Query 030121
Match_columns 182
No_of_seqs 109 out of 202
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 08:51:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030121.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030121hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02099 Josephin: Josephin; 100.0 5.6E-63 1.2E-67 396.3 7.8 152 12-179 1-157 (157)
2 KOG2935 Ataxin 3/Josephin [Gen 100.0 2.2E-52 4.7E-57 353.8 4.9 159 6-180 2-162 (315)
3 KOG2934 Uncharacterized conser 100.0 3.5E-49 7.5E-54 318.6 4.9 162 5-181 23-190 (204)
4 cd02420 Peptidase_C39D A sub-f 80.3 18 0.00039 26.3 8.3 100 16-156 10-111 (125)
5 TIGR02616 tnaC_leader tryptoph 77.2 0.97 2.1E-05 26.1 0.4 11 139-149 8-18 (26)
6 cd02424 Peptidase_C39E A sub-f 75.9 29 0.00064 25.7 9.8 104 16-156 10-115 (129)
7 PF03412 Peptidase_C39: Peptid 71.3 12 0.00026 27.5 5.2 104 12-155 6-111 (131)
8 cd02419 Peptidase_C39C A sub-f 71.2 37 0.0008 24.6 9.7 100 16-156 10-111 (127)
9 cd02549 Peptidase_C39A A sub-f 70.9 39 0.00085 24.8 8.3 133 13-176 2-139 (141)
10 cd02674 Peptidase_C19R A subfa 69.1 6.9 0.00015 31.5 3.8 39 108-152 174-214 (230)
11 cd02418 Peptidase_C39B A sub-f 67.5 46 0.00099 24.3 9.0 109 12-155 5-116 (136)
12 cd02257 Peptidase_C19 Peptidas 65.5 11 0.00024 29.4 4.3 42 108-154 193-236 (255)
13 cd02659 peptidase_C19C A subfa 62.6 12 0.00026 32.1 4.3 40 108-153 252-293 (334)
14 cd02673 Peptidase_C19Q A subfa 62.2 12 0.00027 31.7 4.2 39 109-152 185-226 (245)
15 KOG1415 Ubiquitin C-terminal h 60.0 15 0.00032 31.3 4.1 30 128-157 159-188 (222)
16 cd02417 Peptidase_C39_likeA A 59.3 63 0.0014 23.1 9.1 67 73-156 39-107 (121)
17 cd02667 Peptidase_C19K A subfa 58.9 16 0.00035 30.9 4.4 38 109-152 203-263 (279)
18 cd02661 Peptidase_C19E A subfa 58.6 15 0.00033 30.6 4.2 41 108-153 248-289 (304)
19 cd02259 Peptidase_C39_like Pep 58.5 63 0.0014 22.9 9.3 101 16-156 5-107 (122)
20 cd02658 Peptidase_C19B A subfa 53.8 18 0.0004 30.8 3.9 38 109-151 253-294 (311)
21 cd02657 Peptidase_C19A A subfa 53.6 21 0.00045 30.3 4.2 40 109-153 242-283 (305)
22 cd02663 Peptidase_C19G A subfa 53.5 21 0.00045 30.6 4.2 38 109-152 238-276 (300)
23 cd02423 Peptidase_C39G A sub-f 52.9 84 0.0018 22.6 8.6 103 16-156 10-115 (129)
24 smart00460 TGc Transglutaminas 52.1 62 0.0013 20.8 6.4 19 128-147 48-67 (68)
25 PF13299 CPSF100_C: Cleavage a 51.7 79 0.0017 25.3 7.0 69 63-165 90-158 (161)
26 COG2274 SunT ABC-type bacterio 47.6 1.5E+02 0.0033 29.4 9.5 118 15-179 10-129 (709)
27 cd02660 Peptidase_C19D A subfa 46.9 32 0.00069 29.4 4.3 37 109-151 274-311 (328)
28 cd02668 Peptidase_C19L A subfa 45.5 31 0.00066 29.9 4.0 37 109-151 247-286 (324)
29 PF01473 CW_binding_1: Putativ 43.9 24 0.00052 18.1 2.0 12 136-147 5-16 (19)
30 PF00443 UCH: Ubiquitin carbox 42.1 45 0.00097 26.5 4.3 39 108-152 211-251 (269)
31 cd01427 HAD_like Haloacid deha 41.5 39 0.00084 23.6 3.4 23 158-180 27-49 (139)
32 cd02662 Peptidase_C19F A subfa 41.3 42 0.00092 27.8 4.1 40 108-153 163-224 (240)
33 cd02672 Peptidase_C19P A subfa 40.5 37 0.0008 29.2 3.7 40 108-152 213-258 (268)
34 PF00288 GHMP_kinases_N: GHMP 40.2 42 0.00091 22.2 3.3 29 16-46 21-49 (67)
35 TIGR01684 viral_ppase viral ph 39.0 59 0.0013 29.0 4.8 39 140-179 129-170 (301)
36 PF02251 PA28_alpha: Proteasom 37.0 4.4 9.5E-05 28.0 -2.1 25 21-46 33-57 (64)
37 PF04473 DUF553: Transglutamin 36.8 76 0.0016 25.4 4.7 39 129-174 109-147 (153)
38 PRK10302 hypothetical protein; 36.5 59 0.0013 28.4 4.4 64 26-95 99-163 (272)
39 cd02665 Peptidase_C19I A subfa 36.2 65 0.0014 27.2 4.5 39 109-153 165-205 (228)
40 KOG1865 Ubiquitin carboxyl-ter 35.8 48 0.001 32.0 3.9 42 109-155 353-395 (545)
41 PF01088 Peptidase_C12: Ubiqui 34.8 53 0.0011 27.5 3.7 30 128-157 165-194 (214)
42 cd02425 Peptidase_C39F A sub-f 33.7 1.8E+02 0.0038 20.8 8.7 100 16-155 10-111 (126)
43 PF03698 UPF0180: Uncharacteri 32.1 44 0.00096 24.1 2.4 20 76-95 11-30 (80)
44 PHA03398 viral phosphatase sup 30.9 88 0.0019 28.0 4.6 39 140-179 131-172 (303)
45 cd02669 Peptidase_C19M A subfa 29.1 87 0.0019 28.7 4.4 37 109-151 384-423 (440)
46 COG3012 Uncharacterized protei 28.6 48 0.001 26.7 2.3 16 134-149 115-130 (151)
47 PRK03094 hypothetical protein; 27.5 79 0.0017 22.9 3.0 20 76-95 11-30 (80)
48 PF15649 Tox-REase-7: Restrict 27.2 95 0.0021 22.7 3.5 27 153-179 52-78 (87)
49 COG4840 Uncharacterized protei 24.9 43 0.00094 23.6 1.3 22 25-46 46-67 (71)
50 PF01904 DUF72: Protein of unk 24.5 3.4E+02 0.0073 22.6 6.9 118 26-180 90-213 (230)
51 PF06569 DUF1128: Protein of u 24.3 89 0.0019 22.1 2.8 24 23-46 44-67 (71)
52 PF13529 Peptidase_C39_2: Pept 24.0 2.7E+02 0.0058 19.8 7.8 119 15-146 13-143 (144)
53 COG5077 Ubiquitin carboxyl-ter 23.1 1E+02 0.0022 31.5 3.8 34 109-148 432-467 (1089)
54 cd00086 homeodomain Homeodomai 23.0 1.1E+02 0.0024 19.0 2.9 29 20-48 12-40 (59)
55 PF05152 DUF705: Protein of un 22.6 1.4E+02 0.0029 26.8 4.2 36 140-176 125-163 (297)
56 PF13423 UCH_1: Ubiquitin carb 22.3 1.4E+02 0.003 25.4 4.2 33 109-146 256-292 (295)
57 COG5533 UBP5 Ubiquitin C-termi 22.1 1.1E+02 0.0023 28.1 3.5 41 109-155 358-398 (415)
58 COG1654 BirA Biotin operon rep 21.8 89 0.0019 22.4 2.4 26 154-180 31-56 (79)
59 cd02670 Peptidase_C19N A subfa 21.4 1.9E+02 0.0042 24.6 4.9 39 109-152 168-219 (241)
60 PF12780 AAA_8: P-loop contain 21.4 52 0.0011 28.5 1.4 37 11-47 97-136 (268)
61 PF11380 DUF3184: Protein of u 20.4 50 0.0011 32.3 1.1 31 134-167 420-450 (691)
No 1
>PF02099 Josephin: Josephin; InterPro: IPR006155 Human genes containing triplet repeats can markedly expand in length, leading to neuropsychiatric disease. Expansion of triplet repeats explains the phenomenon of anticipation, i.e. the increasing severity or earlier age of onset in successive generations in a pedigree []. A novel gene containing CAG repeats has been identified and mapped to chromosome 14q32.1, the genetic locus for Machado-Joseph disease (MJD). Normally, the gene contains 13-36 CAG repeats, but most clinically diagnosed patients and all affected members of a family with the clinical and pathological diagnosis of MJD show expansion of the repeat number, from 68-79 []. Similar abnormalities in related genes may give rise to diseases similar to MJD. MJD is a neurodegenerative disorder characterised by cerebellar ataxia, pyramidal and extra-pyramidal signs, peripheral nerve palsy, external ophtalmoplegia, facial and lingual fasciculation and bulging. The disease is autosomal dominant, with late onset of symptoms, generally after the fourth decade.; GO: 0008242 omega peptidase activity; PDB: 3O65_G 1YZB_A 2JRI_A 2DOS_A 2AGA_A.
Probab=100.00 E-value=5.6e-63 Score=396.29 Aligned_cols=152 Identities=45% Similarity=0.784 Sum_probs=132.4
Q ss_pred eccccchHHHHhHhhcCCCCCCCHHHHHHHHHHhcccCCCC---CCCCCCceeeccccCCc-CCCccHHHHHHHHHhCCC
Q 030121 12 RQKLQFCLLHSLNNLFQQEGAFTRASLNEIAEKLVLDYPNK---QTWTPLSVVFKPHHNAL-TGNYDINVLIAALEGRGK 87 (182)
Q Consensus 12 kQ~~~lCalHaLNnLlQ~~~~Ft~~dL~~Ia~~Ld~~e~~~---~~~~~~~~~~~p~~n~~-~GnydinVl~~AL~~~g~ 87 (182)
||+++|||+||||||||| |+||+.||++||++||+.|+.. .++++.+++.+||+||+ +||||||||++||++||+
T Consensus 1 kQ~~~lCalHaLNnLlQ~-~~ft~~dL~~Ia~~Ld~~E~~~~~~~~~~~~~~~~~~s~n~~~~GnysinVL~~AL~~~g~ 79 (157)
T PF02099_consen 1 KQELQLCALHALNNLLQG-PYFTAVDLDEIAQELDEEERSLMAEDSWTPLSFLFNPSRNVDGTGNYSINVLMAALQVWGL 79 (157)
T ss_dssp S-STTSHHHHHHHHHCTS-S-S-HHHHHHHHHHHHHHHHHHHHCTSHHHHHHHTSTSSTCSTTSTCECHHHHHHHHCCT-
T ss_pred CcHHHHHHHHHHHHHhhh-hhcCHHHHHHHHHHhChhhhhhhhccCccchhhccccccCccccCCcCHHHHHHHHHHcCc
Confidence 899999999999999999 8999999999999999988642 45566778899999999 999999999999999999
Q ss_pred eEE-eccCCcccccccCCCCccceEEEEEecccccccccccccceEEEEeeCCEEEEeeCCCCCCeEcCCHHHHHHHHHH
Q 030121 88 SVV-WHDRRNEASAIDLDGGENCLMGIVINVPVTRYAGLWKSRHWVALRKIDGVWYNLDSDFHAPQCFKDSKEVREFLDY 166 (182)
Q Consensus 88 ~~~-w~d~r~~~~~~~~~~~~~~~~gfI~N~~~~~~~~~~~~~HWfaIRki~g~wyNLDS~l~~P~~i~~~~~L~~fL~~ 166 (182)
+++ |+|+|.....++++ ++.|||||. +|||||||||+|+||||||++++|+.|+++| |.+||++
T Consensus 80 ~~~~~~~~~~~~~~~~~~----~~~gfI~N~----------~~HWf~iRki~~~wyNLDS~l~~P~~i~~~~-l~~fL~~ 144 (157)
T PF02099_consen 80 ELVPWFDKRMQEASIDPD----NEFGFICNL----------SRHWFAIRKIGGQWYNLDSKLKEPELISDFY-LSAFLQQ 144 (157)
T ss_dssp EEEETTSHHHHHCC--CC----CSSEEEEEC----------TTEEEEEEEETTEEEEECTTTSS-EEE-HHH-HHHHHHH
T ss_pred eEEEccCccchhhhcCch----hceEEEecc----------CcceEEEEeeCCeeEeccCCCCCCcccCHHH-HHHHHHH
Confidence 999 67777766666655 999999997 9999999999999999999999999999875 9999999
Q ss_pred HHhCCcEEEEEEc
Q 030121 167 IIGLGGEVLLVKN 179 (182)
Q Consensus 167 ~~~~g~~ifvV~~ 179 (182)
++++||+||||+|
T Consensus 145 l~~~g~~ifvV~~ 157 (157)
T PF02099_consen 145 LQSEGYSIFVVRG 157 (157)
T ss_dssp HHCCTEEEEEEES
T ss_pred HHhCCcEEEEEeC
Confidence 9999999999986
No 2
>KOG2935 consensus Ataxin 3/Josephin [General function prediction only]
Probab=100.00 E-value=2.2e-52 Score=353.85 Aligned_cols=159 Identities=26% Similarity=0.395 Sum_probs=144.8
Q ss_pred CcceeeeccccchHHHHhHhhcCCCCCCCHHHHHHHHHHhcccCCCCCCCCCCceeeccccCCc-CCCccHHHHHHHHHh
Q 030121 6 CKIYHERQKLQFCLLHSLNNLFQQEGAFTRASLNEIAEKLVLDYPNKQTWTPLSVVFKPHHNAL-TGNYDINVLIAALEG 84 (182)
Q Consensus 6 ~~iYhEkQ~~~lCalHaLNnLlQ~~~~Ft~~dL~~Ia~~Ld~~e~~~~~~~~~~~~~~p~~n~~-~GnydinVl~~AL~~ 84 (182)
..||||+|+..|||+||||+|||| ++|+..||++-+.+++-.|....+-.+..+...|+.||+ +|+||||||.+||+.
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 GSIFHEVQESNLCAQHCLNTLLQG-PFFSEFDLADGKERMRMAEGGVTGEFYGDFLQQPSENMDDSGFFSIQVLSKALEV 80 (315)
T ss_pred CchhhhhhhhhHHHHHHHHHHhcc-cccChhhhhhHHHHHHHHhcccccccccccccCCCcCcCccCceeHHHHHHHHHh
Confidence 469999999999999999999999 899999999999999887776544445677889999999 999999999999999
Q ss_pred CCCeEEeccCCccc-ccccCCCCccceEEEEEecccccccccccccceEEEEeeCCEEEEeeCCCCCCeEcCCHHHHHHH
Q 030121 85 RGKSVVWHDRRNEA-SAIDLDGGENCLMGIVINVPVTRYAGLWKSRHWVALRKIDGVWYNLDSDFHAPQCFKDSKEVREF 163 (182)
Q Consensus 85 ~g~~~~w~d~r~~~-~~~~~~~~~~~~~gfI~N~~~~~~~~~~~~~HWfaIRki~g~wyNLDS~l~~P~~i~~~~~L~~f 163 (182)
||+++++|.++... ..+|+. +..+||||+ +.|||+|||+|++||||||.|.+|+.|+++| |++|
T Consensus 81 w~Leli~~nnP~~~~~~idP~----~erafICnl----------~eHWF~iRKfg~qWfnlnSllagPellSdty-ls~F 145 (315)
T KOG2935|consen 81 WGLELIPFNNPEYQPLQIDPI----NERAFICNL----------KEHWFTIRKFGKQWFNLNSLLAGPELLSDTY-LSAF 145 (315)
T ss_pred hceeeeecCChhhhhccCCcc----hhhhhhhcc----------hhhhhhHhhhcchhccchhhhcchHHHHHHH-HHHH
Confidence 99999999987554 344444 889999999 9999999999999999999999999999997 9999
Q ss_pred HHHHHhCCcEEEEEEcC
Q 030121 164 LDYIIGLGGEVLLVKND 180 (182)
Q Consensus 164 L~~~~~~g~~ifvV~~~ 180 (182)
|++++.+|||||||.|+
T Consensus 146 L~qlq~egySIFVVkG~ 162 (315)
T KOG2935|consen 146 LAQLQQEGYSIFVVKGD 162 (315)
T ss_pred HHHHHhCCeeEEEEecC
Confidence 99999999999999986
No 3
>KOG2934 consensus Uncharacterized conserved protein, contains Josephin domain [General function prediction only]
Probab=100.00 E-value=3.5e-49 Score=318.63 Aligned_cols=162 Identities=41% Similarity=0.772 Sum_probs=149.9
Q ss_pred CCcceeeeccccchHHHHhHhhcCCCCCCCHHHHHHHHHHhcccCCCCCCCCCCceeeccccCCc-CCCccHHHHHHHHH
Q 030121 5 NCKIYHERQKLQFCLLHSLNNLFQQEGAFTRASLNEIAEKLVLDYPNKQTWTPLSVVFKPHHNAL-TGNYDINVLIAALE 83 (182)
Q Consensus 5 ~~~iYhEkQ~~~lCalHaLNnLlQ~~~~Ft~~dL~~Ia~~Ld~~e~~~~~~~~~~~~~~p~~n~~-~GnydinVl~~AL~ 83 (182)
++.||||||++.|||+|||||++|++..||+..+++||..|.+. .+.+||+++. .||||+||||+|||
T Consensus 23 p~~iYherq~r~lc~lhAlnnv~q~~n~ftr~~~~d~c~~l~p~-----------s~~~Phrs~~g~Gnydvnvimaalq 91 (204)
T KOG2934|consen 23 PPGIYHERQRRELCALHALNNVFQRSNAFTRPVLDDICTRLKPR-----------SWLNPHRSWKGPGNYDVNVIMAALQ 91 (204)
T ss_pred CCccchhHHHHHHHHHHHhhhhhhccccccchhhHHHHhhcCcc-----------cccCccccccCCCcccHHHHHHHHH
Confidence 34699999999999999999999997799999999999999743 3689999999 99999999999999
Q ss_pred hCCCeEEeccCCcccccccCCCCccceEEEEEecccccccc-c---ccccceEEEEeeCCEEEEeeCCCCCCeEcCCHHH
Q 030121 84 GRGKSVVWHDRRNEASAIDLDGGENCLMGIVINVPVTRYAG-L---WKSRHWVALRKIDGVWYNLDSDFHAPQCFKDSKE 159 (182)
Q Consensus 84 ~~g~~~~w~d~r~~~~~~~~~~~~~~~~gfI~N~~~~~~~~-~---~~~~HWfaIRki~g~wyNLDS~l~~P~~i~~~~~ 159 (182)
..|+++||||+|+++..+.+. .+.|||.|+|+....| + ..+|||.|+|+.+|.||||||++.+|++||+..+
T Consensus 92 ~~gl~avw~dRrrd~~~l~L~----~v~gfIlnlp~~~slG~L~Lp~~rrhw~alR~~~g~yynldsklr~P~~ig~e~~ 167 (204)
T KOG2934|consen 92 QCGLEAVWLDRRRDVTALALS----VVFGFILNLPCKFSLGYLRLPVMRRHWLALRSPPGKYYNLDSKLREPECIGTEND 167 (204)
T ss_pred hcCceeeeccccCCcchhhhH----HHHHHHHcCCchhccccccchhHHhhhHhhhCCCCceecccccccCCcccccchh
Confidence 999999999999999988888 9999999999987544 2 5799999999999999999999999999999999
Q ss_pred HHHHHHHHHhCC-cEEEEEEcCC
Q 030121 160 VREFLDYIIGLG-GEVLLVKNDK 181 (182)
Q Consensus 160 L~~fL~~~~~~g-~~ifvV~~~~ 181 (182)
+.+||+..++.+ +++|+|+.+|
T Consensus 168 ~~~fla~hl~~~~~el~lvi~ee 190 (204)
T KOG2934|consen 168 FREFLATHLSMAIEELILVINEE 190 (204)
T ss_pred HHHHHHHHHHhhhhhheeeeccc
Confidence 999999998877 9999998876
No 4
>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=80.31 E-value=18 Score=26.29 Aligned_cols=100 Identities=14% Similarity=0.138 Sum_probs=60.3
Q ss_pred cchHHHHhHhhcCCCCCCCHHHHHHHHHHhcccCCCCCCCCCCceeeccccCCcCCCccHHHHHHHHHhCCCeEEeccCC
Q 030121 16 QFCLLHSLNNLFQQEGAFTRASLNEIAEKLVLDYPNKQTWTPLSVVFKPHHNALTGNYDINVLIAALEGRGKSVVWHDRR 95 (182)
Q Consensus 16 ~lCalHaLNnLlQ~~~~Ft~~dL~~Ia~~Ld~~e~~~~~~~~~~~~~~p~~n~~~GnydinVl~~AL~~~g~~~~w~d~r 95 (182)
.-|++.||=.+++- +=-..+.++|...+.... .| .++..|.+|++..|+++.-....
T Consensus 10 ~~~gl~~l~~i~~~--~g~~~~~~~l~~~~~~~~--------------------~~-~~~~~l~~~a~~~Gl~~~~~~~~ 66 (125)
T cd02420 10 TECGAASLAIILAY--YGRYVPLSELRIACGVSR--------------------DG-SNASNLLKAAREYGLTAKGYKKD 66 (125)
T ss_pred cCHHHHHHHHHHHH--cCCCCCHHHHHHHcCCCC--------------------CC-CCHHHHHHHHHHcCcccceEecC
Confidence 47999999888873 323344444444543110 14 68888999999999988543221
Q ss_pred c-ccccccCCCCccceEEEEEecccccccccccccceEEEEeeC-CEEEEeeCCCCCCeEcCC
Q 030121 96 N-EASAIDLDGGENCLMGIVINVPVTRYAGLWKSRHWVALRKID-GVWYNLDSDFHAPQCFKD 156 (182)
Q Consensus 96 ~-~~~~~~~~~~~~~~~gfI~N~~~~~~~~~~~~~HWfaIRki~-g~wyNLDS~l~~P~~i~~ 156 (182)
. ......+ =.|+- ++..||+-|-+++ +.++-.|+.. +|+.++-
T Consensus 67 ~~~L~~~~l--------P~I~~---------~~~g~~~Vl~~~~~~~~~i~dp~~-~~~~~s~ 111 (125)
T cd02420 67 LEALREVSL--------PAIVF---------WNFNHFLVVEGFDKRKVFLNDPAT-GRRTVSL 111 (125)
T ss_pred HHHHhcCCC--------CEEEE---------eCCCEEEEEEEEeCCEEEEECCCc-CceeecH
Confidence 1 1111111 11221 1368999998885 4778888854 7887754
No 5
>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=77.23 E-value=0.97 Score=26.08 Aligned_cols=11 Identities=27% Similarity=0.930 Sum_probs=9.1
Q ss_pred CEEEEeeCCCC
Q 030121 139 GVWYNLDSDFH 149 (182)
Q Consensus 139 g~wyNLDS~l~ 149 (182)
..|||+|+++.
T Consensus 8 s~WfniD~rIs 18 (26)
T TIGR02616 8 SKWFNIDNRIS 18 (26)
T ss_pred CceEEcchhhe
Confidence 37999999875
No 6
>cd02424 Peptidase_C39E A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family, which contains Colicin V perocessing peptidase.
Probab=75.94 E-value=29 Score=25.66 Aligned_cols=104 Identities=17% Similarity=0.150 Sum_probs=64.4
Q ss_pred cchHHHHhHhhcCCCCCCC-HHHHHHHHHHhcccCCCCCCCCCCceeeccccCCcCCCccHHHHHHHHHhCCCeEEeccC
Q 030121 16 QFCLLHSLNNLFQQEGAFT-RASLNEIAEKLVLDYPNKQTWTPLSVVFKPHHNALTGNYDINVLIAALEGRGKSVVWHDR 94 (182)
Q Consensus 16 ~lCalHaLNnLlQ~~~~Ft-~~dL~~Ia~~Ld~~e~~~~~~~~~~~~~~p~~n~~~GnydinVl~~AL~~~g~~~~w~d~ 94 (182)
.-||+.||=.+++- ||. +.+.+++..++... + .| .|+.-|.++++..|+++.-...
T Consensus 10 ~dcgla~l~~i~~~--~~g~~~~~~~l~~~~~~~-----------------~---~g-~s~~~l~~~a~~~Gl~~k~~~~ 66 (129)
T cd02424 10 NDCGIAVIQMLYNH--YYKKKYDLNELKIKANLK-----------------K---NG-LSIYDLENLAKKFGLETESYQG 66 (129)
T ss_pred cchHHHHHHHHHHH--hcCCCccHHHHHHHhCCC-----------------C---CC-ccHHHHHHHHHHcCCceeEEEc
Confidence 57999999999862 233 44556666555311 0 14 8888999999999998865432
Q ss_pred CcccccccCCCCccceEEEEEecccccccccccccceEEEEee-CCEEEEeeCCCCCCeEcCC
Q 030121 95 RNEASAIDLDGGENCLMGIVINVPVTRYAGLWKSRHWVALRKI-DGVWYNLDSDFHAPQCFKD 156 (182)
Q Consensus 95 r~~~~~~~~~~~~~~~~gfI~N~~~~~~~~~~~~~HWfaIRki-~g~wyNLDS~l~~P~~i~~ 156 (182)
... .+..-+ ...-.|++. ....||+-++++ ++.++-.|. -.+|+.++-
T Consensus 67 ~~~----~l~~~~-~p~P~i~~~--------~~~~hfvVl~~~~~~~v~I~DP-~~g~~~~s~ 115 (129)
T cd02424 67 SFL----EFLELK-NKFIILLKS--------NGLNHFVIVKKIKKNKFIVLDP-KKGKYKITY 115 (129)
T ss_pred CHH----HHhhcc-CCEEEEEec--------CCCCeEEEEEEEECCEEEEECC-CCCCEEeCH
Confidence 210 111000 012234321 124699999999 668888899 667887754
No 7
>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=71.31 E-value=12 Score=27.55 Aligned_cols=104 Identities=20% Similarity=0.131 Sum_probs=59.9
Q ss_pred eccc-cchHHHHhHhhcCCCCCCCHHHHHHHHHHhcccCCCCCCCCCCceeeccccCCcCCCccHHHHHHHHHhCCCeEE
Q 030121 12 RQKL-QFCLLHSLNNLFQQEGAFTRASLNEIAEKLVLDYPNKQTWTPLSVVFKPHHNALTGNYDINVLIAALEGRGKSVV 90 (182)
Q Consensus 12 kQ~~-~lCalHaLNnLlQ~~~~Ft~~dL~~Ia~~Ld~~e~~~~~~~~~~~~~~p~~n~~~GnydinVl~~AL~~~g~~~~ 90 (182)
+|.. .=||+=||=.+++. +--+.+.++|...+...+ . | .|..-|..+++..|++..
T Consensus 6 ~Q~~~~dcg~acl~~l~~~--~g~~~s~~~l~~~~~~~~---------------~-----g-~s~~~L~~~~~~~gl~~~ 62 (131)
T PF03412_consen 6 KQSDSNDCGLACLAMLLKY--YGIPVSEEELRRQLGTSE---------------E-----G-TSLADLKRAARKYGLKAK 62 (131)
T ss_dssp --SSTT-HHHHHHHHHHHH--TT----HHHHHCCTT-BT---------------T-----B---CCCHHHHHHHTTEEEE
T ss_pred EeCCCCCHHHHHHHHHHHH--hCCCchHHHHHHHhcCCc---------------c-----C-CCHHHHHHHHHhccccee
Confidence 4554 67999999999874 345666777776664221 1 1 223338899999999998
Q ss_pred eccCCcccccccCCCCccceEEEEEecccccccccccccceEEEEeeCC-EEEEeeCCCCCCeEcC
Q 030121 91 WHDRRNEASAIDLDGGENCLMGIVINVPVTRYAGLWKSRHWVALRKIDG-VWYNLDSDFHAPQCFK 155 (182)
Q Consensus 91 w~d~r~~~~~~~~~~~~~~~~gfI~N~~~~~~~~~~~~~HWfaIRki~g-~wyNLDS~l~~P~~i~ 155 (182)
.+..... ...... .-+|+-+ ...||+-|-++++ ...-.|. -.+++.++
T Consensus 63 ~~~~~~~-~l~~~~------~P~I~~~---------~~~h~vVi~~~~~~~~~i~dP-~~g~~~~~ 111 (131)
T PF03412_consen 63 AVKLNFE-KLKRLP------LPAIAHL---------KDGHFVVIYKIDDGRVLIYDP-KKGKIKLS 111 (131)
T ss_dssp EEE--GG-GCTCGG------SSEEEEE---------CCCEEEEEEEECCCEEEECCT-TTCEEEEE
T ss_pred eeecchh-hhhhcc------ccEEEEe---------cCcceEEEEeEcCcEEEEEeC-CCCeEEEe
Confidence 7653321 111111 2233332 2789999999865 6777788 67788885
No 8
>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=71.18 E-value=37 Score=24.63 Aligned_cols=100 Identities=16% Similarity=0.133 Sum_probs=59.7
Q ss_pred cchHHHHhHhhcCCCCCCCHHHHHHHHHHhcccCCCCCCCCCCceeeccccCCcCCCccHHHHHHHHHhCCCeEEeccCC
Q 030121 16 QFCLLHSLNNLFQQEGAFTRASLNEIAEKLVLDYPNKQTWTPLSVVFKPHHNALTGNYDINVLIAALEGRGKSVVWHDRR 95 (182)
Q Consensus 16 ~lCalHaLNnLlQ~~~~Ft~~dL~~Ia~~Ld~~e~~~~~~~~~~~~~~p~~n~~~GnydinVl~~AL~~~g~~~~w~d~r 95 (182)
.-|++.||=.+++- +=-..+.+.|...+.. ..+-++...+..+++..|+.+.-....
T Consensus 10 ~~~~l~~l~~~~~~--~g~~~~~~~l~~~~~~---------------------~~~~~~~~~l~~~a~~~Gl~~~~~~~~ 66 (127)
T cd02419 10 AECGLACLAMIASY--HGHHVDLASLRQRFPV---------------------SLKGATLADLIDIAQQLGLSTRALRLD 66 (127)
T ss_pred ccHHHHHHHHHHHH--cCCCCCHHHHHHHcCC---------------------CCCCcCHHHHHHHHHHCCCceeEEEcc
Confidence 46888888888763 2223344444444421 112289999999999999988654422
Q ss_pred c-ccccccCCCCccceEEEEEecccccccccccccceEEEEeeCC-EEEEeeCCCCCCeEcCC
Q 030121 96 N-EASAIDLDGGENCLMGIVINVPVTRYAGLWKSRHWVALRKIDG-VWYNLDSDFHAPQCFKD 156 (182)
Q Consensus 96 ~-~~~~~~~~~~~~~~~gfI~N~~~~~~~~~~~~~HWfaIRki~g-~wyNLDS~l~~P~~i~~ 156 (182)
- ......+ -...+ ++..||+-|-++++ .+.-.|+.. +|+.++.
T Consensus 67 ~~~l~~~~l-----P~i~~------------~~~g~~~Vl~~~~~~~~~i~dp~~-~~~~~~~ 111 (127)
T cd02419 67 LEELGQLKL-----PCILH------------WDMNHFVVLKKVSRRRIVIHDPAL-GKRKLSL 111 (127)
T ss_pred HHHHhhCCC-----CEEEE------------ECCCEEEEEEEEcCCEEEEECCcc-CCEEEcH
Confidence 1 1111111 11111 13689999988865 566668754 6887753
No 9
>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=70.90 E-value=39 Score=24.84 Aligned_cols=133 Identities=15% Similarity=0.072 Sum_probs=73.1
Q ss_pred ccccchHHHHhHhhcCCCCCCCHHHHHHHHHHhcccCCCCCCCCCCceeeccccCCc-CCCccHHHHHHH-HHhCCCeEE
Q 030121 13 QKLQFCLLHSLNNLFQQEGAFTRASLNEIAEKLVLDYPNKQTWTPLSVVFKPHHNAL-TGNYDINVLIAA-LEGRGKSVV 90 (182)
Q Consensus 13 Q~~~lCalHaLNnLlQ~~~~Ft~~dL~~Ia~~Ld~~e~~~~~~~~~~~~~~p~~n~~-~GnydinVl~~A-L~~~g~~~~ 90 (182)
|...-|+..||-.+++. +=-+.+..+++..-. .. ..... .| .+..-|.++ ++..|+.+.
T Consensus 2 ~~~~~C~~~slamvl~~--~g~~~~~~~l~~~~~---~~-------------~~~~~~~g-~~~~~l~~~~a~~~G~~~~ 62 (141)
T cd02549 2 QLENGCGPTSLAMVLSY--LGVKVTKPQLAAEGN---TY-------------DFAKDGYG-TYPKPIVSAAARKYGLVVR 62 (141)
T ss_pred CCCCccHHHHHHHHHHh--cCCCCCHHHHHhhcc---cc-------------ccCCCCCC-cCHHHHHHHHHhhCCCcEE
Confidence 55678999999999974 111223333332210 00 00111 35 556667777 999999998
Q ss_pred eccCCccc-ccccCCCCccceEEEEEecccccccccccccceEEEEeeC--CEEEEeeCCCCCCeEcCCHHHHHHHHHHH
Q 030121 91 WHDRRNEA-SAIDLDGGENCLMGIVINVPVTRYAGLWKSRHWVALRKID--GVWYNLDSDFHAPQCFKDSKEVREFLDYI 167 (182)
Q Consensus 91 w~d~r~~~-~~~~~~~~~~~~~gfI~N~~~~~~~~~~~~~HWfaIRki~--g~wyNLDS~l~~P~~i~~~~~L~~fL~~~ 167 (182)
.......+ ..++.. .=+|+.+... .......||+.|..++ +..+-.|.-...|..++ ..+|.+.-
T Consensus 63 ~~~~~~~~~~~l~~~------~Pvi~~~~~~--~~~~~~gH~vVv~g~~~~~~~~i~DP~~~~~~~~~----~~~f~~~w 130 (141)
T cd02549 63 PLTGLLALLRQLAAG------HPVIVSVNLG--VSITPSGHAMVVIGYDRKGNVYVNDPGGGRRLVVS----FDEFEKAW 130 (141)
T ss_pred ECCCHHHHHHHHHCC------CeEEEEEecC--cccCCCCeEEEEEEEcCCCCEEEECCCCCcCEEEe----HHHHHHHH
Confidence 75432211 111111 2234433110 0112367999999987 46677888766677774 45666666
Q ss_pred HhCCcEEEE
Q 030121 168 IGLGGEVLL 176 (182)
Q Consensus 168 ~~~g~~ifv 176 (182)
...|+..++
T Consensus 131 ~~~~~~~~~ 139 (141)
T cd02549 131 KRMGGQAVV 139 (141)
T ss_pred HHcCCceEE
Confidence 666644444
No 10
>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=69.08 E-value=6.9 Score=31.53 Aligned_cols=39 Identities=21% Similarity=0.297 Sum_probs=28.4
Q ss_pred cceEEEEEecccccccccccccceEEEEeeC--CEEEEeeCCCCCCe
Q 030121 108 NCLMGIVINVPVTRYAGLWKSRHWVALRKID--GVWYNLDSDFHAPQ 152 (182)
Q Consensus 108 ~~~~gfI~N~~~~~~~~~~~~~HWfaIRki~--g~wyNLDS~l~~P~ 152 (182)
-.+.|+|+..-. ....||+|..|.+ +.||.+|=..-.|+
T Consensus 174 Y~L~~vI~H~G~------~~~GHY~~~~~~~~~~~W~~fnD~~V~~i 214 (230)
T cd02674 174 YDLYAVVNHYGS------LNGGHYTAYCKNNETNDWYKFDDSRVTKV 214 (230)
T ss_pred EEEEEEEEeeCC------CCCcEEEEEEECCCCCceEEEcCCeEEEc
Confidence 477899998621 1356999998887 89999986654443
No 11
>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=67.49 E-value=46 Score=24.30 Aligned_cols=109 Identities=19% Similarity=0.119 Sum_probs=60.6
Q ss_pred eccc-cchHHHHhHhhcCCC-CCCCHHHHHHHHHHhcccCCCCCCCCCCceeeccccCCcCCCccHHHHHHHHHhCCCeE
Q 030121 12 RQKL-QFCLLHSLNNLFQQE-GAFTRASLNEIAEKLVLDYPNKQTWTPLSVVFKPHHNALTGNYDINVLIAALEGRGKSV 89 (182)
Q Consensus 12 kQ~~-~lCalHaLNnLlQ~~-~~Ft~~dL~~Ia~~Ld~~e~~~~~~~~~~~~~~p~~n~~~GnydinVl~~AL~~~g~~~ 89 (182)
+|.. .=|++.||=.+++.- -.++.. .|...+... + .| ++...|..+++..|+++
T Consensus 5 ~q~~~~~~gl~~l~~~~~~~g~~~~~~---~l~~~~~~~---------------~-----~~-~~~~~l~~~a~~~Gl~~ 60 (136)
T cd02418 5 LQVDEMDCGAACLAMIAKYYGKNYSLA---KLRELAGTD---------------R-----EG-TSLLGLVKAAEKLGFET 60 (136)
T ss_pred EecCcccHHHHHHHHHHHHhCCCCCHH---HHHHHcCCC---------------C-----CC-cCHHHHHHHHHHCCCee
Confidence 5543 569999998888630 124444 444443210 0 13 78888999999999988
Q ss_pred EeccCCcccccccCCCCccceEEEEEecccccccccccccceEEEEeeCCE-EEEeeCCCCCCeEcC
Q 030121 90 VWHDRRNEASAIDLDGGENCLMGIVINVPVTRYAGLWKSRHWVALRKIDGV-WYNLDSDFHAPQCFK 155 (182)
Q Consensus 90 ~w~d~r~~~~~~~~~~~~~~~~gfI~N~~~~~~~~~~~~~HWfaIRki~g~-wyNLDS~l~~P~~i~ 155 (182)
.-....... ..+...+--...+|-|- ++..||+.|-++++. -+-.|. ...|+.++
T Consensus 61 ~~~~~~~~~--~~l~~~~~P~I~~~~~~--------~~~~~~~Vl~~~~~~~~~i~dp-~~~~~~~~ 116 (136)
T cd02418 61 RAVKADMDL--FELKDIPLPFIAHVIKE--------WKLNHYVVVYKIKKKKILIADP-AVGITKIS 116 (136)
T ss_pred EEEEcccch--hhHhcCCCCEEEEEccC--------CCCCeEEEEEEEcCCEEEEECC-CCCCEEee
Confidence 654322110 01110011112222110 246899999988764 455677 56677774
No 12
>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=65.49 E-value=11 Score=29.36 Aligned_cols=42 Identities=26% Similarity=0.388 Sum_probs=30.5
Q ss_pred cceEEEEEecccccccccccccceEEEEeeC--CEEEEeeCCCCCCeEc
Q 030121 108 NCLMGIVINVPVTRYAGLWKSRHWVALRKID--GVWYNLDSDFHAPQCF 154 (182)
Q Consensus 108 ~~~~gfI~N~~~~~~~~~~~~~HWfaIRki~--g~wyNLDS~l~~P~~i 154 (182)
-++.|+||..... -..-|++|..|-. ++||.+|=..-.|+.-
T Consensus 193 Y~L~~vi~h~G~~-----~~~GHY~~~~~~~~~~~W~~~nD~~V~~v~~ 236 (255)
T cd02257 193 YELVAVVVHSGTS-----ADSGHYVAYVKDPSDGKWYKFNDDKVTEVSE 236 (255)
T ss_pred EEEEEEEEEecCC-----CCCcCeEEEEeCCCCCceEEEeccccEEcCH
Confidence 4788889886211 1356999998876 8999999877666544
No 13
>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=62.57 E-value=12 Score=32.14 Aligned_cols=40 Identities=23% Similarity=0.404 Sum_probs=28.6
Q ss_pred cceEEEEEecccccccccccccceEEEEeeC--CEEEEeeCCCCCCeE
Q 030121 108 NCLMGIVINVPVTRYAGLWKSRHWVALRKID--GVWYNLDSDFHAPQC 153 (182)
Q Consensus 108 ~~~~gfI~N~~~~~~~~~~~~~HWfaIRki~--g~wyNLDS~l~~P~~ 153 (182)
-.+.|+|++.- -...-||+|..|-. +.||.+|=..-.+..
T Consensus 252 Y~L~~vI~H~G------~~~~GHY~~~vk~~~~~~W~~~nD~~V~~i~ 293 (334)
T cd02659 252 YELHGVLVHSG------DAHGGHYYSYIKDRDDGKWYKFNDDVVTPFD 293 (334)
T ss_pred EEEEEEEEecC------CCCCCCeEEEEECCCCCceEEEeCcccEECC
Confidence 36677777752 22468999987764 899999987765543
No 14
>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=62.18 E-value=12 Score=31.70 Aligned_cols=39 Identities=18% Similarity=0.292 Sum_probs=27.2
Q ss_pred ceEEEEEecccccccccccccceEEEEee---CCEEEEeeCCCCCCe
Q 030121 109 CLMGIVINVPVTRYAGLWKSRHWVALRKI---DGVWYNLDSDFHAPQ 152 (182)
Q Consensus 109 ~~~gfI~N~~~~~~~~~~~~~HWfaIRki---~g~wyNLDS~l~~P~ 152 (182)
.+.|+|++.- .-...-|++|.-|. +|+||.+|=..-.|+
T Consensus 185 ~L~~VV~H~G-----~~~~~GHY~a~vk~~~~~~~Wy~fnD~~V~~v 226 (245)
T cd02673 185 SLVAVICHLG-----ESPYDGHYIAYTKELYNGSSWLYCSDDEIRPV 226 (245)
T ss_pred EEEEEEEECC-----CCCCCceEEEEEEcCCCCCeEEEeeCceeeEc
Confidence 5677777651 11235799999876 689999987765554
No 15
>KOG1415 consensus Ubiquitin C-terminal hydrolase UCHL1 [Posttranslational modification, protein turnover, chaperones]
Probab=59.96 E-value=15 Score=31.33 Aligned_cols=30 Identities=20% Similarity=0.341 Sum_probs=27.1
Q ss_pred ccceEEEEeeCCEEEEeeCCCCCCeEcCCH
Q 030121 128 SRHWVALRKIDGVWYNLDSDFHAPQCFKDS 157 (182)
Q Consensus 128 ~~HWfaIRki~g~wyNLDS~l~~P~~i~~~ 157 (182)
.-|++|.-..+|.-|-||+-++.|+..|.+
T Consensus 159 d~HFI~~v~~~G~lYELDgR~~fPi~hG~t 188 (222)
T KOG1415|consen 159 DLHFICFVNKNGHLYELDGRKPFPINHGPT 188 (222)
T ss_pred ceEEEEEEccCCeEEEecCCcCCCccCCCC
Confidence 468888889999999999999999999976
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=59.31 E-value=63 Score=23.13 Aligned_cols=67 Identities=15% Similarity=0.168 Sum_probs=42.0
Q ss_pred ccHHHHHHHHHhCCCeEEeccCCc-ccccccCCCCccceEEEEEecccccccccccccceEEEEeeCC-EEEEeeCCCCC
Q 030121 73 YDINVLIAALEGRGKSVVWHDRRN-EASAIDLDGGENCLMGIVINVPVTRYAGLWKSRHWVALRKIDG-VWYNLDSDFHA 150 (182)
Q Consensus 73 ydinVl~~AL~~~g~~~~w~d~r~-~~~~~~~~~~~~~~~gfI~N~~~~~~~~~~~~~HWfaIRki~g-~wyNLDS~l~~ 150 (182)
++...|.++++..|+.+.-..... ....+.+. .++. ++..||+-|-++++ ..+-.|.....
T Consensus 39 ~~~~~l~~~a~~~Gl~~~~~~~~~~~l~~~~lP-------~I~~----------~~~g~~~Vl~~~~~~~~~i~dp~~~~ 101 (121)
T cd02417 39 FNSTELLLAAKSLGLKAKAVRQPVERLARLPLP-------ALAW----------DDDGGHFILAKLDGQKYLIQDPISQR 101 (121)
T ss_pred CCHHHHHHHHHHcCCeeEEEecCHHHhccCCCC-------EEEE----------ccCCCEEEEEEEcCCCEEEECCCcCC
Confidence 788889999999999886543221 11111111 1121 12679999988865 56777875556
Q ss_pred CeEcCC
Q 030121 151 PQCFKD 156 (182)
Q Consensus 151 P~~i~~ 156 (182)
|+.++.
T Consensus 102 ~~~~~~ 107 (121)
T cd02417 102 PEVLSR 107 (121)
T ss_pred CeecCH
Confidence 888754
No 17
>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=58.93 E-value=16 Score=30.94 Aligned_cols=38 Identities=32% Similarity=0.545 Sum_probs=28.2
Q ss_pred ceEEEEEecccccccccccccceEEEEee-----------------------CCEEEEeeCCCCCCe
Q 030121 109 CLMGIVINVPVTRYAGLWKSRHWVALRKI-----------------------DGVWYNLDSDFHAPQ 152 (182)
Q Consensus 109 ~~~gfI~N~~~~~~~~~~~~~HWfaIRki-----------------------~g~wyNLDS~l~~P~ 152 (182)
++.|+|++. |--..-|++|..|. +|.||.+|=..-.++
T Consensus 203 ~L~~vi~H~------G~~~~GHY~a~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~W~~~dD~~V~~v 263 (279)
T cd02667 203 RLYGVVEHS------GTMRSGHYVAYVKVRPPQQRLSDLTKSKPAADEAGPGSGQWYYISDSDVREV 263 (279)
T ss_pred EEEEEEEEe------CCCCCCEeEEEEEcCccccccccccccccccccCCCCCCcEEEEECCccEEC
Confidence 678888886 22257799999876 679999987665544
No 18
>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=58.61 E-value=15 Score=30.62 Aligned_cols=41 Identities=24% Similarity=0.468 Sum_probs=27.6
Q ss_pred cceEEEEEecccccccccccccceEEEEee-CCEEEEeeCCCCCCeE
Q 030121 108 NCLMGIVINVPVTRYAGLWKSRHWVALRKI-DGVWYNLDSDFHAPQC 153 (182)
Q Consensus 108 ~~~~gfI~N~~~~~~~~~~~~~HWfaIRki-~g~wyNLDS~l~~P~~ 153 (182)
-++.|+|++.-.. -...|++|..+- +|.||.+|=..-.|+.
T Consensus 248 Y~L~~vi~H~G~~-----~~~GHY~~~~~~~~~~W~~~nD~~V~~v~ 289 (304)
T cd02661 248 YKLYAVLVHSGFS-----PHSGHYYCYVKSSNGKWYNMDDSKVSPVS 289 (304)
T ss_pred eeEEEEEEECCCC-----CCCcCCEEEEECCCCCEEEEeCCeeEECC
Confidence 3566777765111 145699999774 8999999887665543
No 19
>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=58.54 E-value=63 Score=22.90 Aligned_cols=101 Identities=16% Similarity=0.142 Sum_probs=60.4
Q ss_pred cchHHHHhHhhcCCCCCCCHHHHHHHHHHhcccCCCCCCCCCCceeeccccCCcCCCccHHHHHHHHHhCCCeEEeccCC
Q 030121 16 QFCLLHSLNNLFQQEGAFTRASLNEIAEKLVLDYPNKQTWTPLSVVFKPHHNALTGNYDINVLIAALEGRGKSVVWHDRR 95 (182)
Q Consensus 16 ~lCalHaLNnLlQ~~~~Ft~~dL~~Ia~~Ld~~e~~~~~~~~~~~~~~p~~n~~~GnydinVl~~AL~~~g~~~~w~d~r 95 (182)
.-|++.||=.+++- +-.+.+.+.|...+... .+-++...|..+.+..|+++.-...+
T Consensus 5 ~~~gl~~l~~i~~~--~g~~~~~~~l~~~~~~~---------------------~~~~~~~~l~~~a~~~gl~~~~~~~~ 61 (122)
T cd02259 5 LDCGLACLQMLLRY--FGIPVRRDVLLNAQQRR---------------------QQGLSLADLVSLANKLGLTAQGVKLP 61 (122)
T ss_pred cchHHHHHHHHHHH--cCCCCCHHHHHHHHhhc---------------------cCCCCHHHHHHHHHHcCCeeeEEEcC
Confidence 46888888777763 22333444444444211 02278888999999999999754422
Q ss_pred c-ccccccCCCCccceEEEEEecccccccccccccceEEEEeeCC-EEEEeeCCCCCCeEcCC
Q 030121 96 N-EASAIDLDGGENCLMGIVINVPVTRYAGLWKSRHWVALRKIDG-VWYNLDSDFHAPQCFKD 156 (182)
Q Consensus 96 ~-~~~~~~~~~~~~~~~gfI~N~~~~~~~~~~~~~HWfaIRki~g-~wyNLDS~l~~P~~i~~ 156 (182)
. ......+. +++. ++..||+.|-++++ ...-.|..-..|+.++-
T Consensus 62 ~~~l~~~~~P-------~i~~----------~~~~~~~Vl~~~~~~~~~i~dp~~~~~~~~~~ 107 (122)
T cd02259 62 LAALSRLQLP-------ALLL----------WKQGHFVILYGADKGQVLIADPLEEGPVTLSE 107 (122)
T ss_pred HHHhccCCCC-------EEEE----------cCCCcEEEEEEEcCCEEEEECCcccCCEEeCH
Confidence 1 11111111 2222 23789999998865 66666765677887754
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=53.85 E-value=18 Score=30.76 Aligned_cols=38 Identities=21% Similarity=0.302 Sum_probs=26.3
Q ss_pred ceEEEEEecccccccccccccceEEEEeeC----CEEEEeeCCCCCC
Q 030121 109 CLMGIVINVPVTRYAGLWKSRHWVALRKID----GVWYNLDSDFHAP 151 (182)
Q Consensus 109 ~~~gfI~N~~~~~~~~~~~~~HWfaIRki~----g~wyNLDS~l~~P 151 (182)
++.|+|++.-. -...-|++|..|.. |+||-+|=..=.|
T Consensus 253 ~L~~vI~H~G~-----~~~~GHY~~~vk~~~~~~~~W~~fnD~~V~~ 294 (311)
T cd02658 253 ELIAFISHKGT-----SVHSGHYVAHIKKEIDGEGKWVLFNDEKVVA 294 (311)
T ss_pred EEEEEEEccCC-----CCCCcceEEEEeCCCCCCCCEEEecCceeEE
Confidence 56677766511 12467999999987 8999998665444
No 21
>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=53.59 E-value=21 Score=30.29 Aligned_cols=40 Identities=23% Similarity=0.328 Sum_probs=27.0
Q ss_pred ceEEEEEecccccccccccccceEEEEeeC--CEEEEeeCCCCCCeE
Q 030121 109 CLMGIVINVPVTRYAGLWKSRHWVALRKID--GVWYNLDSDFHAPQC 153 (182)
Q Consensus 109 ~~~gfI~N~~~~~~~~~~~~~HWfaIRki~--g~wyNLDS~l~~P~~ 153 (182)
++.|+|++.-. --..-|++|..|-. +.||.+|=..-.|+.
T Consensus 242 ~L~~vI~H~G~-----~~~~GHY~~~~~~~~~~~W~~fdD~~V~~~~ 283 (305)
T cd02657 242 ELVAVITHQGR-----SADSGHYVAWVRRKNDGKWIKFDDDKVSEVT 283 (305)
T ss_pred EEEEEEEecCC-----CCCCcEEEEEEEcCCCCeEEEEECCceEEeC
Confidence 46677776510 11245999998887 899999876655544
No 22
>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=53.55 E-value=21 Score=30.57 Aligned_cols=38 Identities=24% Similarity=0.428 Sum_probs=27.5
Q ss_pred ceEEEEEeccccccccc-ccccceEEEEeeCCEEEEeeCCCCCCe
Q 030121 109 CLMGIVINVPVTRYAGL-WKSRHWVALRKIDGVWYNLDSDFHAPQ 152 (182)
Q Consensus 109 ~~~gfI~N~~~~~~~~~-~~~~HWfaIRki~g~wyNLDS~l~~P~ 152 (182)
.+.|+|++. |- -..-|++|..|-+|.||.+|=..-.|.
T Consensus 238 ~L~~vi~H~------G~~~~~GHY~a~~k~~~~W~~fdD~~V~~~ 276 (300)
T cd02663 238 ELVAVVVHI------GGGPNHGHYVSIVKSHGGWLLFDDETVEKI 276 (300)
T ss_pred EEEEEEEEe------cCCCCCCceEEEEECCCcEEEEcCCceEEc
Confidence 455666664 22 347899999888999999987665554
No 23
>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=52.90 E-value=84 Score=22.61 Aligned_cols=103 Identities=15% Similarity=0.120 Sum_probs=61.5
Q ss_pred cchHHHHhHhhcCCCCCC-CHHHHHHHHHHhcccCCCCCCCCCCceeeccccCCcCCCccHHHHHHHHHhCCCeEEeccC
Q 030121 16 QFCLLHSLNNLFQQEGAF-TRASLNEIAEKLVLDYPNKQTWTPLSVVFKPHHNALTGNYDINVLIAALEGRGKSVVWHDR 94 (182)
Q Consensus 16 ~lCalHaLNnLlQ~~~~F-t~~dL~~Ia~~Ld~~e~~~~~~~~~~~~~~p~~n~~~GnydinVl~~AL~~~g~~~~w~d~ 94 (182)
+-|++.|+=.+++- +. -..+.+++..++... + .| ++..-|.++++..|+++.-...
T Consensus 10 ~~~~l~~l~~~~~~--~g~~~~~~~~l~~~~~~~---------------~-----~~-~s~~~l~~~a~~~Gl~~~~~~~ 66 (129)
T cd02423 10 FSCGPAALATLLRY--YGGINITEQEVLKLMLIR---------------S-----EG-FSMLDLKRYAEALGLKANGYRL 66 (129)
T ss_pred CChHHHHHHHHHHh--cCCCCCCHHHHHHHhCcc---------------c-----CC-cCHHHHHHHHHHCCCcceEEEc
Confidence 47999999888873 45 455555555555311 0 13 7888899999999998865432
Q ss_pred Cc-ccccccCCCCccceEEEEEecccccccccccccceEEEEee-CCEEEEeeCCCCCCeEcCC
Q 030121 95 RN-EASAIDLDGGENCLMGIVINVPVTRYAGLWKSRHWVALRKI-DGVWYNLDSDFHAPQCFKD 156 (182)
Q Consensus 95 r~-~~~~~~~~~~~~~~~gfI~N~~~~~~~~~~~~~HWfaIRki-~g~wyNLDS~l~~P~~i~~ 156 (182)
+. ......+ -...++-|- ...||+.|.++ ++.+.-.|+.. .|+.++.
T Consensus 67 ~~~~L~~~~l-----P~i~~~~~~---------~~~~~vvl~~~~~~~~~i~dp~~-~~~~~s~ 115 (129)
T cd02423 67 NLDKLNALQI-----PVIVLVNNG---------GYGHFVVIKGIDGDRVLVGDPAL-GNISMSR 115 (129)
T ss_pred CHHHHhhCCC-----CEEEEEecC---------CCceEEEEEEEeCCEEEEECCCC-CCcccCH
Confidence 21 1111111 122222111 14699999877 55777778744 5666643
No 24
>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=52.13 E-value=62 Score=20.82 Aligned_cols=19 Identities=26% Similarity=0.838 Sum_probs=13.9
Q ss_pred ccc-eEEEEeeCCEEEEeeCC
Q 030121 128 SRH-WVALRKIDGVWYNLDSD 147 (182)
Q Consensus 128 ~~H-WfaIRki~g~wyNLDS~ 147 (182)
..| |..+. +++.|+.+|..
T Consensus 48 ~~H~W~ev~-~~~~W~~~D~~ 67 (68)
T smart00460 48 EAHAWAEVY-LEGGWVPVDPT 67 (68)
T ss_pred CcEEEEEEE-ECCCeEEEeCC
Confidence 445 66665 78999999964
No 25
>PF13299 CPSF100_C: Cleavage and polyadenylation factor 2 C-terminal
Probab=51.66 E-value=79 Score=25.28 Aligned_cols=69 Identities=22% Similarity=0.266 Sum_probs=47.0
Q ss_pred ccccCCcCCCccHHHHHHHHHhCCCeEEeccCCcccccccCCCCccceEEEEEecccccccccccccceEEEEeeCCEEE
Q 030121 63 KPHHNALTGNYDINVLIAALEGRGKSVVWHDRRNEASAIDLDGGENCLMGIVINVPVTRYAGLWKSRHWVALRKIDGVWY 142 (182)
Q Consensus 63 ~p~~n~~~GnydinVl~~AL~~~g~~~~w~d~r~~~~~~~~~~~~~~~~gfI~N~~~~~~~~~~~~~HWfaIRki~g~wy 142 (182)
.+|..++.|+-...-|.++|...|+.+...- .=.++||= . ++|||.+.-=+
T Consensus 90 ~~~~~~~iGd~rL~~lk~~L~~~g~~aEF~g----------------~G~Lv~~~-----------~--V~VrK~~~G~i 140 (161)
T PF13299_consen 90 PGHQSLFIGDLRLSDLKQALQSAGIQAEFRG----------------EGVLVCNG-----------G--VAVRKSEDGRI 140 (161)
T ss_pred CCCCceecCcccHHHHHHHHHHCCCceEEee----------------CCeEEECC-----------E--EEEEEcCCCCE
Confidence 4477777999999999999999998875320 01257883 3 99999974336
Q ss_pred EeeCCCCCCeEcCCHHHHHHHHH
Q 030121 143 NLDSDFHAPQCFKDSKEVREFLD 165 (182)
Q Consensus 143 NLDS~l~~P~~i~~~~~L~~fL~ 165 (182)
.+++.+. .++|.+..-+.
T Consensus 141 ~ieG~~~-----~~yy~VR~~iy 158 (161)
T PF13299_consen 141 VIEGCLS-----EDYYKVRKLIY 158 (161)
T ss_pred EEEecCc-----hhHHHHHHHHH
Confidence 6666554 44555554443
No 26
>COG2274 SunT ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]
Probab=47.60 E-value=1.5e+02 Score=29.38 Aligned_cols=118 Identities=22% Similarity=0.224 Sum_probs=72.3
Q ss_pred ccchHHHHhHhhcCC-CCCCCHHHHHHHHHHhcccCCCCCCCCCCceeeccccCCcCCCccHHHHHHHHHhCCCeEEecc
Q 030121 15 LQFCLLHSLNNLFQQ-EGAFTRASLNEIAEKLVLDYPNKQTWTPLSVVFKPHHNALTGNYDINVLIAALEGRGKSVVWHD 93 (182)
Q Consensus 15 ~~lCalHaLNnLlQ~-~~~Ft~~dL~~Ia~~Ld~~e~~~~~~~~~~~~~~p~~n~~~GnydinVl~~AL~~~g~~~~w~d 93 (182)
..=||+.||..+.+. ...++..+ +-+..... + +-.+..-+..+-+..|++..-+.
T Consensus 10 ~~dcgla~l~mia~~~g~~~~~~~---lr~~~~~~-----------------~----~g~sl~~l~~~a~~lGl~~~~~~ 65 (709)
T COG2274 10 ANDCGLACLAMIANYHGKKISLNE---LRELVGLS-----------------R----NGLSLLELKQAAEKLGLSARAVK 65 (709)
T ss_pred ccchHHHHHHHHHHHhCCCCCHHH---HHHHcCCC-----------------C----CCCChHHHHHHHHHcCCcccccc
Confidence 467999999999873 12344433 33333211 0 12677779999999999987655
Q ss_pred CCcccccccCCCCccceEEEEEecccccccccccccceEEEEeeCCE-EEEeeCCCCCCeEcCCHHHHHHHHHHHHhCCc
Q 030121 94 RRNEASAIDLDGGENCLMGIVINVPVTRYAGLWKSRHWVALRKIDGV-WYNLDSDFHAPQCFKDSKEVREFLDYIIGLGG 172 (182)
Q Consensus 94 ~r~~~~~~~~~~~~~~~~gfI~N~~~~~~~~~~~~~HWfaIRki~g~-wyNLDS~l~~P~~i~~~~~L~~fL~~~~~~g~ 172 (182)
-+ .. .+. . -..=+|++ |...||+.+-++++. |+-+|- -.+|+.++.. +|.+.-. |+
T Consensus 66 ~~--~~--~l~--~-~~lP~ii~---------~~~~h~vVl~~~~~~~~~v~dp-~~g~~~l~~~----e~~~~~t--g~ 122 (709)
T COG2274 66 LS--LE--ELK--Q-LPLPAIIH---------WNGNHFVVLYKIDKNKVVVLDP-AKGIRRLSLE----EFEKLWT--GI 122 (709)
T ss_pred CC--HH--Hhc--c-cCCCEEEE---------EcCCcEEEEEEecCCeEEEEeC-CCCcEEcCHH----HHHHhhh--ee
Confidence 33 11 111 0 01123554 347899999999885 888998 7788888754 3333332 66
Q ss_pred EEEEEEc
Q 030121 173 EVLLVKN 179 (182)
Q Consensus 173 ~ifvV~~ 179 (182)
.+++.-.
T Consensus 123 ~l~l~~~ 129 (709)
T COG2274 123 ALLLAPT 129 (709)
T ss_pred EEEEecc
Confidence 6665544
No 27
>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=46.89 E-value=32 Score=29.42 Aligned_cols=37 Identities=22% Similarity=0.541 Sum_probs=26.3
Q ss_pred ceEEEEEecccccccccccccceEEEEeeC-CEEEEeeCCCCCC
Q 030121 109 CLMGIVINVPVTRYAGLWKSRHWVALRKID-GVWYNLDSDFHAP 151 (182)
Q Consensus 109 ~~~gfI~N~~~~~~~~~~~~~HWfaIRki~-g~wyNLDS~l~~P 151 (182)
++.|+|+.. |-...-|++|..|-. +.||-+|=..-.|
T Consensus 274 ~L~avi~H~------G~~~~GHY~~~~~~~~~~W~~~nD~~V~~ 311 (328)
T cd02660 274 DLFAVVVHK------GTLDTGHYTAYCRQGDGQWFKFDDAMITR 311 (328)
T ss_pred EEEEEEEee------ccCCCCcEEEEEECCCCcEEEEECCeeEE
Confidence 566777665 222468999999887 8999998554443
No 28
>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=45.50 E-value=31 Score=29.86 Aligned_cols=37 Identities=30% Similarity=0.517 Sum_probs=24.8
Q ss_pred ceEEEEEeccccccccc-ccccceEEEEee--CCEEEEeeCCCCCC
Q 030121 109 CLMGIVINVPVTRYAGL-WKSRHWVALRKI--DGVWYNLDSDFHAP 151 (182)
Q Consensus 109 ~~~gfI~N~~~~~~~~~-~~~~HWfaIRki--~g~wyNLDS~l~~P 151 (182)
.+.|+|++. |- -..-||+|.-|- +|.||.+|=..-.+
T Consensus 247 ~L~~vI~H~------G~~~~~GHY~~~~k~~~~~~W~~fdD~~V~~ 286 (324)
T cd02668 247 ELSGVLIHQ------GVSAYSGHYIAHIKDEQTGEWYKFNDEDVEE 286 (324)
T ss_pred EEEEEEEEc------CCCCCCEeeEEEEECCCCCcEEEEECCceEE
Confidence 566777765 21 135799999764 48999998655433
No 29
>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=43.92 E-value=24 Score=18.08 Aligned_cols=12 Identities=50% Similarity=1.068 Sum_probs=9.5
Q ss_pred eeCCEEEEeeCC
Q 030121 136 KIDGVWYNLDSD 147 (182)
Q Consensus 136 ki~g~wyNLDS~ 147 (182)
+++|.||-+++.
T Consensus 5 ~~~~~wYy~~~~ 16 (19)
T PF01473_consen 5 QDNGNWYYFDSD 16 (19)
T ss_dssp EETTEEEEETTT
T ss_pred EECCEEEEeCCC
Confidence 458999999873
No 30
>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=42.06 E-value=45 Score=26.47 Aligned_cols=39 Identities=23% Similarity=0.429 Sum_probs=27.0
Q ss_pred cceEEEEEecccccccccccccceEEEEeeCC--EEEEeeCCCCCCe
Q 030121 108 NCLMGIVINVPVTRYAGLWKSRHWVALRKIDG--VWYNLDSDFHAPQ 152 (182)
Q Consensus 108 ~~~~gfI~N~~~~~~~~~~~~~HWfaIRki~g--~wyNLDS~l~~P~ 152 (182)
-++.|+|+.. |-..+-||+|.-+-.+ .||.+|=..-.++
T Consensus 211 Y~L~avi~H~------G~~~~GHY~a~v~~~~~~~W~~~dD~~v~~~ 251 (269)
T PF00443_consen 211 YRLVAVIVHY------GSADSGHYVAYVRDSDDGKWYKFDDSRVTEV 251 (269)
T ss_dssp EEEEEEEEEE------SSTTSEEEEEEEEETTTTEEEEEETTEEEEE
T ss_pred eeehhhhccc------cccccceEEEeeccccCCeEEEeeCCceEEC
Confidence 4678999986 2234779999876543 6999986554443
No 31
>cd01427 HAD_like Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others, all of which use a nucleophilic aspartate in their phosphoryl transfer reaction. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.
Probab=41.50 E-value=39 Score=23.58 Aligned_cols=23 Identities=26% Similarity=0.263 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHhCCcEEEEEEcC
Q 030121 158 KEVREFLDYIIGLGGEVLLVKND 180 (182)
Q Consensus 158 ~~L~~fL~~~~~~g~~ifvV~~~ 180 (182)
..+.++|+++.++|+.+++|.+.
T Consensus 27 ~~~~~~l~~l~~~g~~i~ivS~~ 49 (139)
T cd01427 27 PGVKEALKELKEKGIKLALATNK 49 (139)
T ss_pred cCHHHHHHHHHHCCCeEEEEeCc
Confidence 35789999999999999999763
No 32
>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=41.30 E-value=42 Score=27.81 Aligned_cols=40 Identities=20% Similarity=0.378 Sum_probs=29.2
Q ss_pred cceEEEEEecccccccccccccceEEEEeeC----------------------CEEEEeeCCCCCCeE
Q 030121 108 NCLMGIVINVPVTRYAGLWKSRHWVALRKID----------------------GVWYNLDSDFHAPQC 153 (182)
Q Consensus 108 ~~~~gfI~N~~~~~~~~~~~~~HWfaIRki~----------------------g~wyNLDS~l~~P~~ 153 (182)
-.+.|+|++. |--..-|.+|..|.. +.||.+|-..-.|+.
T Consensus 163 Y~L~avi~H~------G~~~~GHY~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~W~~fnD~~V~~v~ 224 (240)
T cd02662 163 YRLRAVVVHY------GSHSSGHYVCYRRKPLFSKDKEPGSFVRMREGPSSTSHPWWRISDTTVKEVS 224 (240)
T ss_pred EEEEEEEEEe------ccCCCceEEEEEeCCCcccccccccccccccccCccCCCEEEEechheEEeC
Confidence 3577888775 222578999998876 899999876655553
No 33
>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=40.50 E-value=37 Score=29.16 Aligned_cols=40 Identities=23% Similarity=0.376 Sum_probs=28.7
Q ss_pred cceEEEEEecccccccccccccceEEEEee------CCEEEEeeCCCCCCe
Q 030121 108 NCLMGIVINVPVTRYAGLWKSRHWVALRKI------DGVWYNLDSDFHAPQ 152 (182)
Q Consensus 108 ~~~~gfI~N~~~~~~~~~~~~~HWfaIRki------~g~wyNLDS~l~~P~ 152 (182)
-.+.|+|+++-.. -...|++|.=|. .|+||.+|=.+-.|+
T Consensus 213 Y~L~gvV~hig~~-----~~~GHyva~vk~~~~~~~~~~WylFND~~V~~v 258 (268)
T cd02672 213 YELVGYVCEINDS-----SRGQHNVVFVIKVNEESTHGRWYLFNDFLVTPV 258 (268)
T ss_pred EEEEEEEEEecCC-----CCCCcEEEEEEccCCCCCCCcEEEecCeEEEEc
Confidence 3677888876211 147899999887 579999998776553
No 34
>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=40.23 E-value=42 Score=22.19 Aligned_cols=29 Identities=24% Similarity=0.428 Sum_probs=24.8
Q ss_pred cchHHHHhHhhcCCCCCCCHHHHHHHHHHhc
Q 030121 16 QFCLLHSLNNLFQQEGAFTRASLNEIAEKLV 46 (182)
Q Consensus 16 ~lCalHaLNnLlQ~~~~Ft~~dL~~Ia~~Ld 46 (182)
..|.+.|+|.++.. -+++.+|.++|.+..
T Consensus 21 ~~a~~~a~~~~~~~--~~~~~~l~~~a~~~e 49 (67)
T PF00288_consen 21 AVALAAALNKLFGL--PLSKEELAKLAQEAE 49 (67)
T ss_dssp HHHHHHHHHHHTTT--SSBHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHccc--cccHHHHHHHHHHHH
Confidence 46889999999975 389999999999885
No 35
>TIGR01684 viral_ppase viral phosphatase. These proteins also include an N-terminal domain (ca. 125 aas) that is unique to this clade.
Probab=38.98 E-value=59 Score=29.05 Aligned_cols=39 Identities=21% Similarity=0.283 Sum_probs=31.6
Q ss_pred EEEEeeCCCCCCe---EcCCHHHHHHHHHHHHhCCcEEEEEEc
Q 030121 140 VWYNLDSDFHAPQ---CFKDSKEVREFLDYIIGLGGEVLLVKN 179 (182)
Q Consensus 140 ~wyNLDS~l~~P~---~i~~~~~L~~fL~~~~~~g~~ifvV~~ 179 (182)
.-|.|||+|-..+ .|.+. .+.+.|.++.+.|+.+-++.+
T Consensus 129 IvFDLDgTLi~~~~~v~irdP-gV~EaL~~LkekGikLaIaTS 170 (301)
T TIGR01684 129 VVFDLDSTLITDEEPVRIRDP-RIYDSLTELKKRGCILVLWSY 170 (301)
T ss_pred EEEecCCCCcCCCCccccCCH-HHHHHHHHHHHCCCEEEEEEC
Confidence 4789999995443 36776 499999999999999999874
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=36.96 E-value=4.4 Score=28.02 Aligned_cols=25 Identities=24% Similarity=0.386 Sum_probs=14.7
Q ss_pred HHhHhhcCCCCCCCHHHHHHHHHHhc
Q 030121 21 HSLNNLFQQEGAFTRASLNEIAEKLV 46 (182)
Q Consensus 21 HaLNnLlQ~~~~Ft~~dL~~Ia~~Ld 46 (182)
-=||+|||+ +.|+-.+|.+|-..|+
T Consensus 33 ~eLd~lLk~-~~fn~~dls~i~~~ln 57 (64)
T PF02251_consen 33 VELDELLKS-PSFNLSDLSSIHAPLN 57 (64)
T ss_dssp HHHHHHHHS-GGG--S-GGGS-----
T ss_pred HHHHHHhcC-cccccccHHhhcCcCC
Confidence 348999998 8999999999887776
No 37
>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=36.79 E-value=76 Score=25.41 Aligned_cols=39 Identities=28% Similarity=0.538 Sum_probs=28.1
Q ss_pred cceEEEEeeCCEEEEeeCCCCCCeEcCCHHHHHHHHHHHHhCCcEE
Q 030121 129 RHWVALRKIDGVWYNLDSDFHAPQCFKDSKEVREFLDYIIGLGGEV 174 (182)
Q Consensus 129 ~HWfaIRki~g~wyNLDS~l~~P~~i~~~~~L~~fL~~~~~~g~~i 174 (182)
.|=++.-+++|.||-||=.++ | + +|.+|+.....++..|
T Consensus 109 ~Haa~aV~ing~~yvlDq~~p-~--~----~l~~y~~~~~~~~~~i 147 (153)
T PF04473_consen 109 GHAAVAVKINGKYYVLDQHLP-P--I----DLGDYLKYWKKEGKII 147 (153)
T ss_pred CeEEEEEEECCEEEEEeCCCC-C--c----cHHHHHHHhhhcccee
Confidence 377788899999999997543 2 2 3667777666666654
No 38
>PRK10302 hypothetical protein; Provisional
Probab=36.54 E-value=59 Score=28.37 Aligned_cols=64 Identities=20% Similarity=0.130 Sum_probs=40.7
Q ss_pred hcCCCCCCCHHHHHHHHHHhcccCCCCCCCCCCceeecc-ccCCcCCCccHHHHHHHHHhCCCeEEeccCC
Q 030121 26 LFQQEGAFTRASLNEIAEKLVLDYPNKQTWTPLSVVFKP-HHNALTGNYDINVLIAALEGRGKSVVWHDRR 95 (182)
Q Consensus 26 LlQ~~~~Ft~~dL~~Ia~~Ld~~e~~~~~~~~~~~~~~p-~~n~~~GnydinVl~~AL~~~g~~~~w~d~r 95 (182)
|+|=||.|+..+++.+..-|....++ ..+.++. |.+.+....--+++...|+.+|...|-.|.+
T Consensus 99 L~QfPpsf~~~~~~~l~~fl~~l~~~------~~~AvEfRh~sW~~~~~~~~~l~~lL~~~~~~~v~~D~~ 163 (272)
T PRK10302 99 WLQLPAAFGPRELPALWQFLDALPAG------FTYGVEVRHPEFFAKGEAEQALNRGLHQRGVNRVILDSR 163 (272)
T ss_pred EEEcCCCCCcccHHHHHHHHHhCCCC------CCEEEEccCHHHcCCchhHHHHHHHHHHcCCEEEecCcc
Confidence 46778889876666655555432211 1123443 6666643344457888999999999999986
No 39
>cd02665 Peptidase_C19I A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=36.16 E-value=65 Score=27.24 Aligned_cols=39 Identities=13% Similarity=0.147 Sum_probs=26.4
Q ss_pred ceEEEEEecccccccccccccceEEEEe--eCCEEEEeeCCCCCCeE
Q 030121 109 CLMGIVINVPVTRYAGLWKSRHWVALRK--IDGVWYNLDSDFHAPQC 153 (182)
Q Consensus 109 ~~~gfI~N~~~~~~~~~~~~~HWfaIRk--i~g~wyNLDS~l~~P~~ 153 (182)
.+.|+|++. |--...||+|.-| -++.||.+|-..-.|..
T Consensus 165 ~L~aVi~H~------G~~~~GHY~~~i~~~~~~~W~~fdD~~V~~~~ 205 (228)
T cd02665 165 ELHAVLVHE------GQANAGHYWAYIYKQSRQEWEKYNDISVTESS 205 (228)
T ss_pred EEEEEEEec------CCCCCCEEEEEEEcCCCCEEEEEECCeeEEcC
Confidence 456666654 2235799999643 47899999877655543
No 40
>KOG1865 consensus Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=35.76 E-value=48 Score=31.95 Aligned_cols=42 Identities=17% Similarity=0.485 Sum_probs=29.7
Q ss_pred ceEEEEEecccccccccccccceEE-EEeeCCEEEEeeCCCCCCeEcC
Q 030121 109 CLMGIVINVPVTRYAGLWKSRHWVA-LRKIDGVWYNLDSDFHAPQCFK 155 (182)
Q Consensus 109 ~~~gfI~N~~~~~~~~~~~~~HWfa-IRki~g~wyNLDS~l~~P~~i~ 155 (182)
++.|+|+++-... ..-|.++ ||-..|+||.+|=..-.+..+.
T Consensus 353 ~LYavlVH~g~~~-----~~GHY~cYvks~~g~Wy~~DDS~V~~~~~~ 395 (545)
T KOG1865|consen 353 KLYAVLVHLGTSC-----HSGHYFCYVKSQNGQWYKMDDSEVTQSSIE 395 (545)
T ss_pred EEEEEEEeccccc-----cCCceEEEEEcCCCceEEccCceeeecccc
Confidence 7899999984332 2567666 5778999999987665555443
No 41
>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=34.80 E-value=53 Score=27.45 Aligned_cols=30 Identities=27% Similarity=0.431 Sum_probs=26.2
Q ss_pred ccceEEEEeeCCEEEEeeCCCCCCeEcCCH
Q 030121 128 SRHWVALRKIDGVWYNLDSDFHAPQCFKDS 157 (182)
Q Consensus 128 ~~HWfaIRki~g~wyNLDS~l~~P~~i~~~ 157 (182)
..|++|.-+.+|.=|-||...+.|+..|..
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 579999999999999999999999999876
No 42
>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=33.67 E-value=1.8e+02 Score=20.76 Aligned_cols=100 Identities=17% Similarity=0.099 Sum_probs=56.5
Q ss_pred cchHHHHhHhhcCC-CCCCCHHHHHHHHHHhcccCCCCCCCCCCceeeccccCCcCCCccHHHHHHHHHhCCCeEEeccC
Q 030121 16 QFCLLHSLNNLFQQ-EGAFTRASLNEIAEKLVLDYPNKQTWTPLSVVFKPHHNALTGNYDINVLIAALEGRGKSVVWHDR 94 (182)
Q Consensus 16 ~lCalHaLNnLlQ~-~~~Ft~~dL~~Ia~~Ld~~e~~~~~~~~~~~~~~p~~n~~~GnydinVl~~AL~~~g~~~~w~d~ 94 (182)
.-|++.||=.+++. .-.++..++. .++... + +-.+...+.++++..|+++.-...
T Consensus 10 ~~~~l~~l~~~~~~~~~~~~~~~l~---~~~~~~---------------~------~~~~~~~l~~~a~~~gl~~~~~~~ 65 (126)
T cd02425 10 TECGLACYAMILNYFGYKVSLNELR---EKYELG---------------R------DGLSLSYLKQLLEEYGFKCKVYKI 65 (126)
T ss_pred ccHHHHHHHHHHHHhCCCCCHHHHH---HhccCC---------------C------CCcCHHHHHHHHHHCCCcceEEEE
Confidence 46888888888763 0124554443 333210 1 227888899999999998854322
Q ss_pred CcccccccCCCCccceEEEEEecccccccccccccceEEEEeeCC-EEEEeeCCCCCCeEcC
Q 030121 95 RNEASAIDLDGGENCLMGIVINVPVTRYAGLWKSRHWVALRKIDG-VWYNLDSDFHAPQCFK 155 (182)
Q Consensus 95 r~~~~~~~~~~~~~~~~gfI~N~~~~~~~~~~~~~HWfaIRki~g-~wyNLDS~l~~P~~i~ 155 (182)
... +.+.-...| +|+-. +..||+-|-++++ ..+-.|+.. .+..++
T Consensus 66 ~~~-~~l~~~~lP-----~I~~~---------~~~~~~Vl~~~~~~~~~i~dp~~-~~~~~~ 111 (126)
T cd02425 66 SFK-KNLYPLKLP-----VIIFW---------NNNHFVVLEKIKKNKVTIVDPAI-GRIKIS 111 (126)
T ss_pred chH-HHHhhCCCC-----EEEEE---------cCCcEEEEEEEECCEEEEEcCCC-CCEEEC
Confidence 110 111111011 22222 2569999988754 677788855 466664
No 43
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=32.07 E-value=44 Score=24.07 Aligned_cols=20 Identities=25% Similarity=0.250 Sum_probs=16.7
Q ss_pred HHHHHHHHhCCCeEEeccCC
Q 030121 76 NVLIAALEGRGKSVVWHDRR 95 (182)
Q Consensus 76 nVl~~AL~~~g~~~~w~d~r 95 (182)
.-+..||+.+||+++.++..
T Consensus 11 s~v~~~L~~~GyeVv~l~~~ 30 (80)
T PF03698_consen 11 SNVKEALREKGYEVVDLENE 30 (80)
T ss_pred hHHHHHHHHCCCEEEecCCc
Confidence 34789999999999987754
No 44
>PHA03398 viral phosphatase superfamily protein; Provisional
Probab=30.91 E-value=88 Score=27.99 Aligned_cols=39 Identities=23% Similarity=0.268 Sum_probs=31.6
Q ss_pred EEEEeeCCCCCC---eEcCCHHHHHHHHHHHHhCCcEEEEEEc
Q 030121 140 VWYNLDSDFHAP---QCFKDSKEVREFLDYIIGLGGEVLLVKN 179 (182)
Q Consensus 140 ~wyNLDS~l~~P---~~i~~~~~L~~fL~~~~~~g~~ifvV~~ 179 (182)
.-|.|||+|-.+ +.|.+. ...+.|.++.+.|+.+.++..
T Consensus 131 i~~D~D~TL~~~~~~v~irdp-~V~EtL~eLkekGikLaIvTN 172 (303)
T PHA03398 131 IVFDLDSTLITDEEPVRIRDP-FVYDSLDELKERGCVLVLWSY 172 (303)
T ss_pred EEEecCCCccCCCCccccCCh-hHHHHHHHHHHCCCEEEEEcC
Confidence 578999999554 335566 489999999999999999974
No 45
>cd02669 Peptidase_C19M 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=29.12 E-value=87 Score=28.73 Aligned_cols=37 Identities=11% Similarity=0.274 Sum_probs=24.2
Q ss_pred ceEEEEEecccccccccc-cccceEEEEe--eCCEEEEeeCCCCCC
Q 030121 109 CLMGIVINVPVTRYAGLW-KSRHWVALRK--IDGVWYNLDSDFHAP 151 (182)
Q Consensus 109 ~~~gfI~N~~~~~~~~~~-~~~HWfaIRk--i~g~wyNLDS~l~~P 151 (182)
+++|.|++. |-- ..-||+|.-| -+|+||.+|=..-.|
T Consensus 384 ~L~avI~H~------G~~~~sGHY~a~v~~~~~~~W~~fdD~~V~~ 423 (440)
T cd02669 384 NLVANIVHE------GTPQEDGTWRVQLRHKSTNKWFEIQDLNVKE 423 (440)
T ss_pred EEEEEEEEe------ccCCCCeeEEEEEEcCCCCeEEEEECCeeeE
Confidence 556666664 222 4789999654 378999997654433
No 46
>COG3012 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.62 E-value=48 Score=26.72 Aligned_cols=16 Identities=38% Similarity=0.864 Sum_probs=13.7
Q ss_pred EEeeCCEEEEeeCCCC
Q 030121 134 LRKIDGVWYNLDSDFH 149 (182)
Q Consensus 134 IRki~g~wyNLDS~l~ 149 (182)
.+|++|+||-+|-..+
T Consensus 115 Fvk~ngrWyyiDgtv~ 130 (151)
T COG3012 115 FVKINGRWYYIDGTVP 130 (151)
T ss_pred heEECCEEEEECCCCC
Confidence 3689999999998776
No 47
>PRK03094 hypothetical protein; Provisional
Probab=27.45 E-value=79 Score=22.87 Aligned_cols=20 Identities=25% Similarity=0.225 Sum_probs=16.6
Q ss_pred HHHHHHHHhCCCeEEeccCC
Q 030121 76 NVLIAALEGRGKSVVWHDRR 95 (182)
Q Consensus 76 nVl~~AL~~~g~~~~w~d~r 95 (182)
.-|..+|+.+||+++.+...
T Consensus 11 s~i~~~L~~~GYeVv~l~~~ 30 (80)
T PRK03094 11 TDVQQALKQKGYEVVQLRSE 30 (80)
T ss_pred HHHHHHHHHCCCEEEecCcc
Confidence 44889999999999987653
No 48
>PF15649 Tox-REase-7: Restriction endonuclease fold toxin 7
Probab=27.16 E-value=95 Score=22.68 Aligned_cols=27 Identities=26% Similarity=0.331 Sum_probs=23.3
Q ss_pred EcCCHHHHHHHHHHHHhCCcEEEEEEc
Q 030121 153 CFKDSKEVREFLDYIIGLGGEVLLVKN 179 (182)
Q Consensus 153 ~i~~~~~L~~fL~~~~~~g~~ifvV~~ 179 (182)
.++.+.+|.+|++..++.|+.+.+|+.
T Consensus 52 ~~s~t~Qlr~~~~~A~~~G~~~~Lvv~ 78 (87)
T PF15649_consen 52 YQSLTKQLRDYVKYAKENGYRFNLVVN 78 (87)
T ss_pred hccchHHHHHHHHHHHHcCCcEEEEEc
Confidence 356677999999999999999988876
No 49
>COG4840 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.93 E-value=43 Score=23.61 Aligned_cols=22 Identities=18% Similarity=0.480 Sum_probs=17.8
Q ss_pred hhcCCCCCCCHHHHHHHHHHhc
Q 030121 25 NLFQQEGAFTRASLNEIAEKLV 46 (182)
Q Consensus 25 nLlQ~~~~Ft~~dL~~Ia~~Ld 46 (182)
-+.|.+.-||..+++.||.+|.
T Consensus 46 ~mvkkkenfSpsEmqaiA~eL~ 67 (71)
T COG4840 46 DMVKKKENFSPSEMQAIADELG 67 (71)
T ss_pred HHHHHhccCCHHHHHHHHHHHH
Confidence 4456667899999999999985
No 50
>PF01904 DUF72: Protein of unknown function DUF72; InterPro: IPR002763 The function of this family is unknown. Aquifex aeolicus has two copies of this protein. A probable aspartyl-tRNA synthetase from Escherichia coli [] belongs to this group.; PDB: 1VPY_A 1ZTV_A 1VPQ_A.
Probab=24.54 E-value=3.4e+02 Score=22.58 Aligned_cols=118 Identities=19% Similarity=0.180 Sum_probs=56.0
Q ss_pred hcCCCCC--CCHHHHHHHHHHhcccCCCCCCCCCCceeecc-ccCCcCCCccHHHHHHHHHhCCCeEEeccCCccccccc
Q 030121 26 LFQQEGA--FTRASLNEIAEKLVLDYPNKQTWTPLSVVFKP-HHNALTGNYDINVLIAALEGRGKSVVWHDRRNEASAID 102 (182)
Q Consensus 26 LlQ~~~~--Ft~~dL~~Ia~~Ld~~e~~~~~~~~~~~~~~p-~~n~~~GnydinVl~~AL~~~g~~~~w~d~r~~~~~~~ 102 (182)
|+|=||. +++..++.+..-|+...++ ....+++ |.+.+ + .-+.++|+.+|...|..|.+.......
T Consensus 90 L~Q~Ppsf~~~~~~~~~l~~~l~~~~~~------~~~avE~R~~sW~----~-~~~~~~l~~~~~~~v~~d~~~~~~~p~ 158 (230)
T PF01904_consen 90 LFQFPPSFRFTPENLERLDAFLDRLPRG------FRYAVEFRHPSWF----T-EEVFELLREHGVALVIADSPRLPSLPP 158 (230)
T ss_dssp EEE--TT--S-HHHHHHHHHHHHHTT-T------S-EEEE--BGGGG----C-HHHHHHHHHTT-EEEEEE---BTTC--
T ss_pred EEEcCCCcCCCHHHHHHHHHHHhhcccc------cceEEecCCcchh----h-HHHHHHHHHcCCEEEEeCCcccCCCCC
Confidence 4676665 7888888887777654311 1233443 44433 4 446899999999999998775221111
Q ss_pred CCCCccceEEEEEecccccccccccccceEEEEeeC---CEEEEeeCCCCCCeEcCCHHHHHHHHHHHHhCCcEEEEEEc
Q 030121 103 LDGGENCLMGIVINVPVTRYAGLWKSRHWVALRKID---GVWYNLDSDFHAPQCFKDSKEVREFLDYIIGLGGEVLLVKN 179 (182)
Q Consensus 103 ~~~~~~~~~gfI~N~~~~~~~~~~~~~HWfaIRki~---g~wyNLDS~l~~P~~i~~~~~L~~fL~~~~~~g~~ifvV~~ 179 (182)
.. . +. ...+.-||=.| +.| .++..+.++. .++.+.+.+..++|.+|+|...
T Consensus 159 ~~----~----~~------------~~~~~y~RlhG~~~~~~--~~~~Ys~~eL----~~~a~~i~~~~~~~~~v~v~fn 212 (230)
T PF01904_consen 159 PE----P----QT------------TPDFAYVRLHGRNGEGW--YDYRYSDEEL----EEWAERIRAWAAQGKEVYVFFN 212 (230)
T ss_dssp ------------S------------STTEEEEEE--S-TTTT--TB----HHHH----HHHHHHHHHHHTCSSEEEEEE-
T ss_pred cc----c----cc------------CCCCeEEeeccCccccc--ccccCCHHHH----HHHHHHHHHHHHcCCCEEEEEe
Confidence 10 0 00 11222223222 124 4444444332 3466667777778899999875
Q ss_pred C
Q 030121 180 D 180 (182)
Q Consensus 180 ~ 180 (182)
.
T Consensus 213 N 213 (230)
T PF01904_consen 213 N 213 (230)
T ss_dssp S
T ss_pred C
Confidence 4
No 51
>PF06569 DUF1128: Protein of unknown function (DUF1128); InterPro: IPR009507 This family consists of several short, hypothetical bacterial proteins of unknown function.
Probab=24.25 E-value=89 Score=22.14 Aligned_cols=24 Identities=21% Similarity=0.433 Sum_probs=18.7
Q ss_pred hHhhcCCCCCCCHHHHHHHHHHhc
Q 030121 23 LNNLFQQEGAFTRASLNEIAEKLV 46 (182)
Q Consensus 23 LNnLlQ~~~~Ft~~dL~~Ia~~Ld 46 (182)
|=.+.+.++-||..|++.||.+|.
T Consensus 44 iy~~V~~K~~fS~sEm~aI~~ELG 67 (71)
T PF06569_consen 44 IYEMVMSKDSFSPSEMQAIAEELG 67 (71)
T ss_pred HHHHHHhccCCCHHHHHHHHHHHH
Confidence 344556677899999999999985
No 52
>PF13529 Peptidase_C39_2: Peptidase_C39 like family; PDB: 3ERV_A.
Probab=24.05 E-value=2.7e+02 Score=19.75 Aligned_cols=119 Identities=14% Similarity=0.006 Sum_probs=51.3
Q ss_pred ccchHHHHhHhhcCCC-CCCCHHHHHHHHHHhcccCCCCCCCCCCceeeccccCCcCCCccHHHHHHHHHhCCCeEEecc
Q 030121 15 LQFCLLHSLNNLFQQE-GAFTRASLNEIAEKLVLDYPNKQTWTPLSVVFKPHHNALTGNYDINVLIAALEGRGKSVVWHD 93 (182)
Q Consensus 15 ~~lCalHaLNnLlQ~~-~~Ft~~dL~~Ia~~Ld~~e~~~~~~~~~~~~~~p~~n~~~GnydinVl~~AL~~~g~~~~w~d 93 (182)
..-|+.=|+-++|..- ...++.+ |+..+....... ....++.+++ ...........+..+++..|.......
T Consensus 13 ~~~Cg~as~~mvl~~~g~~~~~~~---l~~~~~~~~~~~---~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~ 85 (144)
T PF13529_consen 13 SYGCGPASAAMVLNYYGKNISQED---LADEAGTNPDGD---PNTGFVGNPY-YDSGYGTSPDDLARYLEKYGYKATDTS 85 (144)
T ss_dssp TT-HHHHHHHHHHHHTT----HHH---HHHHS-EE-E-----TTTSEEB-SS-TS-B----HHHHHHHHHHH-TTEEE-T
T ss_pred CCcCHHHHHHHHHHHcCCCCCHHH---HHHHhhhccCCC---CCcccccCcc-ccCCCccccHHHHHHHHHcCcceeecc
Confidence 3568888887777531 2244444 444443221000 0011233444 111334677888999999998554432
Q ss_pred CCcc---cccccCCCCccceEEEEEeccccc------ccccccccceEEEEeeCC-E-EEEeeC
Q 030121 94 RRNE---ASAIDLDGGENCLMGIVINVPVTR------YAGLWKSRHWVALRKIDG-V-WYNLDS 146 (182)
Q Consensus 94 ~r~~---~~~~~~~~~~~~~~gfI~N~~~~~------~~~~~~~~HWfaIRki~g-~-wyNLDS 146 (182)
...- ...++ .-.-+|+++.... -.......||++|+-.+. . ++-.|+
T Consensus 86 ~~~~~~i~~~i~------~G~Pvi~~~~~~~~~~~~~~~~~~~~~H~vvi~Gy~~~~~~~v~DP 143 (144)
T PF13529_consen 86 DASFDDIKQEID------AGRPVIVSVNSGWRPPNGDGYDGTYGGHYVVIIGYDEDGYVYVNDP 143 (144)
T ss_dssp TS-HHHHHHHHH------TT--EEEEEETTSS--TTEEEEE-TTEEEEEEEEE-SSE-EEEE-T
T ss_pred CCcHHHHHHHHH------CCCcEEEEEEcccccCCCCCcCCCcCCEEEEEEEEeCCCEEEEeCC
Confidence 2211 12222 2245677763221 012345899999998753 3 555554
No 53
>COG5077 Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=23.09 E-value=1e+02 Score=31.55 Aligned_cols=34 Identities=35% Similarity=0.693 Sum_probs=26.5
Q ss_pred ceEEEEEecccccccccccccceEEEEe--eCCEEEEeeCCC
Q 030121 109 CLMGIVINVPVTRYAGLWKSRHWVALRK--IDGVWYNLDSDF 148 (182)
Q Consensus 109 ~~~gfI~N~~~~~~~~~~~~~HWfaIRk--i~g~wyNLDS~l 148 (182)
.+.|.|++- |=...-|.+|+-| ++|+||.+|-..
T Consensus 432 ~LygVlVHs------GDl~~GHyYallKpe~dg~WykfdDtr 467 (1089)
T COG5077 432 VLYGVLVHS------GDLHEGHYYALLKPEKDGRWYKFDDTR 467 (1089)
T ss_pred EEEEEEEec------cccCCceEEEEeccccCCCceeeccee
Confidence 567777764 4345789999999 999999998653
No 54
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=23.04 E-value=1.1e+02 Score=18.98 Aligned_cols=29 Identities=28% Similarity=0.369 Sum_probs=22.9
Q ss_pred HHHhHhhcCCCCCCCHHHHHHHHHHhccc
Q 030121 20 LHSLNNLFQQEGAFTRASLNEIAEKLVLD 48 (182)
Q Consensus 20 lHaLNnLlQ~~~~Ft~~dL~~Ia~~Ld~~ 48 (182)
++.|-..++..++-+..+++.||.++...
T Consensus 12 ~~~Le~~f~~~~~P~~~~~~~la~~~~l~ 40 (59)
T cd00086 12 LEELEKEFEKNPYPSREEREELAKELGLT 40 (59)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHHHHHCcC
Confidence 56667777766788999999999998643
No 55
>PF05152 DUF705: Protein of unknown function (DUF705); InterPro: IPR007827 This family contains uncharacterised baculoviral proteins.
Probab=22.56 E-value=1.4e+02 Score=26.78 Aligned_cols=36 Identities=22% Similarity=0.341 Sum_probs=29.9
Q ss_pred EEEEeeCCC---CCCeEcCCHHHHHHHHHHHHhCCcEEEE
Q 030121 140 VWYNLDSDF---HAPQCFKDSKEVREFLDYIIGLGGEVLL 176 (182)
Q Consensus 140 ~wyNLDS~l---~~P~~i~~~~~L~~fL~~~~~~g~~ifv 176 (182)
.-|.|||+| ..+..|.+.. +.+.|.++.+.|+-+.+
T Consensus 125 IVfDlD~TLItd~~~v~Ir~~~-v~~sL~~Lk~~g~vLvL 163 (297)
T PF05152_consen 125 IVFDLDSTLITDEGDVRIRDPA-VYDSLRELKEQGCVLVL 163 (297)
T ss_pred EEEECCCcccccCCccccCChH-HHHHHHHHHHcCCEEEE
Confidence 589999999 4688898874 99999999999985543
No 56
>PF13423 UCH_1: Ubiquitin carboxyl-terminal hydrolase
Probab=22.29 E-value=1.4e+02 Score=25.40 Aligned_cols=33 Identities=24% Similarity=0.436 Sum_probs=25.3
Q ss_pred ceEEEEEecccccccccccccceEEEEeeC----CEEEEeeC
Q 030121 109 CLMGIVINVPVTRYAGLWKSRHWVALRKID----GVWYNLDS 146 (182)
Q Consensus 109 ~~~gfI~N~~~~~~~~~~~~~HWfaIRki~----g~wyNLDS 146 (182)
.+.|+||.+.. --...|-+|+-|++ .+||-+|=
T Consensus 256 ~L~~~V~~i~~-----~~~~~HlVs~vrv~~~~~~~W~lFND 292 (295)
T PF13423_consen 256 ELRSMVCHIGD-----SIESGHLVSLVRVGPSDDSQWYLFND 292 (295)
T ss_pred EEEEEEEEecC-----CCCCCceEEEEEcCCCCCCcEEEECc
Confidence 57899998743 12378999999986 69999873
No 57
>COG5533 UBP5 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=22.06 E-value=1.1e+02 Score=28.12 Aligned_cols=41 Identities=22% Similarity=0.356 Sum_probs=32.7
Q ss_pred ceEEEEEecccccccccccccceEEEEeeCCEEEEeeCCCCCCeEcC
Q 030121 109 CLMGIVINVPVTRYAGLWKSRHWVALRKIDGVWYNLDSDFHAPQCFK 155 (182)
Q Consensus 109 ~~~gfI~N~~~~~~~~~~~~~HWfaIRki~g~wyNLDS~l~~P~~i~ 155 (182)
.+.|+||.. |-...-|.|+=-+.+|.||-.|-.+-.|.-..
T Consensus 358 ~L~gv~Ch~------G~L~gGHY~s~v~~~~~W~~~dDs~vr~~~~~ 398 (415)
T COG5533 358 SLLGVVCHN------GTLNGGHYFSEVKRSGTWNVYDDSQVRKGSRT 398 (415)
T ss_pred eEEEEEeec------ceecCceeEEeeeecCceEEechhheeeccce
Confidence 678888875 44458999999999999999998776665543
No 58
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=21.77 E-value=89 Score=22.36 Aligned_cols=26 Identities=12% Similarity=0.197 Sum_probs=21.0
Q ss_pred cCCHHHHHHHHHHHHhCCcEEEEEEcC
Q 030121 154 FKDSKEVREFLDYIIGLGGEVLLVKND 180 (182)
Q Consensus 154 i~~~~~L~~fL~~~~~~g~~ifvV~~~ 180 (182)
|+.+ .+-..+++|.+.|++|+.|.++
T Consensus 31 iSRt-aVwK~Iq~Lr~~G~~I~s~~~k 56 (79)
T COG1654 31 ISRT-AVWKHIQQLREEGVDIESVRGK 56 (79)
T ss_pred ccHH-HHHHHHHHHHHhCCceEecCCC
Confidence 4555 3788899999999999999764
No 59
>cd02670 Peptidase_C19N 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=21.43 E-value=1.9e+02 Score=24.57 Aligned_cols=39 Identities=18% Similarity=0.246 Sum_probs=28.3
Q ss_pred ceEEEEEecccccccccccccceEEEEeeC-------------CEEEEeeCCCCCCe
Q 030121 109 CLMGIVINVPVTRYAGLWKSRHWVALRKID-------------GVWYNLDSDFHAPQ 152 (182)
Q Consensus 109 ~~~gfI~N~~~~~~~~~~~~~HWfaIRki~-------------g~wyNLDS~l~~P~ 152 (182)
.+.|+|++.-. -...-|-+|.-|-. +.||-+|+....+.
T Consensus 168 ~L~aVi~H~G~-----s~~sGHYva~vr~~~~~~~~~~~~~~~~~W~~FDD~~v~~~ 219 (241)
T cd02670 168 SLCSAVCHRGT-----SLETGHYVAFVRYGSYSLTETDNEAYNAQWVFFDDMADRDG 219 (241)
T ss_pred EEEEEEEeCCC-----CCCCcCeEEEEECCcccccccccCCCCCeEEEecCcccccc
Confidence 46799988621 13478999997765 69999999865443
No 60
>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=21.37 E-value=52 Score=28.46 Aligned_cols=37 Identities=24% Similarity=0.395 Sum_probs=27.7
Q ss_pred eeccccchHHHHhHhhcCC---CCCCCHHHHHHHHHHhcc
Q 030121 11 ERQKLQFCLLHSLNNLFQQ---EGAFTRASLNEIAEKLVL 47 (182)
Q Consensus 11 EkQ~~~lCalHaLNnLlQ~---~~~Ft~~dL~~Ia~~Ld~ 47 (182)
+.|-..---+..+|+||-. |..|++.|++.|+..+..
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 3444444467899999976 667999999999998864
No 61
>PF11380 DUF3184: Protein of unknown function (DUF3184); InterPro: IPR021520 This eukaryotic family of proteins has no known function. ; GO: 0016772 transferase activity, transferring phosphorus-containing groups
Probab=20.37 E-value=50 Score=32.31 Aligned_cols=31 Identities=19% Similarity=0.607 Sum_probs=25.6
Q ss_pred EEeeCCEEEEeeCCCCCCeEcCCHHHHHHHHHHH
Q 030121 134 LRKIDGVWYNLDSDFHAPQCFKDSKEVREFLDYI 167 (182)
Q Consensus 134 IRki~g~wyNLDS~l~~P~~i~~~~~L~~fL~~~ 167 (182)
||+.+..|||.|++++.|+.= .+|..||..+
T Consensus 420 v~q~~plffNINagfs~~eaa---~qLR~FL~~~ 450 (691)
T PF11380_consen 420 VRQTNPLFFNINAGFSSAEAA---DQLRNFLHGL 450 (691)
T ss_pred HHhcCCceEEeccccCchHHH---HHHHHHHHhh
Confidence 567788999999999998864 4789998765
Done!