Query 032862
Match_columns 132
No_of_seqs 152 out of 904
Neff 8.7
Searched_HMMs 46136
Date Fri Mar 29 06:51:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032862.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032862hhsearch_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 2.3E-30 4.9E-35 200.8 12.2 111 2-127 379-489 (490)
2 KOG0778 Protease, Ulp1 family 100.0 4.7E-31 1E-35 206.0 6.8 113 1-128 399-511 (511)
3 PF02902 Peptidase_C48: Ulp1 p 99.9 2E-24 4.3E-29 154.4 13.1 116 2-126 94-212 (216)
4 COG5160 ULP1 Protease, Ulp1 fa 99.9 2.7E-23 5.9E-28 161.5 3.9 111 2-131 463-573 (578)
5 KOG3246 Sentrin-specific cyste 99.7 7.3E-17 1.6E-21 113.9 8.7 99 2-122 107-211 (223)
6 PF00770 Peptidase_C5: Adenovi 98.0 3.3E-05 7.2E-10 53.4 6.2 84 2-98 33-116 (183)
7 PF03290 Peptidase_C57: Vaccin 96.7 0.0061 1.3E-07 47.3 6.4 25 2-26 241-265 (423)
8 PRK11836 deubiquitinase; Provi 95.9 0.049 1.1E-06 41.1 7.0 87 2-96 229-324 (403)
9 KOG0779 Protease, Ulp1 family 95.1 0.021 4.5E-07 47.2 3.2 41 77-118 528-580 (595)
10 PRK14848 deubiquitinase SseL; 94.9 0.21 4.5E-06 37.1 7.4 77 2-99 198-276 (317)
11 PF03421 YopJ: YopJ Serine/Thr 94.7 0.3 6.6E-06 34.3 7.8 26 74-99 138-163 (177)
12 PRK15371 effector protein YopJ 88.3 4.2 9E-05 30.8 7.7 26 75-100 162-187 (287)
13 KOG4110 NADH:ubiquinone oxidor 87.4 0.55 1.2E-05 30.3 2.2 32 66-97 17-48 (120)
14 cd02424 Peptidase_C39E A sub-f 75.7 5.3 0.00011 25.9 3.8 25 78-102 5-29 (129)
15 COG5418 Predicted secreted pro 67.7 9.2 0.0002 26.1 3.5 42 32-90 75-116 (164)
16 PF03412 Peptidase_C39: Peptid 66.6 5.9 0.00013 25.5 2.4 26 76-102 4-29 (131)
17 KOG3315 Transport protein part 63.0 9.6 0.00021 26.7 2.9 28 75-102 132-159 (191)
18 cd02423 Peptidase_C39G A sub-f 62.8 18 0.00039 23.0 4.2 27 76-102 3-29 (129)
19 PRK13130 H/ACA RNA-protein com 59.8 3.3 7.1E-05 23.5 0.2 40 84-124 10-54 (56)
20 COG2260 Predicted Zn-ribbon RN 56.5 5.1 0.00011 22.9 0.6 39 85-124 11-54 (59)
21 PF12252 SidE: Dot/Icm substra 51.5 58 0.0013 29.5 6.2 25 2-27 62-86 (1439)
22 cd02420 Peptidase_C39D A sub-f 50.6 28 0.00061 22.0 3.5 22 80-102 7-28 (125)
23 cd02418 Peptidase_C39B A sub-f 46.0 36 0.00079 21.7 3.5 24 78-102 5-28 (136)
24 TIGR03796 NHPM_micro_ABC1 NHPM 41.7 34 0.00074 28.9 3.5 24 78-102 6-29 (710)
25 TIGR01193 bacteriocin_ABC ABC- 40.6 46 0.001 28.1 4.2 23 79-102 1-23 (708)
26 cd02259 Peptidase_C39_like Pep 38.0 77 0.0017 19.6 4.1 23 79-102 1-23 (122)
27 cd02419 Peptidase_C39C A sub-f 37.7 54 0.0012 20.6 3.4 25 76-102 4-28 (127)
28 cd02549 Peptidase_C39A A sub-f 36.7 46 0.00099 21.4 2.9 23 2-25 93-116 (141)
29 cd02425 Peptidase_C39F A sub-f 31.4 76 0.0016 19.8 3.3 24 78-102 5-28 (126)
30 PRK14751 tetracycline resistan 31.3 50 0.0011 15.6 1.7 15 9-23 9-23 (28)
31 COG3756 Uncharacterized protei 25.3 79 0.0017 21.6 2.5 19 84-102 22-40 (153)
32 PF12816 Vps8: Golgi CORVET co 24.0 2.6E+02 0.0056 19.8 5.1 45 84-129 112-159 (196)
33 PF05393 Hum_adeno_E3A: Human 23.2 72 0.0016 19.9 1.8 12 82-93 38-49 (94)
34 COG5128 Transport protein part 23.1 1E+02 0.0022 21.7 2.8 28 75-102 145-172 (208)
35 PF09369 DUF1998: Domain of un 22.1 1.4E+02 0.0031 17.6 3.1 16 12-27 33-48 (84)
36 PF07559 FlaE: Flagellar basal 21.5 61 0.0013 20.8 1.4 13 15-27 13-25 (130)
No 1
>PLN03189 Protease specific for SMALL UBIQUITIN-RELATED MODIFIER (SUMO); Provisional
Probab=99.97 E-value=2.3e-30 Score=200.81 Aligned_cols=111 Identities=24% Similarity=0.484 Sum_probs=92.1
Q ss_pred CCeEEEEEEeCCCCeEEEEcCCCCCCChHHHHHhHHHHHHHHHHHHHHhhhccCCCCCCCCccCCCeeEEeeccCCCCCC
Q 032862 2 NDHWVLGVVDILGGKISIYDSMIDLTKDSVLVRQLLPVADMIPLVLQKIAYHETHPDCSEVISKIPWPIVRVRDILQPKS 81 (132)
Q Consensus 2 ~~HW~L~vv~~~~~~i~~~DSl~~~~~~~~~~~~~~~i~~~l~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~Q~n 81 (132)
+.||+|+|||+++++|.|||||++.. ... ++.|.+++. .+. .++.+.+++. +.|....+.++|||+|
T Consensus 379 n~HWsLaVId~k~k~I~yyDSLgg~~-~~v----L~~L~rYL~----~E~-kdK~g~d~D~---s~W~~~~~~~vPQQ~N 445 (490)
T PLN03189 379 EIHWTLAVINKKDQKFQYLDSLKGRD-PKI----LDALAKYYV----DEV-KDKSEKDIDV---SSWEQEFVEDLPEQKN 445 (490)
T ss_pred CCeeEEEEEEcCCCeEEEEeCCCCCC-HHH----HHHHHHHHH----HHH-hhhcCCCcch---hcceeccCCCCCCCCC
Confidence 68999999999999999999999864 323 444544443 343 4555555544 8998776679999999
Q ss_pred CCCcHHHHHHHHHHHhcCCCCCCCccchhHHHHHHHHHHHHHhccc
Q 032862 82 GGDCGVFLLRYLEVLAHGLDVNSYCQQDHVTQFRQALAVKLFGHRS 127 (132)
Q Consensus 82 ~~DCGvfvl~~~e~~~~~~~~~~~~~~~~i~~~R~~l~~~l~~~~~ 127 (132)
|+|||||||+||++++.|.++ +|+|+ ||+.||++|++||+..|+
T Consensus 446 G~DCGVFVL~yAE~~SrG~~L-tFSQe-DMp~fRrRma~EIl~~r~ 489 (490)
T PLN03189 446 GYDCGMFMIKYIDFYSRGLGL-CFGQE-HMPYFRLRTAKEILRLKA 489 (490)
T ss_pred CCCHHHHHHHHHHHHcCCCCC-CcChh-hhHHHHHHHHHHHHHhhc
Confidence 999999999999999999998 89999 999999999999999875
No 2
>KOG0778 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=4.7e-31 Score=205.98 Aligned_cols=113 Identities=26% Similarity=0.522 Sum_probs=97.2
Q ss_pred CCCeEEEEEEeCCCCeEEEEcCCCCCCChHHHHHhHHHHHHHHHHHHHHhhhccCCCCCCCCccCCCeeEEeeccCCCCC
Q 032862 1 MNDHWVLGVVDILGGKISIYDSMIDLTKDSVLVRQLLPVADMIPLVLQKIAYHETHPDCSEVISKIPWPIVRVRDILQPK 80 (132)
Q Consensus 1 ~~~HW~L~vv~~~~~~i~~~DSl~~~~~~~~~~~~~~~i~~~l~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~Q~ 80 (132)
++.||+|+|||+++++|.|||||++..+. . +..|..+|+.+. .++.+..++. +.|.+....++|||.
T Consensus 399 ~~vHW~l~vid~r~k~i~y~DS~~~~~nr-~--------~~aL~~Yl~~E~-~~k~~~~~d~---s~w~~~~~~~iP~Q~ 465 (511)
T KOG0778|consen 399 LGVHWCLAVIDLREKTIEYYDSLGGGPNR-I--------CDALAKYLQDES-RDKSKKDFDV---SGWTIEFVQNIPQQR 465 (511)
T ss_pred cCceEEEEEEEcccceEEEeeccCCCCcc-h--------HHHHHHHHHHHH-hhhhcCCCCc---cchhhhhhhcccccc
Confidence 47899999999999999999999975433 2 234455666675 6666666654 999998889999999
Q ss_pred CCCCcHHHHHHHHHHHhcCCCCCCCccchhHHHHHHHHHHHHHhcccc
Q 032862 81 SGGDCGVFLLRYLEVLAHGLDVNSYCQQDHVTQFRQALAVKLFGHRSW 128 (132)
Q Consensus 81 n~~DCGvfvl~~~e~~~~~~~~~~~~~~~~i~~~R~~l~~~l~~~~~~ 128 (132)
||+|||+|+|+|++|++.|.|+ .|+|+ ||++||++|+.||+..+++
T Consensus 466 Ng~DCG~f~c~~~~~~s~~~p~-~ftq~-dmp~fR~~m~~eI~~~~l~ 511 (511)
T KOG0778|consen 466 NGSDCGMFVCKYADYISRDVPL-TFTQQ-DMPYFRKKMAKEILHLKLL 511 (511)
T ss_pred CCCccceEEeeechhhccCCCc-ccChh-hhHHHHHHHHHHHHhhhcC
Confidence 9999999999999999999999 99999 9999999999999998874
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=99.92 E-value=2e-24 Score=154.37 Aligned_cols=116 Identities=29% Similarity=0.542 Sum_probs=79.4
Q ss_pred CCeEEEEEEeCCCCeEEEEcCCCCCCChHHHHHhHHHHHHHHHHHHHHhhhccCCCCCCCCccCCCeeEEeeccCCCCCC
Q 032862 2 NDHWVLGVVDILGGKISIYDSMIDLTKDSVLVRQLLPVADMIPLVLQKIAYHETHPDCSEVISKIPWPIVRVRDILQPKS 81 (132)
Q Consensus 2 ~~HW~L~vv~~~~~~i~~~DSl~~~~~~~~~~~~~~~i~~~l~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~Q~n 81 (132)
++||+|++||++.++|.+|||+++..........+..+..++..... ...+... +.++|....+.++|||.|
T Consensus 94 ~~HW~l~vi~~~~~~i~~~DSl~~~~~~~~~~~~~~~~~~~l~~~~~-----~~~~~~~---~~~~~~~~~~~~~pqQ~n 165 (216)
T PF02902_consen 94 NNHWVLLVIDLPKKRIYVYDSLGSSNNDKRYKRVIENIIPFLKREYK-----KKEGRDP---DKSPFKIVRPPNVPQQPN 165 (216)
T ss_dssp TTEEEEEEEETTTTEEEEE-TTSTSSH-HHHHHHHHHHHHHHHHHHH-----HHHSSCT----TTTCEEEEECTS-SSSS
T ss_pred hhccceeEEcccccEEEEEeccccccccccchhhhhhhhhhhhhccc-----ccccccc---ccceeeecccccccCCCC
Confidence 78999999999999999999999975412222223333333322211 1111222 237888888889999999
Q ss_pred CCCcHHHHHHHHHHHhcCCCCCC---CccchhHHHHHHHHHHHHHhcc
Q 032862 82 GGDCGVFLLRYLEVLAHGLDVNS---YCQQDHVTQFRQALAVKLFGHR 126 (132)
Q Consensus 82 ~~DCGvfvl~~~e~~~~~~~~~~---~~~~~~i~~~R~~l~~~l~~~~ 126 (132)
++|||+|||+||++++.|.+... ++++ ++..+|++++.++.+..
T Consensus 166 ~~dCGv~vl~~~~~~~~~~~~~~~~~l~~~-~i~~~r~~~a~~~~e~~ 212 (216)
T PF02902_consen 166 GYDCGVYVLKFMECLLEGPSFDFSQELTEE-DIKNFRKKLAVDLYEEL 212 (216)
T ss_dssp SSCHHHHHHHHHHHHHCTHHSTGCCSBTGH-HHHHHHHHHHH------
T ss_pred CCCcHHHHHHHHHHHHhCCCCcccccCCHH-HHHHHHHHHHhhccccc
Confidence 99999999999999999977643 7888 99999999998887654
No 4
>COG5160 ULP1 Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=99.87 E-value=2.7e-23 Score=161.47 Aligned_cols=111 Identities=20% Similarity=0.335 Sum_probs=87.4
Q ss_pred CCeEEEEEEeCCCCeEEEEcCCCCCCChHHHHHhHHHHHHHHHHHHHHhhhccCCCCCCCCccCCCeeEEeeccCCCCCC
Q 032862 2 NDHWVLGVVDILGGKISIYDSMIDLTKDSVLVRQLLPVADMIPLVLQKIAYHETHPDCSEVISKIPWPIVRVRDILQPKS 81 (132)
Q Consensus 2 ~~HW~L~vv~~~~~~i~~~DSl~~~~~~~~~~~~~~~i~~~l~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~Q~n 81 (132)
..||+|++||.++..|.|||||++.. ... .+.+..|+..+. +..+ ++++|.....-++|||.|
T Consensus 463 ~~HW~l~II~~~~~~i~~~DSLan~~-~~v--------~~~L~~Y~ldE~-k~~~-------~k~~~~~~~~~~vPqQ~N 525 (578)
T COG5160 463 SYHWFLAIIDNPKKNILYFDSLANTH-DPV--------LEFLRSYLLDEY-KIQH-------DKDPQIKMKHCKVPQQRN 525 (578)
T ss_pred cceEEEEEeecCcceeEEecccccCc-HHH--------HHHHHHHHHHHH-hccc-------CCchhhhhhcCCCCCCCC
Confidence 37999999999999999999999964 323 233444443342 3333 235565555668999999
Q ss_pred CCCcHHHHHHHHHHHhcCCCCCCCccchhHHHHHHHHHHHHHhccccccc
Q 032862 82 GGDCGVFLLRYLEVLAHGLDVNSYCQQDHVTQFRQALAVKLFGHRSWKKT 131 (132)
Q Consensus 82 ~~DCGvfvl~~~e~~~~~~~~~~~~~~~~i~~~R~~l~~~l~~~~~~~~~ 131 (132)
|+|||||||+|++|++.+.+. .|.+. |++.+|+.|+++|+..++...+
T Consensus 526 g~DCGV~vc~~~~~~~~~~p~-~f~~n-d~~r~Rk~m~h~i~~~qi~y~~ 573 (578)
T COG5160 526 GSDCGVFVCMFIRYFLENPPE-QFSKN-DRPRARKNMAHTIKDLQINYIS 573 (578)
T ss_pred CCccceEEEEeeeecccCChh-hcCcc-chHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999775 99999 9999999999999998876543
No 5
>KOG3246 consensus Sentrin-specific cysteine protease (Ulp1 family) [General function prediction only]
Probab=99.70 E-value=7.3e-17 Score=113.85 Aligned_cols=99 Identities=25% Similarity=0.300 Sum_probs=62.2
Q ss_pred CCeEEEEEEeCCCCeEEEEcCCCCCCChHHHHHhHHHHHHHHHHHHHHhhhccCCCCCCCCccCCCeeEEeeccCCCCCC
Q 032862 2 NDHWVLGVVDILGGKISIYDSMIDLTKDSVLVRQLLPVADMIPLVLQKIAYHETHPDCSEVISKIPWPIVRVRDILQPKS 81 (132)
Q Consensus 2 ~~HW~L~vv~~~~~~i~~~DSl~~~~~~~~~~~~~~~i~~~l~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~Q~n 81 (132)
|+||+|+|++.+++++++|||+.+.+.. .-+.++++++. ++.... ... .....|||+|
T Consensus 107 GsHWSLLV~sr~~~~f~hyDS~~n~nt~-~a~~l~~kl~~----ll~~~~--------------~~~---~~~~~~qQqN 164 (223)
T KOG3246|consen 107 GSHWSLLVFSRPDGKFYHYDSLSNGNTK-DAKSLMKKLRA----LLKKKF--------------AKR---VECKCLQQQN 164 (223)
T ss_pred CcceEEEEEEeeCCcEEEeecccCCCcH-HHHHHHHHHHH----HHhhhh--------------hhc---ccccChhhhc
Confidence 6899999999999999999999997654 32333443333 332111 111 0346788999
Q ss_pred CCCcHHHHHHHHHHHhcCC---CCCCCccc---hhHHHHHHHHHHHH
Q 032862 82 GGDCGVFLLRYLEVLAHGL---DVNSYCQQ---DHVTQFRQALAVKL 122 (132)
Q Consensus 82 ~~DCGvfvl~~~e~~~~~~---~~~~~~~~---~~i~~~R~~l~~~l 122 (132)
|||||+|||.+.+.++... +..+-.+. +-+..+|..+..-|
T Consensus 165 gyDCG~hV~~~t~~l~~~~~~~~~~~~~~~~~~~~i~~lr~~l~~LI 211 (223)
T KOG3246|consen 165 GYDCGLHVCCNTRVLAERLLRCPYATSSQLLVVDLIKALREELLDLI 211 (223)
T ss_pred CCchhHHHHHHHHHHHHHHhccccccccchhhHHHHHHHHHHHHHHH
Confidence 9999999999877665322 33232233 14455555554444
No 6
>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=97.95 E-value=3.3e-05 Score=53.39 Aligned_cols=84 Identities=20% Similarity=0.292 Sum_probs=42.3
Q ss_pred CCeEEEEEEeCCCCeEEEEcCCCCCCChHHHHHhHHHHHHHHHHHHHHhhhccCCCCCCCCccCCCeeEEeeccCCCCCC
Q 032862 2 NDHWVLGVVDILGGKISIYDSMIDLTKDSVLVRQLLPVADMIPLVLQKIAYHETHPDCSEVISKIPWPIVRVRDILQPKS 81 (132)
Q Consensus 2 ~~HW~L~vv~~~~~~i~~~DSl~~~~~~~~~~~~~~~i~~~l~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~Q~n 81 (132)
|.||+.+..|+..++++.||++|=+ ++++..+.+. --..+++..+......+. .+.+.....-|=++
T Consensus 33 GvHWlA~Aw~P~s~t~YmFDPfGfs--d~~L~qiY~F---eYe~llrRSAL~~~~dRC--------v~LvkstqtVQ~p~ 99 (183)
T PF00770_consen 33 GVHWLAFAWDPRSRTFYMFDPFGFS--DQKLKQIYQF---EYEGLLRRSALSSTPDRC--------VTLVKSTQTVQCPC 99 (183)
T ss_dssp -S-EEEEEEETTTTEEEEE-TT-----HHHHHHHH-------HHHHHHHHHHH-TTSE--------EEEEEE-EE-S-TT
T ss_pred ceeEEEEEecCCcceEEEeCCCCCC--HHHHHHHHhh---hHHHHHHHHhhcCCCCce--------EEEEeccceeeccC
Confidence 6899999999999999999999984 3343332110 012333322211111111 12233344455568
Q ss_pred CCCcHHHHHHHHHHHhc
Q 032862 82 GGDCGVFLLRYLEVLAH 98 (132)
Q Consensus 82 ~~DCGvfvl~~~e~~~~ 98 (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 99999999999999864
No 7
>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=96.71 E-value=0.0061 Score=47.25 Aligned_cols=25 Identities=24% Similarity=0.347 Sum_probs=23.2
Q ss_pred CCeEEEEEEeCCCCeEEEEcCCCCC
Q 032862 2 NDHWVLGVVDILGGKISIYDSMIDL 26 (132)
Q Consensus 2 ~~HW~L~vv~~~~~~i~~~DSl~~~ 26 (132)
.+||-++++|-+++-+.+|||-|+.
T Consensus 241 ~~Hwkc~IfDk~~~~v~FydSgG~~ 265 (423)
T PF03290_consen 241 MSHWKCCIFDKEKKIVYFYDSGGNI 265 (423)
T ss_pred hhcceEEEEeccccEEEEEcCCCCC
Confidence 4899999999999999999999884
No 8
>PRK11836 deubiquitinase; Provisional
Probab=95.85 E-value=0.049 Score=41.08 Aligned_cols=87 Identities=18% Similarity=0.250 Sum_probs=44.6
Q ss_pred CCeEEEEEEe--------CCCCeEEEEcCCCCCCChHHHHHhHHHHHHHH-HHHHHHhhhccCCCCCCCCccCCCeeEEe
Q 032862 2 NDHWVLGVVD--------ILGGKISIYDSMIDLTKDSVLVRQLLPVADMI-PLVLQKIAYHETHPDCSEVISKIPWPIVR 72 (132)
Q Consensus 2 ~~HW~L~vv~--------~~~~~i~~~DSl~~~~~~~~~~~~~~~i~~~l-~~ll~~~~~~~~~~~~~~~~~~~~~~~~~ 72 (132)
|+||+|++.. ..+.+..+|.|+..-+.++. ...+.+...+ ..++-... ..+..... .+=.+.+
T Consensus 229 g~HWil~~l~Ki~~~~~~~ekiKC~IFNs~~~l~~d~~--~t~q~ii~a~~~~~~~~~~-~~~ik~~~-----~e~ei~f 300 (403)
T PRK11836 229 GGHWILVSLQKIVNEKNNTQQIKCVIFNSLRALGHDKE--NSLKRVINSFNSELMGEMS-NNNIKVHL-----TEPEIIF 300 (403)
T ss_pred CCcEEEEEeHHhhhcccccceeEEEEEecHhhhccchh--hHHHHHHHhhhhhhhhhcc-hhhhcccc-----cCCceEE
Confidence 6899999762 24567789999987554311 1233333332 12222111 11111111 2222333
Q ss_pred eccCCCCCCCCCcHHHHHHHHHHH
Q 032862 73 VRDILQPKSGGDCGVFLLRYLEVL 96 (132)
Q Consensus 73 ~~~~P~Q~n~~DCGvfvl~~~e~~ 96 (132)
...--||.=...||.||++.+.-+
T Consensus 301 ie~dLQq~vpngCGlFv~~a~Qe~ 324 (403)
T PRK11836 301 LHADLQQYLSQSCGAFVCMAAQEV 324 (403)
T ss_pred EechhhhcCCCccceehHHHHHHH
Confidence 322244545688999999888633
No 9
>KOG0779 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=95.09 E-value=0.021 Score=47.24 Aligned_cols=41 Identities=22% Similarity=0.489 Sum_probs=30.9
Q ss_pred CCCCCCCCcHHHHHHHHHHHhcCCCC------------CCCccchhHHHHHHHH
Q 032862 77 LQPKSGGDCGVFLLRYLEVLAHGLDV------------NSYCQQDHVTQFRQAL 118 (132)
Q Consensus 77 P~Q~n~~DCGvfvl~~~e~~~~~~~~------------~~~~~~~~i~~~R~~l 118 (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 89999999999999999998766432 125555 666666654
No 10
>PRK14848 deubiquitinase SseL; Provisional
Probab=94.86 E-value=0.21 Score=37.06 Aligned_cols=77 Identities=23% Similarity=0.373 Sum_probs=41.6
Q ss_pred CCeEEEEEEeC--CCCeEEEEcCCCCCCChHHHHHhHHHHHHHHHHHHHHhhhccCCCCCCCCccCCCeeEEeeccCCCC
Q 032862 2 NDHWVLGVVDI--LGGKISIYDSMIDLTKDSVLVRQLLPVADMIPLVLQKIAYHETHPDCSEVISKIPWPIVRVRDILQP 79 (132)
Q Consensus 2 ~~HW~L~vv~~--~~~~i~~~DSl~~~~~~~~~~~~~~~i~~~l~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~Q 79 (132)
|+||+|++..- .+.+..+|.|+..-+ +...++ +... . .+. +.. + .=.+.+...--||
T Consensus 198 g~HWil~~~~Ki~~kiKC~iFNs~~~l~-eNs~~~----ii~~-a----k~a-----g~~-~-----e~di~fIe~nLQq 256 (317)
T PRK14848 198 GDHWLLCLFYKLAEKIKCLIFNTYYDLN-ENTKQE----IIEA-A----KIA-----GIS-E-----NEDVNFIETNLQN 256 (317)
T ss_pred CCcEEEEEhHHhhhhceEEEeecHhhhh-hhHHHH----HHHH-H----Hhh-----Ccc-c-----CCceEEeehhhhh
Confidence 78999987633 245678899988754 223222 2111 0 111 110 0 1112222222344
Q ss_pred CCCCCcHHHHHHHHHHHhcC
Q 032862 80 KSGGDCGVFLLRYLEVLAHG 99 (132)
Q Consensus 80 ~n~~DCGvfvl~~~e~~~~~ 99 (132)
.=...||.||+.+++.+...
T Consensus 257 nVpngCGlFv~~aIq~l~~~ 276 (317)
T PRK14848 257 NVPNGCGLFCYHTIQLLSNA 276 (317)
T ss_pred hCCCcchHHHHHHHHHHHhc
Confidence 44578999999999977543
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=94.69 E-value=0.3 Score=34.30 Aligned_cols=26 Identities=27% Similarity=0.439 Sum_probs=22.3
Q ss_pred ccCCCCCCCCCcHHHHHHHHHHHhcC
Q 032862 74 RDILQPKSGGDCGVFLLRYLEVLAHG 99 (132)
Q Consensus 74 ~~~P~Q~n~~DCGvfvl~~~e~~~~~ 99 (132)
-.+..|...+|||+|.|.++......
T Consensus 138 ie~diQkS~~dC~IFsLs~AkK~~~~ 163 (177)
T PF03421_consen 138 IEMDIQKSPSDCGIFSLSLAKKMYKE 163 (177)
T ss_pred EecccccCcCcchhhHHHHHHHHhhc
Confidence 36899999999999999999877654
No 12
>PRK15371 effector protein YopJ; Provisional
Probab=88.31 E-value=4.2 Score=30.84 Aligned_cols=26 Identities=23% Similarity=0.414 Sum_probs=21.3
Q ss_pred cCCCCCCCCCcHHHHHHHHHHHhcCC
Q 032862 75 DILQPKSGGDCGVFLLRYLEVLAHGL 100 (132)
Q Consensus 75 ~~P~Q~n~~DCGvfvl~~~e~~~~~~ 100 (132)
.+-.|...+|||+|.|.++.......
T Consensus 162 e~d~QkS~~dC~mFSL~~AkK~~~e~ 187 (287)
T PRK15371 162 EMDIQRSSSECGIFSLALAKKLYLER 187 (287)
T ss_pred ecccccCcccchhhhHHHHHHHhhhh
Confidence 46789999999999999998765443
No 13
>KOG4110 consensus NADH:ubiquinone oxidoreductase, NDUFS5/15kDa [Energy production and conversion]
Probab=87.36 E-value=0.55 Score=30.26 Aligned_cols=32 Identities=25% Similarity=0.527 Sum_probs=26.6
Q ss_pred CCeeEEeeccCCCCCCCCCcHHHHHHHHHHHh
Q 032862 66 IPWPIVRVRDILQPKSGGDCGVFLLRYLEVLA 97 (132)
Q Consensus 66 ~~~~~~~~~~~P~Q~n~~DCGvfvl~~~e~~~ 97 (132)
..|.+.....+|.-.-++|||.|-..++||.-
T Consensus 17 ~r~p~tds~~~p~~~q~r~cg~FE~e~~eC~e 48 (120)
T KOG4110|consen 17 DRWPTTDSTEQPYKHQGRDCGKFEKEWMECAE 48 (120)
T ss_pred hhccccccccCccccccccccHHHHHHHHHHH
Confidence 56766666778888889999999999999974
No 14
>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=75.73 E-value=5.3 Score=25.86 Aligned_cols=25 Identities=16% Similarity=0.220 Sum_probs=17.1
Q ss_pred CCCCCCCcHHHHHHHHHHHhcCCCC
Q 032862 78 QPKSGGDCGVFLLRYLEVLAHGLDV 102 (132)
Q Consensus 78 ~Q~n~~DCGvfvl~~~e~~~~~~~~ 102 (132)
.|.+..|||+.++..+-....|.+.
T Consensus 5 ~q~~~~dcgla~l~~i~~~~~g~~~ 29 (129)
T cd02424 5 KQTDLNDCGIAVIQMLYNHYYKKKY 29 (129)
T ss_pred EecCccchHHHHHHHHHHHhcCCCc
Confidence 4667779999999877554335443
No 15
>COG5418 Predicted secreted protein [Function unknown]
Probab=67.75 E-value=9.2 Score=26.15 Aligned_cols=42 Identities=24% Similarity=0.275 Sum_probs=26.7
Q ss_pred HHHhHHHHHHHHHHHHHHhhhccCCCCCCCCccCCCeeEEeeccCCCCCCCCCcHHHHH
Q 032862 32 LVRQLLPVADMIPLVLQKIAYHETHPDCSEVISKIPWPIVRVRDILQPKSGGDCGVFLL 90 (132)
Q Consensus 32 ~~~~~~~i~~~l~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~Q~n~~DCGvfvl 90 (132)
++++++.|.+.+.++++.+. . ...+++.+ .++ ++-.||||.-
T Consensus 75 yRr~c~ki~~pi~~~l~e~k-~------------d~~kii~I-GV~---~SpTCgVy~t 116 (164)
T COG5418 75 YRRVCRKIADPIGRVLEEEK-P------------DGIKIIFI-GVK---GSPTCGVYTT 116 (164)
T ss_pred HHHHHHHHHHHHHHHHHHhC-c------------CCceEEEE-ecC---CCCccceEec
Confidence 45667788888877776543 1 33344433 555 7789999964
No 16
>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=66.55 E-value=5.9 Score=25.48 Aligned_cols=26 Identities=27% Similarity=0.526 Sum_probs=15.2
Q ss_pred CCCCCCCCCcHHHHHHHHHHHhcCCCC
Q 032862 76 ILQPKSGGDCGVFLLRYLEVLAHGLDV 102 (132)
Q Consensus 76 ~P~Q~n~~DCGvfvl~~~e~~~~~~~~ 102 (132)
+=.|.+..|||+-++.++-.. .|.++
T Consensus 4 ~v~Q~~~~dcg~acl~~l~~~-~g~~~ 29 (131)
T PF03412_consen 4 VVKQSDSNDCGLACLAMLLKY-YGIPV 29 (131)
T ss_dssp ----SSTT-HHHHHHHHHHHH-TT---
T ss_pred eEEeCCCCCHHHHHHHHHHHH-hCCCc
Confidence 446889999999999888666 46544
No 17
>KOG3315 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=62.95 E-value=9.6 Score=26.74 Aligned_cols=28 Identities=11% Similarity=0.300 Sum_probs=25.0
Q ss_pred cCCCCCCCCCcHHHHHHHHHHHhcCCCC
Q 032862 75 DILQPKSGGDCGVFLLRYLEVLAHGLDV 102 (132)
Q Consensus 75 ~~P~Q~n~~DCGvfvl~~~e~~~~~~~~ 102 (132)
.+|.-.|+-+|+-|++-.++.++.+..+
T Consensus 132 SVPke~~~lnc~~fvaGIiea~L~~agf 159 (191)
T KOG3315|consen 132 SVPKENGTLNCAAFVAGIIEAVLDNAGF 159 (191)
T ss_pred ecccccCcccHHHHHHHHHHHHHHhCCC
Confidence 6799999999999999999999877655
No 18
>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=62.83 E-value=18 Score=22.95 Aligned_cols=27 Identities=19% Similarity=0.303 Sum_probs=17.9
Q ss_pred CCCCCCCCCcHHHHHHHHHHHhcCCCC
Q 032862 76 ILQPKSGGDCGVFLLRYLEVLAHGLDV 102 (132)
Q Consensus 76 ~P~Q~n~~DCGvfvl~~~e~~~~~~~~ 102 (132)
+-.|++..|||+.++.++-....+.+.
T Consensus 3 ~~~q~~~~~~~l~~l~~~~~~~g~~~~ 29 (129)
T cd02423 3 VVRQSYDFSCGPAALATLLRYYGGINI 29 (129)
T ss_pred ceecCCCCChHHHHHHHHHHhcCCCCC
Confidence 345667779999998777555432443
No 19
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=59.81 E-value=3.3 Score=23.55 Aligned_cols=40 Identities=23% Similarity=0.335 Sum_probs=26.2
Q ss_pred CcHHHHHHHHHHHhcCCCC-----CCCccchhHHHHHHHHHHHHHh
Q 032862 84 DCGVFLLRYLEVLAHGLDV-----NSYCQQDHVTQFRQALAVKLFG 124 (132)
Q Consensus 84 DCGvfvl~~~e~~~~~~~~-----~~~~~~~~i~~~R~~l~~~l~~ 124 (132)
+||+|+| -..|=..|.+. ..|+.+|--..+|+.+-.++..
T Consensus 10 ~CgvYTL-k~~CP~CG~~t~~~~P~rfSp~D~y~~yR~~~kk~~~~ 54 (56)
T PRK13130 10 KCGVYTL-KEICPVCGGKTKNPHPPRFSPEDKYGKYRRALKKRRKL 54 (56)
T ss_pred CCCCEEc-cccCcCCCCCCCCCCCCCCCCCCccHHHHHHHHHHhhc
Confidence 8999999 23332224432 3688886778999888766543
No 20
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=56.46 E-value=5.1 Score=22.92 Aligned_cols=39 Identities=23% Similarity=0.404 Sum_probs=26.0
Q ss_pred cHHHHHHHHHHHhcCCC-----CCCCccchhHHHHHHHHHHHHHh
Q 032862 85 CGVFLLRYLEVLAHGLD-----VNSYCQQDHVTQFRQALAVKLFG 124 (132)
Q Consensus 85 CGvfvl~~~e~~~~~~~-----~~~~~~~~~i~~~R~~l~~~l~~ 124 (132)
||+|+|+ =.|=..|.. ...|+.+|--.++|+.+..++..
T Consensus 11 cg~YTLk-e~Cp~CG~~t~~~~PprFSPeD~y~kYR~~lkk~~~~ 54 (59)
T COG2260 11 CGRYTLK-EKCPVCGGDTKVPHPPRFSPEDKYGKYRRELKKRLGL 54 (59)
T ss_pred CCceeec-ccCCCCCCccccCCCCCCCccchHHHHHHHHHHHhcc
Confidence 9999998 222223321 13788886778999988776643
No 21
>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=51.46 E-value=58 Score=29.53 Aligned_cols=25 Identities=16% Similarity=0.509 Sum_probs=19.8
Q ss_pred CCeEEEEEEeCCCCeEEEEcCCCCCC
Q 032862 2 NDHWVLGVVDILGGKISIYDSMIDLT 27 (132)
Q Consensus 2 ~~HW~L~vv~~~~~~i~~~DSl~~~~ 27 (132)
..||+.++ .-..+..+.||+|+..+
T Consensus 62 sghwimli-kg~gn~y~lfdplg~~s 86 (1439)
T PF12252_consen 62 SGHWIMLI-KGQGNQYYLFDPLGKTS 86 (1439)
T ss_pred CceeEEEE-EcCCCceEEeccccccc
Confidence 36999875 55677889999999854
No 22
>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=50.64 E-value=28 Score=22.00 Aligned_cols=22 Identities=23% Similarity=0.309 Sum_probs=15.1
Q ss_pred CCCCCcHHHHHHHHHHHhcCCCC
Q 032862 80 KSGGDCGVFLLRYLEVLAHGLDV 102 (132)
Q Consensus 80 ~n~~DCGvfvl~~~e~~~~~~~~ 102 (132)
.+..|||..++.++-.+ .|.+.
T Consensus 7 ~~~~~~gl~~l~~i~~~-~g~~~ 28 (125)
T cd02420 7 MEATECGAASLAIILAY-YGRYV 28 (125)
T ss_pred CcccCHHHHHHHHHHHH-cCCCC
Confidence 44679999999876555 35443
No 23
>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=45.98 E-value=36 Score=21.69 Aligned_cols=24 Identities=21% Similarity=0.272 Sum_probs=17.5
Q ss_pred CCCCCCCcHHHHHHHHHHHhcCCCC
Q 032862 78 QPKSGGDCGVFLLRYLEVLAHGLDV 102 (132)
Q Consensus 78 ~Q~n~~DCGvfvl~~~e~~~~~~~~ 102 (132)
+|++..|||+.++.++-.+. |.++
T Consensus 5 ~q~~~~~~gl~~l~~~~~~~-g~~~ 28 (136)
T cd02418 5 LQVDEMDCGAACLAMIAKYY-GKNY 28 (136)
T ss_pred EecCcccHHHHHHHHHHHHh-CCCC
Confidence 46677899999998776553 5544
No 24
>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=41.65 E-value=34 Score=28.90 Aligned_cols=24 Identities=21% Similarity=0.235 Sum_probs=16.9
Q ss_pred CCCCCCCcHHHHHHHHHHHhcCCCC
Q 032862 78 QPKSGGDCGVFLLRYLEVLAHGLDV 102 (132)
Q Consensus 78 ~Q~n~~DCGvfvl~~~e~~~~~~~~ 102 (132)
.|.+..|||..++.++-.+ .|.+.
T Consensus 6 ~Q~~~~dCg~acl~mi~~~-~g~~~ 29 (710)
T TIGR03796 6 LQMEAVECGAASLAMILAY-YGRYV 29 (710)
T ss_pred eecccccHHHHHHHHHHHH-cCCCC
Confidence 3777889999999866444 35443
No 25
>TIGR01193 bacteriocin_ABC ABC-type bacteriocin transporter. This model describes ABC-type bacteriocin transporter. The amino terminal domain (pfam03412) processes the N-terminal leader peptide from the bacteriocin while C-terminal domains resemble ABC transporter membrane protein and ATP-binding cassette domain. In general, bacteriocins are agents which are responsible for killing or inhibiting the closely related species or even different strains of the same species. Bacteriocins are usually encoded by bacterial plasmids. Bacteriocins are named after the species and hence in literature one encounters various names e.g., leucocin from Leuconostic geldium; pedicocin from Pedicoccus acidilactici; sakacin from Lactobacillus sake etc.
Probab=40.62 E-value=46 Score=28.12 Aligned_cols=23 Identities=22% Similarity=0.343 Sum_probs=17.0
Q ss_pred CCCCCCcHHHHHHHHHHHhcCCCC
Q 032862 79 PKSGGDCGVFLLRYLEVLAHGLDV 102 (132)
Q Consensus 79 Q~n~~DCGvfvl~~~e~~~~~~~~ 102 (132)
|.+..|||..++.++-.+ .|.+.
T Consensus 1 Q~~~~dCg~~cl~~i~~~-~g~~~ 23 (708)
T TIGR01193 1 QVDEKDCGIAALSMILKK-YGTEY 23 (708)
T ss_pred CCCccchHHHHHHHHHHH-cCCCC
Confidence 778889999999866544 36554
No 26
>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=37.99 E-value=77 Score=19.57 Aligned_cols=23 Identities=30% Similarity=0.390 Sum_probs=16.5
Q ss_pred CCCCCCcHHHHHHHHHHHhcCCCC
Q 032862 79 PKSGGDCGVFLLRYLEVLAHGLDV 102 (132)
Q Consensus 79 Q~n~~DCGvfvl~~~e~~~~~~~~ 102 (132)
|.+..|||+.++.++-.+. |.+.
T Consensus 1 ~~~~~~~gl~~l~~i~~~~-g~~~ 23 (122)
T cd02259 1 GGGPLDCGLACLQMLLRYF-GIPV 23 (122)
T ss_pred CCCccchHHHHHHHHHHHc-CCCC
Confidence 5567799999998776554 5443
No 27
>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=37.69 E-value=54 Score=20.64 Aligned_cols=25 Identities=36% Similarity=0.671 Sum_probs=16.9
Q ss_pred CCCCCCCCCcHHHHHHHHHHHhcCCCC
Q 032862 76 ILQPKSGGDCGVFLLRYLEVLAHGLDV 102 (132)
Q Consensus 76 ~P~Q~n~~DCGvfvl~~~e~~~~~~~~ 102 (132)
++|+ +..|||+.++..+-.+ .|.++
T Consensus 4 ~~q~-~~~~~~l~~l~~~~~~-~g~~~ 28 (127)
T cd02419 4 ILQT-EAAECGLACLAMIASY-HGHHV 28 (127)
T ss_pred EeeC-ccccHHHHHHHHHHHH-cCCCC
Confidence 4444 4679999999876555 36554
No 28
>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=36.66 E-value=46 Score=21.36 Aligned_cols=23 Identities=17% Similarity=0.211 Sum_probs=17.2
Q ss_pred CCeEEEEE-EeCCCCeEEEEcCCCC
Q 032862 2 NDHWVLGV-VDILGGKISIYDSMID 25 (132)
Q Consensus 2 ~~HW~L~v-v~~~~~~i~~~DSl~~ 25 (132)
+.||++++ +| .+..+.+.|+..+
T Consensus 93 ~gH~vVv~g~~-~~~~~~i~DP~~~ 116 (141)
T cd02549 93 SGHAMVVIGYD-RKGNVYVNDPGGG 116 (141)
T ss_pred CCeEEEEEEEc-CCCCEEEECCCCC
Confidence 46998876 44 3677999999765
No 29
>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=31.45 E-value=76 Score=19.83 Aligned_cols=24 Identities=17% Similarity=0.335 Sum_probs=17.0
Q ss_pred CCCCCCCcHHHHHHHHHHHhcCCCC
Q 032862 78 QPKSGGDCGVFLLRYLEVLAHGLDV 102 (132)
Q Consensus 78 ~Q~n~~DCGvfvl~~~e~~~~~~~~ 102 (132)
.|++..|||+.++..+-.+ .|.+.
T Consensus 5 ~q~~~~~~~l~~l~~~~~~-~~~~~ 28 (126)
T cd02425 5 LQNNQTECGLACYAMILNY-FGYKV 28 (126)
T ss_pred eecccccHHHHHHHHHHHH-hCCCC
Confidence 4667779999999876555 35544
No 30
>PRK14751 tetracycline resistance determinant leader peptide; Provisional
Probab=31.29 E-value=50 Score=15.58 Aligned_cols=15 Identities=13% Similarity=-0.028 Sum_probs=11.2
Q ss_pred EEeCCCCeEEEEcCC
Q 032862 9 VVDILGGKISIYDSM 23 (132)
Q Consensus 9 vv~~~~~~i~~~DSl 23 (132)
..++.++.|+.||=+
T Consensus 9 h~~psdksi~hwdf~ 23 (28)
T PRK14751 9 HKNPSDKSIYHWDFY 23 (28)
T ss_pred ecCCCcCceeeeeeh
Confidence 346788899999854
No 31
>COG3756 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.33 E-value=79 Score=21.62 Aligned_cols=19 Identities=21% Similarity=0.380 Sum_probs=16.7
Q ss_pred CcHHHHHHHHHHHhcCCCC
Q 032862 84 DCGVFLLRYLEVLAHGLDV 102 (132)
Q Consensus 84 DCGvfvl~~~e~~~~~~~~ 102 (132)
.=|+|.|..+.+|..+.++
T Consensus 22 EhGaY~LLL~~yw~t~~pi 40 (153)
T COG3756 22 EHGAYLLLLMAYWATEKPI 40 (153)
T ss_pred HHhHHHHHHHHHHhcCCCC
Confidence 4599999999999998876
No 32
>PF12816 Vps8: Golgi CORVET complex core vacuolar protein 8
Probab=23.99 E-value=2.6e+02 Score=19.78 Aligned_cols=45 Identities=18% Similarity=0.219 Sum_probs=36.4
Q ss_pred CcHHHHHHHHHHHhcCCCC--CCC-ccchhHHHHHHHHHHHHHhccccc
Q 032862 84 DCGVFLLRYLEVLAHGLDV--NSY-CQQDHVTQFRQALAVKLFGHRSWK 129 (132)
Q Consensus 84 DCGvfvl~~~e~~~~~~~~--~~~-~~~~~i~~~R~~l~~~l~~~~~~~ 129 (132)
..|--++.|+.+...|..+ .+. +.+ .....|..+..-|+.+....
T Consensus 112 ~~~~kil~Yls~~L~Gr~yP~g~~i~~~-~~~~ak~~i~~~Lfs~~~~~ 159 (196)
T PF12816_consen 112 ELGYKILVYLSYCLTGRQYPSGEIIPEE-KAPSAKREIYSFLFSGTSIP 159 (196)
T ss_pred hhHHHHHHHHHHHHcCCCCCCCCCCChh-HHHHHHHHHHHHHHcCCcCC
Confidence 8899999999999989864 344 445 88999999999999887754
No 33
>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=23.24 E-value=72 Score=19.89 Aligned_cols=12 Identities=33% Similarity=0.639 Sum_probs=8.4
Q ss_pred CCCcHHHHHHHH
Q 032862 82 GGDCGVFLLRYL 93 (132)
Q Consensus 82 ~~DCGvfvl~~~ 93 (132)
..=||+|+|..+
T Consensus 38 lvI~~iFil~Vi 49 (94)
T PF05393_consen 38 LVICGIFILLVI 49 (94)
T ss_pred HHHHHHHHHHHH
Confidence 356999987543
No 34
>COG5128 Transport protein particle (TRAPP) complex subunit [Intracellular trafficking and secretion]
Probab=23.11 E-value=1e+02 Score=21.73 Aligned_cols=28 Identities=7% Similarity=0.147 Sum_probs=23.7
Q ss_pred cCCCCCCCCCcHHHHHHHHHHHhcCCCC
Q 032862 75 DILQPKSGGDCGVFLLRYLEVLAHGLDV 102 (132)
Q Consensus 75 ~~P~Q~n~~DCGvfvl~~~e~~~~~~~~ 102 (132)
.+|.-.|+-+|-.|||-.++.++....+
T Consensus 145 svP~E~n~lsc~~~vcGiI~gfL~~agf 172 (208)
T COG5128 145 SVPDEWNGLSCDSIVCGIIQGFLMAAGF 172 (208)
T ss_pred cCcchhcCcchHHHHHHHHHHHHHhcCC
Confidence 6799999999999999999988765443
No 35
>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=22.12 E-value=1.4e+02 Score=17.64 Aligned_cols=16 Identities=19% Similarity=0.137 Sum_probs=12.4
Q ss_pred CCCCeEEEEcCCCCCC
Q 032862 12 ILGGKISIYDSMIDLT 27 (132)
Q Consensus 12 ~~~~~i~~~DSl~~~~ 27 (132)
.....|++||+..+..
T Consensus 33 ~~~~~i~lyD~~~GG~ 48 (84)
T PF09369_consen 33 QGPPRIFLYDTVPGGA 48 (84)
T ss_pred CCccEEEEEECCCCch
Confidence 3457899999998753
No 36
>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=21.53 E-value=61 Score=20.81 Aligned_cols=13 Identities=31% Similarity=0.547 Sum_probs=7.9
Q ss_pred CeEEEEcCCCCCC
Q 032862 15 GKISIYDSMIDLT 27 (132)
Q Consensus 15 ~~i~~~DSl~~~~ 27 (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 4689999999964
Done!