Query 046745
Match_columns 132
No_of_seqs 165 out of 1030
Neff 9.0
Searched_HMMs 46136
Date Fri Mar 29 04:05:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046745.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046745hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03189 Protease specific for 100.0 1.3E-34 2.8E-39 220.4 12.8 117 1-132 372-488 (490)
2 KOG0778 Protease, Ulp1 family 100.0 8.3E-35 1.8E-39 223.0 8.0 117 1-132 393-509 (511)
3 PF02902 Peptidase_C48: Ulp1 p 100.0 1.1E-27 2.5E-32 168.8 12.6 122 1-131 86-211 (216)
4 COG5160 ULP1 Protease, Ulp1 fa 99.9 2.5E-27 5.4E-32 180.5 5.5 112 1-131 456-567 (578)
5 KOG3246 Sentrin-specific cyste 99.8 1.5E-18 3.2E-23 120.2 10.1 104 1-128 91-207 (223)
6 PRK11836 deubiquitinase; Provi 97.9 0.00013 2.7E-09 53.7 8.1 95 2-105 223-327 (403)
7 PRK14848 deubiquitinase SseL; 97.8 0.00026 5.7E-09 51.0 8.3 83 2-105 192-276 (317)
8 KOG0779 Protease, Ulp1 family 97.6 3.9E-05 8.4E-10 62.0 2.8 41 83-124 528-580 (595)
9 PF00770 Peptidase_C5: Adenovi 97.6 0.00079 1.7E-08 45.9 8.2 82 9-104 34-116 (183)
10 PF03290 Peptidase_C57: Vaccin 97.3 0.001 2.2E-08 50.6 6.8 32 1-32 234-265 (423)
11 PF03421 YopJ: YopJ Serine/Thr 94.1 0.34 7.4E-06 33.5 6.9 26 80-105 138-163 (177)
12 KOG4110 NADH:ubiquinone oxidor 88.7 0.46 9.9E-06 30.1 2.5 33 71-103 16-48 (120)
13 PRK15371 effector protein YopJ 88.4 4.7 0.0001 30.1 7.9 26 81-106 162-187 (287)
14 PF12252 SidE: Dot/Icm substra 84.9 3.1 6.8E-05 36.4 6.0 25 9-34 63-87 (1439)
15 cd02424 Peptidase_C39E A sub-f 74.6 5.9 0.00013 25.3 3.7 24 84-107 5-28 (129)
16 COG4871 Uncharacterized protei 73.5 27 0.00058 24.0 6.9 81 17-106 70-158 (193)
17 PF03412 Peptidase_C39: Peptid 68.0 5.4 0.00012 25.3 2.4 24 83-107 5-28 (131)
18 KOG3315 Transport protein part 62.2 11 0.00023 26.1 2.9 29 81-109 132-160 (191)
19 cd02423 Peptidase_C39G A sub-f 60.6 21 0.00047 22.3 4.2 25 83-107 4-28 (129)
20 COG5418 Predicted secreted pro 52.4 17 0.00038 24.4 2.7 42 38-96 75-116 (164)
21 cd02549 Peptidase_C39A A sub-f 50.6 19 0.00041 22.9 2.7 24 8-32 93-117 (141)
22 PF13280 WYL: WYL domain 43.1 35 0.00076 22.2 3.2 21 2-22 32-55 (172)
23 COG2260 Predicted Zn-ribbon RN 41.1 11 0.00024 21.2 0.4 39 91-129 11-53 (59)
24 PRK13130 H/ACA RNA-protein com 38.4 15 0.00032 20.5 0.6 40 89-129 9-53 (56)
25 TIGR03796 NHPM_micro_ABC1 NHPM 36.2 46 0.00099 27.8 3.4 20 84-103 6-25 (710)
26 cd02418 Peptidase_C39B A sub-f 35.1 37 0.0008 21.4 2.2 23 84-107 5-27 (136)
27 cd02420 Peptidase_C39D A sub-f 34.8 36 0.00078 21.2 2.1 19 85-103 6-24 (125)
28 cd02259 Peptidase_C39_like Pep 30.6 51 0.0011 20.2 2.3 22 85-107 1-22 (122)
29 PF02099 Josephin: Josephin; 28.6 1.7E+02 0.0036 19.8 4.6 27 4-32 103-129 (157)
30 COG5128 Transport protein part 28.1 73 0.0016 22.1 2.7 28 81-108 145-172 (208)
31 PF07559 FlaE: Flagellar basal 27.8 39 0.00085 21.4 1.4 13 21-33 13-25 (130)
32 COG3756 Uncharacterized protei 26.8 69 0.0015 21.5 2.4 20 90-109 22-41 (153)
33 PF09369 DUF1998: Domain of un 26.0 1.5E+02 0.0031 17.4 3.7 15 18-32 33-47 (84)
34 cd02419 Peptidase_C39C A sub-f 25.6 61 0.0013 20.1 2.0 22 85-107 6-27 (127)
35 PHA02634 hypothetical protein; 24.7 33 0.00072 18.4 0.5 11 87-97 21-31 (49)
36 cd02421 Peptidase_C39_likeD A 24.6 1.3E+02 0.0027 18.6 3.3 21 8-29 78-98 (124)
37 PF09778 Guanylate_cyc_2: Guan 24.4 56 0.0012 23.4 1.7 20 84-103 5-24 (212)
38 COG2378 Predicted transcriptio 23.9 1.3E+02 0.0027 22.7 3.7 23 2-24 171-196 (311)
39 cd02425 Peptidase_C39F A sub-f 23.7 72 0.0016 19.7 2.1 23 84-107 5-27 (126)
40 PRK14751 tetracycline resistan 23.6 88 0.0019 14.4 1.7 13 17-29 11-23 (28)
41 PF05412 Peptidase_C33: Equine 22.9 1.1E+02 0.0023 19.5 2.6 20 88-107 7-26 (108)
42 PF05393 Hum_adeno_E3A: Human 22.8 78 0.0017 19.4 1.9 12 88-99 38-49 (94)
43 PF02338 OTU: OTU-like cystein 22.0 1.8E+02 0.0038 17.9 3.6 38 88-131 3-41 (121)
44 PF07984 DUF1693: Domain of un 21.0 87 0.0019 23.9 2.3 31 3-33 127-161 (320)
No 1
>PLN03189 Protease specific for SMALL UBIQUITIN-RELATED MODIFIER (SUMO); Provisional
Probab=100.00 E-value=1.3e-34 Score=220.41 Aligned_cols=117 Identities=26% Similarity=0.507 Sum_probs=97.7
Q ss_pred CEEeeeeCCeeEEEEEeCCCCeEEEEeCCCCCCChHHHHHHHHhHHHHHHHHHHhhhccCCCCCCCCCcccCCccccccc
Q 046745 1 VYLPIFMNDHWVLGVVDILGGKISIYDSMIDLTNDSVLVRQLLPVADMIPLVLQKISYHETNPDCSEVISKIPWPIVRVR 80 (132)
Q Consensus 1 i~iPi~~~~HW~L~vi~~~~~~i~~~DSl~~~~~~~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~ 80 (132)
||||||.+.||+|+|||++.++|.+||||++.. .. +++.|++++...+. ++.+ .+++.+.|+.....
T Consensus 372 IFIPIh~n~HWsLaVId~k~k~I~yyDSLgg~~-~~----vL~~L~rYL~~E~k-----dK~g---~d~D~s~W~~~~~~ 438 (490)
T PLN03189 372 IFVPIHQEIHWTLAVINKKDQKFQYLDSLKGRD-PK----ILDALAKYYVDEVK-----DKSE---KDIDVSSWEQEFVE 438 (490)
T ss_pred EEeeeecCCeeEEEEEEcCCCeEEEEeCCCCCC-HH----HHHHHHHHHHHHHh-----hhcC---CCcchhcceeccCC
Confidence 699999999999999999999999999999863 22 35556665544332 2222 24667889876567
Q ss_pred CCCCCCCCCChhHHHHHHHHHHhccCCCCCCCcccchHHHHHHHHHHHhcCC
Q 046745 81 DIPQQKSGGDCGAFLLRYLEVLAHELDVNSYCQQDHVTQFRQALAVKLFGHR 132 (132)
Q Consensus 81 ~~P~Q~n~~DCGvfvl~~~~~~~~~~~~~~~~~~~~~~~~R~~l~~~l~~~~ 132 (132)
++|||.||+|||||||+||++++.|.++ .|+|+ ||+.||++|+.||+..|
T Consensus 439 ~vPQQ~NG~DCGVFVL~yAE~~SrG~~L-tFSQe-DMp~fRrRma~EIl~~r 488 (490)
T PLN03189 439 DLPEQKNGYDCGMFMIKYIDFYSRGLGL-CFGQE-HMPYFRLRTAKEILRLK 488 (490)
T ss_pred CCCCCCCCCCHHHHHHHHHHHHcCCCCC-CcChh-hhHHHHHHHHHHHHHhh
Confidence 8999999999999999999999999998 69999 99999999999999876
No 2
>KOG0778 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=8.3e-35 Score=222.99 Aligned_cols=117 Identities=29% Similarity=0.589 Sum_probs=99.3
Q ss_pred CEEeeeeCCeeEEEEEeCCCCeEEEEeCCCCCCChHHHHHHHHhHHHHHHHHHHhhhccCCCCCCCCCcccCCccccccc
Q 046745 1 VYLPIFMNDHWVLGVVDILGGKISIYDSMIDLTNDSVLVRQLLPVADMIPLVLQKISYHETNPDCSEVISKIPWPIVRVR 80 (132)
Q Consensus 1 i~iPi~~~~HW~L~vi~~~~~~i~~~DSl~~~~~~~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~ 80 (132)
||||||.+.||+|+|||+++++|.|||||++..+. ++..|++ |+++++ .+++ +.+++.+.|.+....
T Consensus 393 i~vPIH~~vHW~l~vid~r~k~i~y~DS~~~~~nr-----~~~aL~~----Yl~~E~-~~k~---~~~~d~s~w~~~~~~ 459 (511)
T KOG0778|consen 393 IFVPIHLGVHWCLAVIDLREKTIEYYDSLGGGPNR-----ICDALAK----YLQDES-RDKS---KKDFDVSGWTIEFVQ 459 (511)
T ss_pred eEeeeecCceEEEEEEEcccceEEEeeccCCCCcc-----hHHHHHH----HHHHHH-hhhh---cCCCCccchhhhhhh
Confidence 79999999999999999999999999999975443 2344554 454443 2332 235788999998888
Q ss_pred CCCCCCCCCChhHHHHHHHHHHhccCCCCCCCcccchHHHHHHHHHHHhcCC
Q 046745 81 DIPQQKSGGDCGAFLLRYLEVLAHELDVNSYCQQDHVTQFRQALAVKLFGHR 132 (132)
Q Consensus 81 ~~P~Q~n~~DCGvfvl~~~~~~~~~~~~~~~~~~~~~~~~R~~l~~~l~~~~ 132 (132)
++|||.||+|||+|+|+|+++++.|.|+ +|+|. +|++||++||.||++.|
T Consensus 460 ~iP~Q~Ng~DCG~f~c~~~~~~s~~~p~-~ftq~-dmp~fR~~m~~eI~~~~ 509 (511)
T KOG0778|consen 460 NIPQQRNGSDCGMFVCKYADYISRDVPL-TFTQQ-DMPYFRKKMAKEILHLK 509 (511)
T ss_pred ccccccCCCccceEEeeechhhccCCCc-ccChh-hhHHHHHHHHHHHHhhh
Confidence 9999999999999999999999999999 89999 99999999999999864
No 3
>PF02902 Peptidase_C48: Ulp1 protease family, C-terminal catalytic domain This family belongs to family C48 of the peptidase classification.; InterPro: IPR003653 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of proteins contain cysteine peptidases belonging to MEROPS peptidase family C48 (Ulp1 endopeptidase family, clan CE). The protein fold of the peptidase domain for members of this family resembles that of adenain, the type example for clan CE. This group of sequences also contains a number of hypothetical proteins, which have not yet been characterised, and non-peptidase homologues. These are proteins that have either been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity of the peptidases in the family. The Ulp1 endopeptidase family contain the deubiquitinating enzymes (DUB) that can de-conjugate ubiquitin or ubiquitin-like proteins from ubiquitin-conjugated proteins. They can be classified in 3 families according to sequence homology [, ]: Ubiquitin carboxyl-terminal hydrolase (UCH) (see PDOC00127 from PROSITEDOC), Ubiquitin-specific processing protease (UBP) (see PDOC00750 from PROSITEDOC), and ubiquitin-like protease (ULP) specific for de-conjugating ubiquitin-like proteins. In contrast to the UBP pathway, which is very redundant (16 UBP enzymes in yeast), there are few ubiquitin-like proteases (only one in yeast, Ulp1). Ulp1 catalyses two critical functions in the SUMO/Smt3 pathway via its cysteine protease activity. Ulp1 processes the Smt3 C-terminal sequence (-GGATY) to its mature form (-GG), and it de-conjugates Smt3 from the lysine epsilon-amino group of the target protein []. Crystal structure of yeast Ulp1 bound to Smt3 [] revealed that the catalytic and interaction interface is situated in a shallow and narrow cleft where conserved residues recognise the Gly-Gly motif at the C-terminal extremity of Smt3 protein. Ulp1 adopts a novel architecture despite some structural similarity with other cysteine protease. The secondary structure is composed of seven alpha helices and seven beta strands. The catalytic domain includes the central alpha helix, beta-strands 4 to 6, and the catalytic triad (Cys-His-Asp). This profile is directed against the C-terminal part of ULP proteins that displays full proteolytic activity [].; GO: 0008234 cysteine-type peptidase activity, 0006508 proteolysis; PDB: 1EUV_A 2HL8_A 2HKP_A 2HL9_A 1XT9_A 2BKQ_C 2BKR_A 2IO1_E 1TH0_B 1TGZ_A ....
Probab=99.95 E-value=1.1e-27 Score=168.80 Aligned_cols=122 Identities=31% Similarity=0.595 Sum_probs=85.6
Q ss_pred CEEeeee-CCeeEEEEEeCCCCeEEEEeCCCCCCChHHHHHHHHhHHHHHHHHHHhhhccCCCCCCCCCcccCCcccccc
Q 046745 1 VYLPIFM-NDHWVLGVVDILGGKISIYDSMIDLTNDSVLVRQLLPVADMIPLVLQKISYHETNPDCSEVISKIPWPIVRV 79 (132)
Q Consensus 1 i~iPi~~-~~HW~L~vi~~~~~~i~~~DSl~~~~~~~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~ 79 (132)
|++|+|. ++||+|++|+++.++|.+|||+++..........+..+..++...... ..+. ..+..+|.....
T Consensus 86 i~iPin~~~~HW~l~vi~~~~~~i~~~DSl~~~~~~~~~~~~~~~~~~~l~~~~~~-----~~~~---~~~~~~~~~~~~ 157 (216)
T PF02902_consen 86 IFIPININNNHWVLLVIDLPKKRIYVYDSLGSSNNDKRYKRVIENIIPFLKREYKK-----KEGR---DPDKSPFKIVRP 157 (216)
T ss_dssp EEEEEEETTTEEEEEEEETTTTEEEEE-TTSTSSH-HHHHHHHHHHHHHHHHHHHH-----HHSS---CT-TTTCEEEEE
T ss_pred EEEEEechhhccceeEEcccccEEEEEeccccccccccchhhhhhhhhhhhhcccc-----cccc---ccccceeeeccc
Confidence 6899999 999999999999999999999998754122222333333333332211 1111 124467877667
Q ss_pred cCCCCCCCCCChhHHHHHHHHHHhccCCCCC---CCcccchHHHHHHHHHHHhcC
Q 046745 80 RDIPQQKSGGDCGAFLLRYLEVLAHELDVNS---YCQQDHVTQFRQALAVKLFGH 131 (132)
Q Consensus 80 ~~~P~Q~n~~DCGvfvl~~~~~~~~~~~~~~---~~~~~~~~~~R~~l~~~l~~~ 131 (132)
.++|||.|++|||+|||+||++++.|.+... ++++ ++..+|++++.++.+.
T Consensus 158 ~~~pqQ~n~~dCGv~vl~~~~~~~~~~~~~~~~~l~~~-~i~~~r~~~a~~~~e~ 211 (216)
T PF02902_consen 158 PNVPQQPNGYDCGVYVLKFMECLLEGPSFDFSQELTEE-DIKNFRKKLAVDLYEE 211 (216)
T ss_dssp CTS-SSSSSSCHHHHHHHHHHHHHCTHHSTGCCSBTGH-HHHHHHHHHHH-----
T ss_pred ccccCCCCCCCcHHHHHHHHHHHHhCCCCcccccCCHH-HHHHHHHHHHhhcccc
Confidence 7999999999999999999999999977643 7888 9999999999887653
No 4
>COG5160 ULP1 Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=99.94 E-value=2.5e-27 Score=180.55 Aligned_cols=112 Identities=21% Similarity=0.456 Sum_probs=90.2
Q ss_pred CEEeeeeCCeeEEEEEeCCCCeEEEEeCCCCCCChHHHHHHHHhHHHHHHHHHHhhhccCCCCCCCCCcccCCccccccc
Q 046745 1 VYLPIFMNDHWVLGVVDILGGKISIYDSMIDLTNDSVLVRQLLPVADMIPLVLQKISYHETNPDCSEVISKIPWPIVRVR 80 (132)
Q Consensus 1 i~iPi~~~~HW~L~vi~~~~~~i~~~DSl~~~~~~~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~ 80 (132)
||||||...||+|++||.+...|.+||||++... . ++ +++..|+.++ |...+ +.++|.....-
T Consensus 456 I~iPIni~~HW~l~II~~~~~~i~~~DSLan~~~-~----v~----~~L~~Y~ldE-~k~~~-------~k~~~~~~~~~ 518 (578)
T COG5160 456 IFIPINISYHWFLAIIDNPKKNILYFDSLANTHD-P----VL----EFLRSYLLDE-YKIQH-------DKDPQIKMKHC 518 (578)
T ss_pred EEEEecccceEEEEEeecCcceeEEecccccCcH-H----HH----HHHHHHHHHH-Hhccc-------CCchhhhhhcC
Confidence 7999999999999999999999999999998752 2 23 3334455433 22222 33456555567
Q ss_pred CCCCCCCCCChhHHHHHHHHHHhccCCCCCCCcccchHHHHHHHHHHHhcC
Q 046745 81 DIPQQKSGGDCGAFLLRYLEVLAHELDVNSYCQQDHVTQFRQALAVKLFGH 131 (132)
Q Consensus 81 ~~P~Q~n~~DCGvfvl~~~~~~~~~~~~~~~~~~~~~~~~R~~l~~~l~~~ 131 (132)
++|||.||+|||||||+|+++++.+.+. .|.+. +++++|+.|+++|++.
T Consensus 519 ~vPqQ~Ng~DCGV~vc~~~~~~~~~~p~-~f~~n-d~~r~Rk~m~h~i~~~ 567 (578)
T COG5160 519 KVPQQRNGSDCGVFVCMFIRYFLENPPE-QFSKN-DRPRARKNMAHTIKDL 567 (578)
T ss_pred CCCCCCCCCccceEEEEeeeecccCChh-hcCcc-chHHHHHHHHHHHHHH
Confidence 8999999999999999999999999886 89998 9999999999999764
No 5
>KOG3246 consensus Sentrin-specific cysteine protease (Ulp1 family) [General function prediction only]
Probab=99.78 E-value=1.5e-18 Score=120.22 Aligned_cols=104 Identities=30% Similarity=0.367 Sum_probs=68.6
Q ss_pred CEEeeeeC---------CeeEEEEEeCCCCeEEEEeCCCCCCChHHHHHHHHhHHHHHHHHHHhhhccCCCCCCCCCccc
Q 046745 1 VYLPIFMN---------DHWVLGVVDILGGKISIYDSMIDLTNDSVLVRQLLPVADMIPLVLQKISYHETNPDCSEVISK 71 (132)
Q Consensus 1 i~iPi~~~---------~HW~L~vi~~~~~~i~~~DSl~~~~~~~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~ 71 (132)
||+|||.+ +||+|+|+..++++.++|||+.+..... -+.+++++. .++.. +
T Consensus 91 iflpiNDn~~~~~~~GGsHWSLLV~sr~~~~f~hyDS~~n~nt~~-a~~l~~kl~----~ll~~------~--------- 150 (223)
T KOG3246|consen 91 IFLPINDNSNVTRASGGSHWSLLVFSRPDGKFYHYDSLSNGNTKD-AKSLMKKLR----ALLKK------K--------- 150 (223)
T ss_pred EEEEecCCCcccccCCCcceEEEEEEeeCCcEEEeecccCCCcHH-HHHHHHHHH----HHHhh------h---------
Confidence 68999983 3999999999999999999999976543 233444433 33321 1
Q ss_pred CCccccc-ccCCCCCCCCCChhHHHHHHHHHHhccC---CCCCCCcccchHHHHHHHHHHH
Q 046745 72 IPWPIVR-VRDIPQQKSGGDCGAFLLRYLEVLAHEL---DVNSYCQQDHVTQFRQALAVKL 128 (132)
Q Consensus 72 ~~w~~~~-~~~~P~Q~n~~DCGvfvl~~~~~~~~~~---~~~~~~~~~~~~~~R~~l~~~l 128 (132)
...+ ...+|||.||+|||+|||.+.+.++... +..+-.+. ..+.+|.++-.+|
T Consensus 151 ---~~~~~~~~~~qQqNgyDCG~hV~~~t~~l~~~~~~~~~~~~~~~-~~~~~i~~lr~~l 207 (223)
T KOG3246|consen 151 ---FAKRVECKCLQQQNGYDCGLHVCCNTRVLAERLLRCPYATSSQL-LVVDLIKALREEL 207 (223)
T ss_pred ---hhhcccccChhhhcCCchhHHHHHHHHHHHHHHhccccccccch-hhHHHHHHHHHHH
Confidence 1111 3578899999999999999987766432 23233344 4444554444443
No 6
>PRK11836 deubiquitinase; Provisional
Probab=97.85 E-value=0.00013 Score=53.71 Aligned_cols=95 Identities=21% Similarity=0.325 Sum_probs=49.7
Q ss_pred EEeeeeCCeeEEEEEe--------CCCCeEEEEeCCCCCCChH--HHHHHHHhHHHHHHHHHHhhhccCCCCCCCCCccc
Q 046745 2 YLPIFMNDHWVLGVVD--------ILGGKISIYDSMIDLTNDS--VLVRQLLPVADMIPLVLQKISYHETNPDCSEVISK 71 (132)
Q Consensus 2 ~iPi~~~~HW~L~vi~--------~~~~~i~~~DSl~~~~~~~--~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~ 71 (132)
++|||.++||+|+++- ..+.+..+|.|+.....+. ..++++..+. ..++-+++-...++. ...
T Consensus 223 lFpINtg~HWil~~l~Ki~~~~~~~ekiKC~IFNs~~~l~~d~~~t~q~ii~a~~---~~~~~~~~~~~ik~~----~~e 295 (403)
T PRK11836 223 LFPINTGGHWILVSLQKIVNEKNNTQQIKCVIFNSLRALGHDKENSLKRVINSFN---SELMGEMSNNNIKVH----LTE 295 (403)
T ss_pred EEEecCCCcEEEEEeHHhhhcccccceeEEEEEecHhhhccchhhHHHHHHHhhh---hhhhhhcchhhhccc----ccC
Confidence 6899999999999872 3456678899987654331 1222222211 111111110011111 111
Q ss_pred CCcccccccCCCCCCCCCChhHHHHHHHHHHhcc
Q 046745 72 IPWPIVRVRDIPQQKSGGDCGAFLLRYLEVLAHE 105 (132)
Q Consensus 72 ~~w~~~~~~~~P~Q~n~~DCGvfvl~~~~~~~~~ 105 (132)
.. +.+...--||.=...||.||++-+.-++..
T Consensus 296 ~e--i~fie~dLQq~vpngCGlFv~~a~Qe~i~q 327 (403)
T PRK11836 296 PE--IIFLHADLQQYLSQSCGAFVCMAAQEVIEQ 327 (403)
T ss_pred Cc--eEEEechhhhcCCCccceehHHHHHHHHHH
Confidence 11 112222235555689999999888755444
No 7
>PRK14848 deubiquitinase SseL; Provisional
Probab=97.76 E-value=0.00026 Score=51.02 Aligned_cols=83 Identities=17% Similarity=0.214 Sum_probs=47.3
Q ss_pred EEeeeeCCeeEEEEEe--CCCCeEEEEeCCCCCCChHHHHHHHHhHHHHHHHHHHhhhccCCCCCCCCCcccCCcccccc
Q 046745 2 YLPIFMNDHWVLGVVD--ILGGKISIYDSMIDLTNDSVLVRQLLPVADMIPLVLQKISYHETNPDCSEVISKIPWPIVRV 79 (132)
Q Consensus 2 ~iPi~~~~HW~L~vi~--~~~~~i~~~DSl~~~~~~~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~ 79 (132)
++|||.++||+|+++- ..+.+..+|.|+..... ...++++.. -. ..+.+ ...... +.
T Consensus 192 vF~INtg~HWil~~~~Ki~~kiKC~iFNs~~~l~e-Ns~~~ii~~-------ak-------~ag~~----~e~di~--fI 250 (317)
T PRK14848 192 VFLINTGDHWLLCLFYKLAEKIKCLIFNTYYDLNE-NTKQEIIEA-------AK-------IAGIS----ENEDVN--FI 250 (317)
T ss_pred EEEecCCCcEEEEEhHHhhhhceEEEeecHhhhhh-hHHHHHHHH-------HH-------hhCcc----cCCceE--Ee
Confidence 5899999999999863 23456678999886542 222222221 00 00111 001111 11
Q ss_pred cCCCCCCCCCChhHHHHHHHHHHhcc
Q 046745 80 RDIPQQKSGGDCGAFLLRYLEVLAHE 105 (132)
Q Consensus 80 ~~~P~Q~n~~DCGvfvl~~~~~~~~~ 105 (132)
..--||.=...||.|||.+++.+...
T Consensus 251 e~nLQqnVpngCGlFv~~aIq~l~~~ 276 (317)
T PRK14848 251 ETNLQNNVPNGCGLFCYHTIQLLSNA 276 (317)
T ss_pred ehhhhhhCCCcchHHHHHHHHHHHhc
Confidence 12224555689999999999976544
No 8
>KOG0779 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=97.62 E-value=3.9e-05 Score=62.02 Aligned_cols=41 Identities=27% Similarity=0.631 Sum_probs=31.3
Q ss_pred CCCCCCCChhHHHHHHHHHHhccCCC------------CCCCcccchHHHHHHH
Q 046745 83 PQQKSGGDCGAFLLRYLEVLAHELDV------------NSYCQQDHVTQFRQAL 124 (132)
Q Consensus 83 P~Q~n~~DCGvfvl~~~~~~~~~~~~------------~~~~~~~~~~~~R~~l 124 (132)
|||.|..|||+|++.|++.+..+.+. +.|.+. .+..+|..+
T Consensus 528 p~q~n~~dcG~~~~~~v~~f~e~~~e~~~~~~~~~~~l~~~~~~-~~~~~r~~~ 580 (595)
T KOG0779|consen 528 PQQNNDVDCGSFVLEFVERFIEDAPERFNIEDEGTINLEWFPPK-EILKFRDEI 580 (595)
T ss_pred cCccCcccchhhHHHHHHHhhhChhhhcccccccccccccCCch-HHhhhhhhh
Confidence 89999999999999999999876553 235555 666666544
No 9
>PF00770 Peptidase_C5: Adenovirus endoprotease; InterPro: IPR000855 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine aminopeptidases belong to the peptidase family C5 (adenain family, clan CE). Several adenovirus proteins are synthesised as precursors, requiring processing by a protease before the virion is assembled [, ]. Until recently, the adenovirus endopeptidase was classified as a serine protease, having been reported to be inhibited by serine protease inhibitors [, ]. However, it has since been shown to be inhibited by cysteine protease inhibitors, and the catalytic residues are believed to be His-54 and Cys-104 [, ].; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis; PDB: 1NLN_A 1AVP_A.
Probab=97.58 E-value=0.00079 Score=45.87 Aligned_cols=82 Identities=20% Similarity=0.277 Sum_probs=40.5
Q ss_pred CeeEEEEEeCCCCeEEEEeCCCCCCChHHHHHHHHh-HHHHHHHHHHhhhccCCCCCCCCCcccCCcccccccCCCCCCC
Q 046745 9 DHWVLGVVDILGGKISIYDSMIDLTNDSVLVRQLLP-VADMIPLVLQKISYHETNPDCSEVISKIPWPIVRVRDIPQQKS 87 (132)
Q Consensus 9 ~HW~L~vi~~~~~~i~~~DSl~~~~~~~~~~~~~~~-i~~~i~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~P~Q~n 87 (132)
.||....-|++.++++.+|++|=+ +.++..+.+. ... +++..+ .....++ =.+.+...+.-|=.+
T Consensus 34 vHWlA~Aw~P~s~t~YmFDPfGfs--d~~L~qiY~FeYe~----llrRSA-L~~~~dR-------Cv~LvkstqtVQ~p~ 99 (183)
T PF00770_consen 34 VHWLAFAWDPRSRTFYMFDPFGFS--DQKLKQIYQFEYEG----LLRRSA-LSSTPDR-------CVTLVKSTQTVQCPC 99 (183)
T ss_dssp S-EEEEEEETTTTEEEEE-TT-----HHHHHHHH----HH----HHHHHH-HHH-TTS-------EEEEEEE-EE-S-TT
T ss_pred eeEEEEEecCCcceEEEeCCCCCC--HHHHHHHHhhhHHH----HHHHHh-hcCCCCc-------eEEEEeccceeeccC
Confidence 799999999999999999999964 3344333221 111 222111 0100111 012222223334558
Q ss_pred CCChhHHHHHHHHHHhc
Q 046745 88 GGDCGAFLLRYLEVLAH 104 (132)
Q Consensus 88 ~~DCGvfvl~~~~~~~~ 104 (132)
+.-||.|.|.|+.++..
T Consensus 100 SaaCGLFC~lFL~aF~~ 116 (183)
T PF00770_consen 100 SAACGLFCCLFLHAFVH 116 (183)
T ss_dssp ---HHHHHHHHHHHHHH
T ss_pred chhHHHHHHHHHHHHHh
Confidence 99999999999999874
No 10
>PF03290 Peptidase_C57: Vaccinia virus I7 processing peptidase; InterPro: IPR004970 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 is a group of cysteine peptidases which constitute MEROPS peptidase family C57 (clan CE). The type example is vaccinia virus I7 processing peptidase (vaccinia virus); protein I7 is expressed in the late phase of infection [].
Probab=97.32 E-value=0.001 Score=50.58 Aligned_cols=32 Identities=22% Similarity=0.309 Sum_probs=29.2
Q ss_pred CEEeeeeCCeeEEEEEeCCCCeEEEEeCCCCC
Q 046745 1 VYLPIFMNDHWVLGVVDILGGKISIYDSMIDL 32 (132)
Q Consensus 1 i~iPi~~~~HW~L~vi~~~~~~i~~~DSl~~~ 32 (132)
+.+|++-..||..+++|-+++-+.+|||-|..
T Consensus 234 vmFgfcY~~Hwkc~IfDk~~~~v~FydSgG~~ 265 (423)
T PF03290_consen 234 VMFGFCYMSHWKCCIFDKEKKIVYFYDSGGNI 265 (423)
T ss_pred EEeeeeehhcceEEEEeccccEEEEEcCCCCC
Confidence 46789999999999999999999999999874
No 11
>PF03421 YopJ: YopJ Serine/Threonine acetyltransferase; InterPro: IPR005083 The infection of mammalian host cells by Yersinia sp. causes a rapid induction of the mitogen-activated protein kinase (MAPK; including the ERK, JNK and p38 pathways) and nuclear factor kappaB (NF-kappaB) signalling pathways that would typically result in cytokine production and initiation of the innate immune response. However, these pathways are rapidly inhibited promoting apoptosis. YopJ has been shown to block phosphorylation of active site residues []. It has also been shown that YopJ acetyltransferase is activated by eukaryotic host cell inositol hexakisphosphate []. Serine and threonine acetylation is yet another complication to the control of signalling pathways and may be a may be a widespread mode of biochemical regulation of endogenous processes in eukaryotic cells. It has been shown that YopJ is a serine/threonine acetyltransferase []. It acetylates the serine and threonine residues in the phosphorylation sites of MAPK kinases and nuclear factor kappaB, preventing their activation by phosphorylation and the inhibition of these signalling pathways []. This entry contains YopJ and related proteins.
Probab=94.12 E-value=0.34 Score=33.53 Aligned_cols=26 Identities=35% Similarity=0.525 Sum_probs=22.7
Q ss_pred cCCCCCCCCCChhHHHHHHHHHHhcc
Q 046745 80 RDIPQQKSGGDCGAFLLRYLEVLAHE 105 (132)
Q Consensus 80 ~~~P~Q~n~~DCGvfvl~~~~~~~~~ 105 (132)
.+...|...+|||+|.|.++.....+
T Consensus 138 ie~diQkS~~dC~IFsLs~AkK~~~~ 163 (177)
T PF03421_consen 138 IEMDIQKSPSDCGIFSLSLAKKMYKE 163 (177)
T ss_pred EecccccCcCcchhhHHHHHHHHhhc
Confidence 47888999999999999999887654
No 12
>KOG4110 consensus NADH:ubiquinone oxidoreductase, NDUFS5/15kDa [Energy production and conversion]
Probab=88.74 E-value=0.46 Score=30.08 Aligned_cols=33 Identities=27% Similarity=0.624 Sum_probs=26.8
Q ss_pred cCCcccccccCCCCCCCCCChhHHHHHHHHHHh
Q 046745 71 KIPWPIVRVRDIPQQKSGGDCGAFLLRYLEVLA 103 (132)
Q Consensus 71 ~~~w~~~~~~~~P~Q~n~~DCGvfvl~~~~~~~ 103 (132)
...|.+.-...+|.-.-+.|||.|-..++||.-
T Consensus 16 ~~r~p~tds~~~p~~~q~r~cg~FE~e~~eC~e 48 (120)
T KOG4110|consen 16 IDRWPTTDSTEQPYKHQGRDCGKFEKEWMECAE 48 (120)
T ss_pred hhhccccccccCccccccccccHHHHHHHHHHH
Confidence 356777555678888889999999999999963
No 13
>PRK15371 effector protein YopJ; Provisional
Probab=88.40 E-value=4.7 Score=30.11 Aligned_cols=26 Identities=31% Similarity=0.500 Sum_probs=21.3
Q ss_pred CCCCCCCCCChhHHHHHHHHHHhccC
Q 046745 81 DIPQQKSGGDCGAFLLRYLEVLAHEL 106 (132)
Q Consensus 81 ~~P~Q~n~~DCGvfvl~~~~~~~~~~ 106 (132)
..-.|.-.+|||+|.|.+|.......
T Consensus 162 e~d~QkS~~dC~mFSL~~AkK~~~e~ 187 (287)
T PRK15371 162 EMDIQRSSSECGIFSLALAKKLYLER 187 (287)
T ss_pred ecccccCcccchhhhHHHHHHHhhhh
Confidence 45679999999999999998776543
No 14
>PF12252 SidE: Dot/Icm substrate protein; InterPro: IPR021014 This entry represents bacterial proteins that are typically between 397 and 1543 amino acids in length including SidE protein in the Dot/Icm pathway of Legionella pneumophila bacteria. There is little literature describing the family.
Probab=84.92 E-value=3.1 Score=36.38 Aligned_cols=25 Identities=16% Similarity=0.502 Sum_probs=20.0
Q ss_pred CeeEEEEEeCCCCeEEEEeCCCCCCC
Q 046745 9 DHWVLGVVDILGGKISIYDSMIDLTN 34 (132)
Q Consensus 9 ~HW~L~vi~~~~~~i~~~DSl~~~~~ 34 (132)
+||+.++ --+....+.||+||....
T Consensus 63 ghwimli-kg~gn~y~lfdplg~~sg 87 (1439)
T PF12252_consen 63 GHWIMLI-KGQGNQYYLFDPLGKTSG 87 (1439)
T ss_pred ceeEEEE-EcCCCceEEecccccccc
Confidence 8999875 566778899999997643
No 15
>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=74.63 E-value=5.9 Score=25.29 Aligned_cols=24 Identities=21% Similarity=0.263 Sum_probs=17.4
Q ss_pred CCCCCCChhHHHHHHHHHHhccCC
Q 046745 84 QQKSGGDCGAFLLRYLEVLAHELD 107 (132)
Q Consensus 84 ~Q~n~~DCGvfvl~~~~~~~~~~~ 107 (132)
.|.+..|||+.++..+-.+..|..
T Consensus 5 ~q~~~~dcgla~l~~i~~~~~g~~ 28 (129)
T cd02424 5 KQTDLNDCGIAVIQMLYNHYYKKK 28 (129)
T ss_pred EecCccchHHHHHHHHHHHhcCCC
Confidence 466778999999988776633543
No 16
>COG4871 Uncharacterized protein conserved in archaea [Function unknown]
Probab=73.48 E-value=27 Score=24.02 Aligned_cols=81 Identities=19% Similarity=0.158 Sum_probs=42.0
Q ss_pred eCCCCeEEEEeCCC----CCCChHHHHHHHHhHHHHHHHHHHhhhccCCCCCCCCCc---ccCCcccccccCCCCCCCCC
Q 046745 17 DILGGKISIYDSMI----DLTNDSVLVRQLLPVADMIPLVLQKISYHETNPDCSEVI---SKIPWPIVRVRDIPQQKSGG 89 (132)
Q Consensus 17 ~~~~~~i~~~DSl~----~~~~~~~~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~---~~~~w~~~~~~~~P~Q~n~~ 89 (132)
--..+.|.+|-|-. .-.+.++.++++..+.+-+...+ ++.++.+.+. ..+++.+ -+.--|+|..
T Consensus 70 ~kgerIitiy~sGkVsm~~ikdedEAkeilgel~d~ineA~------~kg~d~s~prek~rV~p~dV---ykyLP~tNCg 140 (193)
T COG4871 70 QKGERIITIYGSGKVSMTMIKDEDEAKEILGELMDIINEAI------AKGGDASDPREKVRVGPMDV---YKYLPQTNCG 140 (193)
T ss_pred eeccEEEEEccCCeEEeeeecCHHHHHHHHHHHHHHHHHHH------HccCCCCCchhhcccChHHH---HHhCCCCccc
Confidence 34566778887643 22233344455555554333322 3333322111 1233332 2334489999
Q ss_pred ChhHHHH-HHHHHHhccC
Q 046745 90 DCGAFLL-RYLEVLAHEL 106 (132)
Q Consensus 90 DCGvfvl-~~~~~~~~~~ 106 (132)
+||==+| .|+--++.|.
T Consensus 141 ~CGEqtCmaFAiKLlnge 158 (193)
T COG4871 141 KCGEQTCMAFAIKLLNGE 158 (193)
T ss_pred cchhHHHHHHHHHHHcCc
Confidence 9999866 5676676663
No 17
>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=67.97 E-value=5.4 Score=25.32 Aligned_cols=24 Identities=25% Similarity=0.326 Sum_probs=15.3
Q ss_pred CCCCCCCChhHHHHHHHHHHhccCC
Q 046745 83 PQQKSGGDCGAFLLRYLEVLAHELD 107 (132)
Q Consensus 83 P~Q~n~~DCGvfvl~~~~~~~~~~~ 107 (132)
=+|.+..|||+-++.++-.. .|.+
T Consensus 5 v~Q~~~~dcg~acl~~l~~~-~g~~ 28 (131)
T PF03412_consen 5 VKQSDSNDCGLACLAMLLKY-YGIP 28 (131)
T ss_dssp ---SSTT-HHHHHHHHHHHH-TT--
T ss_pred EEeCCCCCHHHHHHHHHHHH-hCCC
Confidence 36889999999999988776 3544
No 18
>KOG3315 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=62.21 E-value=11 Score=26.13 Aligned_cols=29 Identities=17% Similarity=0.450 Sum_probs=25.7
Q ss_pred CCCCCCCCCChhHHHHHHHHHHhccCCCC
Q 046745 81 DIPQQKSGGDCGAFLLRYLEVLAHELDVN 109 (132)
Q Consensus 81 ~~P~Q~n~~DCGvfvl~~~~~~~~~~~~~ 109 (132)
.+|.-.|+-+|+-||+=.++.++.+..++
T Consensus 132 SVPke~~~lnc~~fvaGIiea~L~~agfp 160 (191)
T KOG3315|consen 132 SVPKENGTLNCAAFVAGIIEAVLDNAGFP 160 (191)
T ss_pred ecccccCcccHHHHHHHHHHHHHHhCCCC
Confidence 67999999999999999999998876654
No 19
>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=60.58 E-value=21 Score=22.27 Aligned_cols=25 Identities=20% Similarity=0.165 Sum_probs=17.7
Q ss_pred CCCCCCCChhHHHHHHHHHHhccCC
Q 046745 83 PQQKSGGDCGAFLLRYLEVLAHELD 107 (132)
Q Consensus 83 P~Q~n~~DCGvfvl~~~~~~~~~~~ 107 (132)
-.|++..|||+.++.++-.+..+.+
T Consensus 4 ~~q~~~~~~~l~~l~~~~~~~g~~~ 28 (129)
T cd02423 4 VRQSYDFSCGPAALATLLRYYGGIN 28 (129)
T ss_pred eecCCCCChHHHHHHHHHHhcCCCC
Confidence 3566777999999887766654344
No 20
>COG5418 Predicted secreted protein [Function unknown]
Probab=52.36 E-value=17 Score=24.44 Aligned_cols=42 Identities=21% Similarity=0.226 Sum_probs=24.6
Q ss_pred HHHHHHhHHHHHHHHHHhhhccCCCCCCCCCcccCCcccccccCCCCCCCCCChhHHHH
Q 046745 38 LVRQLLPVADMIPLVLQKISYHETNPDCSEVISKIPWPIVRVRDIPQQKSGGDCGAFLL 96 (132)
Q Consensus 38 ~~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~P~Q~n~~DCGvfvl 96 (132)
++++++.++..|.++++++. ..+..++. ..++ ++-.||||.-
T Consensus 75 yRr~c~ki~~pi~~~l~e~k-------------~d~~kii~-IGV~---~SpTCgVy~t 116 (164)
T COG5418 75 YRRVCRKIADPIGRVLEEEK-------------PDGIKIIF-IGVK---GSPTCGVYTT 116 (164)
T ss_pred HHHHHHHHHHHHHHHHHHhC-------------cCCceEEE-EecC---CCCccceEec
Confidence 45567777777777776422 12333332 2443 6778999964
No 21
>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=50.60 E-value=19 Score=22.95 Aligned_cols=24 Identities=17% Similarity=0.171 Sum_probs=18.2
Q ss_pred CCeeEEEE-EeCCCCeEEEEeCCCCC
Q 046745 8 NDHWVLGV-VDILGGKISIYDSMIDL 32 (132)
Q Consensus 8 ~~HW~L~v-i~~~~~~i~~~DSl~~~ 32 (132)
++||++++ ++ .+..+.+.|+..+.
T Consensus 93 ~gH~vVv~g~~-~~~~~~i~DP~~~~ 117 (141)
T cd02549 93 SGHAMVVIGYD-RKGNVYVNDPGGGR 117 (141)
T ss_pred CCeEEEEEEEc-CCCCEEEECCCCCc
Confidence 57999886 44 36779999997653
No 22
>PF13280 WYL: WYL domain
Probab=43.12 E-value=35 Score=22.23 Aligned_cols=21 Identities=24% Similarity=0.262 Sum_probs=15.7
Q ss_pred EEeeee---CCeeEEEEEeCCCCe
Q 046745 2 YLPIFM---NDHWVLGVVDILGGK 22 (132)
Q Consensus 2 ~iPi~~---~~HW~L~vi~~~~~~ 22 (132)
+.|+.. +++|+|++.+...+.
T Consensus 32 v~P~~l~~~~~~~Yl~~~~~~~~~ 55 (172)
T PF13280_consen 32 VDPYRLYYYNGRWYLIAYDREREE 55 (172)
T ss_pred EEEEEEEEECCEEEEEEEeccccc
Confidence 456666 699999999876543
No 23
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=41.14 E-value=11 Score=21.19 Aligned_cols=39 Identities=18% Similarity=0.323 Sum_probs=24.3
Q ss_pred hhHHHHHHHHHHhccCC----CCCCCcccchHHHHHHHHHHHh
Q 046745 91 CGAFLLRYLEVLAHELD----VNSYCQQDHVTQFRQALAVKLF 129 (132)
Q Consensus 91 CGvfvl~~~~~~~~~~~----~~~~~~~~~~~~~R~~l~~~l~ 129 (132)
||+|+|+=.--...|.. ...|+.+|--.++|+.+..++.
T Consensus 11 cg~YTLke~Cp~CG~~t~~~~PprFSPeD~y~kYR~~lkk~~~ 53 (59)
T COG2260 11 CGRYTLKEKCPVCGGDTKVPHPPRFSPEDKYGKYRRELKKRLG 53 (59)
T ss_pred CCceeecccCCCCCCccccCCCCCCCccchHHHHHHHHHHHhc
Confidence 99999982211122211 1368988567889988876654
No 24
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=38.42 E-value=15 Score=20.51 Aligned_cols=40 Identities=18% Similarity=0.294 Sum_probs=24.4
Q ss_pred CChhHHHHHHHHHHhccCC-----CCCCCcccchHHHHHHHHHHHh
Q 046745 89 GDCGAFLLRYLEVLAHELD-----VNSYCQQDHVTQFRQALAVKLF 129 (132)
Q Consensus 89 ~DCGvfvl~~~~~~~~~~~-----~~~~~~~~~~~~~R~~l~~~l~ 129 (132)
.+||+|+++ ..|=.-|.+ ...|+.+|...++|..+-.++.
T Consensus 9 ~~CgvYTLk-~~CP~CG~~t~~~~P~rfSp~D~y~~yR~~~kk~~~ 53 (56)
T PRK13130 9 PKCGVYTLK-EICPVCGGKTKNPHPPRFSPEDKYGKYRRALKKRRK 53 (56)
T ss_pred CCCCCEEcc-ccCcCCCCCCCCCCCCCCCCCCccHHHHHHHHHHhh
Confidence 389999882 222221322 1268888667888887766553
No 25
>TIGR03796 NHPM_micro_ABC1 NHPM bacteriocin system ABC transporter, peptidase/ATP-binding protein. This protein describes an multidomain ABC transporter subunit that is one of three protein families associated with some regularity with a distinctive family of putative bacteriocins. It includes a bacteriocin-processing peptidase domain at the N-terminus. Model TIGR03793 describes a conserved propeptide region for this bacteriocin family, unusual because it shows obvious homology a region of the enzyme nitrile hydratase up to the classic Gly-Gly cleavage motif. This family is therefore predicted to be a subunit of a bacteriocin processing and export system characteristic to this system that we designate NHPM, Nitrile Hydratase Propeptide Microcin.
Probab=36.17 E-value=46 Score=27.81 Aligned_cols=20 Identities=25% Similarity=0.285 Sum_probs=15.3
Q ss_pred CCCCCCChhHHHHHHHHHHh
Q 046745 84 QQKSGGDCGAFLLRYLEVLA 103 (132)
Q Consensus 84 ~Q~n~~DCGvfvl~~~~~~~ 103 (132)
.|.+..|||..++.++-.+.
T Consensus 6 ~Q~~~~dCg~acl~mi~~~~ 25 (710)
T TIGR03796 6 LQMEAVECGAASLAMILAYY 25 (710)
T ss_pred eecccccHHHHHHHHHHHHc
Confidence 47788899999998655443
No 26
>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=35.08 E-value=37 Score=21.38 Aligned_cols=23 Identities=26% Similarity=0.268 Sum_probs=17.4
Q ss_pred CCCCCCChhHHHHHHHHHHhccCC
Q 046745 84 QQKSGGDCGAFLLRYLEVLAHELD 107 (132)
Q Consensus 84 ~Q~n~~DCGvfvl~~~~~~~~~~~ 107 (132)
+|++..|||+.++.++-.+. |.+
T Consensus 5 ~q~~~~~~gl~~l~~~~~~~-g~~ 27 (136)
T cd02418 5 LQVDEMDCGAACLAMIAKYY-GKN 27 (136)
T ss_pred EecCcccHHHHHHHHHHHHh-CCC
Confidence 57777899999998876654 444
No 27
>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=34.84 E-value=36 Score=21.19 Aligned_cols=19 Identities=26% Similarity=0.357 Sum_probs=13.9
Q ss_pred CCCCCChhHHHHHHHHHHh
Q 046745 85 QKSGGDCGAFLLRYLEVLA 103 (132)
Q Consensus 85 Q~n~~DCGvfvl~~~~~~~ 103 (132)
|.+..|||..++.++-.+.
T Consensus 6 q~~~~~~gl~~l~~i~~~~ 24 (125)
T cd02420 6 QMEATECGAASLAIILAYY 24 (125)
T ss_pred eCcccCHHHHHHHHHHHHc
Confidence 3456799999998776553
No 28
>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=30.59 E-value=51 Score=20.15 Aligned_cols=22 Identities=23% Similarity=0.208 Sum_probs=16.1
Q ss_pred CCCCCChhHHHHHHHHHHhccCC
Q 046745 85 QKSGGDCGAFLLRYLEVLAHELD 107 (132)
Q Consensus 85 Q~n~~DCGvfvl~~~~~~~~~~~ 107 (132)
|.+..|||+.++.++-.+. |.+
T Consensus 1 ~~~~~~~gl~~l~~i~~~~-g~~ 22 (122)
T cd02259 1 GGGPLDCGLACLQMLLRYF-GIP 22 (122)
T ss_pred CCCccchHHHHHHHHHHHc-CCC
Confidence 5566799999998876665 434
No 29
>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=28.56 E-value=1.7e+02 Score=19.84 Aligned_cols=27 Identities=22% Similarity=0.299 Sum_probs=20.8
Q ss_pred eeeeCCeeEEEEEeCCCCeEEEEeCCCCC
Q 046745 4 PIFMNDHWVLGVVDILGGKISIYDSMIDL 32 (132)
Q Consensus 4 Pi~~~~HW~L~vi~~~~~~i~~~DSl~~~ 32 (132)
-+|...||+.+= --.+.-+-+||+-..
T Consensus 103 I~N~~~HWf~iR--ki~~~wyNLDS~l~~ 129 (157)
T PF02099_consen 103 ICNLSRHWFAIR--KIGGQWYNLDSKLKE 129 (157)
T ss_dssp EEECTTEEEEEE--EETTEEEEECTTTSS
T ss_pred EeccCcceEEEE--eeCCeeEeccCCCCC
Confidence 356689999872 227889999999876
No 30
>COG5128 Transport protein particle (TRAPP) complex subunit [Intracellular trafficking and secretion]
Probab=28.08 E-value=73 Score=22.07 Aligned_cols=28 Identities=11% Similarity=0.310 Sum_probs=24.3
Q ss_pred CCCCCCCCCChhHHHHHHHHHHhccCCC
Q 046745 81 DIPQQKSGGDCGAFLLRYLEVLAHELDV 108 (132)
Q Consensus 81 ~~P~Q~n~~DCGvfvl~~~~~~~~~~~~ 108 (132)
.+|.-.|+-+|-.|||-.++.++....+
T Consensus 145 svP~E~n~lsc~~~vcGiI~gfL~~agf 172 (208)
T COG5128 145 SVPDEWNGLSCDSIVCGIIQGFLMAAGF 172 (208)
T ss_pred cCcchhcCcchHHHHHHHHHHHHHhcCC
Confidence 6799999999999999999998876544
No 31
>PF07559 FlaE: Flagellar basal body protein FlaE; InterPro: IPR011491 This domain is found in several bacterial FlaE flagellar proteins. These proteins are part of the flagellar basal body rod complex.; GO: 0030694 bacterial-type flagellum basal body, rod; PDB: 2BGY_A 1WLG_B 2BGZ_A 3A69_A.
Probab=27.84 E-value=39 Score=21.43 Aligned_cols=13 Identities=31% Similarity=0.547 Sum_probs=7.8
Q ss_pred CeEEEEeCCCCCC
Q 046745 21 GKISIYDSMIDLT 33 (132)
Q Consensus 21 ~~i~~~DSl~~~~ 33 (132)
..+.+|||++...
T Consensus 13 ts~~vYDSlG~~h 25 (130)
T PF07559_consen 13 TSITVYDSLGNAH 25 (130)
T ss_dssp EEEEEE-TT--EE
T ss_pred eeEEEECCCCCEE
Confidence 4688999999864
No 32
>COG3756 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.79 E-value=69 Score=21.55 Aligned_cols=20 Identities=30% Similarity=0.458 Sum_probs=17.4
Q ss_pred ChhHHHHHHHHHHhccCCCC
Q 046745 90 DCGAFLLRYLEVLAHELDVN 109 (132)
Q Consensus 90 DCGvfvl~~~~~~~~~~~~~ 109 (132)
.=|+|.|..+.+|..+.+++
T Consensus 22 EhGaY~LLL~~yw~t~~pip 41 (153)
T COG3756 22 EHGAYLLLLMAYWATEKPIP 41 (153)
T ss_pred HHhHHHHHHHHHHhcCCCCC
Confidence 45999999999999998874
No 33
>PF09369 DUF1998: Domain of unknown function (DUF1998); InterPro: IPR018973 This entry represents a family of DEAD/DEAH-box-containing family of helicases. It includes Hrq1 from Saccharomyces, a putative RecQ helicase []. RecQ helicases are involved in maintaining genomic integrity.
Probab=26.04 E-value=1.5e+02 Score=17.35 Aligned_cols=15 Identities=20% Similarity=0.133 Sum_probs=11.9
Q ss_pred CCCCeEEEEeCCCCC
Q 046745 18 ILGGKISIYDSMIDL 32 (132)
Q Consensus 18 ~~~~~i~~~DSl~~~ 32 (132)
.....|++||+.++.
T Consensus 33 ~~~~~i~lyD~~~GG 47 (84)
T PF09369_consen 33 QGPPRIFLYDTVPGG 47 (84)
T ss_pred CCccEEEEEECCCCc
Confidence 455789999999874
No 34
>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=25.58 E-value=61 Score=20.11 Aligned_cols=22 Identities=18% Similarity=0.330 Sum_probs=15.5
Q ss_pred CCCCCChhHHHHHHHHHHhccCC
Q 046745 85 QKSGGDCGAFLLRYLEVLAHELD 107 (132)
Q Consensus 85 Q~n~~DCGvfvl~~~~~~~~~~~ 107 (132)
|.+..|||+.++..+-.+. |.+
T Consensus 6 q~~~~~~~l~~l~~~~~~~-g~~ 27 (127)
T cd02419 6 QTEAAECGLACLAMIASYH-GHH 27 (127)
T ss_pred eCccccHHHHHHHHHHHHc-CCC
Confidence 4456799999998766553 544
No 35
>PHA02634 hypothetical protein; Provisional
Probab=24.71 E-value=33 Score=18.45 Aligned_cols=11 Identities=27% Similarity=0.395 Sum_probs=8.1
Q ss_pred CCCChhHHHHH
Q 046745 87 SGGDCGAFLLR 97 (132)
Q Consensus 87 n~~DCGvfvl~ 97 (132)
++.|||+=.+.
T Consensus 21 ~~~nCgi~Ifl 31 (49)
T PHA02634 21 QELNCDASILL 31 (49)
T ss_pred CCCCcCHhHhH
Confidence 78899876553
No 36
>cd02421 Peptidase_C39_likeD A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in this sub-family.
Probab=24.59 E-value=1.3e+02 Score=18.57 Aligned_cols=21 Identities=19% Similarity=0.204 Sum_probs=15.6
Q ss_pred CCeeEEEEEeCCCCeEEEEeCC
Q 046745 8 NDHWVLGVVDILGGKISIYDSM 29 (132)
Q Consensus 8 ~~HW~L~vi~~~~~~i~~~DSl 29 (132)
++||+++. ...+..+.++|+.
T Consensus 78 ~g~~~Vl~-~~~~~~~~i~dp~ 98 (124)
T cd02421 78 NGRACVLL-GVDDGHARILDPE 98 (124)
T ss_pred CCCEEEEE-EecCCeEEEEccC
Confidence 57997765 3445779999997
No 37
>PF09778 Guanylate_cyc_2: Guanylylate cyclase; InterPro: IPR018616 Members of this family of proteins catalyse the conversion of guanosine triphosphate (GTP) to 3',5'-cyclic guanosine monophosphate (cGMP) and pyrophosphate.
Probab=24.40 E-value=56 Score=23.40 Aligned_cols=20 Identities=25% Similarity=0.262 Sum_probs=15.7
Q ss_pred CCCCCCChhHHHHHHHHHHh
Q 046745 84 QQKSGGDCGAFLLRYLEVLA 103 (132)
Q Consensus 84 ~Q~n~~DCGvfvl~~~~~~~ 103 (132)
+|.-.+|||+=.+..+-..+
T Consensus 5 ~Q~~~WDCGlACv~MvL~~~ 24 (212)
T PF09778_consen 5 QQRYNWDCGLACVLMVLRYL 24 (212)
T ss_pred eeeccccccHHHHHHHHHHc
Confidence 78999999998776665554
No 38
>COG2378 Predicted transcriptional regulator [Transcription]
Probab=23.93 E-value=1.3e+02 Score=22.72 Aligned_cols=23 Identities=22% Similarity=0.281 Sum_probs=16.2
Q ss_pred EEeeee---CCeeEEEEEeCCCCeEE
Q 046745 2 YLPIFM---NDHWVLGVVDILGGKIS 24 (132)
Q Consensus 2 ~iPi~~---~~HW~L~vi~~~~~~i~ 24 (132)
+-|+.. ++||+|+.-|.....+.
T Consensus 171 V~P~~l~~~~~~wylva~c~~r~~~R 196 (311)
T COG2378 171 VEPLGLVFKGGHWYLVAWCELRQDFR 196 (311)
T ss_pred EeeeEEEEECCEEEEEeeecccCcee
Confidence 346555 69999999887665443
No 39
>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=23.71 E-value=72 Score=19.66 Aligned_cols=23 Identities=13% Similarity=0.160 Sum_probs=16.7
Q ss_pred CCCCCCChhHHHHHHHHHHhccCC
Q 046745 84 QQKSGGDCGAFLLRYLEVLAHELD 107 (132)
Q Consensus 84 ~Q~n~~DCGvfvl~~~~~~~~~~~ 107 (132)
.|.+..|||+.++..+-.+. |.+
T Consensus 5 ~q~~~~~~~l~~l~~~~~~~-~~~ 27 (126)
T cd02425 5 LQNNQTECGLACYAMILNYF-GYK 27 (126)
T ss_pred eecccccHHHHHHHHHHHHh-CCC
Confidence 46777899999998766553 444
No 40
>PRK14751 tetracycline resistance determinant leader peptide; Provisional
Probab=23.63 E-value=88 Score=14.44 Aligned_cols=13 Identities=15% Similarity=0.061 Sum_probs=9.4
Q ss_pred eCCCCeEEEEeCC
Q 046745 17 DILGGKISIYDSM 29 (132)
Q Consensus 17 ~~~~~~i~~~DSl 29 (132)
++.++.|..||=+
T Consensus 11 ~psdksi~hwdf~ 23 (28)
T PRK14751 11 NPSDKSIYHWDFY 23 (28)
T ss_pred CCCcCceeeeeeh
Confidence 5677888888744
No 41
>PF05412 Peptidase_C33: Equine arterivirus Nsp2-type cysteine proteinase; InterPro: IPR008743 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 corresponds to MEROPS peptidase family C33 (clan CA). The type example is equine arteritis virus Nsp2-type cysteine proteinase, which is involved in viral polyprotein processing [].; GO: 0016032 viral reproduction, 0019082 viral protein processing
Probab=22.86 E-value=1.1e+02 Score=19.50 Aligned_cols=20 Identities=15% Similarity=0.207 Sum_probs=15.1
Q ss_pred CCChhHHHHHHHHHHhccCC
Q 046745 88 GGDCGAFLLRYLEVLAHELD 107 (132)
Q Consensus 88 ~~DCGvfvl~~~~~~~~~~~ 107 (132)
...||+.++.++..-+.|-.
T Consensus 7 DG~CG~H~i~aI~n~m~~~~ 26 (108)
T PF05412_consen 7 DGSCGWHCIAAIMNHMMGGE 26 (108)
T ss_pred CCchHHHHHHHHHHHhhccC
Confidence 46899999999776665533
No 42
>PF05393 Hum_adeno_E3A: Human adenovirus early E3A glycoprotein; InterPro: IPR008652 This family consists of several early glycoproteins (E3A), from human adenovirus type 2.; GO: 0016021 integral to membrane
Probab=22.76 E-value=78 Score=19.40 Aligned_cols=12 Identities=33% Similarity=0.531 Sum_probs=8.4
Q ss_pred CCChhHHHHHHH
Q 046745 88 GGDCGAFLLRYL 99 (132)
Q Consensus 88 ~~DCGvfvl~~~ 99 (132)
..=||+|+|..+
T Consensus 38 lvI~~iFil~Vi 49 (94)
T PF05393_consen 38 LVICGIFILLVI 49 (94)
T ss_pred HHHHHHHHHHHH
Confidence 356999977544
No 43
>PF02338 OTU: OTU-like cysteine protease; InterPro: IPR003323 This is a group of proteins found primarily in viruses, eukaryotes and in the pathogenic bacterium Chlamydia pneumoniae. In viruses they are annotated as replicase or RNA-dependent RNA polymerase. The eukaryotic sequences are related to the Ovarian Tumour (OTU) gene in Drosophila, cezanne deubiquitinating peptidase and tumor necrosis factor, alpha-induced protein 3 (MEROPS peptidase family C64) and otubain 1 and otubain 2 (MEROPS peptidase family C65). None of these proteins has a known biochemical function but low sequence similarity with the polyprotein regions of arteriviruses, and conserved cysteine and histidine, and possibly the aspartate, residues suggests that those not yet recognised as peptidases could possess cysteine protease activity [].; PDB: 2VFJ_C 3DKB_F 3PHW_A 3PHU_B 3PHX_A 3BY4_A 3C0R_C 3PRM_C 3PRP_C 3ZRH_A ....
Probab=22.02 E-value=1.8e+02 Score=17.94 Aligned_cols=38 Identities=13% Similarity=0.035 Sum_probs=26.0
Q ss_pred CCChhHHHHHHHHHHhccCCCCCCCcccchHHHHHHHHHHHh-cC
Q 046745 88 GGDCGAFLLRYLEVLAHELDVNSYCQQDHVTQFRQALAVKLF-GH 131 (132)
Q Consensus 88 ~~DCGvfvl~~~~~~~~~~~~~~~~~~~~~~~~R~~l~~~l~-~~ 131 (132)
..+|.+.++...-....+ -++. +...+|+.++..|. .+
T Consensus 3 DGnClF~Avs~~l~~~~~-----~~~~-~~~~lR~~~~~~l~~~~ 41 (121)
T PF02338_consen 3 DGNCLFRAVSDQLYGDGG-----GSED-NHQELRKAVVDYLRDKN 41 (121)
T ss_dssp STTHHHHHHHHHHCTT-S-----SSTT-THHHHHHHHHHHHHTHT
T ss_pred CccHHHHHHHHHHHHhcC-----CCHH-HHHHHHHHHHHHHHHhc
Confidence 468988888776543332 3445 77899999988876 44
No 44
>PF07984 DUF1693: Domain of unknown function (DUF1693) ; InterPro: IPR012937 This domain occurs in many hypothetical proteins. It also occurs in some prion-like proteins.
Probab=21.05 E-value=87 Score=23.91 Aligned_cols=31 Identities=19% Similarity=0.303 Sum_probs=23.5
Q ss_pred Eeeee-CCeeEEEEEeCCCC---eEEEEeCCCCCC
Q 046745 3 LPIFM-NDHWVLGVVDILGG---KISIYDSMIDLT 33 (132)
Q Consensus 3 iPi~~-~~HW~L~vi~~~~~---~i~~~DSl~~~~ 33 (132)
++++. +.+|+|+.+....+ .+-+-|||..+.
T Consensus 127 VkV~~d~D~WSLiSL~n~~GknvELKFV~~mrRqf 161 (320)
T PF07984_consen 127 VKVNNDDDRWSLISLSNNNGKNVELKFVDRMRRQF 161 (320)
T ss_pred ccccCCCCcEEEEecCCCCCCceEEEehhhccCCc
Confidence 46666 68999999976555 567888988753
Done!