Query psy16758
Match_columns 186
No_of_seqs 110 out of 204
Neff 5.2
Searched_HMMs 46136
Date Fri Aug 16 21:15:38 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16758.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16758hhsearch_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 2.8E-59 6E-64 378.2 9.5 142 15-174 1-157 (157)
2 KOG2934|consensus 100.0 3.2E-56 6.9E-61 364.3 6.7 171 9-180 24-194 (204)
3 KOG2935|consensus 100.0 8.9E-48 1.9E-52 329.9 4.4 151 9-177 2-164 (315)
4 cd02424 Peptidase_C39E A sub-f 92.6 1.8 3.9E-05 32.6 9.6 102 18-150 9-115 (129)
5 cd02420 Peptidase_C39D A sub-f 86.9 6.8 0.00015 28.8 8.5 99 19-150 10-111 (125)
6 cd02419 Peptidase_C39C A sub-f 84.6 13 0.00029 27.2 9.1 99 19-150 10-111 (127)
7 cd02549 Peptidase_C39A A sub-f 84.0 13 0.00028 27.7 8.9 117 16-150 2-123 (141)
8 cd02418 Peptidase_C39B A sub-f 79.6 22 0.00048 26.2 11.5 106 15-150 5-117 (136)
9 PF03412 Peptidase_C39: Peptid 77.3 11 0.00024 27.9 6.4 104 15-150 6-112 (131)
10 cd02423 Peptidase_C39G A sub-f 71.9 34 0.00074 24.9 7.8 102 19-150 10-115 (129)
11 cd02259 Peptidase_C39_like Pep 70.6 36 0.00079 24.4 8.9 100 19-150 5-107 (122)
12 COG2274 SunT ABC-type bacterio 65.9 50 0.0011 33.0 9.7 117 18-174 10-129 (709)
13 cd02425 Peptidase_C39F A sub-f 64.5 52 0.0011 23.8 8.2 98 19-150 10-112 (126)
14 TIGR02616 tnaC_leader tryptoph 64.3 3.1 6.6E-05 24.5 0.6 11 133-143 8-18 (26)
15 cd02257 Peptidase_C19 Peptidas 63.5 10 0.00022 29.7 3.7 41 98-148 194-236 (255)
16 cd02417 Peptidase_C39_likeA A 59.4 64 0.0014 23.3 9.1 96 21-150 7-107 (121)
17 cd02673 Peptidase_C19Q A subfa 57.3 16 0.00034 31.3 4.0 39 98-146 185-226 (245)
18 PF00288 GHMP_kinases_N: GHMP 54.4 17 0.00038 24.4 3.1 29 19-49 21-49 (67)
19 cd02674 Peptidase_C19R A subfa 53.7 18 0.0004 29.2 3.7 38 98-146 175-214 (230)
20 cd02658 Peptidase_C19B A subfa 49.6 21 0.00045 30.6 3.6 39 98-146 253-295 (311)
21 cd02659 peptidase_C19C A subfa 48.8 24 0.00052 30.4 3.9 38 98-146 253-292 (334)
22 TIGR03796 NHPM_micro_ABC1 NHPM 48.3 1.7E+02 0.0036 28.5 9.9 99 18-150 10-112 (710)
23 cd02663 Peptidase_C19G A subfa 47.3 25 0.00053 30.3 3.7 38 99-146 239-276 (300)
24 KOG1415|consensus 45.7 22 0.00047 30.8 3.0 103 8-150 76-187 (222)
25 cd02667 Peptidase_C19K A subfa 44.3 30 0.00065 29.5 3.7 38 98-146 203-263 (279)
26 cd02661 Peptidase_C19E A subfa 43.8 31 0.00068 28.9 3.7 39 98-146 249-288 (304)
27 PF01473 CW_binding_1: Putativ 42.8 28 0.00061 18.1 2.2 12 130-141 5-16 (19)
28 cd02657 Peptidase_C19A A subfa 42.8 35 0.00076 29.1 3.9 38 99-146 243-282 (305)
29 smart00460 TGc Transglutaminas 37.9 1.1E+02 0.0024 19.7 6.1 54 68-141 13-67 (68)
30 PRK03094 hypothetical protein; 34.7 48 0.001 24.3 3.0 22 68-89 10-31 (80)
31 PF13529 Peptidase_C39_2: Pept 34.4 1.3E+02 0.0028 21.6 5.4 119 18-140 13-143 (144)
32 cd02672 Peptidase_C19P A subfa 34.3 47 0.001 28.8 3.4 39 98-146 214-258 (268)
33 PF01088 Peptidase_C12: Ubiqui 34.1 60 0.0013 27.4 3.9 30 122-151 165-194 (214)
34 cd02668 Peptidase_C19L A subfa 34.0 52 0.0011 28.6 3.7 38 99-146 248-287 (324)
35 PF10742 DUF2555: Protein of u 33.8 34 0.00075 23.7 2.0 22 35-56 8-29 (57)
36 PF02251 PA28_alpha: Proteasom 32.2 5.7 0.00012 27.8 -2.1 25 24-49 33-57 (64)
37 PF11814 DUF3335: Peptidase_C3 31.8 1.3E+02 0.0028 25.8 5.6 53 63-142 114-167 (207)
38 KOG1865|consensus 31.6 78 0.0017 30.9 4.6 57 98-174 353-410 (545)
39 PF03698 UPF0180: Uncharacteri 30.5 61 0.0013 23.7 3.0 21 69-89 11-31 (80)
40 cd02421 Peptidase_C39_likeD A 29.2 2.2E+02 0.0048 20.5 8.8 96 21-150 7-108 (124)
41 cd01750 GATase1_CobQ Type 1 gl 29.0 95 0.0021 25.3 4.2 26 63-90 9-34 (194)
42 PF13299 CPSF100_C: Cleavage a 27.9 3.2E+02 0.007 22.0 7.4 59 54-143 89-147 (161)
43 cd02660 Peptidase_C19D A subfa 27.5 83 0.0018 27.0 3.8 38 98-146 274-312 (328)
44 COG3012 Uncharacterized protei 26.1 58 0.0013 26.7 2.4 16 128-143 115-130 (151)
45 cd02662 Peptidase_C19F A subfa 25.4 87 0.0019 26.1 3.5 38 98-146 164-223 (240)
46 PF00443 UCH: Ubiquitin carbox 25.2 93 0.002 24.7 3.5 37 99-146 213-251 (269)
47 smart00850 LytTR LytTr DNA-bin 25.0 12 0.00025 26.2 -1.6 46 10-61 11-56 (96)
48 PF13132 DUF3950: Domain of un 25.0 52 0.0011 20.0 1.4 14 62-75 13-26 (30)
49 PRK14609 4-diphosphocytidyl-2- 24.3 83 0.0018 27.2 3.2 31 19-51 104-134 (269)
50 TIGR01684 viral_ppase viral ph 24.1 1.3E+02 0.0027 27.3 4.4 41 134-176 129-172 (301)
51 PF12295 Symplekin_C: Sympleki 24.0 1.5E+02 0.0032 24.5 4.5 55 23-78 34-102 (183)
52 PF04473 DUF553: Transglutamin 23.9 1.2E+02 0.0025 24.6 3.8 39 123-169 109-147 (153)
53 PRK00650 4-diphosphocytidyl-2- 23.1 90 0.002 27.7 3.3 31 19-51 102-132 (288)
54 PF12780 AAA_8: P-loop contain 23.0 46 0.001 29.1 1.4 37 14-50 97-136 (268)
55 PF13423 UCH_1: Ubiquitin carb 22.7 1.3E+02 0.0028 25.8 4.1 33 98-140 256-292 (295)
56 PF00770 Peptidase_C5: Adenovi 22.1 1.1E+02 0.0024 25.8 3.3 51 85-150 6-58 (183)
57 PRK04181 4-diphosphocytidyl-2- 21.9 1.1E+02 0.0024 26.5 3.6 31 20-52 109-139 (257)
58 PRK14616 4-diphosphocytidyl-2- 21.3 1.2E+02 0.0025 26.3 3.6 31 19-51 105-135 (287)
59 COG4947 Uncharacterized protei 21.0 39 0.00085 29.0 0.5 24 16-39 106-129 (227)
60 PF07283 TrbH: Conjugal transf 20.2 1E+02 0.0022 24.2 2.7 23 69-91 39-61 (121)
61 PF06938 DUF1285: Protein of u 20.2 47 0.001 26.8 0.8 39 131-176 5-44 (148)
62 COG3915 Uncharacterized protei 20.2 4.3E+02 0.0093 21.7 6.2 83 36-140 38-132 (155)
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=2.8e-59 Score=378.21 Aligned_cols=142 Identities=48% Similarity=0.794 Sum_probs=124.0
Q ss_pred ecchhhHHHHHhhhhhCCCCCCCHHHHHHHHhhcCccC--------------ccCCCCCcCCCCCccHHHHHHHHHhcCC
Q psy16758 15 KQMKELCALHALNNLFQNPKTFSKADLDEICINLSPQT--------------WLNPHRSILGLGNYDINVIMTALQKKGF 80 (186)
Q Consensus 15 kQ~~~lCalHaLNnLlQ~~~~ft~~dL~~Ia~~Ld~~~--------------~~nph~n~~~~GNydinVL~~AL~~~g~ 80 (186)
||+++|||+|||||||||| +||+.||++||++||+.| +.+||+||+++||||||||++||++||+
T Consensus 1 kQ~~~lCalHaLNnLlQ~~-~ft~~dL~~Ia~~Ld~~E~~~~~~~~~~~~~~~~~~s~n~~~~GnysinVL~~AL~~~g~ 79 (157)
T PF02099_consen 1 KQELQLCALHALNNLLQGP-YFTAVDLDEIAQELDEEERSLMAEDSWTPLSFLFNPSRNVDGTGNYSINVLMAALQVWGL 79 (157)
T ss_dssp S-STTSHHHHHHHHHCTSS--S-HHHHHHHHHHHHHHHHHHHHCTSHHHHHHHTSTSSTCSTTSTCECHHHHHHHHCCT-
T ss_pred CcHHHHHHHHHHHHHhhhh-hcCHHHHHHHHHHhChhhhhhhhccCccchhhccccccCccccCCcCHHHHHHHHHHcCc
Confidence 7999999999999999999 899999999999999853 3589999999999999999999999999
Q ss_pred eeE-EecCCCCCcccCCcCceEEEeecccccccccccCCCCCCCceEEEEEECCEEEEecCCCCCCeeeCChhHHHHHHH
Q psy16758 81 ESN-WFDRRKDPKCIDQQKVEGYILNIPSQFKIGKYVPTPIKRRHWLTVRNINGIYYNLDSKLDNPEHIGREEDLVEYLR 159 (186)
Q Consensus 81 ~~~-w~d~r~~~~~i~~~~~~gfI~N~~~~~~~g~~~~l~~~~~HWfaIRki~g~wyNLDS~l~~P~~i~~~~~l~~yL~ 159 (186)
+++ |+|+|.....++++++.|||||. +|||||||||+|+||||||++++|+.|++ ++|..||.
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~~gfI~N~---------------~~HWf~iRki~~~wyNLDS~l~~P~~i~~-~~l~~fL~ 143 (157)
T PF02099_consen 80 ELVPWFDKRMQEASIDPDNEFGFICNL---------------SRHWFAIRKIGGQWYNLDSKLKEPELISD-FYLSAFLQ 143 (157)
T ss_dssp EEEETTSHHHHHCC--CCCSSEEEEEC---------------TTEEEEEEEETTEEEEECTTTSS-EEE-H-HHHHHHHH
T ss_pred eEEEccCccchhhhcCchhceEEEecc---------------CcceEEEEeeCCeeEeccCCCCCCcccCH-HHHHHHHH
Confidence 999 66777667888999999999994 89999999999999999999999999987 79999996
Q ss_pred HHhccCCcEEEEEEe
Q psy16758 160 DVLSDIDKELFVVTR 174 (186)
Q Consensus 160 ~~L~~~g~~iFvV~~ 174 (186)
++..+||+||||++
T Consensus 144 -~l~~~g~~ifvV~~ 157 (157)
T PF02099_consen 144 -QLQSEGYSIFVVRG 157 (157)
T ss_dssp -HHHCCTEEEEEEES
T ss_pred -HHHhCCcEEEEEeC
Confidence 56678999999985
No 2
>KOG2934|consensus
Probab=100.00 E-value=3.2e-56 Score=364.26 Aligned_cols=171 Identities=53% Similarity=0.925 Sum_probs=166.4
Q ss_pred ccceeeecchhhHHHHHhhhhhCCCCCCCHHHHHHHHhhcCccCccCCCCCcCCCCCccHHHHHHHHHhcCCeeEEecCC
Q psy16758 9 EIIYHEKQMKELCALHALNNLFQNPKTFSKADLDEICINLSPQTWLNPHRSILGLGNYDINVIMTALQKKGFESNWFDRR 88 (186)
Q Consensus 9 ~~iYhEkQ~~~lCalHaLNnLlQ~~~~ft~~dL~~Ia~~Ld~~~~~nph~n~~~~GNydinVL~~AL~~~g~~~~w~d~r 88 (186)
..||||||++.+||+|||||++|++..||+..+++||.+|.|+.|+|||+++.|.||||+||||+|||+.|++++|||+|
T Consensus 24 ~~iYherq~r~lc~lhAlnnv~q~~n~ftr~~~~d~c~~l~p~s~~~Phrs~~g~Gnydvnvimaalq~~gl~avw~dRr 103 (204)
T KOG2934|consen 24 PGIYHERQRRELCALHALNNVFQRSNAFTRPVLDDICTRLKPRSWLNPHRSWKGPGNYDVNVIMAALQQCGLEAVWLDRR 103 (204)
T ss_pred CccchhHHHHHHHHHHHhhhhhhccccccchhhHHHHhhcCcccccCccccccCCCcccHHHHHHHHHhcCceeeecccc
Confidence 46999999999999999999999998999999999999999999999999999999999999999999999999999999
Q ss_pred CCCcccCCcCceEEEeecccccccccccCCCCCCCceEEEEEECCEEEEecCCCCCCeeeCChhHHHHHHHHHhccCCcE
Q psy16758 89 KDPKCIDQQKVEGYILNIPSQFKIGKYVPTPIKRRHWLTVRNINGIYYNLDSKLDNPEHIGREEDLVEYLRDVLSDIDKE 168 (186)
Q Consensus 89 ~~~~~i~~~~~~gfI~N~~~~~~~g~~~~l~~~~~HWfaIRki~g~wyNLDS~l~~P~~i~~~~~l~~yL~~~L~~~g~~ 168 (186)
+++..+.++.++|||.|+|+++.+| .++||..+|||+|+|+.+|.|||||||+.+|++||++.++.+||..+++.+-++
T Consensus 104 rd~~~l~L~~v~gfIlnlp~~~slG-~L~Lp~~rrhw~alR~~~g~yynldsklr~P~~ig~e~~~~~fla~hl~~~~~e 182 (204)
T KOG2934|consen 104 RDVTALALSVVFGFILNLPCKFSLG-YLRLPVMRRHWLALRSPPGKYYNLDSKLREPECIGTENDFREFLATHLSMAIEE 182 (204)
T ss_pred CCcchhhhHHHHHHHHcCCchhccc-cccchhHHhhhHhhhCCCCceecccccccCCcccccchhHHHHHHHHHHhhhhh
Confidence 9999999999999999999999999 699999999999999999999999999999999999999999999999987899
Q ss_pred EEEEEecCcccc
Q psy16758 169 LFVVTRIENSKS 180 (186)
Q Consensus 169 iFvV~~~~~~~~ 180 (186)
+|+|..+|+++.
T Consensus 183 l~lvi~ee~~~k 194 (204)
T KOG2934|consen 183 LILVINEESSCK 194 (204)
T ss_pred heeeeccccccc
Confidence 999999998854
No 3
>KOG2935|consensus
Probab=100.00 E-value=8.9e-48 Score=329.90 Aligned_cols=151 Identities=30% Similarity=0.460 Sum_probs=138.9
Q ss_pred ccceeeecchhhHHHHHhhhhhCCCCCCCHHHHHHHHhhcCccC-----------ccCCCCCcCCCCCccHHHHHHHHHh
Q psy16758 9 EIIYHEKQMKELCALHALNNLFQNPKTFSKADLDEICINLSPQT-----------WLNPHRSILGLGNYDINVIMTALQK 77 (186)
Q Consensus 9 ~~iYhEkQ~~~lCalHaLNnLlQ~~~~ft~~dL~~Ia~~Ld~~~-----------~~nph~n~~~~GNydinVL~~AL~~ 77 (186)
+.||||+|+..|||+||||+||||+ +|+..||++-+.+++-.+ +-.|+.||+++|+||||||.+||+.
T Consensus 2 ~~ifhE~QE~~LCAqHclN~lLQg~-~fs~~dLaD~~erm~m~Eg~v~g~~~~~fl~~~SeNm~~sG~FSIQVl~kALe~ 80 (315)
T KOG2935|consen 2 GSIFHEVQESNLCAQHCLNTLLQGP-FFSEFDLADGKERMRMAEGGVTGEFYGDFLQQPSENMDDSGFFSIQVLSKALEV 80 (315)
T ss_pred CchhhhhhhhhHHHHHHHHHHhccc-ccChhhhhhHHHHHHHHhcccccccccccccCCCcCcCccCceeHHHHHHHHHh
Confidence 4799999999999999999999999 999999999988876321 2258999999999999999999999
Q ss_pred cCCeeEEecCCCCC-cccCCcCceEEEeecccccccccccCCCCCCCceEEEEEECCEEEEecCCCCCCeeeCChhHHHH
Q psy16758 78 KGFESNWFDRRKDP-KCIDQQKVEGYILNIPSQFKIGKYVPTPIKRRHWLTVRNINGIYYNLDSKLDNPEHIGREEDLVE 156 (186)
Q Consensus 78 ~g~~~~w~d~r~~~-~~i~~~~~~gfI~N~~~~~~~g~~~~l~~~~~HWfaIRki~g~wyNLDS~l~~P~~i~~~~~l~~ 156 (186)
||++++.|..+... ..|||.+..+||||+ +.|||+|||+|++||||||.|.+|+.|++ .+|..
T Consensus 81 w~Leli~~nnP~~~~~~idP~~erafICnl---------------~eHWF~iRKfg~qWfnlnSllagPellSd-tyls~ 144 (315)
T KOG2935|consen 81 WGLELIPFNNPEYQPLQIDPINERAFICNL---------------KEHWFTIRKFGKQWFNLNSLLAGPELLSD-TYLSA 144 (315)
T ss_pred hceeeeecCChhhhhccCCcchhhhhhhcc---------------hhhhhhHhhhcchhccchhhhcchHHHHH-HHHHH
Confidence 99999999999876 578999999999996 89999999999999999999999999999 69999
Q ss_pred HHHHHhccCCcEEEEEEecCc
Q psy16758 157 YLRDVLSDIDKELFVVTRIEN 177 (186)
Q Consensus 157 yL~~~L~~~g~~iFvV~~~~~ 177 (186)
||. +|+++||+||||.|..|
T Consensus 145 FL~-qlq~egySIFVVkG~lP 164 (315)
T KOG2935|consen 145 FLA-QLQQEGYSIFVVKGDLP 164 (315)
T ss_pred HHH-HHHhCCeeEEEEecCCC
Confidence 994 68889999999999887
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=92.64 E-value=1.8 Score=32.62 Aligned_cols=102 Identities=15% Similarity=0.166 Sum_probs=65.5
Q ss_pred hhhHHHHHhhhhhCC---CCCCCHHHHHHHHhhcCccCccCCCCCcCCCCCccHHHHHHHHHhcCCeeEEecCCCCCccc
Q psy16758 18 KELCALHALNNLFQN---PKTFSKADLDEICINLSPQTWLNPHRSILGLGNYDINVIMTALQKKGFESNWFDRRKDPKCI 94 (186)
Q Consensus 18 ~~lCalHaLNnLlQ~---~~~ft~~dL~~Ia~~Ld~~~~~nph~n~~~~GNydinVL~~AL~~~g~~~~w~d~r~~~~~i 94 (186)
..-||+.||=.+++- . ..+.++|...+ .. ...| .|+.-|.++++..|+++.-..... +.+
T Consensus 9 ~~dcgla~l~~i~~~~~g~-~~~~~~l~~~~---~~----------~~~g-~s~~~l~~~a~~~Gl~~k~~~~~~--~~l 71 (129)
T cd02424 9 LNDCGIAVIQMLYNHYYKK-KYDLNELKIKA---NL----------KKNG-LSIYDLENLAKKFGLETESYQGSF--LEF 71 (129)
T ss_pred ccchHHHHHHHHHHHhcCC-CccHHHHHHHh---CC----------CCCC-ccHHHHHHHHHHcCCceeEEEcCH--HHH
Confidence 346999998888753 3 25555555433 21 1235 899999999999999988764322 112
Q ss_pred C-CcCceEEEeecccccccccccCCCCCCCceEEEEEE-CCEEEEecCCCCCCeeeCC
Q psy16758 95 D-QQKVEGYILNIPSQFKIGKYVPTPIKRRHWLTVRNI-NGIYYNLDSKLDNPEHIGR 150 (186)
Q Consensus 95 ~-~~~~~gfI~N~~~~~~~g~~~~l~~~~~HWfaIRki-~g~wyNLDS~l~~P~~i~~ 150 (186)
. .....-.|++. ....||+.++++ ++.++-.|. -.+|+.++.
T Consensus 72 ~~~~~p~P~i~~~-------------~~~~hfvVl~~~~~~~v~I~DP-~~g~~~~s~ 115 (129)
T cd02424 72 LELKNKFIILLKS-------------NGLNHFVIVKKIKKNKFIVLDP-KKGKYKITY 115 (129)
T ss_pred hhccCCEEEEEec-------------CCCCeEEEEEEEECCEEEEECC-CCCCEEeCH
Confidence 1 11122233321 135799999999 667888999 677887765
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=86.89 E-value=6.8 Score=28.80 Aligned_cols=99 Identities=11% Similarity=0.142 Sum_probs=61.3
Q ss_pred hhHHHHHhhhhhCCCC-CCCHHHHHHHHhhcCccCccCCCCCcCCCCCccHHHHHHHHHhcCCeeEEecCCC-CCcccCC
Q psy16758 19 ELCALHALNNLFQNPK-TFSKADLDEICINLSPQTWLNPHRSILGLGNYDINVIMTALQKKGFESNWFDRRK-DPKCIDQ 96 (186)
Q Consensus 19 ~lCalHaLNnLlQ~~~-~ft~~dL~~Ia~~Ld~~~~~nph~n~~~~GNydinVL~~AL~~~g~~~~w~d~r~-~~~~i~~ 96 (186)
.-|++.||=.+++--. -.|.++|.. .+... ..| .+...|.+|++..|+++.-..... .+..+.+
T Consensus 10 ~~~gl~~l~~i~~~~g~~~~~~~l~~---~~~~~----------~~~-~~~~~l~~~a~~~Gl~~~~~~~~~~~L~~~~l 75 (125)
T cd02420 10 TECGAASLAIILAYYGRYVPLSELRI---ACGVS----------RDG-SNASNLLKAAREYGLTAKGYKKDLEALREVSL 75 (125)
T ss_pred cCHHHHHHHHHHHHcCCCCCHHHHHH---HcCCC----------CCC-CCHHHHHHHHHHcCcccceEecCHHHHhcCCC
Confidence 4688888877775320 266666653 33211 134 699999999999999886553321 1122222
Q ss_pred cCceEEEeecccccccccccCCCCCCCceEEEEEEC-CEEEEecCCCCCCeeeCC
Q psy16758 97 QKVEGYILNIPSQFKIGKYVPTPIKRRHWLTVRNIN-GIYYNLDSKLDNPEHIGR 150 (186)
Q Consensus 97 ~~~~gfI~N~~~~~~~g~~~~l~~~~~HWfaIRki~-g~wyNLDS~l~~P~~i~~ 150 (186)
+ .|+- +...||+.|-+++ +.++-.|+.. +|+.++-
T Consensus 76 P----~I~~--------------~~~g~~~Vl~~~~~~~~~i~dp~~-~~~~~s~ 111 (125)
T cd02420 76 P----AIVF--------------WNFNHFLVVEGFDKRKVFLNDPAT-GRRTVSL 111 (125)
T ss_pred C----EEEE--------------eCCCEEEEEEEEeCCEEEEECCCc-CceeecH
Confidence 1 2221 1368999999985 4678888854 7887764
No 6
>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=84.63 E-value=13 Score=27.21 Aligned_cols=99 Identities=11% Similarity=0.153 Sum_probs=59.7
Q ss_pred hhHHHHHhhhhhCCCC-CCCHHHHHHHHhhcCccCccCCCCCcCCCCCccHHHHHHHHHhcCCeeEEecCCC-CCcccCC
Q psy16758 19 ELCALHALNNLFQNPK-TFSKADLDEICINLSPQTWLNPHRSILGLGNYDINVIMTALQKKGFESNWFDRRK-DPKCIDQ 96 (186)
Q Consensus 19 ~lCalHaLNnLlQ~~~-~ft~~dL~~Ia~~Ld~~~~~nph~n~~~~GNydinVL~~AL~~~g~~~~w~d~r~-~~~~i~~ 96 (186)
.-|++.||=.+++--. -++.+++.. .+.. +.+-++...|..+++..|+++......- .+..+.+
T Consensus 10 ~~~~l~~l~~~~~~~g~~~~~~~l~~---~~~~-----------~~~~~~~~~l~~~a~~~Gl~~~~~~~~~~~l~~~~l 75 (127)
T cd02419 10 AECGLACLAMIASYHGHHVDLASLRQ---RFPV-----------SLKGATLADLIDIAQQLGLSTRALRLDLEELGQLKL 75 (127)
T ss_pred ccHHHHHHHHHHHHcCCCCCHHHHHH---HcCC-----------CCCCcCHHHHHHHHHHCCCceeEEEccHHHHhhCCC
Confidence 3577777766664210 155555543 3321 1244999999999999999987764321 1222222
Q ss_pred cCceEEEeecccccccccccCCCCCCCceEEEEEECC-EEEEecCCCCCCeeeCC
Q psy16758 97 QKVEGYILNIPSQFKIGKYVPTPIKRRHWLTVRNING-IYYNLDSKLDNPEHIGR 150 (186)
Q Consensus 97 ~~~~gfI~N~~~~~~~g~~~~l~~~~~HWfaIRki~g-~wyNLDS~l~~P~~i~~ 150 (186)
+ .++. ++..||+.|-++++ .+.-.|+.. +|+.++.
T Consensus 76 P---~i~~---------------~~~g~~~Vl~~~~~~~~~i~dp~~-~~~~~~~ 111 (127)
T cd02419 76 P---CILH---------------WDMNHFVVLKKVSRRRIVIHDPAL-GKRKLSL 111 (127)
T ss_pred C---EEEE---------------ECCCEEEEEEEEcCCEEEEECCcc-CCEEEcH
Confidence 1 1221 13579999999865 566668754 6888865
No 7
>cd02549 Peptidase_C39A A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family of proteins with a single peptidase domain, which are
Probab=83.96 E-value=13 Score=27.67 Aligned_cols=117 Identities=15% Similarity=0.094 Sum_probs=67.1
Q ss_pred cchhhHHHHHhhhhhCCCC-CCCHHHHHHHHhhcCccCccCCCCCcCCCCCccHHHHHHH-HHhcCCeeEEecCCCCC-c
Q psy16758 16 QMKELCALHALNNLFQNPK-TFSKADLDEICINLSPQTWLNPHRSILGLGNYDINVIMTA-LQKKGFESNWFDRRKDP-K 92 (186)
Q Consensus 16 Q~~~lCalHaLNnLlQ~~~-~ft~~dL~~Ia~~Ld~~~~~nph~n~~~~GNydinVL~~A-L~~~g~~~~w~d~r~~~-~ 92 (186)
|...-|+..||-.+++.-. -.+..++... .... .....+.| .+..-|.++ ++..|+++........+ .
T Consensus 2 ~~~~~C~~~slamvl~~~g~~~~~~~l~~~---~~~~-----~~~~~~~g-~~~~~l~~~~a~~~G~~~~~~~~~~~~~~ 72 (141)
T cd02549 2 QLENGCGPTSLAMVLSYLGVKVTKPQLAAE---GNTY-----DFAKDGYG-TYPKPIVSAAARKYGLVVRPLTGLLALLR 72 (141)
T ss_pred CCCCccHHHHHHHHHHhcCCCCCHHHHHhh---cccc-----ccCCCCCC-cCHHHHHHHHHhhCCCcEEECCCHHHHHH
Confidence 5567899999999986431 1344444332 1101 11223356 566667777 99999999876432211 2
Q ss_pred ccCCcCceEEEeecccccccccccCCCCCCCceEEEEEEC--CEEEEecCCCCCCeeeCC
Q psy16758 93 CIDQQKVEGYILNIPSQFKIGKYVPTPIKRRHWLTVRNIN--GIYYNLDSKLDNPEHIGR 150 (186)
Q Consensus 93 ~i~~~~~~gfI~N~~~~~~~g~~~~l~~~~~HWfaIRki~--g~wyNLDS~l~~P~~i~~ 150 (186)
.++. -.=+|+.+...... ....||+.|..++ +..+-.|.-...+..++-
T Consensus 73 ~l~~--~~Pvi~~~~~~~~~-------~~~gH~vVv~g~~~~~~~~i~DP~~~~~~~~~~ 123 (141)
T cd02549 73 QLAA--GHPVIVSVNLGVSI-------TPSGHAMVVIGYDRKGNVYVNDPGGGRRLVVSF 123 (141)
T ss_pred HHHC--CCeEEEEEecCccc-------CCCCeEEEEEEEcCCCCEEEECCCCCcCEEEeH
Confidence 2222 12234433111111 1368999999997 567788887667777754
No 8
>cd02418 Peptidase_C39B A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=79.59 E-value=22 Score=26.19 Aligned_cols=106 Identities=20% Similarity=0.187 Sum_probs=63.2
Q ss_pred ecc-hhhHHHHHhhhhhCC--CCCCCHHHHHHHHhhcCccCccCCCCCcCCCCCccHHHHHHHHHhcCCeeEEecCCCC-
Q psy16758 15 KQM-KELCALHALNNLFQN--PKTFSKADLDEICINLSPQTWLNPHRSILGLGNYDINVIMTALQKKGFESNWFDRRKD- 90 (186)
Q Consensus 15 kQ~-~~lCalHaLNnLlQ~--~~~ft~~dL~~Ia~~Ld~~~~~nph~n~~~~GNydinVL~~AL~~~g~~~~w~d~r~~- 90 (186)
+|. ..-|++.||=.+++. - -++.+++.. .+... .+-++...|.++++..|+++.-......
T Consensus 5 ~q~~~~~~gl~~l~~~~~~~g~-~~~~~~l~~---~~~~~-----------~~~~~~~~l~~~a~~~Gl~~~~~~~~~~~ 69 (136)
T cd02418 5 LQVDEMDCGAACLAMIAKYYGK-NYSLAKLRE---LAGTD-----------REGTSLLGLVKAAEKLGFETRAVKADMDL 69 (136)
T ss_pred EecCcccHHHHHHHHHHHHhCC-CCCHHHHHH---HcCCC-----------CCCcCHHHHHHHHHHCCCeeEEEEcccch
Confidence 444 346888888777653 2 266666543 32211 1238899999999999999877654322
Q ss_pred --CcccCCcCceEEEeecccccccccccCCCCCCCceEEEEEECCEE-EEecCCCCCCeeeCC
Q psy16758 91 --PKCIDQQKVEGYILNIPSQFKIGKYVPTPIKRRHWLTVRNINGIY-YNLDSKLDNPEHIGR 150 (186)
Q Consensus 91 --~~~i~~~~~~gfI~N~~~~~~~g~~~~l~~~~~HWfaIRki~g~w-yNLDS~l~~P~~i~~ 150 (186)
...+..+ +..+|-| .+...||+.|-++++.. +-.|. ...|+.++-
T Consensus 70 ~~l~~~~~P-~I~~~~~-------------~~~~~~~~Vl~~~~~~~~~i~dp-~~~~~~~~~ 117 (136)
T cd02418 70 FELKDIPLP-FIAHVIK-------------EWKLNHYVVVYKIKKKKILIADP-AVGITKISK 117 (136)
T ss_pred hhHhcCCCC-EEEEEcc-------------CCCCCeEEEEEEEcCCEEEEECC-CCCCEEeeH
Confidence 2222211 1222211 02468999999997654 55677 667877754
No 9
>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=77.30 E-value=11 Score=27.93 Aligned_cols=104 Identities=16% Similarity=0.176 Sum_probs=60.7
Q ss_pred ecc-hhhHHHHHhhhhhCCCCCCCHHHHHHHHhhcCccCccCCCCCcCCCCCccHHHHHHHHHhcCCeeEEecCCCC-Cc
Q psy16758 15 KQM-KELCALHALNNLFQNPKTFSKADLDEICINLSPQTWLNPHRSILGLGNYDINVIMTALQKKGFESNWFDRRKD-PK 92 (186)
Q Consensus 15 kQ~-~~lCalHaLNnLlQ~~~~ft~~dL~~Ia~~Ld~~~~~nph~n~~~~GNydinVL~~AL~~~g~~~~w~d~r~~-~~ 92 (186)
+|. ..=||+=||=.+++.- =-+.+.++|...+...+ +..|..-|..|++..|+++..+..... ..
T Consensus 6 ~Q~~~~dcg~acl~~l~~~~--g~~~s~~~l~~~~~~~~-----------~g~s~~~L~~~~~~~gl~~~~~~~~~~~l~ 72 (131)
T PF03412_consen 6 KQSDSNDCGLACLAMLLKYY--GIPVSEEELRRQLGTSE-----------EGTSLADLKRAARKYGLKAKAVKLNFEKLK 72 (131)
T ss_dssp --SSTT-HHHHHHHHHHHHT--T----HHHHHCCTT-BT-----------TB--CCCHHHHHHHTTEEEEEEE--GGGCT
T ss_pred EeCCCCCHHHHHHHHHHHHh--CCCchHHHHHHHhcCCc-----------cCCCHHHHHHHHHhcccceeeeecchhhhh
Confidence 455 4578888888888753 23445566666554221 123444588999999999998753321 12
Q ss_pred ccCCcCceEEEeecccccccccccCCCCCCCceEEEEEECC-EEEEecCCCCCCeeeCC
Q psy16758 93 CIDQQKVEGYILNIPSQFKIGKYVPTPIKRRHWLTVRNING-IYYNLDSKLDNPEHIGR 150 (186)
Q Consensus 93 ~i~~~~~~gfI~N~~~~~~~g~~~~l~~~~~HWfaIRki~g-~wyNLDS~l~~P~~i~~ 150 (186)
.+. .-+|+-+ ...||+-|-++++ ..+-.|. ..+++.++.
T Consensus 73 ~~~----~P~I~~~--------------~~~h~vVi~~~~~~~~~i~dP-~~g~~~~~~ 112 (131)
T PF03412_consen 73 RLP----LPAIAHL--------------KDGHFVVIYKIDDGRVLIYDP-KKGKIKLSK 112 (131)
T ss_dssp CGG----SSEEEEE--------------CCCEEEEEEEECCCEEEECCT-TTCEEEEEH
T ss_pred hcc----ccEEEEe--------------cCcceEEEEeEcCcEEEEEeC-CCCeEEEeH
Confidence 221 2244432 3689999999965 6777888 777888864
No 10
>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=71.88 E-value=34 Score=24.93 Aligned_cols=102 Identities=15% Similarity=0.190 Sum_probs=60.6
Q ss_pred hhHHHHHhhhhhCCC--CCCCHHHHHHHHhhcCccCccCCCCCcCCCCCccHHHHHHHHHhcCCeeEEecCCC-CCcccC
Q psy16758 19 ELCALHALNNLFQNP--KTFSKADLDEICINLSPQTWLNPHRSILGLGNYDINVIMTALQKKGFESNWFDRRK-DPKCID 95 (186)
Q Consensus 19 ~lCalHaLNnLlQ~~--~~ft~~dL~~Ia~~Ld~~~~~nph~n~~~~GNydinVL~~AL~~~g~~~~w~d~r~-~~~~i~ 95 (186)
+-|++.|+=.+++.- .-++..+|.. ++... ..| ++..-|.++++..|+++.-...+. .+..+.
T Consensus 10 ~~~~l~~l~~~~~~~g~~~~~~~~l~~---~~~~~----------~~~-~s~~~l~~~a~~~Gl~~~~~~~~~~~L~~~~ 75 (129)
T cd02423 10 FSCGPAALATLLRYYGGINITEQEVLK---LMLIR----------SEG-FSMLDLKRYAEALGLKANGYRLNLDKLNALQ 75 (129)
T ss_pred CChHHHHHHHHHHhcCCCCCCHHHHHH---HhCcc----------cCC-cCHHHHHHHHHHCCCcceEEEcCHHHHhhCC
Confidence 368888877666432 0256666643 33211 123 889999999999999998764432 112222
Q ss_pred CcCceEEEeecccccccccccCCCCCCCceEEEEEE-CCEEEEecCCCCCCeeeCC
Q psy16758 96 QQKVEGYILNIPSQFKIGKYVPTPIKRRHWLTVRNI-NGIYYNLDSKLDNPEHIGR 150 (186)
Q Consensus 96 ~~~~~gfI~N~~~~~~~g~~~~l~~~~~HWfaIRki-~g~wyNLDS~l~~P~~i~~ 150 (186)
++ +..++-| | ...||+.|.++ ++.+.-.|+.. .|+.++.
T Consensus 76 lP-~i~~~~~-------~-------~~~~~vvl~~~~~~~~~i~dp~~-~~~~~s~ 115 (129)
T cd02423 76 IP-VIVLVNN-------G-------GYGHFVVIKGIDGDRVLVGDPAL-GNISMSR 115 (129)
T ss_pred CC-EEEEEec-------C-------CCceEEEEEEEeCCEEEEECCCC-CCcccCH
Confidence 22 2222211 1 25799999977 56777788744 5666654
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=70.60 E-value=36 Score=24.36 Aligned_cols=100 Identities=12% Similarity=0.123 Sum_probs=60.8
Q ss_pred hhHHHHHhhhhhCCCC-CCCHHHHHHHHhhcCccCccCCCCCcCCCCCccHHHHHHHHHhcCCeeEEecCCC-CCcccCC
Q psy16758 19 ELCALHALNNLFQNPK-TFSKADLDEICINLSPQTWLNPHRSILGLGNYDINVIMTALQKKGFESNWFDRRK-DPKCIDQ 96 (186)
Q Consensus 19 ~lCalHaLNnLlQ~~~-~ft~~dL~~Ia~~Ld~~~~~nph~n~~~~GNydinVL~~AL~~~g~~~~w~d~r~-~~~~i~~ 96 (186)
.-|++.||=.+++--. -++.+++. ..+... .+-++...|.++.+..|+++.-...+. .+..+..
T Consensus 5 ~~~gl~~l~~i~~~~g~~~~~~~l~---~~~~~~-----------~~~~~~~~l~~~a~~~gl~~~~~~~~~~~l~~~~~ 70 (122)
T cd02259 5 LDCGLACLQMLLRYFGIPVRRDVLL---NAQQRR-----------QQGLSLADLVSLANKLGLTAQGVKLPLAALSRLQL 70 (122)
T ss_pred cchHHHHHHHHHHHcCCCCCHHHHH---HHHhhc-----------cCCCCHHHHHHHHHHcCCeeeEEEcCHHHhccCCC
Confidence 3577777766554320 16666653 222211 233889999999999999998764432 1222222
Q ss_pred cCceEEEeecccccccccccCCCCCCCceEEEEEECC-EEEEecCCCCCCeeeCC
Q psy16758 97 QKVEGYILNIPSQFKIGKYVPTPIKRRHWLTVRNING-IYYNLDSKLDNPEHIGR 150 (186)
Q Consensus 97 ~~~~gfI~N~~~~~~~g~~~~l~~~~~HWfaIRki~g-~wyNLDS~l~~P~~i~~ 150 (186)
+ +++. +...||+.|-++++ .....|..-..|+.++.
T Consensus 71 P---~i~~---------------~~~~~~~Vl~~~~~~~~~i~dp~~~~~~~~~~ 107 (122)
T cd02259 71 P---ALLL---------------WKQGHFVILYGADKGQVLIADPLEEGPVTLSE 107 (122)
T ss_pred C---EEEE---------------cCCCcEEEEEEEcCCEEEEECCcccCCEEeCH
Confidence 2 2222 13689999999965 56666775677887765
No 12
>COG2274 SunT ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]
Probab=65.87 E-value=50 Score=32.98 Aligned_cols=117 Identities=15% Similarity=0.161 Sum_probs=76.7
Q ss_pred hhhHHHHHhhhhhC--CCCCCCHHHHHHHHhhcCccCccCCCCCcCCCCCccHHHHHHHHHhcCCeeEEecCCCCCcccC
Q psy16758 18 KELCALHALNNLFQ--NPKTFSKADLDEICINLSPQTWLNPHRSILGLGNYDINVIMTALQKKGFESNWFDRRKDPKCID 95 (186)
Q Consensus 18 ~~lCalHaLNnLlQ--~~~~ft~~dL~~Ia~~Ld~~~~~nph~n~~~~GNydinVL~~AL~~~g~~~~w~d~r~~~~~i~ 95 (186)
..=||+.||..+.+ |. -++.++|.+.+.. . .+-.+..-|..+-++.|+++.-+.-. ...+.
T Consensus 10 ~~dcgla~l~mia~~~g~-~~~~~~lr~~~~~---------~-----~~g~sl~~l~~~a~~lGl~~~~~~~~--~~~l~ 72 (709)
T COG2274 10 ANDCGLACLAMIANYHGK-KISLNELRELVGL---------S-----RNGLSLLELKQAAEKLGLSARAVKLS--LEELK 72 (709)
T ss_pred ccchHHHHHHHHHHHhCC-CCCHHHHHHHcCC---------C-----CCCCChHHHHHHHHHcCCccccccCC--HHHhc
Confidence 45799999998887 44 3666666554321 1 12578888999999999998877544 22221
Q ss_pred CcCceEEEeecccccccccccCCCCCCCceEEEEEECCE-EEEecCCCCCCeeeCChhHHHHHHHHHhccCCcEEEEEEe
Q psy16758 96 QQKVEGYILNIPSQFKIGKYVPTPIKRRHWLTVRNINGI-YYNLDSKLDNPEHIGREEDLVEYLRDVLSDIDKELFVVTR 174 (186)
Q Consensus 96 ~~~~~gfI~N~~~~~~~g~~~~l~~~~~HWfaIRki~g~-wyNLDS~l~~P~~i~~~~~l~~yL~~~L~~~g~~iFvV~~ 174 (186)
... .=+|++ |...||+.+-++++. |+-+|- -..++.++.. +|.+... |+.+++.-.
T Consensus 73 ~~~-lP~ii~--------------~~~~h~vVl~~~~~~~~~v~dp-~~g~~~l~~~----e~~~~~t---g~~l~l~~~ 129 (709)
T COG2274 73 QLP-LPAIIH--------------WNGNHFVVLYKIDKNKVVVLDP-AKGIRRLSLE----EFEKLWT---GIALLLAPT 129 (709)
T ss_pred ccC-CCEEEE--------------EcCCcEEEEEEecCCeEEEEeC-CCCcEEcCHH----HHHHhhh---eeEEEEecc
Confidence 111 124554 346899999999886 889999 7889999873 3443322 565555554
No 13
>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=64.52 E-value=52 Score=23.83 Aligned_cols=98 Identities=13% Similarity=0.187 Sum_probs=59.8
Q ss_pred hhHHHHHhhhhhC--CCCCCCHHHHHHHHhhcCccCccCCCCCcCCCCCccHHHHHHHHHhcCCeeEEecCCC--CCccc
Q psy16758 19 ELCALHALNNLFQ--NPKTFSKADLDEICINLSPQTWLNPHRSILGLGNYDINVIMTALQKKGFESNWFDRRK--DPKCI 94 (186)
Q Consensus 19 ~lCalHaLNnLlQ--~~~~ft~~dL~~Ia~~Ld~~~~~nph~n~~~~GNydinVL~~AL~~~g~~~~w~d~r~--~~~~i 94 (186)
.-|++.||=.+++ +- -++..++... +... .+..+...+.++++..|+++.-..... .+..+
T Consensus 10 ~~~~l~~l~~~~~~~~~-~~~~~~l~~~---~~~~-----------~~~~~~~~l~~~a~~~gl~~~~~~~~~~~~l~~~ 74 (126)
T cd02425 10 TECGLACYAMILNYFGY-KVSLNELREK---YELG-----------RDGLSLSYLKQLLEEYGFKCKVYKISFKKNLYPL 74 (126)
T ss_pred ccHHHHHHHHHHHHhCC-CCCHHHHHHh---ccCC-----------CCCcCHHHHHHHHHHCCCcceEEEEchHHHHhhC
Confidence 3588888777665 33 2777766542 2211 123888999999999999887654322 11222
Q ss_pred CCcCceEEEeecccccccccccCCCCCCCceEEEEEECC-EEEEecCCCCCCeeeCC
Q psy16758 95 DQQKVEGYILNIPSQFKIGKYVPTPIKRRHWLTVRNING-IYYNLDSKLDNPEHIGR 150 (186)
Q Consensus 95 ~~~~~~gfI~N~~~~~~~g~~~~l~~~~~HWfaIRki~g-~wyNLDS~l~~P~~i~~ 150 (186)
.++ +|+-. ...||+.|-++++ ..+-.|+.. +++.++.
T Consensus 75 ~lP----~I~~~--------------~~~~~~Vl~~~~~~~~~i~dp~~-~~~~~~~ 112 (126)
T cd02425 75 KLP----VIIFW--------------NNNHFVVLEKIKKNKVTIVDPAI-GRIKISI 112 (126)
T ss_pred CCC----EEEEE--------------cCCcEEEEEEEECCEEEEEcCCC-CCEEECH
Confidence 221 23211 2569999988754 577888855 5666754
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=64.28 E-value=3.1 Score=24.50 Aligned_cols=11 Identities=18% Similarity=0.779 Sum_probs=9.1
Q ss_pred CEEEEecCCCC
Q psy16758 133 GIYYNLDSKLD 143 (186)
Q Consensus 133 g~wyNLDS~l~ 143 (186)
..|||+|+++.
T Consensus 8 s~WfniD~rIs 18 (26)
T TIGR02616 8 SKWFNIDNRIS 18 (26)
T ss_pred CceEEcchhhe
Confidence 37999999875
No 15
>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=63.55 E-value=10 Score=29.68 Aligned_cols=41 Identities=7% Similarity=0.177 Sum_probs=30.7
Q ss_pred CceEEEeecccccccccccCCCCCCCceEEEEEEC--CEEEEecCCCCCCeee
Q psy16758 98 KVEGYILNIPSQFKIGKYVPTPIKRRHWLTVRNIN--GIYYNLDSKLDNPEHI 148 (186)
Q Consensus 98 ~~~gfI~N~~~~~~~g~~~~l~~~~~HWfaIRki~--g~wyNLDS~l~~P~~i 148 (186)
...|+||..... ....|++|..|-. +.||..|-..-.++.-
T Consensus 194 ~L~~vi~h~G~~----------~~~GHY~~~~~~~~~~~W~~~nD~~V~~v~~ 236 (255)
T cd02257 194 ELVAVVVHSGTS----------ADSGHYVAYVKDPSDGKWYKFNDDKVTEVSE 236 (255)
T ss_pred EEEEEEEEecCC----------CCCcCeEEEEeCCCCCceEEEeccccEEcCH
Confidence 578999986432 1467999998887 8999999877666633
No 16
>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=59.44 E-value=64 Score=23.26 Aligned_cols=96 Identities=14% Similarity=0.122 Sum_probs=58.0
Q ss_pred HHHHHhhhhh---CCCCCCCHHHHHHHHhhcCccCccCCCCCcCCCCCccHHHHHHHHHhcCCeeEEecCCC-CCcccCC
Q psy16758 21 CALHALNNLF---QNPKTFSKADLDEICINLSPQTWLNPHRSILGLGNYDINVIMTALQKKGFESNWFDRRK-DPKCIDQ 96 (186)
Q Consensus 21 CalHaLNnLl---Q~~~~ft~~dL~~Ia~~Ld~~~~~nph~n~~~~GNydinVL~~AL~~~g~~~~w~d~r~-~~~~i~~ 96 (186)
|++.||=.++ ..+ ++.+.|... +... .+-++...|.++++..|+.+......- .+..+.+
T Consensus 7 ~~l~~l~~i~~~~g~~--~~~~~l~~~---~~~~-----------~~~~~~~~l~~~a~~~Gl~~~~~~~~~~~l~~~~l 70 (121)
T cd02417 7 SGLLALVLLARYHGIA--ADPEQLRHE---FGLA-----------GEPFNSTELLLAAKSLGLKAKAVRQPVERLARLPL 70 (121)
T ss_pred cHHHHHHHHHHHcCCC--CCHHHHHHH---hcCC-----------CCCCCHHHHHHHHHHcCCeeEEEecCHHHhccCCC
Confidence 5555544443 344 677666643 3211 344899999999999999988664321 1222222
Q ss_pred cCceEEEeecccccccccccCCCCCCCceEEEEEECC-EEEEecCCCCCCeeeCC
Q psy16758 97 QKVEGYILNIPSQFKIGKYVPTPIKRRHWLTVRNING-IYYNLDSKLDNPEHIGR 150 (186)
Q Consensus 97 ~~~~gfI~N~~~~~~~g~~~~l~~~~~HWfaIRki~g-~wyNLDS~l~~P~~i~~ 150 (186)
+ .++. +...||+-|-++++ ..+-.|.....|+.++.
T Consensus 71 P---~I~~---------------~~~g~~~Vl~~~~~~~~~i~dp~~~~~~~~~~ 107 (121)
T cd02417 71 P---ALAW---------------DDDGGHFILAKLDGQKYLIQDPISQRPEVLSR 107 (121)
T ss_pred C---EEEE---------------ccCCCEEEEEEEcCCCEEEECCCcCCCeecCH
Confidence 1 2221 13579999998865 56777875556888765
No 17
>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=57.33 E-value=16 Score=31.35 Aligned_cols=39 Identities=8% Similarity=0.089 Sum_probs=28.5
Q ss_pred CceEEEeecccccccccccCCCCCCCceEEEEEE---CCEEEEecCCCCCCe
Q psy16758 98 KVEGYILNIPSQFKIGKYVPTPIKRRHWLTVRNI---NGIYYNLDSKLDNPE 146 (186)
Q Consensus 98 ~~~gfI~N~~~~~~~g~~~~l~~~~~HWfaIRki---~g~wyNLDS~l~~P~ 146 (186)
...|+|+..... ...-|++|.-|. +|.||.+|=..-.|+
T Consensus 185 ~L~~VV~H~G~~----------~~~GHY~a~vk~~~~~~~Wy~fnD~~V~~v 226 (245)
T cd02673 185 SLVAVICHLGES----------PYDGHYIAYTKELYNGSSWLYCSDDEIRPV 226 (245)
T ss_pred EEEEEEEECCCC----------CCCceEEEEEEcCCCCCeEEEeeCceeeEc
Confidence 467888876321 246799999887 689999998776654
No 18
>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=54.44 E-value=17 Score=24.35 Aligned_cols=29 Identities=31% Similarity=0.472 Sum_probs=25.6
Q ss_pred hhHHHHHhhhhhCCCCCCCHHHHHHHHhhcC
Q psy16758 19 ELCALHALNNLFQNPKTFSKADLDEICINLS 49 (186)
Q Consensus 19 ~lCalHaLNnLlQ~~~~ft~~dL~~Ia~~Ld 49 (186)
..|.+.|+|.++..+ +++.+|.++|.+..
T Consensus 21 ~~a~~~a~~~~~~~~--~~~~~l~~~a~~~e 49 (67)
T PF00288_consen 21 AVALAAALNKLFGLP--LSKEELAKLAQEAE 49 (67)
T ss_dssp HHHHHHHHHHHTTTS--SBHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcccc--ccHHHHHHHHHHHH
Confidence 478899999999887 89999999998765
No 19
>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=53.73 E-value=18 Score=29.18 Aligned_cols=38 Identities=13% Similarity=0.132 Sum_probs=28.5
Q ss_pred CceEEEeecccccccccccCCCCCCCceEEEEEEC--CEEEEecCCCCCCe
Q psy16758 98 KVEGYILNIPSQFKIGKYVPTPIKRRHWLTVRNIN--GIYYNLDSKLDNPE 146 (186)
Q Consensus 98 ~~~gfI~N~~~~~~~g~~~~l~~~~~HWfaIRki~--g~wyNLDS~l~~P~ 146 (186)
...|+|+..... ...||+|..+.+ +.||-+|=..-.++
T Consensus 175 ~L~~vI~H~G~~-----------~~GHY~~~~~~~~~~~W~~fnD~~V~~i 214 (230)
T cd02674 175 DLYAVVNHYGSL-----------NGGHYTAYCKNNETNDWYKFDDSRVTKV 214 (230)
T ss_pred EEEEEEEeeCCC-----------CCcEEEEEEECCCCCceEEEcCCeEEEc
Confidence 468999886322 357999999987 89999987665544
No 20
>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=49.59 E-value=21 Score=30.63 Aligned_cols=39 Identities=8% Similarity=0.180 Sum_probs=28.2
Q ss_pred CceEEEeecccccccccccCCCCCCCceEEEEEEC----CEEEEecCCCCCCe
Q psy16758 98 KVEGYILNIPSQFKIGKYVPTPIKRRHWLTVRNIN----GIYYNLDSKLDNPE 146 (186)
Q Consensus 98 ~~~gfI~N~~~~~~~g~~~~l~~~~~HWfaIRki~----g~wyNLDS~l~~P~ 146 (186)
...|+|+..... ....|+++.-|.. |.||-.|=..=.|.
T Consensus 253 ~L~~vI~H~G~~----------~~~GHY~~~vk~~~~~~~~W~~fnD~~V~~~ 295 (311)
T cd02658 253 ELIAFISHKGTS----------VHSGHYVAHIKKEIDGEGKWVLFNDEKVVAS 295 (311)
T ss_pred EEEEEEEccCCC----------CCCcceEEEEeCCCCCCCCEEEecCceeEEC
Confidence 367888875321 2467999999988 89999987665443
No 21
>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=48.84 E-value=24 Score=30.43 Aligned_cols=38 Identities=13% Similarity=0.357 Sum_probs=27.9
Q ss_pred CceEEEeecccccccccccCCCCCCCceEEEEEEC--CEEEEecCCCCCCe
Q psy16758 98 KVEGYILNIPSQFKIGKYVPTPIKRRHWLTVRNIN--GIYYNLDSKLDNPE 146 (186)
Q Consensus 98 ~~~gfI~N~~~~~~~g~~~~l~~~~~HWfaIRki~--g~wyNLDS~l~~P~ 146 (186)
...|+|+...+ ..+.||+|..|-. +.||.+|-..-.+.
T Consensus 253 ~L~~vI~H~G~-----------~~~GHY~~~vk~~~~~~W~~~nD~~V~~i 292 (334)
T cd02659 253 ELHGVLVHSGD-----------AHGGHYYSYIKDRDDGKWYKFNDDVVTPF 292 (334)
T ss_pred EEEEEEEecCC-----------CCCCCeEEEEECCCCCceEEEeCcccEEC
Confidence 36778877531 2468999988865 89999998776555
No 22
>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=48.29 E-value=1.7e+02 Score=28.50 Aligned_cols=99 Identities=18% Similarity=0.246 Sum_probs=64.5
Q ss_pred hhhHHHHHhhhhhCC--CCCCCHHHHHHHHhhcCccCccCCCCCcCCCCCccHHHHHHHHHhcCCeeEEecCCC-CCccc
Q psy16758 18 KELCALHALNNLFQN--PKTFSKADLDEICINLSPQTWLNPHRSILGLGNYDINVIMTALQKKGFESNWFDRRK-DPKCI 94 (186)
Q Consensus 18 ~~lCalHaLNnLlQ~--~~~ft~~dL~~Ia~~Ld~~~~~nph~n~~~~GNydinVL~~AL~~~g~~~~w~d~r~-~~~~i 94 (186)
..=||+=||=.+++- . -.+..+|.+. +... ..| .++.-|.+|++..|+++.-+.... ....+
T Consensus 10 ~~dCg~acl~mi~~~~g~-~~~~~~lr~~---~~~~----------~~g-~s~~~l~~~~~~~g~~~~~~~~~~~~l~~~ 74 (710)
T TIGR03796 10 AVECGAASLAMILAYYGR-YVPLEELREE---CGVS----------RDG-SKASNLLKAARSYGLEAKGFRKELDALAEL 74 (710)
T ss_pred cccHHHHHHHHHHHHcCC-CCCHHHHHHH---cCCC----------CCC-CCHHHHHHHHHHCCCEeEEEecCHHHhccC
Confidence 457999888877763 3 2555555432 2211 134 799999999999999998775431 12222
Q ss_pred CCcCceEEEeecccccccccccCCCCCCCceEEEEEEC-CEEEEecCCCCCCeeeCC
Q psy16758 95 DQQKVEGYILNIPSQFKIGKYVPTPIKRRHWLTVRNIN-GIYYNLDSKLDNPEHIGR 150 (186)
Q Consensus 95 ~~~~~~gfI~N~~~~~~~g~~~~l~~~~~HWfaIRki~-g~wyNLDS~l~~P~~i~~ 150 (186)
.+ -.|+- |...|++.+.++. +..+-.|... ++..++-
T Consensus 75 ~l----P~i~~--------------~~~~h~vvl~~~~~~~~~i~dP~~-g~~~~~~ 112 (710)
T TIGR03796 75 PL----PYIVF--------------WNFNHFVVVEGFRGGRVYLNDPAL-GPRTVSL 112 (710)
T ss_pred CC----CEEEE--------------EcCCcEEEEEEEeCCEEEEECCCC-CCEEccH
Confidence 22 23432 3469999999986 5677888754 7888865
No 23
>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=47.33 E-value=25 Score=30.32 Aligned_cols=38 Identities=11% Similarity=0.218 Sum_probs=28.4
Q ss_pred ceEEEeecccccccccccCCCCCCCceEEEEEECCEEEEecCCCCCCe
Q psy16758 99 VEGYILNIPSQFKIGKYVPTPIKRRHWLTVRNINGIYYNLDSKLDNPE 146 (186)
Q Consensus 99 ~~gfI~N~~~~~~~g~~~~l~~~~~HWfaIRki~g~wyNLDS~l~~P~ 146 (186)
..|+|+...+. ..+-|++|..|-+|.||..|=..-.|.
T Consensus 239 L~~vi~H~G~~----------~~~GHY~a~~k~~~~W~~fdD~~V~~~ 276 (300)
T cd02663 239 LVAVVVHIGGG----------PNHGHYVSIVKSHGGWLLFDDETVEKI 276 (300)
T ss_pred EEEEEEEecCC----------CCCCceEEEEECCCcEEEEcCCceEEc
Confidence 56777775321 247899999999999999998766554
No 24
>KOG1415|consensus
Probab=45.74 E-value=22 Score=30.76 Aligned_cols=103 Identities=24% Similarity=0.365 Sum_probs=63.6
Q ss_pred cccceeeecc-hhhHH----HHHhhhhhCCCCCCCHH-HHHHH---HhhcCccCccCCCCCcCCCCCccHHHHHHHHHhc
Q psy16758 8 QEIIYHEKQM-KELCA----LHALNNLFQNPKTFSKA-DLDEI---CINLSPQTWLNPHRSILGLGNYDINVIMTALQKK 78 (186)
Q Consensus 8 ~~~iYhEkQ~-~~lCa----lHaLNnLlQ~~~~ft~~-dL~~I---a~~Ld~~~~~nph~n~~~~GNydinVL~~AL~~~ 78 (186)
++++||=||. ..-|| +|+|-|.=-.-. +..- .|+.. +..+++++ |.=+=.++=.+..+-+|....
T Consensus 76 ~~~V~fmkQti~NACGTiaLlHslaN~~~r~~-l~~Gs~l~~fl~~~~~~s~ee-----Ra~~le~d~~l~~~H~a~a~e 149 (222)
T KOG1415|consen 76 SDKVFFMKQTIGNACGTIALLHSLANNEDRVK-LEDGSFLKKFLEEAEKMSPEE-----RADLLENDEELEAAHEAAAQE 149 (222)
T ss_pred CCceEEEeccccchhHHHHHHHHHhccccccc-cCCchHHHHHHHHhhcCCHHH-----HHHHhcccHHHHHHHHHHHhc
Confidence 4689999999 56776 688877644332 4433 45544 23333333 221113444566666666664
Q ss_pred CCeeEEecCCCCCcccCCcCceEEEeecccccccccccCCCCCCCceEEEEEECCEEEEecCCCCCCeeeCC
Q psy16758 79 GFESNWFDRRKDPKCIDQQKVEGYILNIPSQFKIGKYVPTPIKRRHWLTVRNINGIYYNLDSKLDNPEHIGR 150 (186)
Q Consensus 79 g~~~~w~d~r~~~~~i~~~~~~gfI~N~~~~~~~g~~~~l~~~~~HWfaIRki~g~wyNLDS~l~~P~~i~~ 150 (186)
|=+- .+-+ -.-|+++.-+.+|.-|-||+-.+.|+..|.
T Consensus 150 Gqte-----------~~~~-----------------------vd~HFI~~v~~~G~lYELDgR~~fPi~hG~ 187 (222)
T KOG1415|consen 150 GQTE-----------ADED-----------------------VDLHFICFVNKNGHLYELDGRKPFPINHGP 187 (222)
T ss_pred CCCC-----------Cccc-----------------------cceEEEEEEccCCeEEEecCCcCCCccCCC
Confidence 4221 0111 135777777899999999999999999986
No 25
>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=44.25 E-value=30 Score=29.53 Aligned_cols=38 Identities=11% Similarity=0.280 Sum_probs=28.3
Q ss_pred CceEEEeecccccccccccCCCCCCCceEEEEEE-----------------------CCEEEEecCCCCCCe
Q psy16758 98 KVEGYILNIPSQFKIGKYVPTPIKRRHWLTVRNI-----------------------NGIYYNLDSKLDNPE 146 (186)
Q Consensus 98 ~~~gfI~N~~~~~~~g~~~~l~~~~~HWfaIRki-----------------------~g~wyNLDS~l~~P~ 146 (186)
...|+|+...+. ..-|++|..|. +|.||.+|=..-.++
T Consensus 203 ~L~~vi~H~G~~-----------~~GHY~a~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~W~~~dD~~V~~v 263 (279)
T cd02667 203 RLYGVVEHSGTM-----------RSGHYVAYVKVRPPQQRLSDLTKSKPAADEAGPGSGQWYYISDSDVREV 263 (279)
T ss_pred EEEEEEEEeCCC-----------CCCEeEEEEEcCccccccccccccccccccCCCCCCcEEEEECCccEEC
Confidence 478999886321 46799999886 679999987665544
No 26
>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=43.80 E-value=31 Score=28.90 Aligned_cols=39 Identities=21% Similarity=0.322 Sum_probs=27.6
Q ss_pred CceEEEeecccccccccccCCCCCCCceEEEEEE-CCEEEEecCCCCCCe
Q psy16758 98 KVEGYILNIPSQFKIGKYVPTPIKRRHWLTVRNI-NGIYYNLDSKLDNPE 146 (186)
Q Consensus 98 ~~~gfI~N~~~~~~~g~~~~l~~~~~HWfaIRki-~g~wyNLDS~l~~P~ 146 (186)
+..|+|+..... ..+.|++|..+- +|.||.+|-..-.++
T Consensus 249 ~L~~vi~H~G~~----------~~~GHY~~~~~~~~~~W~~~nD~~V~~v 288 (304)
T cd02661 249 KLYAVLVHSGFS----------PHSGHYYCYVKSSNGKWYNMDDSKVSPV 288 (304)
T ss_pred eEEEEEEECCCC----------CCCcCCEEEEECCCCCEEEEeCCeeEEC
Confidence 367888875221 146799999775 889999988665554
No 27
>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=42.84 E-value=28 Score=18.14 Aligned_cols=12 Identities=42% Similarity=0.678 Sum_probs=9.6
Q ss_pred EECCEEEEecCC
Q psy16758 130 NINGIYYNLDSK 141 (186)
Q Consensus 130 ki~g~wyNLDS~ 141 (186)
+++|.||-+|+.
T Consensus 5 ~~~~~wYy~~~~ 16 (19)
T PF01473_consen 5 QDNGNWYYFDSD 16 (19)
T ss_dssp EETTEEEEETTT
T ss_pred EECCEEEEeCCC
Confidence 458999999873
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=42.83 E-value=35 Score=29.09 Aligned_cols=38 Identities=11% Similarity=0.131 Sum_probs=27.6
Q ss_pred ceEEEeecccccccccccCCCCCCCceEEEEEEC--CEEEEecCCCCCCe
Q psy16758 99 VEGYILNIPSQFKIGKYVPTPIKRRHWLTVRNIN--GIYYNLDSKLDNPE 146 (186)
Q Consensus 99 ~~gfI~N~~~~~~~g~~~~l~~~~~HWfaIRki~--g~wyNLDS~l~~P~ 146 (186)
..|+|+..... ..+-|++|..|-. +.||.+|=..-.|+
T Consensus 243 L~~vI~H~G~~----------~~~GHY~~~~~~~~~~~W~~fdD~~V~~~ 282 (305)
T cd02657 243 LVAVITHQGRS----------ADSGHYVAWVRRKNDGKWIKFDDDKVSEV 282 (305)
T ss_pred EEEEEEecCCC----------CCCcEEEEEEEcCCCCeEEEEECCceEEe
Confidence 67888875211 1356999999887 89999997665555
No 29
>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=37.91 E-value=1.1e+02 Score=19.72 Aligned_cols=54 Identities=19% Similarity=0.346 Sum_probs=31.0
Q ss_pred HHHHHHHHHhcCCeeEEecCCCCCcccCCcCceEEEeecccccccccccCCCCCCCc-eEEEEEECCEEEEecCC
Q psy16758 68 INVIMTALQKKGFESNWFDRRKDPKCIDQQKVEGYILNIPSQFKIGKYVPTPIKRRH-WLTVRNINGIYYNLDSK 141 (186)
Q Consensus 68 inVL~~AL~~~g~~~~w~d~r~~~~~i~~~~~~gfI~N~~~~~~~g~~~~l~~~~~H-WfaIRki~g~wyNLDS~ 141 (186)
+.++.+.|...|+.+... .|+..+-.....- ......| |..+. +++.|+.+|..
T Consensus 13 a~l~~~llr~~GIpar~v--------------~g~~~~~~~~~~~-----~~~~~~H~W~ev~-~~~~W~~~D~~ 67 (68)
T smart00460 13 AALFVALLRSLGIPARVV--------------SGYLKAPDTIGGL-----RSIWEAHAWAEVY-LEGGWVPVDPT 67 (68)
T ss_pred HHHHHHHHHHCCCCeEEE--------------eeeecCCCCCccc-----ccCCCcEEEEEEE-ECCCeEEEeCC
Confidence 456777888899888754 2343332111000 0012456 66665 78999999964
No 30
>PRK03094 hypothetical protein; Provisional
Probab=34.67 E-value=48 Score=24.33 Aligned_cols=22 Identities=23% Similarity=0.424 Sum_probs=17.6
Q ss_pred HHHHHHHHHhcCCeeEEecCCC
Q psy16758 68 INVIMTALQKKGFESNWFDRRK 89 (186)
Q Consensus 68 inVL~~AL~~~g~~~~w~d~r~ 89 (186)
..-|..+|+++||+++.++...
T Consensus 10 Ls~i~~~L~~~GYeVv~l~~~~ 31 (80)
T PRK03094 10 LTDVQQALKQKGYEVVQLRSEQ 31 (80)
T ss_pred cHHHHHHHHHCCCEEEecCccc
Confidence 3458899999999999886543
No 31
>PF13529 Peptidase_C39_2: Peptidase_C39 like family; PDB: 3ERV_A.
Probab=34.35 E-value=1.3e+02 Score=21.59 Aligned_cols=119 Identities=14% Similarity=0.074 Sum_probs=52.1
Q ss_pred hhhHHHHHhhhhhC--CCCCCCHHHHHHHHhhcC---ccC--ccCCCCCcCCCCCccHHHHHHHHHhcCCeeEEecCCCC
Q psy16758 18 KELCALHALNNLFQ--NPKTFSKADLDEICINLS---PQT--WLNPHRSILGLGNYDINVIMTALQKKGFESNWFDRRKD 90 (186)
Q Consensus 18 ~~lCalHaLNnLlQ--~~~~ft~~dL~~Ia~~Ld---~~~--~~nph~n~~~~GNydinVL~~AL~~~g~~~~w~d~r~~ 90 (186)
..-|+.=|+-++|. |. ..|+.+|.+.+.... +.. .-+++ ...........+.++++..|........ ..
T Consensus 13 ~~~Cg~as~~mvl~~~g~-~~~~~~l~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~ 88 (144)
T PF13529_consen 13 SYGCGPASAAMVLNYYGK-NISQEDLADEAGTNPDGDPNTGFVGNPY--YDSGYGTSPDDLARYLEKYGYKATDTSD-AS 88 (144)
T ss_dssp TT-HHHHHHHHHHHHTT-----HHHHHHHS-EE-E--TTTSEEB-SS--TS-B----HHHHHHHHHHH-TTEEE-TT-S-
T ss_pred CCcCHHHHHHHHHHHcCC-CCCHHHHHHHhhhccCCCCCcccccCcc--ccCCCccccHHHHHHHHHcCcceeeccC-Cc
Confidence 45687777776664 45 367777776665543 111 11232 1122345778889999999985544322 12
Q ss_pred Cccc--CCcCceEEEeecccccccc-cccCCCCCCCceEEEEEECC-E-EEEecC
Q psy16758 91 PKCI--DQQKVEGYILNIPSQFKIG-KYVPTPIKRRHWLTVRNING-I-YYNLDS 140 (186)
Q Consensus 91 ~~~i--~~~~~~gfI~N~~~~~~~g-~~~~l~~~~~HWfaIRki~g-~-wyNLDS 140 (186)
.+.+ .+++=.-+|+++.....-+ ....-.....||++|+-.+. . ++-.|+
T Consensus 89 ~~~i~~~i~~G~Pvi~~~~~~~~~~~~~~~~~~~~~H~vvi~Gy~~~~~~~v~DP 143 (144)
T PF13529_consen 89 FDDIKQEIDAGRPVIVSVNSGWRPPNGDGYDGTYGGHYVVIIGYDEDGYVYVNDP 143 (144)
T ss_dssp HHHHHHHHHTT--EEEEEETTSS--TTEEEEE-TTEEEEEEEEE-SSE-EEEE-T
T ss_pred HHHHHHHHHCCCcEEEEEEcccccCCCCCcCCCcCCEEEEEEEEeCCCEEEEeCC
Confidence 2221 1334456777774221100 00000124799999998753 3 555554
No 32
>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=34.29 E-value=47 Score=28.80 Aligned_cols=39 Identities=21% Similarity=0.374 Sum_probs=28.7
Q ss_pred CceEEEeecccccccccccCCCCCCCceEEEEEE------CCEEEEecCCCCCCe
Q psy16758 98 KVEGYILNIPSQFKIGKYVPTPIKRRHWLTVRNI------NGIYYNLDSKLDNPE 146 (186)
Q Consensus 98 ~~~gfI~N~~~~~~~g~~~~l~~~~~HWfaIRki------~g~wyNLDS~l~~P~ 146 (186)
...|+|+++... ..+.|++|.=|. .|+||.+|-.+-.|+
T Consensus 214 ~L~gvV~hig~~----------~~~GHyva~vk~~~~~~~~~~WylFND~~V~~v 258 (268)
T cd02672 214 ELVGYVCEINDS----------SRGQHNVVFVIKVNEESTHGRWYLFNDFLVTPV 258 (268)
T ss_pred EEEEEEEEecCC----------CCCCcEEEEEEccCCCCCCCcEEEecCeEEEEc
Confidence 467888876321 147899998887 579999998776664
No 33
>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=34.10 E-value=60 Score=27.40 Aligned_cols=30 Identities=23% Similarity=0.462 Sum_probs=25.6
Q ss_pred CCceEEEEEECCEEEEecCCCCCCeeeCCh
Q psy16758 122 RRHWLTVRNINGIYYNLDSKLDNPEHIGRE 151 (186)
Q Consensus 122 ~~HWfaIRki~g~wyNLDS~l~~P~~i~~~ 151 (186)
..|.+|.-+.+|.=|-||...+.|+..|..
T Consensus 165 ~~HFI~fV~~~G~LyELDG~k~~Pi~~G~~ 194 (214)
T PF01088_consen 165 DFHFIAFVPVDGHLYELDGRKSGPIDHGPC 194 (214)
T ss_dssp CEEEEEEEEETTEEEEEETTSSS-EEEEE-
T ss_pred CccEEEEEeECCeEEEcCCCCCCCeEcCcC
Confidence 468888888999999999999999999874
No 34
>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=34.05 E-value=52 Score=28.60 Aligned_cols=38 Identities=11% Similarity=0.234 Sum_probs=25.8
Q ss_pred ceEEEeecccccccccccCCCCCCCceEEEEEE--CCEEEEecCCCCCCe
Q psy16758 99 VEGYILNIPSQFKIGKYVPTPIKRRHWLTVRNI--NGIYYNLDSKLDNPE 146 (186)
Q Consensus 99 ~~gfI~N~~~~~~~g~~~~l~~~~~HWfaIRki--~g~wyNLDS~l~~P~ 146 (186)
..|+|+..... ..+-||+|.-|- +|.||.+|=..-.+.
T Consensus 248 L~~vI~H~G~~----------~~~GHY~~~~k~~~~~~W~~fdD~~V~~i 287 (324)
T cd02668 248 LSGVLIHQGVS----------AYSGHYIAHIKDEQTGEWYKFNDEDVEEM 287 (324)
T ss_pred EEEEEEEcCCC----------CCCEeeEEEEECCCCCcEEEEECCceEEc
Confidence 67788775211 146799998775 479999997554433
No 35
>PF10742 DUF2555: Protein of unknown function (DUF2555); InterPro: IPR019678 This entry represents conserved proteins found in Cyanobacteria. The function is not known.
Probab=33.82 E-value=34 Score=23.66 Aligned_cols=22 Identities=23% Similarity=0.561 Sum_probs=19.2
Q ss_pred CCCHHHHHHHHhhcCccCccCC
Q psy16758 35 TFSKADLDEICINLSPQTWLNP 56 (186)
Q Consensus 35 ~ft~~dL~~Ia~~Ld~~~~~np 56 (186)
.||+++-+++|.+|..+.+-+|
T Consensus 8 ~~t~~~va~LA~RLE~DdY~~p 29 (57)
T PF10742_consen 8 AFTEEDVAKLAKRLEEDDYPNP 29 (57)
T ss_pred hcCHHHHHHHHHhhhhccCCch
Confidence 5999999999999999876555
No 36
>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=32.22 E-value=5.7 Score=27.85 Aligned_cols=25 Identities=32% Similarity=0.598 Sum_probs=14.8
Q ss_pred HHhhhhhCCCCCCCHHHHHHHHhhcC
Q psy16758 24 HALNNLFQNPKTFSKADLDEICINLS 49 (186)
Q Consensus 24 HaLNnLlQ~~~~ft~~dL~~Ia~~Ld 49 (186)
-=||+|||++ .|+-.+|.+|-..|+
T Consensus 33 ~eLd~lLk~~-~fn~~dls~i~~~ln 57 (64)
T PF02251_consen 33 VELDELLKSP-SFNLSDLSSIHAPLN 57 (64)
T ss_dssp HHHHHHHHSG-GG--S-GGGS-----
T ss_pred HHHHHHhcCc-ccccccHHhhcCcCC
Confidence 4589999999 699999998877665
No 37
>PF11814 DUF3335: Peptidase_C39 like family; InterPro: IPR021770 This family of proteins are functionally uncharacterised. This family is only found in bacteria. This presumed domain is typically between 226 to 230 amino acids in length.
Probab=31.81 E-value=1.3e+02 Score=25.80 Aligned_cols=53 Identities=19% Similarity=0.364 Sum_probs=33.3
Q ss_pred CCCccHHHHHHHHHhcCCeeEEecCCCCCcccCCcCceEEEeecccccccccccCCCCCCCceEEEEEECCEE-EEecCC
Q psy16758 63 LGNYDINVIMTALQKKGFESNWFDRRKDPKCIDQQKVEGYILNIPSQFKIGKYVPTPIKRRHWLTVRNINGIY-YNLDSK 141 (186)
Q Consensus 63 ~GNydinVL~~AL~~~g~~~~w~d~r~~~~~i~~~~~~gfI~N~~~~~~~g~~~~l~~~~~HWfaIRki~g~w-yNLDS~ 141 (186)
.+.++++-|.+||+.-+.-++-++ .+-+| | -+..||+.+.-+++.+ |-.|--
T Consensus 114 ~~~~~~~~l~~~l~~G~~~lvLIS--------------~y~~~-------g------~k~PHWV~v~g~d~~~vyihDP~ 166 (207)
T PF11814_consen 114 YRPLSLADLRAALAAGAIVLVLIS--------------TYRMD-------G------KKVPHWVVVTGVDDDFVYIHDPD 166 (207)
T ss_pred cCCCCHHHHHHHHHCCCEEEEEEe--------------ecccC-------C------CCCCeEEEEEEecCCEEEEeCCC
Confidence 566777777777777555544332 12233 2 3579999999998876 455544
Q ss_pred C
Q psy16758 142 L 142 (186)
Q Consensus 142 l 142 (186)
.
T Consensus 167 ~ 167 (207)
T PF11814_consen 167 V 167 (207)
T ss_pred C
Confidence 3
No 38
>KOG1865|consensus
Probab=31.56 E-value=78 Score=30.92 Aligned_cols=57 Identities=23% Similarity=0.406 Sum_probs=38.7
Q ss_pred CceEEEeecccccccccccCCCCCCCceEE-EEEECCEEEEecCCCCCCeeeCChhHHHHHHHHHhccCCcEEEEEEe
Q psy16758 98 KVEGYILNIPSQFKIGKYVPTPIKRRHWLT-VRNINGIYYNLDSKLDNPEHIGREEDLVEYLRDVLSDIDKELFVVTR 174 (186)
Q Consensus 98 ~~~gfI~N~~~~~~~g~~~~l~~~~~HWfa-IRki~g~wyNLDS~l~~P~~i~~~~~l~~yL~~~L~~~g~~iFvV~~ 174 (186)
...|+|+.+.... ..-|.++ ||-..|+||.+|--.-.+..+. .+|.++-|-+|-++.
T Consensus 353 ~LYavlVH~g~~~----------~~GHY~cYvks~~g~Wy~~DDS~V~~~~~~----------~VLsq~AYmLfY~R~ 410 (545)
T KOG1865|consen 353 KLYAVLVHLGTSC----------HSGHYFCYVKSQNGQWYKMDDSEVTQSSIE----------SVLSQQAYILFYARK 410 (545)
T ss_pred EEEEEEEeccccc----------cCCceEEEEEcCCCceEEccCceeeecccc----------ceecccceEEEEEee
Confidence 4789999974332 3446655 6778999999997666665443 245566677777765
No 39
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=30.53 E-value=61 Score=23.68 Aligned_cols=21 Identities=24% Similarity=0.420 Sum_probs=17.3
Q ss_pred HHHHHHHHhcCCeeEEecCCC
Q psy16758 69 NVIMTALQKKGFESNWFDRRK 89 (186)
Q Consensus 69 nVL~~AL~~~g~~~~w~d~r~ 89 (186)
.-+..||+.+||+++.++...
T Consensus 11 s~v~~~L~~~GyeVv~l~~~~ 31 (80)
T PF03698_consen 11 SNVKEALREKGYEVVDLENEQ 31 (80)
T ss_pred hHHHHHHHHCCCEEEecCCcc
Confidence 457899999999999887554
No 40
>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=29.16 E-value=2.2e+02 Score=20.50 Aligned_cols=96 Identities=18% Similarity=0.140 Sum_probs=58.4
Q ss_pred HHHHHhhhhhC---CCCCCCHHHHHHHHhhcCccCccCCCCCcCCCCCccHHHHHHHHHhcCCeeEEecCCC-CCcccCC
Q psy16758 21 CALHALNNLFQ---NPKTFSKADLDEICINLSPQTWLNPHRSILGLGNYDINVIMTALQKKGFESNWFDRRK-DPKCIDQ 96 (186)
Q Consensus 21 CalHaLNnLlQ---~~~~ft~~dL~~Ia~~Ld~~~~~nph~n~~~~GNydinVL~~AL~~~g~~~~w~d~r~-~~~~i~~ 96 (186)
|++.||=.+++ -+ ++.++|. +++.. +.+.++...|..+++..|+++.-..... .+..+.+
T Consensus 7 ~~l~~l~~i~~~~g~~--~~~~~l~---~~~~~-----------~~~~~~~~~l~~~a~~~Gl~~~~~~~~~~~l~~~~l 70 (124)
T cd02421 7 PLLDCLVLLARQFGKP--ASRDSLV---AGLPL-----------DDGRLSPALFPRAAARAGLSARVVRRPLDAIPTLLL 70 (124)
T ss_pred hHHHHHHHHHHHhCCC--CCHHHHH---hcCCC-----------CCCCcCHHHHHHHHHHCCCcceeeeCCHHHCCcccC
Confidence 66666655553 34 6666554 23221 1245999999999999999887654321 1222222
Q ss_pred cCceEEEeecccccccccccCCCCCCCceEEEEEEC-CEEEEecCC-CCCCeeeCC
Q psy16758 97 QKVEGYILNIPSQFKIGKYVPTPIKRRHWLTVRNIN-GIYYNLDSK-LDNPEHIGR 150 (186)
Q Consensus 97 ~~~~gfI~N~~~~~~~g~~~~l~~~~~HWfaIRki~-g~wyNLDS~-l~~P~~i~~ 150 (186)
+ +++. +...||+-|=+++ +.+...|.. -..|+.++.
T Consensus 71 P---~i~~---------------~~~g~~~Vl~~~~~~~~~i~dp~~~~~~~~~~~ 108 (124)
T cd02421 71 P---AILL---------------LKNGRACVLLGVDDGHARILDPESGGGEVEISL 108 (124)
T ss_pred C---EEEE---------------EcCCCEEEEEEecCCeEEEEccCCCCCcEEEcH
Confidence 2 2221 1356999888885 456777876 678888765
No 41
>cd01750 GATase1_CobQ Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ). Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ). CobQ plays a role in cobalamin biosythesis. CobQ catalyses amidations at positions B, D, E, and G on adenosylcobyrinic A,C-diamide in the biosynthesis of cobalamin. CobQ belongs to the triad family of amidotransferases. Two of the three residues of the catalytic triad that are involved in glutamine binding, hydrolysis and transfer of the resulting ammonia to the acceptor substrate in other triad aminodotransferases are conserved in CobQ.
Probab=29.03 E-value=95 Score=25.29 Aligned_cols=26 Identities=8% Similarity=0.300 Sum_probs=22.5
Q ss_pred CCCccHHHHHHHHHhcCCeeEEecCCCC
Q psy16758 63 LGNYDINVIMTALQKKGFESNWFDRRKD 90 (186)
Q Consensus 63 ~GNydinVL~~AL~~~g~~~~w~d~r~~ 90 (186)
.||+ ..+.++++..|.++++++..++
T Consensus 9 ~gN~--~~l~~~~~~~G~~~~~~~~~~~ 34 (194)
T cd01750 9 ISNF--TDLDPLAREPGVDVRYVEVPEG 34 (194)
T ss_pred ccCH--HHHHHHHhcCCceEEEEeCCCC
Confidence 5776 7899999999999999987765
No 42
>PF13299 CPSF100_C: Cleavage and polyadenylation factor 2 C-terminal
Probab=27.89 E-value=3.2e+02 Score=21.97 Aligned_cols=59 Identities=20% Similarity=0.328 Sum_probs=42.2
Q ss_pred cCCCCCcCCCCCccHHHHHHHHHhcCCeeEEecCCCCCcccCCcCceEEEeecccccccccccCCCCCCCceEEEEEECC
Q psy16758 54 LNPHRSILGLGNYDINVIMTALQKKGFESNWFDRRKDPKCIDQQKVEGYILNIPSQFKIGKYVPTPIKRRHWLTVRNING 133 (186)
Q Consensus 54 ~nph~n~~~~GNydinVL~~AL~~~g~~~~w~d~r~~~~~i~~~~~~gfI~N~~~~~~~g~~~~l~~~~~HWfaIRki~g 133 (186)
..+|..++ .|+-...-|-++|...|+.+...- .-.++|| | . ++|||...
T Consensus 89 ~~~~~~~~-iGd~rL~~lk~~L~~~g~~aEF~g------------~G~Lv~~-------~---------~--V~VrK~~~ 137 (161)
T PF13299_consen 89 RPGHQSLF-IGDLRLSDLKQALQSAGIQAEFRG------------EGVLVCN-------G---------G--VAVRKSED 137 (161)
T ss_pred cCCCCcee-cCcccHHHHHHHHHHCCCceEEee------------CCeEEEC-------C---------E--EEEEEcCC
Confidence 34566666 899999999999999999988551 1136787 2 2 99999974
Q ss_pred EEEEecCCCC
Q psy16758 134 IYYNLDSKLD 143 (186)
Q Consensus 134 ~wyNLDS~l~ 143 (186)
-=+.+++.+.
T Consensus 138 G~i~ieG~~~ 147 (161)
T PF13299_consen 138 GRIVIEGCLS 147 (161)
T ss_pred CCEEEEecCc
Confidence 3255565443
No 43
>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=27.54 E-value=83 Score=26.99 Aligned_cols=38 Identities=8% Similarity=0.238 Sum_probs=27.3
Q ss_pred CceEEEeecccccccccccCCCCCCCceEEEEEEC-CEEEEecCCCCCCe
Q psy16758 98 KVEGYILNIPSQFKIGKYVPTPIKRRHWLTVRNIN-GIYYNLDSKLDNPE 146 (186)
Q Consensus 98 ~~~gfI~N~~~~~~~g~~~~l~~~~~HWfaIRki~-g~wyNLDS~l~~P~ 146 (186)
...|+|+...+ ..+.|+++..|-. +.||-+|=..-.|.
T Consensus 274 ~L~avi~H~G~-----------~~~GHY~~~~~~~~~~W~~~nD~~V~~~ 312 (328)
T cd02660 274 DLFAVVVHKGT-----------LDTGHYTAYCRQGDGQWFKFDDAMITRV 312 (328)
T ss_pred EEEEEEEeecc-----------CCCCcEEEEEECCCCcEEEEECCeeEEC
Confidence 36777777532 1468999999988 89999996654444
No 44
>COG3012 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.09 E-value=58 Score=26.65 Aligned_cols=16 Identities=31% Similarity=0.636 Sum_probs=13.7
Q ss_pred EEEECCEEEEecCCCC
Q psy16758 128 VRNINGIYYNLDSKLD 143 (186)
Q Consensus 128 IRki~g~wyNLDS~l~ 143 (186)
.+|++|+||-+|-..+
T Consensus 115 Fvk~ngrWyyiDgtv~ 130 (151)
T COG3012 115 FVKINGRWYYIDGTVP 130 (151)
T ss_pred heEECCEEEEECCCCC
Confidence 4688999999998776
No 45
>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=25.39 E-value=87 Score=26.13 Aligned_cols=38 Identities=8% Similarity=0.224 Sum_probs=28.7
Q ss_pred CceEEEeecccccccccccCCCCCCCceEEEEEEC----------------------CEEEEecCCCCCCe
Q psy16758 98 KVEGYILNIPSQFKIGKYVPTPIKRRHWLTVRNIN----------------------GIYYNLDSKLDNPE 146 (186)
Q Consensus 98 ~~~gfI~N~~~~~~~g~~~~l~~~~~HWfaIRki~----------------------g~wyNLDS~l~~P~ 146 (186)
...|+|+...+. ..-|.+|.-|.. +.||..|-..-.|+
T Consensus 164 ~L~avi~H~G~~-----------~~GHY~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~W~~fnD~~V~~v 223 (240)
T cd02662 164 RLRAVVVHYGSH-----------SSGHYVCYRRKPLFSKDKEPGSFVRMREGPSSTSHPWWRISDTTVKEV 223 (240)
T ss_pred EEEEEEEEeccC-----------CCceEEEEEeCCCcccccccccccccccccCccCCCEEEEechheEEe
Confidence 478888886322 468999999886 89999987665555
No 46
>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=25.17 E-value=93 Score=24.71 Aligned_cols=37 Identities=11% Similarity=0.187 Sum_probs=26.5
Q ss_pred ceEEEeecccccccccccCCCCCCCceEEEEEECC--EEEEecCCCCCCe
Q psy16758 99 VEGYILNIPSQFKIGKYVPTPIKRRHWLTVRNING--IYYNLDSKLDNPE 146 (186)
Q Consensus 99 ~~gfI~N~~~~~~~g~~~~l~~~~~HWfaIRki~g--~wyNLDS~l~~P~ 146 (186)
+.|+|+... . ..+.||+|.-+-.+ .||-+|=..-.++
T Consensus 213 L~avi~H~G-~----------~~~GHY~a~v~~~~~~~W~~~dD~~v~~~ 251 (269)
T PF00443_consen 213 LVAVIVHYG-S----------ADSGHYVAYVRDSDDGKWYKFDDSRVTEV 251 (269)
T ss_dssp EEEEEEEES-S----------TTSEEEEEEEEETTTTEEEEEETTEEEEE
T ss_pred ehhhhcccc-c----------cccceEEEeeccccCCeEEEeeCCceEEC
Confidence 589999863 1 24779998886654 6999997655444
No 47
>smart00850 LytTR LytTr DNA-binding domain. This domain is found in a variety of bacterial transcriptional regulators. The domain binds to a specific DNA sequence pattern.
Probab=24.99 E-value=12 Score=26.25 Aligned_cols=46 Identities=24% Similarity=0.468 Sum_probs=35.6
Q ss_pred cceeeecchhhHHHHHhhhhhCCCCCCCHHHHHHHHhhcCccCccCCCCCcC
Q psy16758 10 IIYHEKQMKELCALHALNNLFQNPKTFSKADLDEICINLSPQTWLNPHRSIL 61 (186)
Q Consensus 10 ~iYhEkQ~~~lCalHaLNnLlQ~~~~ft~~dL~~Ia~~Ld~~~~~nph~n~~ 61 (186)
-+|.|.+. ..|-+|+-+ +. +.....|.++..+|++..++..|||..
T Consensus 11 I~yie~~~-~~~~i~~~~----~~-~~~~~~l~~~~~~L~~~~F~r~hrs~i 56 (96)
T smart00850 11 ILYIEAEG-NYVTIHTKD----GT-YLVRGTLKELEEKLDPTNFFRIHRSYI 56 (96)
T ss_pred EEEEEecC-CEEEEEECC----cE-EEehhhHHHHHhhCCCCceEEechhHE
Confidence 67888876 455667754 45 577789999999998878889999765
No 48
>PF13132 DUF3950: Domain of unknown function (DUF3950)
Probab=24.96 E-value=52 Score=19.96 Aligned_cols=14 Identities=29% Similarity=0.318 Sum_probs=11.7
Q ss_pred CCCCccHHHHHHHH
Q psy16758 62 GLGNYDINVIMTAL 75 (186)
Q Consensus 62 ~~GNydinVL~~AL 75 (186)
+.||||.=|+++.=
T Consensus 13 ~~~NFSaWV~dACr 26 (30)
T PF13132_consen 13 GSGNFSAWVKDACR 26 (30)
T ss_pred cCcChHHHHHHHHH
Confidence 48999999998753
No 49
>PRK14609 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional
Probab=24.33 E-value=83 Score=27.20 Aligned_cols=31 Identities=23% Similarity=0.334 Sum_probs=26.7
Q ss_pred hhHHHHHhhhhhCCCCCCCHHHHHHHHhhcCcc
Q psy16758 19 ELCALHALNNLFQNPKTFSKADLDEICINLSPQ 51 (186)
Q Consensus 19 ~lCalHaLNnLlQ~~~~ft~~dL~~Ia~~Ld~~ 51 (186)
..+++.|+|.+++.+ +|.++|.++|.++-.+
T Consensus 104 aaa~l~al~~~~~~~--l~~~~l~~la~~iGaD 134 (269)
T PRK14609 104 AAFMLKLLNDKFNLG--LSDEELEAYAATLGAD 134 (269)
T ss_pred HHHHHHHHHHHhCCC--cCHHHHHHHHHHhCCC
Confidence 367889999999887 8999999999999654
No 50
>TIGR01684 viral_ppase viral phosphatase. These proteins also include an N-terminal domain (ca. 125 aas) that is unique to this clade.
Probab=24.11 E-value=1.3e+02 Score=27.30 Aligned_cols=41 Identities=20% Similarity=0.191 Sum_probs=29.0
Q ss_pred EEEEecCCCCCC---eeeCChhHHHHHHHHHhccCCcEEEEEEecC
Q psy16758 134 IYYNLDSKLDNP---EHIGREEDLVEYLRDVLSDIDKELFVVTRIE 176 (186)
Q Consensus 134 ~wyNLDS~l~~P---~~i~~~~~l~~yL~~~L~~~g~~iFvV~~~~ 176 (186)
.-+.|||+|=.. +.|.+ ..+.+.|. .|++.|+.+-|+++..
T Consensus 129 IvFDLDgTLi~~~~~v~ird-PgV~EaL~-~LkekGikLaIaTS~~ 172 (301)
T TIGR01684 129 VVFDLDSTLITDEEPVRIRD-PRIYDSLT-ELKKRGCILVLWSYGD 172 (301)
T ss_pred EEEecCCCCcCCCCccccCC-HHHHHHHH-HHHHCCCEEEEEECCC
Confidence 468999998433 33666 46777775 5777899888887543
No 51
>PF12295 Symplekin_C: Symplekin tight junction protein C terminal; InterPro: IPR022075 This domain family is found in eukaryotes, and is approximately 180 amino acids in length. There is a single completely conserved residue P that may be functionally important. Symplekn has been localized, by light and electron microscopy, to the plaque associated with the cytoplasmic face of the tight junction-containing zone (zonula occludens) of polar epithelial cells and of Sertoli cells of testis. However, both the mRNA and the protein can also be detected in a wide range of cell types that do not form tight junctions. Careful analyses have revealed that the protein occurs in all these diverse cells in the nucleoplasm, and only in those cells forming tight junctions is it recruited, partly but specifically, to the plaque structure of the zonula occludens.
Probab=23.97 E-value=1.5e+02 Score=24.49 Aligned_cols=55 Identities=20% Similarity=0.256 Sum_probs=39.6
Q ss_pred HHHhhhhhC------CCCCCCHHHHHHHHhhcCccCccCCCCC--------cCCCCCccHHHHHHHHHhc
Q psy16758 23 LHALNNLFQ------NPKTFSKADLDEICINLSPQTWLNPHRS--------ILGLGNYDINVIMTALQKK 78 (186)
Q Consensus 23 lHaLNnLlQ------~~~~ft~~dL~~Ia~~Ld~~~~~nph~n--------~~~~GNydinVL~~AL~~~ 78 (186)
.||++++++ +...+|+.||=-..+.+|+..= .+-++ +...+-|.-+||.+||++-
T Consensus 34 k~~~~rll~~~~~~~~~~~ltp~ElLv~lH~id~~~~-~~~k~~~~a~~~Cf~~~~vf~~evla~~l~ql 102 (183)
T PF12295_consen 34 KEVFNRLLQAPSSSTGESPLTPSELLVALHNIDPEKD-VPLKKIIEALDLCFSMRDVFTQEVLASALQQL 102 (183)
T ss_pred HHHHHHHhcCCCCCCCCCCCCHHHHHHHHHhCCcccc-ccHHHHHHHHHHHHcccccCCHHHHHHHHHHH
Confidence 589999998 2337999999999999976532 22221 2223469999999999986
No 52
>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=23.89 E-value=1.2e+02 Score=24.62 Aligned_cols=39 Identities=33% Similarity=0.453 Sum_probs=27.5
Q ss_pred CceEEEEEECCEEEEecCCCCCCeeeCChhHHHHHHHHHhccCCcEE
Q psy16758 123 RHWLTVRNINGIYYNLDSKLDNPEHIGREEDLVEYLRDVLSDIDKEL 169 (186)
Q Consensus 123 ~HWfaIRki~g~wyNLDS~l~~P~~i~~~~~l~~yL~~~L~~~g~~i 169 (186)
.|=++.-+++|.||-||=.++ |..+ -+|+....+ ++..|
T Consensus 109 ~Haa~aV~ing~~yvlDq~~p-~~~l------~~y~~~~~~-~~~~i 147 (153)
T PF04473_consen 109 GHAAVAVKINGKYYVLDQHLP-PIDL------GDYLKYWKK-EGKII 147 (153)
T ss_pred CeEEEEEEECCEEEEEeCCCC-CccH------HHHHHHhhh-cccee
Confidence 588888899999999998654 4434 357755554 55544
No 53
>PRK00650 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional
Probab=23.13 E-value=90 Score=27.74 Aligned_cols=31 Identities=29% Similarity=0.445 Sum_probs=27.9
Q ss_pred hhHHHHHhhhhhCCCCCCCHHHHHHHHhhcCcc
Q psy16758 19 ELCALHALNNLFQNPKTFSKADLDEICINLSPQ 51 (186)
Q Consensus 19 ~lCalHaLNnLlQ~~~~ft~~dL~~Ia~~Ld~~ 51 (186)
.-+++-++|.+++.+ ++.++|.+||.+|-.+
T Consensus 102 aAa~L~~ln~l~~~~--ls~~eL~~lA~~lGaD 132 (288)
T PRK00650 102 AATALFALNQIFQTG--LSDEELRSLAEKIGMD 132 (288)
T ss_pred HHHHHHHHHHHhCCC--cCHHHHHHHHHHhCCc
Confidence 368899999999888 9999999999999865
No 54
>PF12780 AAA_8: P-loop containing dynein motor region D4; InterPro: IPR024317 The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four (D1 - D4) correspond to the ATP binding sites with P-loop signatures described previously, and two (D5, D6) are modules in which the P loop has been lost in evolution. This particular entry represents the D4 ATP-binding domain of the motor [].; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.
Probab=22.99 E-value=46 Score=29.08 Aligned_cols=37 Identities=30% Similarity=0.533 Sum_probs=27.4
Q ss_pred eecchhhHHHHHhhhhhCC---CCCCCHHHHHHHHhhcCc
Q psy16758 14 EKQMKELCALHALNNLFQN---PKTFSKADLDEICINLSP 50 (186)
Q Consensus 14 EkQ~~~lCalHaLNnLlQ~---~~~ft~~dL~~Ia~~Ld~ 50 (186)
+.|-..---+..+|+||-. |..|+++|++.|+..+.+
T Consensus 97 d~qi~~~~fLe~in~LL~sGeip~LF~~eE~~~i~~~l~~ 136 (268)
T PF12780_consen 97 DSQIVDESFLEDINSLLSSGEIPNLFTKEELDNIISSLRE 136 (268)
T ss_dssp CCCSSSCHHHHHHHHHHHCSS-TTTS-TCHHHHHHHHHHH
T ss_pred CcccchHhHHHHHHHHHhCCCCCCCccHHHHHHHHHHhHH
Confidence 4444444567899999976 568999999999988854
No 55
>PF13423 UCH_1: Ubiquitin carboxyl-terminal hydrolase
Probab=22.71 E-value=1.3e+02 Score=25.79 Aligned_cols=33 Identities=12% Similarity=0.383 Sum_probs=26.2
Q ss_pred CceEEEeecccccccccccCCCCCCCceEEEEEEC----CEEEEecC
Q psy16758 98 KVEGYILNIPSQFKIGKYVPTPIKRRHWLTVRNIN----GIYYNLDS 140 (186)
Q Consensus 98 ~~~gfI~N~~~~~~~g~~~~l~~~~~HWfaIRki~----g~wyNLDS 140 (186)
...|+||.+... ..+.|-+|+=|++ .+||.+|=
T Consensus 256 ~L~~~V~~i~~~----------~~~~HlVs~vrv~~~~~~~W~lFND 292 (295)
T PF13423_consen 256 ELRSMVCHIGDS----------IESGHLVSLVRVGPSDDSQWYLFND 292 (295)
T ss_pred EEEEEEEEecCC----------CCCCceEEEEEcCCCCCCcEEEECc
Confidence 478999998542 2478999999996 69999884
No 56
>PF00770 Peptidase_C5: Adenovirus endoprotease; InterPro: IPR000855 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 aminopeptidases belong to the peptidase family C5 (adenain family, clan CE). Several adenovirus proteins are synthesised as precursors, requiring processing by a protease before the virion is assembled [, ]. Until recently, the adenovirus endopeptidase was classified as a serine protease, having been reported to be inhibited by serine protease inhibitors [, ]. However, it has since been shown to be inhibited by cysteine protease inhibitors, and the catalytic residues are believed to be His-54 and Cys-104 [, ].; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis; PDB: 1NLN_A 1AVP_A.
Probab=22.09 E-value=1.1e+02 Score=25.83 Aligned_cols=51 Identities=25% Similarity=0.410 Sum_probs=24.8
Q ss_pred ecCCCCCcccCCcCceEEEeecccccccccccCCCCCCCceEEEE--EECCEEEEecCCCCCCeeeCC
Q psy16758 85 FDRRKDPKCIDQQKVEGYILNIPSQFKIGKYVPTPIKRRHWLTVR--NINGIYYNLDSKLDNPEHIGR 150 (186)
Q Consensus 85 ~d~r~~~~~i~~~~~~gfI~N~~~~~~~g~~~~l~~~~~HWfaIR--ki~g~wyNLDS~l~~P~~i~~ 150 (186)
||+| =+.-++.++..--|+|+-++-.- +-||+|+- ......|.+| |--.++
T Consensus 6 FDkr-FPGFl~~~k~acAIVNT~~retG---------GvHWlA~Aw~P~s~t~YmFD-----PfGfsd 58 (183)
T PF00770_consen 6 FDKR-FPGFLSKHKPACAIVNTGGRETG---------GVHWLAFAWDPRSRTFYMFD-----PFGFSD 58 (183)
T ss_dssp E-TT-------TTS-EEEEEESS-TTT-----------S-EEEEEEETTTTEEEEE------TT---H
T ss_pred ccCC-CCCccCCCCcceEEEecCCcccC---------ceeEEEEEecCCcceEEEeC-----CCCCCH
Confidence 5555 23445677787889998666543 49999985 2455777777 555555
No 57
>PRK04181 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional
Probab=21.93 E-value=1.1e+02 Score=26.46 Aligned_cols=31 Identities=23% Similarity=0.265 Sum_probs=27.6
Q ss_pred hHHHHHhhhhhCCCCCCCHHHHHHHHhhcCccC
Q psy16758 20 LCALHALNNLFQNPKTFSKADLDEICINLSPQT 52 (186)
Q Consensus 20 lCalHaLNnLlQ~~~~ft~~dL~~Ia~~Ld~~~ 52 (186)
-.++-++|.+++-+ ++.++|.++|.+|-.+-
T Consensus 109 AA~L~aln~l~~~~--ls~~eL~~lA~~lGaDv 139 (257)
T PRK04181 109 ATFLLMLNEILNLK--LSLEELAEIGSKVGADV 139 (257)
T ss_pred HHHHHHHHHHhCCC--cCHHHHHHHHHHhCCCc
Confidence 56889999999877 99999999999998773
No 58
>PRK14616 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional
Probab=21.34 E-value=1.2e+02 Score=26.26 Aligned_cols=31 Identities=26% Similarity=0.434 Sum_probs=27.9
Q ss_pred hhHHHHHhhhhhCCCCCCCHHHHHHHHhhcCcc
Q psy16758 19 ELCALHALNNLFQNPKTFSKADLDEICINLSPQ 51 (186)
Q Consensus 19 ~lCalHaLNnLlQ~~~~ft~~dL~~Ia~~Ld~~ 51 (186)
..|++-|+|.++..+ ++.++|.++|.++-.+
T Consensus 105 aaA~l~al~~l~g~~--ls~~el~~~a~~ig~D 135 (287)
T PRK14616 105 AATVLRVLNELWEIN--APSADLHRLAVKLGAD 135 (287)
T ss_pred HHHHHHHHHHHhCCC--cCHHHHHHHHHHhCCC
Confidence 478999999999887 9999999999998765
No 59
>COG4947 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.96 E-value=39 Score=28.95 Aligned_cols=24 Identities=33% Similarity=0.493 Sum_probs=20.2
Q ss_pred cchhhHHHHHhhhhhCCCCCCCHH
Q psy16758 16 QMKELCALHALNNLFQNPKTFSKA 39 (186)
Q Consensus 16 Q~~~lCalHaLNnLlQ~~~~ft~~ 39 (186)
|.-++=|.||+|-+||-|++||+.
T Consensus 106 sgcsmGayhA~nfvfrhP~lftkv 129 (227)
T COG4947 106 SGCSMGAYHAANFVFRHPHLFTKV 129 (227)
T ss_pred cccchhhhhhhhhheeChhHhhhh
Confidence 455778999999999999888764
No 60
>PF07283 TrbH: Conjugal transfer protein TrbH; InterPro: IPR010837 This entry represents TrbH, a bacterial conjugal transfer protein approximately 150 residues long. TrbH contains a putative membrane lipoprotein lipid attachment site [].
Probab=20.22 E-value=1e+02 Score=24.16 Aligned_cols=23 Identities=22% Similarity=0.261 Sum_probs=19.7
Q ss_pred HHHHHHHHhcCCeeEEecCCCCC
Q psy16758 69 NVIMTALQKKGFESNWFDRRKDP 91 (186)
Q Consensus 69 nVL~~AL~~~g~~~~w~d~r~~~ 91 (186)
..|+++|+.|||.++-.++....
T Consensus 39 ~aL~~~LR~~GYaV~e~~~~~~~ 61 (121)
T PF07283_consen 39 QALENALRAKGYAVIEDDPPDNS 61 (121)
T ss_pred HHHHHHHHhcCcEEEecCCcccc
Confidence 67999999999999999876543
No 61
>PF06938 DUF1285: Protein of unknown function (DUF1285); InterPro: IPR010707 This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.; PDB: 2RA9_A 2RE3_B.
Probab=20.21 E-value=47 Score=26.82 Aligned_cols=39 Identities=28% Similarity=0.560 Sum_probs=24.2
Q ss_pred ECCEEEEecCCCCCCeeeCChhHHHHHHHHHhccCCc-EEEEEEecC
Q psy16758 131 INGIYYNLDSKLDNPEHIGREEDLVEYLRDVLSDIDK-ELFVVTRIE 176 (186)
Q Consensus 131 i~g~wyNLDS~l~~P~~i~~~~~l~~yL~~~L~~~g~-~iFvV~~~~ 176 (186)
-+|.||--.|....|. |...+.+.|..++. +-|+|++.|
T Consensus 5 ~dG~W~h~G~pI~R~~-------lv~LFasiL~~e~~G~y~LvTPvE 44 (148)
T PF06938_consen 5 RDGRWFHEGSPIPRPK-------LVRLFASILRREDDGEYYLVTPVE 44 (148)
T ss_dssp TTS-EEETTEE---HH-------HHHHHHTTEEEETT-EEEEE-SS-
T ss_pred CCCcEEECCcCcCcHH-------HHHHHHhhEEEcCCCcEEEEccce
Confidence 3689999999666554 45666778875555 899998754
No 62
>COG3915 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.20 E-value=4.3e+02 Score=21.66 Aligned_cols=83 Identities=17% Similarity=0.244 Sum_probs=52.6
Q ss_pred CCHHHHHHHHhhcCccCcc--CC--CCCcCCCCCccHHHHHHHHHhcCCeeEEecCCCCC-----cccC-CcCceEEEee
Q psy16758 36 FSKADLDEICINLSPQTWL--NP--HRSILGLGNYDINVIMTALQKKGFESNWFDRRKDP-----KCID-QQKVEGYILN 105 (186)
Q Consensus 36 ft~~dL~~Ia~~Ld~~~~~--np--h~n~~~~GNydinVL~~AL~~~g~~~~w~d~r~~~-----~~i~-~~~~~gfI~N 105 (186)
||..||+. |...++- -| +.|.- +--+++.-|.+.|..++-++.-+--.+-. +.++ .+-+.|+=.|
T Consensus 38 ft~qeLea----l~~~T~ete~Pw~~gn~r-f~Gvsls~Ll~~l~ak~tslt~iALNdY~a~Ip~sDi~kynpIlA~~~n 112 (155)
T COG3915 38 FTLQELEA----LPDETIETETPWTQGNTR-FKGVSLSALLAWLGAKQTSLTVIALNDYWAEIPYSDIEKYNPILAIQNN 112 (155)
T ss_pred ecHHHHhc----CCcceEEEecCcccCcee-ecceeHHHHHHHhhccCcceEEEEecceeccCcHHHhhhcccEEEEEeC
Confidence 77777765 3332211 12 34433 44489999999999998877766444322 2222 3446666555
Q ss_pred cccccccccccCCCCCCCceEEEEEECCEE--EEecC
Q psy16758 106 IPSQFKIGKYVPTPIKRRHWLTVRNINGIY--YNLDS 140 (186)
Q Consensus 106 ~~~~~~~g~~~~l~~~~~HWfaIRki~g~w--yNLDS 140 (186)
-.-.+||.-|--| |++||
T Consensus 113 -----------------Gn~M~IRerGPl~~IYplds 132 (155)
T COG3915 113 -----------------GNYMQIRERGPLWSIYPLDS 132 (155)
T ss_pred -----------------CcEEEEeccCceEEEeecCC
Confidence 4567899988876 89998
Done!