKRMQEASIDPDNEFGFICNLSRHWFAIRKIGGQWYNLDSKLKEPELISDFYLSAFLQQLQSEGYSIFVVRG 157 (157)
T ss_dssp T-EEEETTSHHHHHCC--CCCSSEEEEECTTEEEEEEEETTEEEEECTTTSS-EEE-HHHHHHHHHHHHCCTEEEEEEES
T ss_pred CceEEEccCccchhhhcCchhceEEEeccCcceEEEEeeCCeeEeccCCCCCCcccCHHHHHHHHHHHHhCCcEEEEEeC
Confidence 99999887777788889999999999999999999999999999999999999999999999999999999999999986
No 2
>KOG2935 consensus Ataxin 3/Josephin [General function prediction only]
Probab=100.00 E-value=4.7e-62 Score=416.81 Aligned_cols=164 Identities=59% Similarity=1.007 Sum_probs=161.0
Q ss_pred CCceeeeccchhhHHHHHHhhhCCCCCCHHHHHHHHhhhCHHHHHHhhhCCCCCCCCCccccccccccCCCCCchHHHHH
Q 045385 8 GMLYHEVQESKLCAVHCVNTVLQGPFFSEFDLAALASDLDRSERQVMLEGRVPAASSGDFLTEESHNVSLDGDFSIQVLQ 87 (188)
Q Consensus 8 ~~iYhEkQ~~~lCalHaLNnLlQ~~~ft~~dL~~Ia~~Ld~~er~~~~~~~~~~~~~~~~~~~~s~n~~~~GNydinVL~ 87 (188)
+.||||+|+..|||+||||+||||++|++.||+ |..||..|++|++.+..|.+|++++|+||+++|+||||||.
T Consensus 2 ~~ifhE~QE~~LCAqHclN~lLQg~~fs~~dLa------D~~erm~m~Eg~v~g~~~~~fl~~~SeNm~~sG~FSIQVl~ 75 (315)
T KOG2935|consen 2 GSIFHEVQESNLCAQHCLNTLLQGPFFSEFDLA------DGKERMRMAEGGVTGEFYGDFLQQPSENMDDSGFFSIQVLS 75 (315)
T ss_pred CchhhhhhhhhHHHHHHHHHHhcccccChhhhh------hHHHHHHHHhcccccccccccccCCCcCcCccCceeHHHHH
Confidence 479999999999999999999999999999999 88899999999999999999999999999999999999999
Q ss_pred HHHhhCCceeEEcCCCCCCCCCCCcccceeeeeccCCceEEEEeeCCEEEEeeCCCCCceEcchhhHHHHHHHHHhCCeE
Q 045385 88 KALEVWDLQVIPLNCPIAEPAQIDPELENAFICHLHDHWFCIRKVNGEWYNFDSLYAAPEHLSKFYLSAYLDSLKGFGWS 167 (188)
Q Consensus 88 ~AL~~~~~~~~~~d~~~~~~~~~~~~~~~gFI~N~~rHWfaIRki~g~wyNLDS~l~~P~~i~~~~L~~~L~~l~~~g~s 167 (188)
+||++||++++++++|++.++.+||.++++||||+++|||+|||+|++||||||.+.+|+.|+++||++||+||+++|||
T Consensus 76 kALe~w~Leli~~nnP~~~~~~idP~~erafICnl~eHWF~iRKfg~qWfnlnSllagPellSdtyls~FL~qlq~egyS 155 (315)
T KOG2935|consen 76 KALEVWGLELIPFNNPEYQPLQIDPINERAFICNLKEHWFTIRKFGKQWFNLNSLLAGPELLSDTYLSAFLAQLQQEGYS 155 (315)
T ss_pred HHHHhhceeeeecCChhhhhccCCcchhhhhhhcchhhhhhHhhhcchhccchhhhcchHHHHHHHHHHHHHHHHhCCee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEECCCCC
Q 045385 168 IFIVRGNFPK 177 (188)
Q Consensus 168 IFvV~g~lp~ 177 (188)
||||.|+||+
T Consensus 156 IFVVkG~lP~ 165 (315)
T KOG2935|consen 156 IFVVKGDLPD 165 (315)
T ss_pred EEEEecCCCC
Confidence 9999999995
No 3
>KOG2934 consensus Uncharacterized conserved protein, contains Josephin domain [General function prediction only]
Probab=100.00 E-value=2.6e-42 Score=281.68 Aligned_cols=148 Identities=26% Similarity=0.429 Sum_probs=132.4
Q ss_pred CCCceeeeccchhhHHHHHHhhhCCC-CCCHHHHHHHHhhhCHHHHHHhhhCCCCCCCCCccccccccc-cCCCCCchHH
Q 045385 7 GGMLYHEVQESKLCAVHCVNTVLQGP-FFSEFDLAALASDLDRSERQVMLEGRVPAASSGDFLTEESHN-VSLDGDFSIQ 84 (188)
Q Consensus 7 ~~~iYhEkQ~~~lCalHaLNnLlQ~~-~ft~~dL~~Ia~~Ld~~er~~~~~~~~~~~~~~~~~~~~s~n-~~~~GNydin 84 (188)
...||||||++.+||+|||||+||++ .||+..+++||..|.+.. |.+ ||+ +...||||+|
T Consensus 23 p~~iYherq~r~lc~lhAlnnv~q~~n~ftr~~~~d~c~~l~p~s---~~~---------------Phrs~~g~Gnydvn 84 (204)
T KOG2934|consen 23 PPGIYHERQRRELCALHALNNVFQRSNAFTRPVLDDICTRLKPRS---WLN---------------PHRSWKGPGNYDVN 84 (204)
T ss_pred CCccchhHHHHHHHHHHHhhhhhhccccccchhhHHHHhhcCccc---ccC---------------ccccccCCCcccHH
Confidence 34699999999999999999999997 999999999999999985 444 454 4568999999
Q ss_pred HHHHHHhhCCceeEEcCCCCCCCCCCCcccceeeeecc--------------CCceEEEEeeCCEEEEeeCCCCCceEcc
Q 045385 85 VLQKALEVWDLQVIPLNCPIAEPAQIDPELENAFICHL--------------HDHWFCIRKVNGEWYNFDSLYAAPEHLS 150 (188)
Q Consensus 85 VL~~AL~~~~~~~~~~d~~~~~~~~~~~~~~~gFI~N~--------------~rHWfaIRki~g~wyNLDS~l~~P~~i~ 150 (188)
|||+|||..|++++|||+|. ....+....+.|||.|+ +|||+|+|+.+|.|||||||+.+|++|+
T Consensus 85 vimaalq~~gl~avw~dRrr-d~~~l~L~~v~gfIlnlp~~~slG~L~Lp~~rrhw~alR~~~g~yynldsklr~P~~ig 163 (204)
T KOG2934|consen 85 VIMAALQQCGLEAVWLDRRR-DVTALALSVVFGFILNLPCKFSLGYLRLPVMRRHWLALRSPPGKYYNLDSKLREPECIG 163 (204)
T ss_pred HHHHHHHhcCceeeeccccC-CcchhhhHHHHHHHHcCCchhccccccchhHHhhhHhhhCCCCceecccccccCCcccc
Confidence 99999999999999999987 56778888999999996 8999999999999999999999999999
Q ss_pred h-hhHHHHHH-HHHhCCeEEEEEEC
Q 045385 151 K-FYLSAYLD-SLKGFGWSIFIVRG 173 (188)
Q Consensus 151 ~-~~L~~~L~-~l~~~g~sIFvV~g 173 (188)
+ ..+.+||+ ++...-+++|+|..
T Consensus 164 ~e~~~~~fla~hl~~~~~el~lvi~ 188 (204)
T KOG2934|consen 164 TENDFREFLATHLSMAIEELILVIN 188 (204)
T ss_pred cchhHHHHHHHHHHhhhhhheeeec
Confidence 7 68999998 56666699988853
No 4
>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=91.96 E-value=1.6 Score=32.92 Aligned_cols=102 Identities=11% Similarity=0.198 Sum_probs=64.3
Q ss_pred chhhHHHHHHhhhCC---CCCCHHHHHHHHhhhCHHHHHHhhhCCCCCCCCCccccccccccCCCCCchHHHHHHHHhhC
Q 045385 17 SKLCAVHCVNTVLQG---PFFSEFDLAALASDLDRSERQVMLEGRVPAASSGDFLTEESHNVSLDGDFSIQVLQKALEVW 93 (188)
Q Consensus 17 ~~lCalHaLNnLlQ~---~~ft~~dL~~Ia~~Ld~~er~~~~~~~~~~~~~~~~~~~~s~n~~~~GNydinVL~~AL~~~ 93 (188)
..-||+.||=.+++- ...+..+|... +. ....| +|+.-|.++++..
T Consensus 9 ~~dcgla~l~~i~~~~~g~~~~~~~l~~~---~~---------------------------~~~~g-~s~~~l~~~a~~~ 57 (129)
T cd02424 9 LNDCGIAVIQMLYNHYYKKKYDLNELKIK---AN---------------------------LKKNG-LSIYDLENLAKKF 57 (129)
T ss_pred ccchHHHHHHHHHHHhcCCCccHHHHHHH---hC---------------------------CCCCC-ccHHHHHHHHHHc
Confidence 457999999988854 34555555431 11 01235 8899999999999
Q ss_pred CceeEEcCCCCCCCCCCCcccceeeeec--cCCceEEEEee-CCEEEEeeCCCCCceEcchh
Q 045385 94 DLQVIPLNCPIAEPAQIDPELENAFICH--LHDHWFCIRKV-NGEWYNFDSLYAAPEHLSKF 152 (188)
Q Consensus 94 ~~~~~~~d~~~~~~~~~~~~~~~gFI~N--~~rHWfaIRki-~g~wyNLDS~l~~P~~i~~~ 152 (188)
|+++.-+..+......+ +. ..-.|++ -..||+-++++ ++.++-.|. -.+|+.++..
T Consensus 58 Gl~~k~~~~~~~~l~~~-~~-p~P~i~~~~~~~hfvVl~~~~~~~v~I~DP-~~g~~~~s~~ 116 (129)
T cd02424 58 GLETESYQGSFLEFLEL-KN-KFIILLKSNGLNHFVIVKKIKKNKFIVLDP-KKGKYKITYK 116 (129)
T ss_pred CCceeEEEcCHHHHhhc-cC-CEEEEEecCCCCeEEEEEEEECCEEEEECC-CCCCEEeCHH
Confidence 99876654322111111 01 2233443 23699999999 668889999 6788888753
No 5
>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=87.80 E-value=2.6 Score=31.09 Aligned_cols=101 Identities=15% Similarity=0.154 Sum_probs=63.3
Q ss_pred chhhHHHHHHhhhCC--CCCCHHHHHHHHhhhCHHHHHHhhhCCCCCCCCCccccccccccCCCCCchHHHHHHHHhhCC
Q 045385 17 SKLCAVHCVNTVLQG--PFFSEFDLAALASDLDRSERQVMLEGRVPAASSGDFLTEESHNVSLDGDFSIQVLQKALEVWD 94 (188)
Q Consensus 17 ~~lCalHaLNnLlQ~--~~ft~~dL~~Ia~~Ld~~er~~~~~~~~~~~~~~~~~~~~s~n~~~~GNydinVL~~AL~~~~ 94 (188)
..-|++.||=.+++- -..|..+|... +. ....| +++..|.+|++..|
T Consensus 9 ~~~~gl~~l~~i~~~~g~~~~~~~l~~~---~~---------------------------~~~~~-~~~~~l~~~a~~~G 57 (125)
T cd02420 9 ATECGAASLAIILAYYGRYVPLSELRIA---CG---------------------------VSRDG-SNASNLLKAAREYG 57 (125)
T ss_pred ccCHHHHHHHHHHHHcCCCCCHHHHHHH---cC---------------------------CCCCC-CCHHHHHHHHHHcC
Confidence 357999999988875 35666666431 10 01134 68889999999999
Q ss_pred ceeEEcCCCCCCCCCCCcccceeeeeccCCceEEEEeeC-CEEEEeeCCCCCceEcchh
Q 045385 95 LQVIPLNCPIAEPAQIDPELENAFICHLHDHWFCIRKVN-GEWYNFDSLYAAPEHLSKF 152 (188)
Q Consensus 95 ~~~~~~d~~~~~~~~~~~~~~~gFI~N~~rHWfaIRki~-g~wyNLDS~l~~P~~i~~~ 152 (188)
+++.-...+-. .++....=..+.....||+-|-+++ +.++..|... +|+.++..
T Consensus 58 l~~~~~~~~~~---~L~~~~lP~I~~~~~g~~~Vl~~~~~~~~~i~dp~~-~~~~~s~~ 112 (125)
T cd02420 58 LTAKGYKKDLE---ALREVSLPAIVFWNFNHFLVVEGFDKRKVFLNDPAT-GRRTVSLE 112 (125)
T ss_pred cccceEecCHH---HHhcCCCCEEEEeCCCEEEEEEEEeCCEEEEECCCc-CceeecHH
Confidence 87654433211 1111111122233467999999985 5788889864 78888754
No 6
>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=87.25 E-value=5.3 Score=29.84 Aligned_cols=125 Identities=18% Similarity=0.092 Sum_probs=73.6
Q ss_pred ccchhhHHHHHHhhhCCC--CCCHHHHHHHHhhhCHHHHHHhhhCCCCCCCCCccccccccccCCCCCchHHHHHHH-Hh
Q 045385 15 QESKLCAVHCVNTVLQGP--FFSEFDLAALASDLDRSERQVMLEGRVPAASSGDFLTEESHNVSLDGDFSIQVLQKA-LE 91 (188)
Q Consensus 15 Q~~~lCalHaLNnLlQ~~--~ft~~dL~~Ia~~Ld~~er~~~~~~~~~~~~~~~~~~~~s~n~~~~GNydinVL~~A-L~ 91 (188)
|...-|+..||-.+++.- ..+..++... ... ........| .+..-|..+ ++
T Consensus 2 ~~~~~C~~~slamvl~~~g~~~~~~~l~~~------------~~~-------------~~~~~~~~g-~~~~~l~~~~a~ 55 (141)
T cd02549 2 QLENGCGPTSLAMVLSYLGVKVTKPQLAAE------------GNT-------------YDFAKDGYG-TYPKPIVSAAAR 55 (141)
T ss_pred CCCCccHHHHHHHHHHhcCCCCCHHHHHhh------------ccc-------------cccCCCCCC-cCHHHHHHHHHh
Confidence 566789999999999863 3344444321 000 011122346 556667777 99
Q ss_pred hCCceeEEcCCCCCCCCCCCcccceeeeecc--------CCceEEEEeeC--CEEEEeeCCCCCceEcchhhHHHHHHHH
Q 045385 92 VWDLQVIPLNCPIAEPAQIDPELENAFICHL--------HDHWFCIRKVN--GEWYNFDSLYAAPEHLSKFYLSAYLDSL 161 (188)
Q Consensus 92 ~~~~~~~~~d~~~~~~~~~~~~~~~gFI~N~--------~rHWfaIRki~--g~wyNLDS~l~~P~~i~~~~L~~~L~~l 161 (188)
.+|+++..+.....-... .+.-.-+|+.+ ..||+.|..++ +..+-.|.....|..++. ..|.+..
T Consensus 56 ~~G~~~~~~~~~~~~~~~--l~~~~Pvi~~~~~~~~~~~~gH~vVv~g~~~~~~~~i~DP~~~~~~~~~~---~~f~~~w 130 (141)
T cd02549 56 KYGLVVRPLTGLLALLRQ--LAAGHPVIVSVNLGVSITPSGHAMVVIGYDRKGNVYVNDPGGGRRLVVSF---DEFEKAW 130 (141)
T ss_pred hCCCcEEECCCHHHHHHH--HHCCCeEEEEEecCcccCCCCeEEEEEEEcCCCCEEEECCCCCcCEEEeH---HHHHHHH
Confidence 999988876543210011 11223445543 56999999987 567788887667777774 3455555
Q ss_pred HhCCeEEEE
Q 045385 162 KGFGWSIFI 170 (188)
Q Consensus 162 ~~~g~sIFv 170 (188)
...|+-.++
T Consensus 131 ~~~~~~~~~ 139 (141)
T cd02549 131 KRMGGQAVV 139 (141)
T ss_pred HHcCCceEE
Confidence 566644443
No 7
>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=86.20 E-value=5 Score=29.57 Aligned_cols=82 Identities=12% Similarity=0.079 Sum_probs=50.2
Q ss_pred chHHHHHHHHhhCCceeEEcCCCCCCCCCCCcccceeeeeccCCceEEEEeeCC-EEEEeeCCCCCceEcchhhHHHHHH
Q 045385 81 FSIQVLQKALEVWDLQVIPLNCPIAEPAQIDPELENAFICHLHDHWFCIRKVNG-EWYNFDSLYAAPEHLSKFYLSAYLD 159 (188)
Q Consensus 81 ydinVL~~AL~~~~~~~~~~d~~~~~~~~~~~~~~~gFI~N~~rHWfaIRki~g-~wyNLDS~l~~P~~i~~~~L~~~L~ 159 (188)
++...|..+++..|+++.-...+-. .+.....=.++.....||+.|-++++ .+...|+.. +|+.++..+ |.+
T Consensus 44 ~~~~~l~~~a~~~Gl~~~~~~~~~~---~l~~~~lP~i~~~~~g~~~Vl~~~~~~~~~i~dp~~-~~~~~~~~e---l~~ 116 (127)
T cd02419 44 ATLADLIDIAQQLGLSTRALRLDLE---ELGQLKLPCILHWDMNHFVVLKKVSRRRIVIHDPAL-GKRKLSLEE---ASR 116 (127)
T ss_pred cCHHHHHHHHHHCCCceeEEEccHH---HHhhCCCCEEEEECCCEEEEEEEEcCCEEEEECCcc-CCEEEcHHH---HHh
Confidence 8999999999999987765443211 11111112333345579999999865 566668754 688887533 323
Q ss_pred HHHhCCeEEEEE
Q 045385 160 SLKGFGWSIFIV 171 (188)
Q Consensus 160 ~l~~~g~sIFvV 171 (188)
.. .|+.+++.
T Consensus 117 ~~--~g~~i~~~ 126 (127)
T cd02419 117 HF--TGVALELW 126 (127)
T ss_pred hC--CcEEEEEe
Confidence 22 35655543
No 8
>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=84.52 E-value=4 Score=30.35 Aligned_cols=120 Identities=21% Similarity=0.279 Sum_probs=68.2
Q ss_pred ecc-chhhHHHHHHhhhCCCCCCHHHHHHHHhhhCHHHHHHhhhCCCCCCCCCccccccccccCCCCCchHHHHHHHHhh
Q 045385 14 VQE-SKLCAVHCVNTVLQGPFFSEFDLAALASDLDRSERQVMLEGRVPAASSGDFLTEESHNVSLDGDFSIQVLQKALEV 92 (188)
Q Consensus 14 kQ~-~~lCalHaLNnLlQ~~~ft~~dL~~Ia~~Ld~~er~~~~~~~~~~~~~~~~~~~~s~n~~~~GNydinVL~~AL~~ 92 (188)
+|. ..=||+=||=.+++. +--+.+.++|.+.+...+ +-++..-|..+++.
T Consensus 6 ~Q~~~~dcg~acl~~l~~~-~g~~~s~~~l~~~~~~~~----------------------------~g~s~~~L~~~~~~ 56 (131)
T PF03412_consen 6 KQSDSNDCGLACLAMLLKY-YGIPVSEEELRRQLGTSE----------------------------EGTSLADLKRAARK 56 (131)
T ss_dssp --SSTT-HHHHHHHHHHHH-TT----HHHHHCCTT-BT----------------------------TB--CCCHHHHHHH
T ss_pred EeCCCCCHHHHHHHHHHHH-hCCCchHHHHHHHhcCCc----------------------------cCCCHHHHHHHHHh
Confidence 455 467999999888887 223444444444442111 11334458889999
Q ss_pred CCceeEEcCCCCCCCCCCCcccceeeeec-cCCceEEEEeeCC-EEEEeeCCCCCceEcchhhHHHHHHHHHhCCeEEEE
Q 045385 93 WDLQVIPLNCPIAEPAQIDPELENAFICH-LHDHWFCIRKVNG-EWYNFDSLYAAPEHLSKFYLSAYLDSLKGFGWSIFI 170 (188)
Q Consensus 93 ~~~~~~~~d~~~~~~~~~~~~~~~gFI~N-~~rHWfaIRki~g-~wyNLDS~l~~P~~i~~~~L~~~L~~l~~~g~sIFv 170 (188)
.|++...+...... + .+...-+|+. ...||+-|-++++ ..+-.|. ..+++.++.. +|.+.. .|+-|++
T Consensus 57 ~gl~~~~~~~~~~~---l-~~~~~P~I~~~~~~h~vVi~~~~~~~~~i~dP-~~g~~~~~~~---~f~~~w--~G~~l~~ 126 (131)
T PF03412_consen 57 YGLKAKAVKLNFEK---L-KRLPLPAIAHLKDGHFVVIYKIDDGRVLIYDP-KKGKIKLSKE---EFEEIW--TGEVLLI 126 (131)
T ss_dssp TTEEEEEEE--GGG---C-TCGGSSEEEEECCCEEEEEEEECCCEEEECCT-TTCEEEEEHH---HHHHHE--EEEEEEE
T ss_pred cccceeeeecchhh---h-hhccccEEEEecCcceEEEEeEcCcEEEEEeC-CCCeEEEeHH---HHHhhC--CCEEEEE
Confidence 99988776543321 1 2233455555 5679999999964 6778888 6788888743 344433 3566555
Q ss_pred EE
Q 045385 171 VR 172 (188)
Q Consensus 171 V~ 172 (188)
-.
T Consensus 127 ~~ 128 (131)
T PF03412_consen 127 KP 128 (131)
T ss_dssp EE
T ss_pred Ee
Confidence 43
No 9
>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=82.52 E-value=9.8 Score=28.19 Aligned_cols=105 Identities=17% Similarity=0.206 Sum_probs=62.6
Q ss_pred ecc-chhhHHHHHHhhhCC--CCCCHHHHHHHHhhhCHHHHHHhhhCCCCCCCCCccccccccccCCCCCchHHHHHHHH
Q 045385 14 VQE-SKLCAVHCVNTVLQG--PFFSEFDLAALASDLDRSERQVMLEGRVPAASSGDFLTEESHNVSLDGDFSIQVLQKAL 90 (188)
Q Consensus 14 kQ~-~~lCalHaLNnLlQ~--~~ft~~dL~~Ia~~Ld~~er~~~~~~~~~~~~~~~~~~~~s~n~~~~GNydinVL~~AL 90 (188)
+|. ..-|++.||=.+++. ..++..++.. .+. .+ ..| ++...|..++
T Consensus 5 ~q~~~~~~gl~~l~~~~~~~g~~~~~~~l~~---~~~------------------------~~---~~~-~~~~~l~~~a 53 (136)
T cd02418 5 LQVDEMDCGAACLAMIAKYYGKNYSLAKLRE---LAG------------------------TD---REG-TSLLGLVKAA 53 (136)
T ss_pred EecCcccHHHHHHHHHHHHhCCCCCHHHHHH---HcC------------------------CC---CCC-cCHHHHHHHH
Confidence 554 356999999888875 3456555432 110 00 123 7888999999
Q ss_pred hhCCceeEEcCCCCCCCCCCCcccceeeee-----ccCCceEEEEeeCCE-EEEeeCCCCCceEcchh
Q 045385 91 EVWDLQVIPLNCPIAEPAQIDPELENAFIC-----HLHDHWFCIRKVNGE-WYNFDSLYAAPEHLSKF 152 (188)
Q Consensus 91 ~~~~~~~~~~d~~~~~~~~~~~~~~~gFI~-----N~~rHWfaIRki~g~-wyNLDS~l~~P~~i~~~ 152 (188)
+..|+++.-...+... ..+.. ...-+|+ ....||+.|-++++. -+..|. ...|+.++..
T Consensus 54 ~~~Gl~~~~~~~~~~~-~~l~~-~~~P~I~~~~~~~~~~~~~Vl~~~~~~~~~i~dp-~~~~~~~~~~ 118 (136)
T cd02418 54 EKLGFETRAVKADMDL-FELKD-IPLPFIAHVIKEWKLNHYVVVYKIKKKKILIADP-AVGITKISKE 118 (136)
T ss_pred HHCCCeeEEEEcccch-hhHhc-CCCCEEEEEccCCCCCeEEEEEEEcCCEEEEECC-CCCCEEeeHH
Confidence 9999887654432210 01111 1122333 345799999999764 455677 6678888743
No 10
>PF01088 Peptidase_C12: Ubiquitin carboxyl-terminal hydrolase, family 1; InterPro: IPR001578 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 MEROPS peptidase family C12 (ubiquitin C-terminal hydrolase family, clan CA). Families within the CA clan are loosely termed papain-like as protein fold of the peptidase unit resembles that of papain, the type example for clan CA. The type example is the human ubiquitin C-terminal hydrolase UCH-L1. Ubiquitin is highly conserved, commonly found conjugated to proteins in eukaryotic cells, where it may act as a marker for rapid degradation, or it may have a chaperone function in protein assembly []. The ubiquitin is released by cleavage from the bound protein by a protease []. A number of deubiquitinising proteases are known: all are activated by thiol compounds [, ], and inhibited by thiol-blocking agents and ubiquitin aldehyde [, ], and as such have the properties of cysteine proteases []. The deubiquitinsing proteases can be split into 2 size ranges (20-30 kDa and 100-200 kDa, IPR001394 from INTERPRO) []: this family are the 20-30 kDa ppeptides which includes the yeast yuh1. Yeast yuh1 protease is known to be active only against small ubiquitin conjugates, being inactive against conjugated beta-galactosidase []. A mammalian homologue, UCH (ubiquitin conjugate hydrolase), is one of the most abundant proteins in the brain []. Only one conserved cysteine can be identified, along with two conserved histidines. The spacing between the cysteine and the second histidine is thought to be more representative of the cysteine/histidine spacing of a cysteine protease catalytic dyad [].; GO: 0004221 ubiquitin thiolesterase activity, 0006511 ubiquitin-dependent protein catabolic process, 0005622 intracellular; PDB: 1CMX_A 4DM9_A 2ETL_A 3IRT_A 3KW5_A 3IFW_A 2LEN_A 3KVF_A 2WDT_C 2WE6_B ....
Probab=82.15 E-value=2.9 Score=35.33 Aligned_cols=110 Identities=17% Similarity=0.222 Sum_probs=63.7
Q ss_pred CCCCCceeeecc-chhhH----HHHHHhhhCCCCC----CHHHHHHHHhhhCHHHHHHhhhCCCCCCCCCcccccccccc
Q 045385 5 SNGGMLYHEVQE-SKLCA----VHCVNTVLQGPFF----SEFDLAALASDLDRSERQVMLEGRVPAASSGDFLTEESHNV 75 (188)
Q Consensus 5 s~~~~iYhEkQ~-~~lCa----lHaLNnLlQ~~~f----t~~dL~~Ia~~Ld~~er~~~~~~~~~~~~~~~~~~~~s~n~ 75 (188)
..+..|||=||. .--|| +|||-|.-..-.. .-..|-+-+..+++.+|...++.. +.+. .-||.
T Consensus 75 ~~~~~v~f~kQti~NACgt~AlLh~l~N~~~~~~i~~gs~L~~f~~~t~~~~p~~Rg~~l~~~-------~~l~-~aH~s 146 (214)
T PF01088_consen 75 DIPENVFFAKQTIGNACGTIALLHALLNNPDRIEIEPGSILDQFKEFTKDLSPEERGKALENS-------KELR-KAHNS 146 (214)
T ss_dssp TCGTTS-EES-SSBTGHHHHHHHHHHHTCCCTTCBBTTSHHHHHHHHHTTSTHHHHHHHHHTH-------HHHH-HHHHH
T ss_pred CCCCCceEeeecCCchhhHHHHHHHHhcccccccccCCchHHHHHHHHhcCCHHHHHHHHhCc-------HHHH-HHHHH
Confidence 345679999999 57887 5666664321112 356677778899999998876531 1111 11221
Q ss_pred CCCCCchHHHHHHHHhhCCceeEEcCCCCCCCCCCCcccceeeeeccCCceEEEEeeCCEEEEeeCCCCCceEcch
Q 045385 76 SLDGDFSIQVLQKALEVWDLQVIPLNCPIAEPAQIDPELENAFICHLHDHWFCIRKVNGEWYNFDSLYAAPEHLSK 151 (188)
Q Consensus 76 ~~~GNydinVL~~AL~~~~~~~~~~d~~~~~~~~~~~~~~~gFI~N~~rHWfaIRki~g~wyNLDS~l~~P~~i~~ 151 (188)
.-..| +... ..... +.. ..-|.+|.-+++|.=|-||..++.|+..|.
T Consensus 147 --------------~A~~g------~t~~-~~~~~--~~~------~~~HFI~fV~~~G~LyELDG~k~~Pi~~G~ 193 (214)
T PF01088_consen 147 --------------FARQG------QTEA-PDDEA--DDE------VDFHFIAFVPVDGHLYELDGRKSGPIDHGP 193 (214)
T ss_dssp --------------HHCHC------SSTS--H--T--TSC------GCEEEEEEEEETTEEEEEETTSSS-EEEEE
T ss_pred --------------HhccC------CcCC-Ccccc--CCC------CCccEEEEEeECCeEEEcCCCCCCCeEcCc
Confidence 11111 1111 00000 111 235999999999999999999999999985
No 11
>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=80.86 E-value=15 Score=26.44 Aligned_cols=69 Identities=17% Similarity=0.176 Sum_probs=47.2
Q ss_pred chHHHHHHHHhhCCceeEEcCCCCCCCCCCCcccceeeeeccCCceEEEEeeCC-EEEEeeCCCCCceEcchh
Q 045385 81 FSIQVLQKALEVWDLQVIPLNCPIAEPAQIDPELENAFICHLHDHWFCIRKVNG-EWYNFDSLYAAPEHLSKF 152 (188)
Q Consensus 81 ydinVL~~AL~~~~~~~~~~d~~~~~~~~~~~~~~~gFI~N~~rHWfaIRki~g-~wyNLDS~l~~P~~i~~~ 152 (188)
++...|..+.+..|+++.-...+.. .+.....=+++.....||+.|-++++ .....|..-..|+.++..
T Consensus 39 ~~~~~l~~~a~~~gl~~~~~~~~~~---~l~~~~~P~i~~~~~~~~~Vl~~~~~~~~~i~dp~~~~~~~~~~~ 108 (122)
T cd02259 39 LSLADLVSLANKLGLTAQGVKLPLA---ALSRLQLPALLLWKQGHFVILYGADKGQVLIADPLEEGPVTLSES 108 (122)
T ss_pred CCHHHHHHHHHHcCCeeeEEEcCHH---HhccCCCCEEEEcCCCcEEEEEEEcCCEEEEECCcccCCEEeCHH
Confidence 7888999999999998876543321 12222222444467889999999965 666667756788888754
No 12
>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=78.79 E-value=18 Score=26.35 Aligned_cols=100 Identities=17% Similarity=0.227 Sum_probs=60.0
Q ss_pred hhhHHHHHHhhhCC--CCCCHHHHHHHHhhhCHHHHHHhhhCCCCCCCCCccccccccccCCCCCchHHHHHHHHhhCCc
Q 045385 18 KLCAVHCVNTVLQG--PFFSEFDLAALASDLDRSERQVMLEGRVPAASSGDFLTEESHNVSLDGDFSIQVLQKALEVWDL 95 (188)
Q Consensus 18 ~lCalHaLNnLlQ~--~~ft~~dL~~Ia~~Ld~~er~~~~~~~~~~~~~~~~~~~~s~n~~~~GNydinVL~~AL~~~~~ 95 (188)
.-|++.||-.+++. -.++..++... +. . ...| ++...|.++++..|+
T Consensus 10 ~~~~l~~l~~~~~~~~~~~~~~~l~~~---~~------------------------~---~~~~-~~~~~l~~~a~~~gl 58 (126)
T cd02425 10 TECGLACYAMILNYFGYKVSLNELREK---YE------------------------L---GRDG-LSLSYLKQLLEEYGF 58 (126)
T ss_pred ccHHHHHHHHHHHHhCCCCCHHHHHHh---cc------------------------C---CCCC-cCHHHHHHHHHHCCC
Confidence 46999999888875 34666655431 10 0 0123 788899999999998
Q ss_pred eeEEcCCCCCCCCCCCcccceeeeecc-CCceEEEEeeCC-EEEEeeCCCCCceEcchh
Q 045385 96 QVIPLNCPIAEPAQIDPELENAFICHL-HDHWFCIRKVNG-EWYNFDSLYAAPEHLSKF 152 (188)
Q Consensus 96 ~~~~~d~~~~~~~~~~~~~~~gFI~N~-~rHWfaIRki~g-~wyNLDS~l~~P~~i~~~ 152 (188)
++.-...+.. ..++... .-+|+-. ..||+.|-++++ .++..|+.. .++.++..
T Consensus 59 ~~~~~~~~~~--~~l~~~~-lP~I~~~~~~~~~Vl~~~~~~~~~i~dp~~-~~~~~~~~ 113 (126)
T cd02425 59 KCKVYKISFK--KNLYPLK-LPVIIFWNNNHFVVLEKIKKNKVTIVDPAI-GRIKISID 113 (126)
T ss_pred cceEEEEchH--HHHhhCC-CCEEEEEcCCcEEEEEEEECCEEEEEcCCC-CCEEECHH
Confidence 7654332210 1122111 2334333 469999988754 677888865 56677743
No 13
>COG2274 SunT ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]
Probab=76.07 E-value=25 Score=35.03 Aligned_cols=117 Identities=16% Similarity=0.208 Sum_probs=78.9
Q ss_pred chhhHHHHHHhhhCC--CCCCHHHHHHHHhhhCHHHHHHhhhCCCCCCCCCccccccccccCCCCCchHHHHHHHHhhCC
Q 045385 17 SKLCAVHCVNTVLQG--PFFSEFDLAALASDLDRSERQVMLEGRVPAASSGDFLTEESHNVSLDGDFSIQVLQKALEVWD 94 (188)
Q Consensus 17 ~~lCalHaLNnLlQ~--~~ft~~dL~~Ia~~Ld~~er~~~~~~~~~~~~~~~~~~~~s~n~~~~GNydinVL~~AL~~~~ 94 (188)
..=|++.||..+.+. ..++..++.+.+. . + .+-.+..-|..+-+..|
T Consensus 10 ~~dcgla~l~mia~~~g~~~~~~~lr~~~~-----------~---------------~-----~~g~sl~~l~~~a~~lG 58 (709)
T COG2274 10 ANDCGLACLAMIANYHGKKISLNELRELVG-----------L---------------S-----RNGLSLLELKQAAEKLG 58 (709)
T ss_pred ccchHHHHHHHHHHHhCCCCCHHHHHHHcC-----------C---------------C-----CCCCChHHHHHHHHHcC
Confidence 567999999999985 4677766654311 0 1 12367778899999999
Q ss_pred ceeEEcCCCCCCCCCCCcccceeeeeccCCceEEEEeeCCE-EEEeeCCCCCceEcchhhHHHHHHHHHhCCeEEEEEEC
Q 045385 95 LQVIPLNCPIAEPAQIDPELENAFICHLHDHWFCIRKVNGE-WYNFDSLYAAPEHLSKFYLSAYLDSLKGFGWSIFIVRG 173 (188)
Q Consensus 95 ~~~~~~d~~~~~~~~~~~~~~~gFI~N~~rHWfaIRki~g~-wyNLDS~l~~P~~i~~~~L~~~L~~l~~~g~sIFvV~g 173 (188)
++...+.-+. ..+.....-+++..-..||+.+-++++. |+-+|- -.+|+.++.. +|.+... |+.+++...
T Consensus 59 l~~~~~~~~~---~~l~~~~lP~ii~~~~~h~vVl~~~~~~~~~v~dp-~~g~~~l~~~---e~~~~~t--g~~l~l~~~ 129 (709)
T COG2274 59 LSARAVKLSL---EELKQLPLPAIIHWNGNHFVVLYKIDKNKVVVLDP-AKGIRRLSLE---EFEKLWT--GIALLLAPT 129 (709)
T ss_pred CccccccCCH---HHhcccCCCEEEEEcCCcEEEEEEecCCeEEEEeC-CCCcEEcCHH---HHHHhhh--eeEEEEecc
Confidence 9887766552 1222222234444467899999999886 899999 7889999864 3344332 777777765
No 14
>TIGR02616 tnaC_leader tryptophanase leader peptide. Members of this family are the apparent leader peptides of tryptophanase operons in Esherichia coli, Vibrio cholerae, Photobacterium profundum, Haemophilus influenzae type b, and related species. All members of the seed alignment are examples ORFs upstream of tryptophanase, with a start codon, a conserved single Trp residue, and several other conserved residues. It is suggested (Konan KV and Yanofsky C) that the nascent peptide interacts with the ribosome once (if) the ribosome reaches the stop codon. Note that this model describes a much broader set (and shorter protein region) than Pfam model pfam08053.
Probab=73.15 E-value=1.4 Score=25.75 Aligned_cols=11 Identities=27% Similarity=0.893 Sum_probs=9.1
Q ss_pred CEEEEeeCCCC
Q 045385 134 GEWYNFDSLYA 144 (188)
Q Consensus 134 g~wyNLDS~l~ 144 (188)
..|||+|+++.
T Consensus 8 s~WfniD~rIs 18 (26)
T TIGR02616 8 SKWFNIDNRIS 18 (26)
T ss_pred CceEEcchhhe
Confidence 37999999874
No 15
>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=71.74 E-value=29 Score=25.34 Aligned_cols=70 Identities=13% Similarity=0.102 Sum_probs=42.5
Q ss_pred chHHHHHHHHhhCCceeEEcCCCCCCCCCCCcccceeeeec-cCCceEEEEee-CCEEEEeeCCCCCceEcchh
Q 045385 81 FSIQVLQKALEVWDLQVIPLNCPIAEPAQIDPELENAFICH-LHDHWFCIRKV-NGEWYNFDSLYAAPEHLSKF 152 (188)
Q Consensus 81 ydinVL~~AL~~~~~~~~~~d~~~~~~~~~~~~~~~gFI~N-~~rHWfaIRki-~g~wyNLDS~l~~P~~i~~~ 152 (188)
++..-|.++++..|+++.-...+......+. --...++-| ...||+.|.++ ++.+...|+.. .|+.++..
T Consensus 45 ~s~~~l~~~a~~~Gl~~~~~~~~~~~L~~~~-lP~i~~~~~~~~~~~vvl~~~~~~~~~i~dp~~-~~~~~s~~ 116 (129)
T cd02423 45 FSMLDLKRYAEALGLKANGYRLNLDKLNALQ-IPVIVLVNNGGYGHFVVIKGIDGDRVLVGDPAL-GNISMSRE 116 (129)
T ss_pred cCHHHHHHHHHHCCCcceEEEcCHHHHhhCC-CCEEEEEecCCCceEEEEEEEeCCEEEEECCCC-CCcccCHH
Confidence 7888999999999987765443221111111 011222212 25699999977 56778888754 57777754
No 16
>cd02674 Peptidase_C19R A subfamily of peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=63.25 E-value=8.1 Score=31.34 Aligned_cols=34 Identities=26% Similarity=0.464 Sum_probs=26.8
Q ss_pred ceeeeeccCC----ceEEEEeeC--CEEEEeeCCCCCceE
Q 045385 115 ENAFICHLHD----HWFCIRKVN--GEWYNFDSLYAAPEH 148 (188)
Q Consensus 115 ~~gFI~N~~r----HWfaIRki~--g~wyNLDS~l~~P~~ 148 (188)
..|+|++.+. ||++..+.+ +.||-+|=..-.|+.
T Consensus 176 L~~vI~H~G~~~~GHY~~~~~~~~~~~W~~fnD~~V~~i~ 215 (230)
T cd02674 176 LYAVVNHYGSLNGGHYTAYCKNNETNDWYKFDDSRVTKVS 215 (230)
T ss_pred EEEEEEeeCCCCCcEEEEEEECCCCCceEEEcCCeEEEcC
Confidence 4699998755 999999987 899999876654443
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=61.19 E-value=60 Score=23.45 Aligned_cols=70 Identities=20% Similarity=0.247 Sum_probs=45.6
Q ss_pred CchHHHHHHHHhhCCceeEEcCCCCCCCCCCCcccceeeeeccCCceEEEEeeCC-EEEEeeCCCCCceEcchh
Q 045385 80 DFSIQVLQKALEVWDLQVIPLNCPIAEPAQIDPELENAFICHLHDHWFCIRKVNG-EWYNFDSLYAAPEHLSKF 152 (188)
Q Consensus 80 NydinVL~~AL~~~~~~~~~~d~~~~~~~~~~~~~~~gFI~N~~rHWfaIRki~g-~wyNLDS~l~~P~~i~~~ 152 (188)
-++...|..+++..|+++....-+-. .++....=.++.....||+-|-++++ ..+..|.....|+.++..
T Consensus 38 ~~~~~~l~~~a~~~Gl~~~~~~~~~~---~l~~~~lP~I~~~~~g~~~Vl~~~~~~~~~i~dp~~~~~~~~~~~ 108 (121)
T cd02417 38 PFNSTELLLAAKSLGLKAKAVRQPVE---RLARLPLPALAWDDDGGHFILAKLDGQKYLIQDPISQRPEVLSRE 108 (121)
T ss_pred CCCHHHHHHHHHHcCCeeEEEecCHH---HhccCCCCEEEEccCCCEEEEEEEcCCCEEEECCCcCCCeecCHH
Confidence 37888999999999998765443221 12111122333355679999999865 567778755568888753
No 18
>TIGR01684 viral_ppase viral phosphatase. These proteins also include an N-terminal domain (ca. 125 aas) that is unique to this clade.
Probab=60.21 E-value=16 Score=32.95 Aligned_cols=40 Identities=15% Similarity=0.124 Sum_probs=33.1
Q ss_pred EEEEeeCCCCCc---eEcchhhHHHHHHHHHhCCeEEEEEECC
Q 045385 135 EWYNFDSLYAAP---EHLSKFYLSAYLDSLKGFGWSIFIVRGN 174 (188)
Q Consensus 135 ~wyNLDS~l~~P---~~i~~~~L~~~L~~l~~~g~sIFvV~g~ 174 (188)
.-|.||++|-.. +.|.+..+.+.|++|++.|+.+-|+.+.
T Consensus 129 IvFDLDgTLi~~~~~v~irdPgV~EaL~~LkekGikLaIaTS~ 171 (301)
T TIGR01684 129 VVFDLDSTLITDEEPVRIRDPRIYDSLTELKKRGCILVLWSYG 171 (301)
T ss_pred EEEecCCCCcCCCCccccCCHHHHHHHHHHHHCCCEEEEEECC
Confidence 679999999433 3477888999999999999999999754
No 19
>KOG1415 consensus Ubiquitin C-terminal hydrolase UCHL1 [Posttranslational modification, protein turnover, chaperones]
Probab=59.53 E-value=15 Score=31.60 Aligned_cols=104 Identities=18% Similarity=0.260 Sum_probs=64.3
Q ss_pred CCCceeeecc-chhhH----HHHHHhhhCCCCCCHH-HHHH---HHhhhCHHHHHHhhhCCCCCCCCCccccccccccCC
Q 045385 7 GGMLYHEVQE-SKLCA----VHCVNTVLQGPFFSEF-DLAA---LASDLDRSERQVMLEGRVPAASSGDFLTEESHNVSL 77 (188)
Q Consensus 7 ~~~iYhEkQ~-~~lCa----lHaLNnLlQ~~~ft~~-dL~~---Ia~~Ld~~er~~~~~~~~~~~~~~~~~~~~s~n~~~ 77 (188)
+..|||=||. ..-|| +|+|-|+=-.--+..- .|+. =+....++||...++
T Consensus 76 ~~~V~fmkQti~NACGTiaLlHslaN~~~r~~l~~Gs~l~~fl~~~~~~s~eeRa~~le--------------------- 134 (222)
T KOG1415|consen 76 SDKVFFMKQTIGNACGTIALLHSLANNEDRVKLEDGSFLKKFLEEAEKMSPEERADLLE--------------------- 134 (222)
T ss_pred CCceEEEeccccchhHHHHHHHHHhccccccccCCchHHHHHHHHhhcCCHHHHHHHhc---------------------
Confidence 3479999999 56675 7888776432233332 3333 244566666644433
Q ss_pred CCCchHHHHHHHHhhCCceeEEcCCCCCCCCCCCcccceeeeeccCCceEEEEeeCCEEEEeeCCCCCceEcchh
Q 045385 78 DGDFSIQVLQKALEVWDLQVIPLNCPIAEPAQIDPELENAFICHLHDHWFCIRKVNGEWYNFDSLYAAPEHLSKF 152 (188)
Q Consensus 78 ~GNydinVL~~AL~~~~~~~~~~d~~~~~~~~~~~~~~~gFI~N~~rHWfaIRki~g~wyNLDS~l~~P~~i~~~ 152 (188)
++=.+..+.+|.-.-|= .. .+-+. .-|+|+.-..+|.-|-||+-++.|+.+|.+
T Consensus 135 -~d~~l~~~H~a~a~eGq-----------te-~~~~v--------d~HFI~~v~~~G~lYELDgR~~fPi~hG~t 188 (222)
T KOG1415|consen 135 -NDEELEAAHEAAAQEGQ-----------TE-ADEDV--------DLHFICFVNKNGHLYELDGRKPFPINHGPT 188 (222)
T ss_pred -ccHHHHHHHHHHHhcCC-----------CC-Ccccc--------ceEEEEEEccCCeEEEecCCcCCCccCCCC
Confidence 33455566665544221 00 11111 247778888999999999999999999854
No 20
>cd02257 Peptidase_C19 Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=58.37 E-value=12 Score=29.35 Aligned_cols=36 Identities=22% Similarity=0.385 Sum_probs=28.0
Q ss_pred ceeeeecc-----CCceEEEEeeC--CEEEEeeCCCCCceEcc
Q 045385 115 ENAFICHL-----HDHWFCIRKVN--GEWYNFDSLYAAPEHLS 150 (188)
Q Consensus 115 ~~gFI~N~-----~rHWfaIRki~--g~wyNLDS~l~~P~~i~ 150 (188)
..|+||+. .-|++|..|-. +.||.+|=..-.++.-.
T Consensus 195 L~~vi~h~G~~~~~GHY~~~~~~~~~~~W~~~nD~~V~~v~~~ 237 (255)
T cd02257 195 LVAVVVHSGTSADSGHYVAYVKDPSDGKWYKFNDDKVTEVSEE 237 (255)
T ss_pred EEEEEEEecCCCCCcCeEEEEeCCCCCceEEEeccccEEcCHH
Confidence 56999986 44999999887 89999998776665443
No 21
>KOG2778 consensus Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=58.19 E-value=36 Score=30.85 Aligned_cols=109 Identities=19% Similarity=0.309 Sum_probs=68.4
Q ss_pred CCceeeecc-chhhHHHHHHhhhCCCC-------CCHHHHHHHHhhhCHHHHHHhhhCCCCCCCCCccccccccccCCCC
Q 045385 8 GMLYHEVQE-SKLCAVHCVNTVLQGPF-------FSEFDLAALASDLDRSERQVMLEGRVPAASSGDFLTEESHNVSLDG 79 (188)
Q Consensus 8 ~~iYhEkQ~-~~lCalHaLNnLlQ~~~-------ft~~dL~~Ia~~Ld~~er~~~~~~~~~~~~~~~~~~~~s~n~~~~G 79 (188)
+.||+-+|- -.-||-|||=++|=.-. =|-.+|.+.|..+||+-+.+-+ |
T Consensus 69 ~niFFA~QvInNACATqAlLsvLlN~~~~~idLG~tLs~~K~f~k~f~Pe~KGlal-----------------------~ 125 (328)
T KOG2778|consen 69 SNIFFAKQVINNACATQALLSVLLNCSHEDIDLGPTLSELKEFTKGFDPELKGLAL-----------------------G 125 (328)
T ss_pred cchhhhhhhcccHHHHHHHHHHHHcCCccccchhhHHHHHHHHhhcCChhhccccc-----------------------C
Confidence 369999999 58999999988885432 4567888888888888654322 2
Q ss_pred CchHHHHHHHHhhCCc-ee-EEcCCCCCCCCCCCcccceeeeeccCCceEEEEeeCCEEEEeeCCCCCceEcch
Q 045385 80 DFSIQVLQKALEVWDL-QV-IPLNCPIAEPAQIDPELENAFICHLHDHWFCIRKVNGEWYNFDSLYAAPEHLSK 151 (188)
Q Consensus 80 NydinVL~~AL~~~~~-~~-~~~d~~~~~~~~~~~~~~~gFI~N~~rHWfaIRki~g~wyNLDS~l~~P~~i~~ 151 (188)
|=+ .|..|=+.+-- +. +++.-....... + ... =|+++--.|+|+-|-||-....|+-++.
T Consensus 126 Nse--~Ir~~HNSfARp~~~~~~e~~a~~~~~-~---dd~------yHFVsyvPI~g~lyELDGLke~PI~lg~ 187 (328)
T KOG2778|consen 126 NSE--EIRCAHNSFARPEPFRPEEVDAATSAK-E---DDV------YHFVSYVPINGRLYELDGLKEGPIDLGP 187 (328)
T ss_pred CcH--HHHHHhccccCCCCcchhhhhcccccc-c---ccc------eeEEEEEeeCCEEEeccCCccCCcccCC
Confidence 211 33333322211 00 000000000001 1 112 3999999999999999999999999985
No 22
>cd02673 Peptidase_C19Q A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=55.85 E-value=15 Score=31.49 Aligned_cols=33 Identities=27% Similarity=0.459 Sum_probs=26.1
Q ss_pred ceeeeeccC-----CceEEEEee---CCEEEEeeCCCCCce
Q 045385 115 ENAFICHLH-----DHWFCIRKV---NGEWYNFDSLYAAPE 147 (188)
Q Consensus 115 ~~gFI~N~~-----rHWfaIRki---~g~wyNLDS~l~~P~ 147 (188)
..|+|++.+ -|++|.-|. +|.||.+|=..-.|+
T Consensus 186 L~~VV~H~G~~~~~GHY~a~vk~~~~~~~Wy~fnD~~V~~v 226 (245)
T cd02673 186 LVAVICHLGESPYDGHYIAYTKELYNGSSWLYCSDDEIRPV 226 (245)
T ss_pred EEEEEEECCCCCCCceEEEEEEcCCCCCeEEEeeCceeeEc
Confidence 568888764 499999887 689999998776554
No 23
>PHA03398 viral phosphatase superfamily protein; Provisional
Probab=52.22 E-value=24 Score=31.88 Aligned_cols=40 Identities=18% Similarity=0.214 Sum_probs=33.3
Q ss_pred EEEEeeCCCCCc---eEcchhhHHHHHHHHHhCCeEEEEEECC
Q 045385 135 EWYNFDSLYAAP---EHLSKFYLSAYLDSLKGFGWSIFIVRGN 174 (188)
Q Consensus 135 ~wyNLDS~l~~P---~~i~~~~L~~~L~~l~~~g~sIFvV~g~ 174 (188)
.-|.||++|-.+ +.|.+....+.|++|+++|+.+-|+.+.
T Consensus 131 i~~D~D~TL~~~~~~v~irdp~V~EtL~eLkekGikLaIvTNg 173 (303)
T PHA03398 131 IVFDLDSTLITDEEPVRIRDPFVYDSLDELKERGCVLVLWSYG 173 (303)
T ss_pred EEEecCCCccCCCCccccCChhHHHHHHHHHHCCCEEEEEcCC
Confidence 679999999444 4466788999999999999999999744
No 24
>cd02661 Peptidase_C19E A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=51.14 E-value=17 Score=30.62 Aligned_cols=34 Identities=35% Similarity=0.751 Sum_probs=26.1
Q ss_pred ceeeeeccC-----CceEEEEee-CCEEEEeeCCCCCceE
Q 045385 115 ENAFICHLH-----DHWFCIRKV-NGEWYNFDSLYAAPEH 148 (188)
Q Consensus 115 ~~gFI~N~~-----rHWfaIRki-~g~wyNLDS~l~~P~~ 148 (188)
..|+||+.+ .|++|..+- +|.||.+|-..-.++.
T Consensus 250 L~~vi~H~G~~~~~GHY~~~~~~~~~~W~~~nD~~V~~v~ 289 (304)
T cd02661 250 LYAVLVHSGFSPHSGHYYCYVKSSNGKWYNMDDSKVSPVS 289 (304)
T ss_pred EEEEEEECCCCCCCcCCEEEEECCCCCEEEEeCCeeEECC
Confidence 458888864 499999775 8999999987765553
No 25
>cd01427 HAD_like Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.
Probab=50.41 E-value=23 Score=24.95 Aligned_cols=25 Identities=16% Similarity=0.073 Sum_probs=21.0
Q ss_pred hhHHHHHHHHHhCCeEEEEEECCCC
Q 045385 152 FYLSAYLDSLKGFGWSIFIVRGNFP 176 (188)
Q Consensus 152 ~~L~~~L~~l~~~g~sIFvV~g~lp 176 (188)
..+..+|++|++.|+.|++|.+..+
T Consensus 27 ~~~~~~l~~l~~~g~~i~ivS~~~~ 51 (139)
T cd01427 27 PGVKEALKELKEKGIKLALATNKSR 51 (139)
T ss_pred cCHHHHHHHHHHCCCeEEEEeCchH
Confidence 4678899999999999999987653
No 26
>PF13529 Peptidase_C39_2: Peptidase_C39 like family; PDB: 3ERV_A.
Probab=49.67 E-value=27 Score=25.41 Aligned_cols=29 Identities=31% Similarity=0.192 Sum_probs=14.9
Q ss_pred cchhhHHHHHHhhhCC--CCCCHHHHHHHHh
Q 045385 16 ESKLCAVHCVNTVLQG--PFFSEFDLAALAS 44 (188)
Q Consensus 16 ~~~lCalHaLNnLlQ~--~~ft~~dL~~Ia~ 44 (188)
...-|+.=|+-++|.. ...++.+|.+.+.
T Consensus 12 ~~~~Cg~as~~mvl~~~g~~~~~~~l~~~~~ 42 (144)
T PF13529_consen 12 TSYGCGPASAAMVLNYYGKNISQEDLADEAG 42 (144)
T ss_dssp -TT-HHHHHHHHHHHHTT----HHHHHHHS-
T ss_pred CCCcCHHHHHHHHHHHcCCCCCHHHHHHHhh
Confidence 3566888888777764 4566666655443
No 27
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=49.59 E-value=20 Score=26.06 Aligned_cols=25 Identities=28% Similarity=0.303 Sum_probs=21.1
Q ss_pred cchhhHHHHHHHHHhCCeEEEEEEC
Q 045385 149 LSKFYLSAYLDSLKGFGWSIFIVRG 173 (188)
Q Consensus 149 i~~~~L~~~L~~l~~~g~sIFvV~g 173 (188)
|+.+-+-..+++|++.|+.|+.|++
T Consensus 31 iSRtaVwK~Iq~Lr~~G~~I~s~~~ 55 (79)
T COG1654 31 ISRTAVWKHIQQLREEGVDIESVRG 55 (79)
T ss_pred ccHHHHHHHHHHHHHhCCceEecCC
Confidence 3446677889999999999999987
No 28
>cd02657 Peptidase_C19A A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=48.15 E-value=23 Score=30.26 Aligned_cols=34 Identities=24% Similarity=0.386 Sum_probs=26.6
Q ss_pred ceeeeeccC-----CceEEEEeeC--CEEEEeeCCCCCceE
Q 045385 115 ENAFICHLH-----DHWFCIRKVN--GEWYNFDSLYAAPEH 148 (188)
Q Consensus 115 ~~gFI~N~~-----rHWfaIRki~--g~wyNLDS~l~~P~~ 148 (188)
..|+|++.+ -|+++..|-. +.||.+|=..-.|+.
T Consensus 243 L~~vI~H~G~~~~~GHY~~~~~~~~~~~W~~fdD~~V~~~~ 283 (305)
T cd02657 243 LVAVITHQGRSADSGHYVAWVRRKNDGKWIKFDDDKVSEVT 283 (305)
T ss_pred EEEEEEecCCCCCCcEEEEEEEcCCCCeEEEEECCceEEeC
Confidence 468899764 3999999987 899999976655544
No 29
>PF02251 PA28_alpha: Proteasome activator pa28 alpha subunit; InterPro: IPR003185 PA28 activator complex (also known as 11S regulator of 20S proteasome) is a ring shaped hexameric structure of alternating alpha (PA28alpha) and beta (PA28beta) subunits. The catalytic properties of PA28alpha and PA28beta-activated proteosome are similar [, ]. This entry represents the alpha subunit. The activator complex binds to the 20S proteasome and stimulates peptidase activity in and ATP-independent manner.; GO: 0008537 proteasome activator complex; PDB: 1AVO_K.
Probab=46.18 E-value=2.6 Score=29.50 Aligned_cols=25 Identities=24% Similarity=0.444 Sum_probs=15.0
Q ss_pred HHHHhhhCCCCCCHHHHHHHHhhhC
Q 045385 23 HCVNTVLQGPFFSEFDLAALASDLD 47 (188)
Q Consensus 23 HaLNnLlQ~~~ft~~dL~~Ia~~Ld 47 (188)
-=||+|||.+.|+-.+|.+|-..|+
T Consensus 33 ~eLd~lLk~~~fn~~dls~i~~~ln 57 (64)
T PF02251_consen 33 VELDELLKSPSFNLSDLSSIHAPLN 57 (64)
T ss_dssp HHHHHHHHSGGG--S-GGGS-----
T ss_pred HHHHHHhcCcccccccHHhhcCcCC
Confidence 3589999999999999998876664
No 30
>cd02659 peptidase_C19C A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=45.79 E-value=23 Score=30.56 Aligned_cols=34 Identities=24% Similarity=0.561 Sum_probs=25.9
Q ss_pred ceeeeecc----CCceEEEEeeC--CEEEEeeCCCCCceE
Q 045385 115 ENAFICHL----HDHWFCIRKVN--GEWYNFDSLYAAPEH 148 (188)
Q Consensus 115 ~~gFI~N~----~rHWfaIRki~--g~wyNLDS~l~~P~~ 148 (188)
..|+|++. +-||++..|-. +.||.+|=..-.++.
T Consensus 254 L~~vI~H~G~~~~GHY~~~vk~~~~~~W~~~nD~~V~~i~ 293 (334)
T cd02659 254 LHGVLVHSGDAHGGHYYSYIKDRDDGKWYKFNDDVVTPFD 293 (334)
T ss_pred EEEEEEecCCCCCCCeEEEEECCCCCceEEEeCcccEECC
Confidence 45888875 56999988764 999999987755543
No 31
>cd02667 Peptidase_C19K A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=45.26 E-value=25 Score=30.04 Aligned_cols=34 Identities=21% Similarity=0.381 Sum_probs=26.2
Q ss_pred ceeeeecc----CCceEEEEee-----------------------CCEEEEeeCCCCCceE
Q 045385 115 ENAFICHL----HDHWFCIRKV-----------------------NGEWYNFDSLYAAPEH 148 (188)
Q Consensus 115 ~~gFI~N~----~rHWfaIRki-----------------------~g~wyNLDS~l~~P~~ 148 (188)
..|+|++. .-|++|..|. +|.||.+|=..-.++.
T Consensus 204 L~~vi~H~G~~~~GHY~a~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~W~~~dD~~V~~v~ 264 (279)
T cd02667 204 LYGVVEHSGTMRSGHYVAYVKVRPPQQRLSDLTKSKPAADEAGPGSGQWYYISDSDVREVS 264 (279)
T ss_pred EEEEEEEeCCCCCCEeEEEEEcCccccccccccccccccccCCCCCCcEEEEECCccEECC
Confidence 56888876 5599999886 6799999877655543
No 32
>cd02658 Peptidase_C19B A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=42.46 E-value=29 Score=29.78 Aligned_cols=33 Identities=27% Similarity=0.441 Sum_probs=26.0
Q ss_pred ceeeeecc-----CCceEEEEeeC----CEEEEeeCCCCCce
Q 045385 115 ENAFICHL-----HDHWFCIRKVN----GEWYNFDSLYAAPE 147 (188)
Q Consensus 115 ~~gFI~N~-----~rHWfaIRki~----g~wyNLDS~l~~P~ 147 (188)
..|+|++. .-|+++.-|.. |.||-+|=..-.|.
T Consensus 254 L~~vI~H~G~~~~~GHY~~~vk~~~~~~~~W~~fnD~~V~~~ 295 (311)
T cd02658 254 LIAFISHKGTSVHSGHYVAHIKKEIDGEGKWVLFNDEKVVAS 295 (311)
T ss_pred EEEEEEccCCCCCCcceEEEEeCCCCCCCCEEEecCceeEEC
Confidence 45899876 45999999988 99999987664443
No 33
>cd02668 Peptidase_C19L A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=39.97 E-value=34 Score=29.84 Aligned_cols=33 Identities=24% Similarity=0.478 Sum_probs=24.4
Q ss_pred ceeeeecc-----CCceEEEEee--CCEEEEeeCCCCCce
Q 045385 115 ENAFICHL-----HDHWFCIRKV--NGEWYNFDSLYAAPE 147 (188)
Q Consensus 115 ~~gFI~N~-----~rHWfaIRki--~g~wyNLDS~l~~P~ 147 (188)
..|+|++. +-||++.-|- +|.||.+|=..-.++
T Consensus 248 L~~vI~H~G~~~~~GHY~~~~k~~~~~~W~~fdD~~V~~i 287 (324)
T cd02668 248 LSGVLIHQGVSAYSGHYIAHIKDEQTGEWYKFNDEDVEEM 287 (324)
T ss_pred EEEEEEEcCCCCCCEeeEEEEECCCCCcEEEEECCceEEc
Confidence 45889876 3599998775 589999997654443
No 34
>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=38.87 E-value=3.8e+02 Score=26.08 Aligned_cols=114 Identities=18% Similarity=0.237 Sum_probs=72.7
Q ss_pred chhhHHHHHHhhhCC--CCCCHHHHHHHHhhhCHHHHHHhhhCCCCCCCCCccccccccccCCCCCchHHHHHHHHhhCC
Q 045385 17 SKLCAVHCVNTVLQG--PFFSEFDLAALASDLDRSERQVMLEGRVPAASSGDFLTEESHNVSLDGDFSIQVLQKALEVWD 94 (188)
Q Consensus 17 ~~lCalHaLNnLlQ~--~~ft~~dL~~Ia~~Ld~~er~~~~~~~~~~~~~~~~~~~~s~n~~~~GNydinVL~~AL~~~~ 94 (188)
..=||+=||=.+++- ...+..+|.+. ..+...| .++.-|.+|++..|
T Consensus 10 ~~dCg~acl~mi~~~~g~~~~~~~lr~~------------------------------~~~~~~g-~s~~~l~~~~~~~g 58 (710)
T TIGR03796 10 AVECGAASLAMILAYYGRYVPLEELREE------------------------------CGVSRDG-SKASNLLKAARSYG 58 (710)
T ss_pred cccHHHHHHHHHHHHcCCCCCHHHHHHH------------------------------cCCCCCC-CCHHHHHHHHHHCC
Confidence 467999999988875 45666666442 0111235 78899999999999
Q ss_pred ceeEEcCCCCCCCCCCCcccceeeeec-cCCceEEEEeeC-CEEEEeeCCCCCceEcchhhHHHHHHHHHhCCeEEEEE
Q 045385 95 LQVIPLNCPIAEPAQIDPELENAFICH-LHDHWFCIRKVN-GEWYNFDSLYAAPEHLSKFYLSAYLDSLKGFGWSIFIV 171 (188)
Q Consensus 95 ~~~~~~d~~~~~~~~~~~~~~~gFI~N-~~rHWfaIRki~-g~wyNLDS~l~~P~~i~~~~L~~~L~~l~~~g~sIFvV 171 (188)
+++..+..+.. .+.. ...-.|+. -..|+..|.++. +..+-.|... ++..++..+ |.+.. .|+-+++-
T Consensus 59 ~~~~~~~~~~~---~l~~-~~lP~i~~~~~~h~vvl~~~~~~~~~i~dP~~-g~~~~~~~e---~~~~~--~g~~l~~~ 127 (710)
T TIGR03796 59 LEAKGFRKELD---ALAE-LPLPYIVFWNFNHFVVVEGFRGGRVYLNDPAL-GPRTVSLEE---FDESF--TGVVLTFE 127 (710)
T ss_pred CEeEEEecCHH---Hhcc-CCCCEEEEEcCCcEEEEEEEeCCEEEEECCCC-CCEEccHHH---HHhhC--CCeEEEEE
Confidence 98876654321 1111 12244443 467999999986 5788888854 788887532 33322 56655554
No 35
>PF05152 DUF705: Protein of unknown function (DUF705); InterPro: IPR007827 This family contains uncharacterised baculoviral proteins.
Probab=37.37 E-value=48 Score=29.88 Aligned_cols=37 Identities=16% Similarity=0.167 Sum_probs=31.9
Q ss_pred EEEEeeCCC---CCceEcchhhHHHHHHHHHhCCeEEEEE
Q 045385 135 EWYNFDSLY---AAPEHLSKFYLSAYLDSLKGFGWSIFIV 171 (188)
Q Consensus 135 ~wyNLDS~l---~~P~~i~~~~L~~~L~~l~~~g~sIFvV 171 (188)
.-|.|||+| ..++.|.+..+...|..|++.|+.+.+=
T Consensus 125 IVfDlD~TLItd~~~v~Ir~~~v~~sL~~Lk~~g~vLvLW 164 (297)
T PF05152_consen 125 IVFDLDSTLITDEGDVRIRDPAVYDSLRELKEQGCVLVLW 164 (297)
T ss_pred EEEECCCcccccCCccccCChHHHHHHHHHHHcCCEEEEe
Confidence 689999999 5788899999999999999999866553
No 36
>PF00288 GHMP_kinases_N: GHMP kinases N terminal domain; InterPro: IPR006204 The galacto- (2.7.1.6 from EC), homoserine (2.7.1.39 from EC), mevalonate (2.7.1.36 from EC) and phosphomevalonate (2.7.4.2 from EC) kinases contain, in their N-terminal section, a conserved Gly/Ser-rich region which is probably involved in the binding of ATP [, ]. This group of kinases has been called 'GHMP' (from the first letter of their substrates).; GO: 0005524 ATP binding, 0016301 kinase activity, 0016310 phosphorylation; PDB: 3F0N_B 1PIE_A 2AJ4_A 1K47_E 3GON_A 2R3V_C 3HUL_A 1KVK_A 2R42_A 3D4J_A ....
Probab=36.83 E-value=50 Score=22.01 Aligned_cols=29 Identities=21% Similarity=0.252 Sum_probs=24.7
Q ss_pred hhhHHHHHHhhhCCCCCCHHHHHHHHhhhC
Q 045385 18 KLCAVHCVNTVLQGPFFSEFDLAALASDLD 47 (188)
Q Consensus 18 ~lCalHaLNnLlQ~~~ft~~dL~~Ia~~Ld 47 (188)
..|.+.|+|.++.. -+++.+|.++|.+..
T Consensus 21 ~~a~~~a~~~~~~~-~~~~~~l~~~a~~~e 49 (67)
T PF00288_consen 21 AVALAAALNKLFGL-PLSKEELAKLAQEAE 49 (67)
T ss_dssp HHHHHHHHHHHTTT-SSBHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHccc-cccHHHHHHHHHHHH
Confidence 56889999999977 479999999988874
No 37
>cd02663 Peptidase_C19G A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=35.35 E-value=41 Score=28.95 Aligned_cols=32 Identities=31% Similarity=0.577 Sum_probs=25.6
Q ss_pred eeeeecc-----CCceEEEEeeCCEEEEeeCCCCCce
Q 045385 116 NAFICHL-----HDHWFCIRKVNGEWYNFDSLYAAPE 147 (188)
Q Consensus 116 ~gFI~N~-----~rHWfaIRki~g~wyNLDS~l~~P~ 147 (188)
.|+|++. .-|++|..|-+|.||..|=..-.|+
T Consensus 240 ~~vi~H~G~~~~~GHY~a~~k~~~~W~~fdD~~V~~~ 276 (300)
T cd02663 240 VAVVVHIGGGPNHGHYVSIVKSHGGWLLFDDETVEKI 276 (300)
T ss_pred EEEEEEecCCCCCCceEEEEECCCcEEEEcCCceEEc
Confidence 4778764 5799999999999999997765553
No 38
>PF01473 CW_binding_1: Putative cell wall binding repeat; InterPro: IPR018337 The cell wall-binding repeat (CW) is an about 20 amino acid residue module, essentially found in two bacterial Gram-positive protein families; the choline binding proteins and glucosyltransferases (2.4.1.5 from EC). In choline-binding proteins cell wall binding repeats bind to choline moieties of both teichoic and lipoteichoic acids, two components peculiar to the cell surface of Gram-positive bacteria [, ]. In glucosyltransferases the region spanning the CW repeats is a glucan binding domain []. Several crystal structures of CW have been solved [, ]. In the choline binding protein LytA, the repeats adopt a solenoid fold consisting exclusively of beta-hairpins that stack to form a left-handed superhelix with a boomerang-like shape. The choline groups bind between beta-hairpin 'steps' of the superhelix []. In Cpl-1 CW repeats assemble in two sub-domains: an N-terminal superhelical moiety similar to the LytA one and a C-terminal beta-sheet involved in interactions with the lysozyme domain. Choline is bound between repeats 1 and 2, and, 2 and 3 of the superhelical sub-domain []. Some proteins known to contain cell-wall binding repeats include: Pneumococcal N-acetylmuramoyl-L-alanine amidase (autolysin, lytA) (3.5.1.28 from EC). It is a surface-exposed enzyme that rules the self-destruction of pneumococcal cells through degradation of their peptidoglycan backbone. It mediates the release of toxic substances that damage the host tissues. Pneumococcal endo-beta-N-acetylglucosaminidase (lytB) (3.2.1.96 from EC). It plays an important role in cell wall degradation and cell separation. Pneumococcal teichoic acid phosphorylcholine esterase (pce or cbpE), a cell wall hydrolase important for cellular adhesion and colonisation. Lactobacillales glucosyltransferase. It catalyses the transfer of glucosyl units from the cleavage of sucrose to a growing chain of glucan. Clostridium difficile toxin A (tcdA) and toxin B (tcdb). They are the causative agents of the antibiotic-associated pseudomembranous colitis. They are intracellular acting toxins that reach their targets after receptor-mediated endocytosis. Clostridium acetobutylicum cspA protein. Siphoviridae bacteriophages N-acetylmuramoyl-L-alanine amidase. It lyses the bacterial host cell wall. Podoviridae lysozyme protein (cpl-1). It is capable of digesting the pneumococcal cell wall. The cell wall binding repeats are also known as the choline-binding repeats (ChBr) or the choline-binding domain (ChBD). ; PDB: 1GVM_C 2BML_B 1HCX_A 1OBA_A 1H09_A 2J8F_A 2IXU_A 2J8G_A 2IXV_A 2X8O_A ....
Probab=34.82 E-value=41 Score=17.42 Aligned_cols=12 Identities=58% Similarity=1.121 Sum_probs=9.6
Q ss_pred eeCCEEEEeeCC
Q 045385 131 KVNGEWYNFDSL 142 (188)
Q Consensus 131 ki~g~wyNLDS~ 142 (188)
+++|.||-+++.
T Consensus 5 ~~~~~wYy~~~~ 16 (19)
T PF01473_consen 5 QDNGNWYYFDSD 16 (19)
T ss_dssp EETTEEEEETTT
T ss_pred EECCEEEEeCCC
Confidence 458999999874
No 39
>cd08324 CARD_NOD1_CARD4 Caspase activation and recruitment domain similar to that found in NOD1. Caspase activation and recruitment domain (CARD) found in human NOD1 (CARD4) and similar proteins. NOD1 is a member of the Nod-like receptor (NLR) family, which plays a central role in the innate immune response. NLRs typically contain an N-terminal effector domain, a central nucleotide-binding domain and a C-terminal ligand-binding region of several leucine-rich repeats (LRRs). In NOD1, as well as NOD2, the N-terminal effector domain is a CARD. Nod1-CARD has been shown to interact with the CARD domain of the downstream effector RICK (RIP2, CARDIAK), a serine/threonine kinase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form hom
Probab=33.93 E-value=46 Score=24.70 Aligned_cols=30 Identities=17% Similarity=0.294 Sum_probs=26.6
Q ss_pred HHHhhhCCCCCCHHHHHHHHhhhCHHHHHH
Q 045385 24 CVNTVLQGPFFSEFDLAALASDLDRSERQV 53 (188)
Q Consensus 24 aLNnLlQ~~~ft~~dL~~Ia~~Ld~~er~~ 53 (188)
-|.||+|..++|.+|-+.|+.+=.+.++.+
T Consensus 20 lLD~Ll~n~~it~E~y~~V~a~~T~qdkmR 49 (85)
T cd08324 20 LVDNLLKNDYFSTEDAEIVCACPTQPDKVR 49 (85)
T ss_pred HHHHHhccCCccHHHHHHHHhCCCCHHHHH
Confidence 478999999999999999999999888644
No 40
>PF00443 UCH: Ubiquitin carboxyl-terminal hydrolase; InterPro: IPR001394 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 MEROPS peptidase family C19 (ubiquitin-specific protease family, clan CA). Families within the CA clan are loosely termed papain-like as protein fold of the peptidase unit resembles that of papain, the type example for clan CA. Predicted active site residues for members of this family and family C1 occur in the same order in the sequence: N/Q, C, H. The type example is human ubiquitin-specific protease 14. Ubiquitin is highly conserved, commonly found conjugated to proteins in eukaryotic cells, where it may act as a marker for rapid degradation, or it may have a chaperone function in protein assembly []. The ubiquitin is released by cleavage from the bound protein by a protease []. A number of deubiquitinising proteases are known: all are activated by thiol compounds [, ], and inhibited by thiol-blocking agents and ubiquitin aldehyde [, ], and as such have the properties of cysteine proteases []. The deubiquitinsing proteases can be split into 2 size ranges (20-30 kDa, IPR001578 from INTERPRO, and 100-200 kDa) []: this family are the 100-200 kDa peptides which includes the Ubp1 ubiquitin peptidase from yeast. Only one conserved cysteine can be identified, along with two conserved histidines. The spacing between the cysteine and the second histidine is thought to be more representative of the cysteine/histidine spacing of a cysteine protease catalytic dyad [].; GO: 0004221 ubiquitin thiolesterase activity, 0006511 ubiquitin-dependent protein catabolic process; PDB: 2LBC_A 3MHH_A 3MHS_A 3M99_A 2Y6E_D 2VHF_A 2HD5_A 3NHE_A 2IBI_A 1NBF_B ....
Probab=33.27 E-value=50 Score=26.35 Aligned_cols=34 Identities=24% Similarity=0.446 Sum_probs=24.5
Q ss_pred ceeeeeccC----CceEEEEeeCC--EEEEeeCCCCCceE
Q 045385 115 ENAFICHLH----DHWFCIRKVNG--EWYNFDSLYAAPEH 148 (188)
Q Consensus 115 ~~gFI~N~~----rHWfaIRki~g--~wyNLDS~l~~P~~ 148 (188)
..|+|++.+ -||+|.-+-.+ .||-+|=..-.++.
T Consensus 213 L~avi~H~G~~~~GHY~a~v~~~~~~~W~~~dD~~v~~~~ 252 (269)
T PF00443_consen 213 LVAVIVHYGSADSGHYVAYVRDSDDGKWYKFDDSRVTEVS 252 (269)
T ss_dssp EEEEEEEESSTTSEEEEEEEEETTTTEEEEEETTEEEEES
T ss_pred ehhhhccccccccceEEEeeccccCCeEEEeeCCceEECC
Confidence 369999764 49998886654 69999976544443
No 41
>cd02660 Peptidase_C19D A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=31.63 E-value=53 Score=28.26 Aligned_cols=34 Identities=21% Similarity=0.457 Sum_probs=25.2
Q ss_pred ceeeeecc----CCceEEEEeeC-CEEEEeeCCCCCceE
Q 045385 115 ENAFICHL----HDHWFCIRKVN-GEWYNFDSLYAAPEH 148 (188)
Q Consensus 115 ~~gFI~N~----~rHWfaIRki~-g~wyNLDS~l~~P~~ 148 (188)
..|+|.+. .-|+++..|-. +.||-+|=..-.|+.
T Consensus 275 L~avi~H~G~~~~GHY~~~~~~~~~~W~~~nD~~V~~~~ 313 (328)
T cd02660 275 LFAVVVHKGTLDTGHYTAYCRQGDGQWFKFDDAMITRVS 313 (328)
T ss_pred EEEEEEeeccCCCCcEEEEEECCCCcEEEEECCeeEECC
Confidence 34777765 45999999988 999999966544443
No 42
>PF04473 DUF553: Transglutaminase-like domain; InterPro: IPR007562 This entry represents a transglutaminase-like domain found in a family of uncharacterised archaeal proteins that had previously been called DUF553 and UPF0252.
Probab=27.63 E-value=1.2e+02 Score=24.52 Aligned_cols=39 Identities=33% Similarity=0.453 Sum_probs=28.0
Q ss_pred CceEEEEeeCCEEEEeeCCCCCceEcchhhHHHHHHHHHhCCeEE
Q 045385 124 DHWFCIRKVNGEWYNFDSLYAAPEHLSKFYLSAYLDSLKGFGWSI 168 (188)
Q Consensus 124 rHWfaIRki~g~wyNLDS~l~~P~~i~~~~L~~~L~~l~~~g~sI 168 (188)
.|=++.-+++|.||-||=.+| |..+ ..|+.....+|..|
T Consensus 109 ~Haa~aV~ing~~yvlDq~~p-~~~l-----~~y~~~~~~~~~~i 147 (153)
T PF04473_consen 109 GHAAVAVKINGKYYVLDQHLP-PIDL-----GDYLKYWKKEGKII 147 (153)
T ss_pred CeEEEEEEECCEEEEEeCCCC-CccH-----HHHHHHhhhcccee
Confidence 388888899999999997643 4444 45776655577665
No 43
>cd02672 Peptidase_C19P A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=27.06 E-value=59 Score=28.16 Aligned_cols=33 Identities=21% Similarity=0.616 Sum_probs=26.1
Q ss_pred ceeeeecc-----CCceEEEEee------CCEEEEeeCCCCCce
Q 045385 115 ENAFICHL-----HDHWFCIRKV------NGEWYNFDSLYAAPE 147 (188)
Q Consensus 115 ~~gFI~N~-----~rHWfaIRki------~g~wyNLDS~l~~P~ 147 (188)
..|+|+++ ..|++|.=|. .|+||.+|-.+-.|+
T Consensus 215 L~gvV~hig~~~~~GHyva~vk~~~~~~~~~~WylFND~~V~~v 258 (268)
T cd02672 215 LVGYVCEINDSSRGQHNVVFVIKVNEESTHGRWYLFNDFLVTPV 258 (268)
T ss_pred EEEEEEEecCCCCCCcEEEEEEccCCCCCCCcEEEecCeEEEEc
Confidence 45888875 5699998887 589999998876654
No 44
>smart00460 TGc Transglutaminase/protease-like homologues. Transglutaminases are enzymes that establish covalent links between proteins. A subset of transglutaminase homologues appear to catalyse the reverse reaction, the hydrolysis of peptide bonds. Proteins with this domain are both extracellular and intracellular, and it is likely that the eukaryotic intracellular proteins are involved in signalling events.
Probab=25.94 E-value=1.9e+02 Score=18.60 Aligned_cols=53 Identities=13% Similarity=0.242 Sum_probs=29.1
Q ss_pred HHHHHHHHhhCCceeEEcCCCCCCCC-CCCcccceeeeeccCCc-eEEEEeeCCEEEEeeCC
Q 045385 83 IQVLQKALEVWDLQVIPLNCPIAEPA-QIDPELENAFICHLHDH-WFCIRKVNGEWYNFDSL 142 (188)
Q Consensus 83 inVL~~AL~~~~~~~~~~d~~~~~~~-~~~~~~~~gFI~N~~rH-WfaIRki~g~wyNLDS~ 142 (188)
+.++.+.|...|+.+........... ...+. -+...| |..|. +++.|+.+|..
T Consensus 13 a~l~~~llr~~GIpar~v~g~~~~~~~~~~~~------~~~~~H~W~ev~-~~~~W~~~D~~ 67 (68)
T smart00460 13 AALFVALLRSLGIPARVVSGYLKAPDTIGGLR------SIWEAHAWAEVY-LEGGWVPVDPT 67 (68)
T ss_pred HHHHHHHHHHCCCCeEEEeeeecCCCCCcccc------cCCCcEEEEEEE-ECCCeEEEeCC
Confidence 34666677888987765432111100 00000 123456 65555 78999999964
No 45
>cd02665 Peptidase_C19I A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=25.19 E-value=96 Score=26.48 Aligned_cols=34 Identities=15% Similarity=0.377 Sum_probs=25.0
Q ss_pred ceeeeecc----CCceEEEEe--eCCEEEEeeCCCCCceE
Q 045385 115 ENAFICHL----HDHWFCIRK--VNGEWYNFDSLYAAPEH 148 (188)
Q Consensus 115 ~~gFI~N~----~rHWfaIRk--i~g~wyNLDS~l~~P~~ 148 (188)
..|+|++. +.||++.-+ .++.||.+|-..-.|+.
T Consensus 166 L~aVi~H~G~~~~GHY~~~i~~~~~~~W~~fdD~~V~~~~ 205 (228)
T cd02665 166 LHAVLVHEGQANAGHYWAYIYKQSRQEWEKYNDISVTESS 205 (228)
T ss_pred EEEEEEecCCCCCCEEEEEEEcCCCCEEEEEECCeeEEcC
Confidence 45777765 789999643 48999999887655553
No 46
>COG3012 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.19 E-value=61 Score=26.47 Aligned_cols=16 Identities=38% Similarity=0.848 Sum_probs=13.7
Q ss_pred EEeeCCEEEEeeCCCC
Q 045385 129 IRKVNGEWYNFDSLYA 144 (188)
Q Consensus 129 IRki~g~wyNLDS~l~ 144 (188)
.+|++|+||-+|-..+
T Consensus 115 Fvk~ngrWyyiDgtv~ 130 (151)
T COG3012 115 FVKINGRWYYIDGTVP 130 (151)
T ss_pred heEECCEEEEECCCCC
Confidence 4688999999998876
No 47
>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=24.21 E-value=2.8e+02 Score=19.97 Aligned_cols=72 Identities=17% Similarity=0.086 Sum_probs=46.4
Q ss_pred CCchHHHHHHHHhhCCceeEEcCCCCCCCCCCCcccceeeeeccCCceEEEEeeC-CEEEEeeCC-CCCceEcchhh
Q 045385 79 GDFSIQVLQKALEVWDLQVIPLNCPIAEPAQIDPELENAFICHLHDHWFCIRKVN-GEWYNFDSL-YAAPEHLSKFY 153 (188)
Q Consensus 79 GNydinVL~~AL~~~~~~~~~~d~~~~~~~~~~~~~~~gFI~N~~rHWfaIRki~-g~wyNLDS~-l~~P~~i~~~~ 153 (188)
+.++...|..+++..|+++.-...+.. .+.....=+++.-...||+-|=+++ +.+...|.. -..|+.++..+
T Consensus 37 ~~~~~~~l~~~a~~~Gl~~~~~~~~~~---~l~~~~lP~i~~~~~g~~~Vl~~~~~~~~~i~dp~~~~~~~~~~~~e 110 (124)
T cd02421 37 GRLSPALFPRAAARAGLSARVVRRPLD---AIPTLLLPAILLLKNGRACVLLGVDDGHARILDPESGGGEVEISLEE 110 (124)
T ss_pred CCcCHHHHHHHHHHCCCcceeeeCCHH---HCCcccCCEEEEEcCCCEEEEEEecCCeEEEEccCCCCCcEEEcHHH
Confidence 348899999999999987755443221 1222222233334456999888885 466777876 67888888543
No 48
>TIGR01670 YrbI-phosphatas 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase, YrbI family. The Methanosarcina sequence is distinctive in that it is linked to an N-terminal cytidylyltransferase domain (pfam02348) and is annotated as acylneuraminate cytidylyltransferase. This may give some clue as the function of these phosphatases. Several eukaryotic sequences scoring between trusted and noise are also closely related to this function such as the CMP-N-acetylneuraminic acid synthetase from mouse, but in these cases the phosphatase domain is clearly inactive as many of the active site residues are not conserved.
Probab=23.99 E-value=97 Score=24.11 Aligned_cols=21 Identities=19% Similarity=0.180 Sum_probs=17.4
Q ss_pred HHHHHHhCCeEEEEEECCCCC
Q 045385 157 YLDSLKGFGWSIFIVRGNFPK 177 (188)
Q Consensus 157 ~L~~l~~~g~sIFvV~g~lp~ 177 (188)
-|++|+++|+.|+||.+.-..
T Consensus 36 ~i~~Lk~~G~~i~IvTn~~~~ 56 (154)
T TIGR01670 36 GIRCALKSGIEVAIITGRKAK 56 (154)
T ss_pred HHHHHHHCCCEEEEEECCCCH
Confidence 578888999999999886543
No 49
>cd02662 Peptidase_C19F A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=22.83 E-value=91 Score=26.02 Aligned_cols=35 Identities=17% Similarity=0.426 Sum_probs=27.0
Q ss_pred ceeeeecc----CCceEEEEeeC----------------------CEEEEeeCCCCCceEc
Q 045385 115 ENAFICHL----HDHWFCIRKVN----------------------GEWYNFDSLYAAPEHL 149 (188)
Q Consensus 115 ~~gFI~N~----~rHWfaIRki~----------------------g~wyNLDS~l~~P~~i 149 (188)
..|+|++. .-|+++.-|.. +.||..|-..-.|+..
T Consensus 165 L~avi~H~G~~~~GHY~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~W~~fnD~~V~~v~~ 225 (240)
T cd02662 165 LRAVVVHYGSHSSGHYVCYRRKPLFSKDKEPGSFVRMREGPSSTSHPWWRISDTTVKEVSE 225 (240)
T ss_pred EEEEEEEeccCCCceEEEEEeCCCcccccccccccccccccCccCCCEEEEechheEEeCH
Confidence 45888875 67999999886 8999998766555543
No 50
>PF01624 MutS_I: MutS domain I C-terminus.; InterPro: IPR007695 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the N-terminal domain of proteins in the MutS family of DNA mismatch repair proteins, as well as closely related proteins. The N-terminal domain of MutS is responsible for mismatch recognition and forms a 6-stranded mixed beta-sheet surrounded by three alpha-helices, which is similar to the structure of tRNA endonuclease. Yeast MSH3 [], bacterial proteins involved in DNA mismatch repair, and the predicted protein product of the Rep-3 gene of mouse share extensive sequence similarity. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein.; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1FW6_A 1EWQ_A 1EWR_B 1NNE_B 3THY_B 3THZ_B 3THW_B 3THX_B 2WTU_A 1OH7_A ....
Probab=22.71 E-value=1.2e+02 Score=22.47 Aligned_cols=24 Identities=29% Similarity=0.390 Sum_probs=19.6
Q ss_pred chhhHHHHHHHHHhCCeEEEEEEC
Q 045385 150 SKFYLSAYLDSLKGFGWSIFIVRG 173 (188)
Q Consensus 150 ~~~~L~~~L~~l~~~g~sIFvV~g 173 (188)
....|..||..|...||.|-|+..
T Consensus 62 p~~~l~~~l~~Ll~~G~~V~i~~q 85 (113)
T PF01624_consen 62 PKSQLDKYLKKLLEAGYRVAIYEQ 85 (113)
T ss_dssp EGGGHHHHHHHHHHTT-EEEEEEE
T ss_pred cHHHHHHHHHHHHHcCCEEEEEEe
Confidence 457899999999999999998853
No 51
>COG1105 FruK Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB) [Carbohydrate transport and metabolism]
Probab=22.59 E-value=1.2e+02 Score=27.36 Aligned_cols=43 Identities=26% Similarity=0.499 Sum_probs=30.6
Q ss_pred EEEEeeCCCCCceEcchhhHHHHHHHHHh--CCeEEEEEECCCCCCCC
Q 045385 135 EWYNFDSLYAAPEHLSKFYLSAYLDSLKG--FGWSIFIVRGNFPKECP 180 (188)
Q Consensus 135 ~wyNLDS~l~~P~~i~~~~L~~~L~~l~~--~g~sIFvV~g~lp~~~~ 180 (188)
.=+.+| .++| .|++..+..|+++++. +...++|+.|.+|..-|
T Consensus 100 ~~Tein--~~Gp-~is~~~~~~~l~~~~~~l~~~d~VvlsGSlP~g~~ 144 (310)
T COG1105 100 EETEIN--FPGP-EISEAELEQFLEQLKALLESDDIVVLSGSLPPGVP 144 (310)
T ss_pred cEEEec--CCCC-CCCHHHHHHHHHHHHHhcccCCEEEEeCCCCCCCC
Confidence 345444 2344 5777788888887754 67888999999999754
No 52
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=22.47 E-value=1.2e+02 Score=19.07 Aligned_cols=30 Identities=23% Similarity=0.354 Sum_probs=23.2
Q ss_pred HHHHHhhhCC-CCCCHHHHHHHHhhhCHHHH
Q 045385 22 VHCVNTVLQG-PFFSEFDLAALASDLDRSER 51 (188)
Q Consensus 22 lHaLNnLlQ~-~~ft~~dL~~Ia~~Ld~~er 51 (188)
++.|-+.|+. ++-+..++++||.++.-.++
T Consensus 12 ~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~ 42 (59)
T cd00086 12 LEELEKEFEKNPYPSREEREELAKELGLTER 42 (59)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHHHHHCcCHH
Confidence 5666777766 77899999999999865543
No 53
>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=22.10 E-value=1.5e+02 Score=23.44 Aligned_cols=32 Identities=19% Similarity=0.349 Sum_probs=23.7
Q ss_pred eeeeecc-CCceEEEEe--eCCEEEEeeCCCCCce
Q 045385 116 NAFICHL-HDHWFCIRK--VNGEWYNFDSLYAAPE 147 (188)
Q Consensus 116 ~gFI~N~-~rHWfaIRk--i~g~wyNLDS~l~~P~ 147 (188)
.-|.+|. ..||+.+-- -.+..+-+||......
T Consensus 86 i~iPin~~~~HW~l~vi~~~~~~i~~~DSl~~~~~ 120 (216)
T PF02902_consen 86 IFIPININNNHWVLLVIDLPKKRIYVYDSLGSSNN 120 (216)
T ss_dssp EEEEEEETTTEEEEEEEETTTTEEEEE-TTSTSSH
T ss_pred EEEEEechhhccceeEEcccccEEEEEeccccccc
Confidence 4556788 999998842 2579999999887666
No 54
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=21.36 E-value=1.3e+02 Score=19.45 Aligned_cols=30 Identities=23% Similarity=0.184 Sum_probs=20.4
Q ss_pred hHHHHHHhhhCCC--CCCHHHHHHHHhhhCHH
Q 045385 20 CAVHCVNTVLQGP--FFSEFDLAALASDLDRS 49 (188)
Q Consensus 20 CalHaLNnLlQ~~--~ft~~dL~~Ia~~Ld~~ 49 (188)
....+++.++-++ .++...|+.||.-|+-.
T Consensus 22 is~~tl~~~~~~~~~~~~~~~l~~ia~~l~~~ 53 (63)
T PF13443_consen 22 ISRSTLSRILNGKPSNPSLDTLEKIAKALNCS 53 (63)
T ss_dssp --HHHHHHHHTTT-----HHHHHHHHHHHT--
T ss_pred cCHHHHHHHHhcccccccHHHHHHHHHHcCCC
Confidence 3567899999997 79999999999988765
No 55
>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=20.88 E-value=6.3e+02 Score=24.52 Aligned_cols=84 Identities=20% Similarity=0.228 Sum_probs=54.4
Q ss_pred chHHHHHHHHhhCCceeEEcCCCCCCCCCCCcccceeeeeccCCceEEEEee-CCEEEEeeCCCCCceEcchhhHHHHHH
Q 045385 81 FSIQVLQKALEVWDLQVIPLNCPIAEPAQIDPELENAFICHLHDHWFCIRKV-NGEWYNFDSLYAAPEHLSKFYLSAYLD 159 (188)
Q Consensus 81 ydinVL~~AL~~~~~~~~~~d~~~~~~~~~~~~~~~gFI~N~~rHWfaIRki-~g~wyNLDS~l~~P~~i~~~~L~~~L~ 159 (188)
.++.-|..+++..|+++..+..+.. .++. ...-+|+....|++.|-++ ++..+-.|....+++.++..++..
T Consensus 32 ~~~~~l~~~~~~~G~~~~~~~~~~~---~l~~-~~lP~i~~~~~~~vvl~~~~~~~~~i~Dp~~g~~~~i~~~e~~~--- 104 (694)
T TIGR01846 32 LDDLEILLAAKQLGLKAKAVKVSIG---RLNK-LPLPALIDGEGGWFVLGKLTANGVTIYDPPGDAPEVLSREVLEA--- 104 (694)
T ss_pred CCHHHHHHHHHHCCCEEEEEeCCHH---HccC-CCCCEEEEECCcEEEEEEEcCCEEEEEcCCCCCceeeCHHHHHh---
Confidence 7888899999999998877654221 1111 1224555546788888887 468999998766788888543322
Q ss_pred HHHhCCeEEEEEEC
Q 045385 160 SLKGFGWSIFIVRG 173 (188)
Q Consensus 160 ~l~~~g~sIFvV~g 173 (188)
.. .|+-+++...
T Consensus 105 ~~--~g~~l~~~~~ 116 (694)
T TIGR01846 105 LW--SGTVILLATR 116 (694)
T ss_pred hC--CCeEEEEecC
Confidence 11 4665555543
No 56
>PRK03669 mannosyl-3-phosphoglycerate phosphatase; Reviewed
Probab=20.84 E-value=1.3e+02 Score=25.40 Aligned_cols=49 Identities=6% Similarity=0.050 Sum_probs=33.3
Q ss_pred EEeeCCEEEEeeCCCCCceEcchhhHHHHHHHHHhCCeEEEEEECCCCC
Q 045385 129 IRKVNGEWYNFDSLYAAPEHLSKFYLSAYLDSLKGFGWSIFIVRGNFPK 177 (188)
Q Consensus 129 IRki~g~wyNLDS~l~~P~~i~~~~L~~~L~~l~~~g~sIFvV~g~lp~ 177 (188)
+|.+.=....||-+|-.|.......-...|++|+++|..|+++.|.-+.
T Consensus 4 ~~~~~lI~~DlDGTLL~~~~~i~~~~~~ai~~l~~~Gi~~viaTGR~~~ 52 (271)
T PRK03669 4 LQDPLLIFTDLDGTLLDSHTYDWQPAAPWLTRLREAQVPVILCSSKTAA 52 (271)
T ss_pred cCCCeEEEEeCccCCcCCCCcCcHHHHHHHHHHHHcCCeEEEEcCCCHH
Confidence 4444445667777775554433223456689999999999999887654
No 57
>PF08645 PNK3P: Polynucleotide kinase 3 phosphatase; InterPro: IPR013954 Polynucleotide kinase 3 phosphatases play a role in the repair of single breaks in DNA induced by DNA-damaging agents such as gamma radiation and camptothecin []. ; PDB: 2FPW_A 2FPR_A 2FPX_A 2FPS_A 2FPU_B 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B 3U7G_A ....
Probab=20.52 E-value=1.3e+02 Score=23.86 Aligned_cols=21 Identities=29% Similarity=0.360 Sum_probs=18.2
Q ss_pred hHHHHHHHHHhCCeEEEEEEC
Q 045385 153 YLSAYLDSLKGFGWSIFIVRG 173 (188)
Q Consensus 153 ~L~~~L~~l~~~g~sIFvV~g 173 (188)
.+..-|++|.++||.|++|..
T Consensus 33 ~v~~~L~~l~~~Gy~IvIvTN 53 (159)
T PF08645_consen 33 GVPEALRELHKKGYKIVIVTN 53 (159)
T ss_dssp THHHHHHHHHHTTEEEEEEEE
T ss_pred hHHHHHHHHHhcCCeEEEEeC
Confidence 478899999999999999953
Done!