Query 027072
Match_columns 228
No_of_seqs 115 out of 1147
Neff 8.4
Searched_HMMs 46136
Date Fri Mar 29 04:34:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027072.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027072hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3246 Sentrin-specific cyste 100.0 9.3E-48 2E-52 303.7 19.3 210 4-226 5-216 (223)
2 KOG0778 Protease, Ulp1 family 100.0 3.2E-39 7E-44 286.1 12.3 194 4-225 306-509 (511)
3 PLN03189 Protease specific for 100.0 4.5E-37 9.7E-42 270.4 19.2 191 7-225 277-488 (490)
4 COG5160 ULP1 Protease, Ulp1 fa 100.0 6.5E-35 1.4E-39 255.5 11.3 183 14-225 379-568 (578)
5 PF02902 Peptidase_C48: Ulp1 p 100.0 2.5E-29 5.4E-34 205.7 15.9 176 30-225 1-212 (216)
6 KOG0779 Protease, Ulp1 family 99.3 4.7E-12 1E-16 117.6 6.1 194 15-227 352-590 (595)
7 PF03290 Peptidase_C57: Vaccin 97.9 4.6E-05 9.9E-10 66.1 7.3 95 81-187 227-348 (423)
8 PRK11836 deubiquitinase; Provi 97.9 0.00029 6.3E-09 59.2 11.7 143 28-185 162-328 (403)
9 PRK14848 deubiquitinase SseL; 97.8 0.00021 4.6E-09 58.9 10.1 138 28-184 133-276 (317)
10 PF00770 Peptidase_C5: Adenovi 97.0 0.0019 4.1E-08 50.4 5.8 94 89-187 21-120 (183)
11 PF03421 YopJ: YopJ Serine/Thr 94.8 1.7 3.6E-05 34.7 13.2 87 86-183 72-162 (177)
12 PRK15371 effector protein YopJ 92.4 6.3 0.00014 33.8 13.4 79 104-185 107-187 (287)
13 PF12252 SidE: Dot/Icm substra 85.9 6.4 0.00014 39.4 9.4 77 89-177 49-125 (1439)
14 PF03412 Peptidase_C39: Peptid 42.1 17 0.00036 26.5 1.6 24 160-183 3-26 (131)
15 KOG3315 Transport protein part 37.8 34 0.00073 27.0 2.7 27 158-184 130-156 (191)
16 PF13529 Peptidase_C39_2: Pept 27.8 57 0.0012 23.5 2.5 21 103-124 122-143 (144)
17 KOG4110 NADH:ubiquinone oxidor 27.4 65 0.0014 23.4 2.5 72 152-223 18-92 (120)
18 COG3840 ThiQ ABC-type thiamine 26.7 73 0.0016 26.0 3.0 42 175-228 138-179 (231)
19 cd00542 Ntn_PVA Penicillin V a 25.9 1.2E+02 0.0026 26.1 4.5 55 61-124 106-167 (303)
20 cd02424 Peptidase_C39E A sub-f 24.9 55 0.0012 23.8 2.0 20 162-181 4-23 (129)
21 COG1551 CsrA RNA-binding globa 24.8 75 0.0016 21.3 2.3 20 207-226 37-56 (73)
22 PF03206 NifW: Nitrogen fixati 23.3 93 0.002 22.5 2.8 31 195-225 15-45 (105)
23 PHA02130 hypothetical protein 23.1 43 0.00094 22.0 0.9 37 70-115 16-53 (81)
24 PF15644 Tox-PL: Papain fold t 20.9 1.6E+02 0.0035 21.1 3.7 22 105-128 88-109 (111)
25 PRK00810 nifW nitrogenase stab 20.8 1.1E+02 0.0023 22.5 2.7 30 195-224 19-48 (113)
26 cd02423 Peptidase_C39G A sub-f 20.3 89 0.0019 22.3 2.3 22 162-183 4-25 (129)
27 COG0851 MinE Septum formation 20.0 1.2E+02 0.0027 21.2 2.7 21 204-224 33-53 (88)
No 1
>KOG3246 consensus Sentrin-specific cysteine protease (Ulp1 family) [General function prediction only]
Probab=100.00 E-value=9.3e-48 Score=303.72 Aligned_cols=210 Identities=34% Similarity=0.615 Sum_probs=185.5
Q ss_pred CCCCCceEEECCeEEehhhhhccCCCCccChHHHHHHHHHHhh-hccC-CCeeeeChhhhHHHhcCCChHHHHHhhccCC
Q 027072 4 SAADDKILSYNDVVLRRSDLDILSGPYFLNDRIIEFYFSYLSS-CLVS-QDILLVPPSIAFWILNCPDATYLKEFIEPLK 81 (228)
Q Consensus 4 ~~~~~~v~~~~~~~l~~~Dl~~L~~~~wLnD~iI~~~~~~L~~-~~~~-~~i~~~~p~~~~~~~~~~~~~~~~~~~~~~~ 81 (228)
|..++.+++|.|++|+.+|+++|+++.|+||.+|+||.+||.+ .+++ .+.+|+.|+.+|++++++++++++.++.+.+
T Consensus 5 s~~~pv~Lsy~dv~Lr~sDVdlL~~p~wlnD~~I~F~~e~l~~~~~~s~~~~~ll~P~~t~~l~~~~~~~e~~~~~~pl~ 84 (223)
T KOG3246|consen 5 SLSDPVVLSYFDVSLRQSDVDLLQPPEWLNDRLIDFYYEYLEHRRSRSEPDLHLLRPSLTFFLRHAPNPEEIAMVLDPLD 84 (223)
T ss_pred ccCCceEEEeeehhhhhhhhhhcCCCchhhhhHHHHHHHHHHHhhcccCcchhccCHHHHHHHHhCCCcHHHHHhcChhh
Confidence 4455679999999999999999999999999999999999997 4442 3468999999999999999999999999999
Q ss_pred CCCCcEEEEeeecCCCcCcCCCCceeEEEEEEcCCCeEEEEeCCCCCCHHHHHHHHHHHHHhhcCcCCCCCCeeecCCCC
Q 027072 82 LPEKKLVIFPVNDNDDMSLAEGGSHWSLIVYERNGNVFVHHDSNHRMNKIKARKLFSAVVGFMGDSTSASNGKYLDCVDS 161 (228)
Q Consensus 82 ~~~~~~I~iPin~n~~~~~~~~~~HW~Llvv~~~~~~i~~~DSl~~~~~~~~~~i~~~l~~~l~~~~~~~~~~~v~~~~~ 161 (228)
+.++++||+|||+|++.++++||+||+|+|++.++++++||||+.+.|...++++++.++.+++.. ...+. ...|
T Consensus 85 l~~k~~iflpiNDn~~~~~~~GGsHWSLLV~sr~~~~f~hyDS~~n~nt~~a~~l~~kl~~ll~~~----~~~~~-~~~~ 159 (223)
T KOG3246|consen 85 LNDKDFIFLPINDNSNVTRASGGSHWSLLVFSRPDGKFYHYDSLSNGNTKDAKSLMKKLRALLKKK----FAKRV-ECKC 159 (223)
T ss_pred cCCCceEEEEecCCCcccccCCCcceEEEEEEeeCCcEEEeecccCCCcHHHHHHHHHHHHHHhhh----hhhcc-cccC
Confidence 999999999999999999999999999999999999999999999999999999999999999732 22222 4789
Q ss_pred CCCCCCCccHHHHHHHHHHHHHHhhcccCcccccchhhhhccccChHHHHHHHHHHHHHHHHhhh
Q 027072 162 PQQTNGYDCGVYVIAIARAICCWYESSEHKDAEGMWFSFVKEQVTSTVVSQMRKEILQLIKGLME 226 (228)
Q Consensus 162 pqQ~n~~DCGvfvl~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~R~~i~~~i~~l~~ 226 (228)
|||.||+|||+|||++++.+++++..+..+.. .....++.|+++|++|.++|..|..
T Consensus 160 ~qQqNgyDCG~hV~~~t~~l~~~~~~~~~~~~--------~~~~~~~~i~~lr~~l~~LI~slg~ 216 (223)
T KOG3246|consen 160 LQQQNGYDCGLHVCCNTRVLAERLLRCPYATS--------SQLLVVDLIKALREELLDLIQSLGS 216 (223)
T ss_pred hhhhcCCchhHHHHHHHHHHHHHHhccccccc--------cchhhHHHHHHHHHHHHHHHHHhCc
Confidence 99999999999999999999999988654331 1345688999999999999999984
No 2
>KOG0778 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=3.2e-39 Score=286.05 Aligned_cols=194 Identities=21% Similarity=0.260 Sum_probs=161.7
Q ss_pred CCCCCceEEECCeEEehhhhhccCCCCccChHHHHHHHHHHhhhccCC----CeeeeChhhhHHHhcCC--ChHHHHHhh
Q 027072 4 SAADDKILSYNDVVLRRSDLDILSGPYFLNDRIIEFYFSYLSSCLVSQ----DILLVPPSIAFWILNCP--DATYLKEFI 77 (228)
Q Consensus 4 ~~~~~~v~~~~~~~l~~~Dl~~L~~~~wLnD~iI~~~~~~L~~~~~~~----~i~~~~p~~~~~~~~~~--~~~~~~~~~ 77 (228)
....+.++..+++.||.+|+.+|.+++||||+||+|||++|.+..+.. .++++ ++||+.++. +++.|++|+
T Consensus 306 ~~~~~~~~~~~~i~It~~dl~tl~~~~WLNDevINfYm~ll~ers~~~~~yp~~h~F---nTFFy~kL~~~gy~~VkRWT 382 (511)
T KOG0778|consen 306 RNSTEILVTHFNIDITGKDLQTLRPGNWLNDEVINFYMELLKERSKKDSKYPKVHAF---NTFFYTKLVGRGYAGVKRWT 382 (511)
T ss_pred CCcccceehhccccccHHHHhhccCccchhHHHHHHHHHHHHhhccccCCCceEEEE---echhhhhhhhcchHHHHhHh
Confidence 455677788888999999999999999999999999999999987643 25554 567887764 478999999
Q ss_pred ccCCCCCCcEEEEeeecCCCcCcCCCCceeEEEEEEcCCCeEEEEeCCCCCCHHHHHHHHHHHHHhhcCc----CCCCCC
Q 027072 78 EPLKLPEKKLVIFPVNDNDDMSLAEGGSHWSLIVYERNGNVFVHHDSNHRMNKIKARKLFSAVVGFMGDS----TSASNG 153 (228)
Q Consensus 78 ~~~~~~~~~~I~iPin~n~~~~~~~~~~HW~Llvv~~~~~~i~~~DSl~~~~~~~~~~i~~~l~~~l~~~----~~~~~~ 153 (228)
++++++++++||+|||. +.||+|+|||.++++|.|||||++.....+..|+++|....... .+-.+|
T Consensus 383 k~v~if~~d~i~vPIH~---------~vHW~l~vid~r~k~i~y~DS~~~~~nr~~~aL~~Yl~~E~~~k~~~~~d~s~w 453 (511)
T KOG0778|consen 383 KKVDIFDKDIIFVPIHL---------GVHWCLAVIDLREKTIEYYDSLGGGPNRICDALAKYLQDESRDKSKKDFDVSGW 453 (511)
T ss_pred hccCccccceeEeeeec---------CceEEEEEEEcccceEEEeeccCCCCcchHHHHHHHHHHHHhhhhcCCCCccch
Confidence 99999999999999998 89999999999999999999999764455688888887765221 123567
Q ss_pred eeecCCCCCCCCCCCccHHHHHHHHHHHHHHhhcccCcccccchhhhhccccChHHHHHHHHHHHHHHHHhh
Q 027072 154 KYLDCVDSPQQTNGYDCGVYVIAIARAICCWYESSEHKDAEGMWFSFVKEQVTSTVVSQMRKEILQLIKGLM 225 (228)
Q Consensus 154 ~~v~~~~~pqQ~n~~DCGvfvl~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~R~~i~~~i~~l~ 225 (228)
......++|||.||+|||+|+|+|++++.+..+ -.+|++++-.||+.|...|...+
T Consensus 454 ~~~~~~~iP~Q~Ng~DCG~f~c~~~~~~s~~~p----------------~~ftq~dmp~fR~~m~~eI~~~~ 509 (511)
T KOG0778|consen 454 TIEFVQNIPQQRNGSDCGMFVCKYADYISRDVP----------------LTFTQQDMPYFRKKMAKEILHLK 509 (511)
T ss_pred hhhhhhccccccCCCccceEEeeechhhccCCC----------------cccChhhhHHHHHHHHHHHHhhh
Confidence 765567899999999999999999999998432 36678999999999999998754
No 3
>PLN03189 Protease specific for SMALL UBIQUITIN-RELATED MODIFIER (SUMO); Provisional
Probab=100.00 E-value=4.5e-37 Score=270.41 Aligned_cols=191 Identities=19% Similarity=0.250 Sum_probs=149.1
Q ss_pred CCceEEEC--CeEEehhhhhccCCCCccChHHHHHHHHHHhhhcc---C--CCeeeeChhhhHHHhcCC------ChHHH
Q 027072 7 DDKILSYN--DVVLRRSDLDILSGPYFLNDRIIEFYFSYLSSCLV---S--QDILLVPPSIAFWILNCP------DATYL 73 (228)
Q Consensus 7 ~~~v~~~~--~~~l~~~Dl~~L~~~~wLnD~iI~~~~~~L~~~~~---~--~~i~~~~p~~~~~~~~~~------~~~~~ 73 (228)
.+.+++.. ++.||.+|+.+|.+++||||.|||||+.+|.+... . ..+++++ +||+.++. +++.+
T Consensus 277 ~~vlvs~~~~~i~IT~~DL~~L~Pg~WLNDeVINfYm~LL~er~~~~p~~~~k~h~FN---TFFytkL~~~~~~ygY~~V 353 (490)
T PLN03189 277 RKVLVTHENSNIDITGEILRCLKPGAWLNDEVINLYLELLKEREAREPKKFLKCHFFN---TFFYKKLVSGKSGYDYKAV 353 (490)
T ss_pred cceeeecCCCceEEEHHHhhccCCCCccCHHHHHHHHHHHHHhhhcCcccccceEEEe---hHHHHHHhhcCCcCChHHH
Confidence 34555443 78999999999999999999999999999986432 1 3566664 45655442 36789
Q ss_pred HHhhcc----CCCCCCcEEEEeeecCCCcCcCCCCceeEEEEEEcCCCeEEEEeCCCCCCHHHHHHHHHHHHHhhcCc--
Q 027072 74 KEFIEP----LKLPEKKLVIFPVNDNDDMSLAEGGSHWSLIVYERNGNVFVHHDSNHRMNKIKARKLFSAVVGFMGDS-- 147 (228)
Q Consensus 74 ~~~~~~----~~~~~~~~I~iPin~n~~~~~~~~~~HW~Llvv~~~~~~i~~~DSl~~~~~~~~~~i~~~l~~~l~~~-- 147 (228)
++|+++ +.++++++||||||. +.||+|+||+.+.++|.|||||++.+...++.+..++.......
T Consensus 354 rRWTk~kKigv~Lfs~D~IFIPIh~---------n~HWsLaVId~k~k~I~yyDSLgg~~~~vL~~L~rYL~~E~kdK~g 424 (490)
T PLN03189 354 RRWTTQKKLGYHLIDCDKIFVPIHQ---------EIHWTLAVINKKDQKFQYLDSLKGRDPKILDALAKYYVDEVKDKSE 424 (490)
T ss_pred HHHhhhcccccccccCceEEeeeec---------CCeeEEEEEEcCCCeEEEEeCCCCCCHHHHHHHHHHHHHHHhhhcC
Confidence 999864 358899999999997 69999999999999999999999988776666666665443221
Q ss_pred --CCCCCCeeecCCCCCCCCCCCccHHHHHHHHHHHHHHhhcccCcccccchhhhhccccChHHHHHHHHHHHHHHHHhh
Q 027072 148 --TSASNGKYLDCVDSPQQTNGYDCGVYVIAIARAICCWYESSEHKDAEGMWFSFVKEQVTSTVVSQMRKEILQLIKGLM 225 (228)
Q Consensus 148 --~~~~~~~~v~~~~~pqQ~n~~DCGvfvl~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~R~~i~~~i~~l~ 225 (228)
.....|.......+|||.||+|||||||+||+++.++.. -.++++.|..+|++|...|..+.
T Consensus 425 ~d~D~s~W~~~~~~~vPQQ~NG~DCGVFVL~yAE~~SrG~~----------------LtFSQeDMp~fRrRma~EIl~~r 488 (490)
T PLN03189 425 KDIDVSSWEQEFVEDLPEQKNGYDCGMFMIKYIDFYSRGLG----------------LCFGQEHMPYFRLRTAKEILRLK 488 (490)
T ss_pred CCcchhcceeccCCCCCCCCCCCCHHHHHHHHHHHHcCCCC----------------CCcChhhhHHHHHHHHHHHHHhh
Confidence 112456553346899999999999999999999987432 24789999999999999998763
No 4
>COG5160 ULP1 Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=6.5e-35 Score=255.55 Aligned_cols=183 Identities=23% Similarity=0.328 Sum_probs=144.3
Q ss_pred CCeEEehhhhhccCCCCccChHHHHHHHHHHhhhcc----CCCeeeeChhhhHHHhcCC--ChHHHHHhhccCCCCCCcE
Q 027072 14 NDVVLRRSDLDILSGPYFLNDRIIEFYFSYLSSCLV----SQDILLVPPSIAFWILNCP--DATYLKEFIEPLKLPEKKL 87 (228)
Q Consensus 14 ~~~~l~~~Dl~~L~~~~wLnD~iI~~~~~~L~~~~~----~~~i~~~~p~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~ 87 (228)
.++.|+.+|+.+|.+++||||.||+|||++|.+..+ .++++++ ++||+..+. .++.|++|+++++++++++
T Consensus 379 ~~i~IT~~D~~~L~~~~wLNDtIIdFy~k~ls~~sk~~s~~~~vh~F---nTFFYT~LsrrGy~gVrrW~kk~dif~~k~ 455 (578)
T COG5160 379 SSIEITNQDFKRLRNGDWLNDTIIDFYMKLLSKISKNTSKREQVHLF---NTFFYTKLSRRGYSGVRRWTKKTDIFSKKY 455 (578)
T ss_pred CcceeehHhhhhhccccchhhHHHHHHHHHHHHhccCcccccceEEe---ehhhHHHHHHHHhHHHHHHHhccCccccce
Confidence 489999999999999999999999999999976554 3567776 467777664 3678999999999999999
Q ss_pred EEEeeecCCCcCcCCCCceeEEEEEEcCCCeEEEEeCCCCCCHHHHHHHHHHHHHhhc-CcCCCCCCeeecCCCCCCCCC
Q 027072 88 VIFPVNDNDDMSLAEGGSHWSLIVYERNGNVFVHHDSNHRMNKIKARKLFSAVVGFMG-DSTSASNGKYLDCVDSPQQTN 166 (228)
Q Consensus 88 I~iPin~n~~~~~~~~~~HW~Llvv~~~~~~i~~~DSl~~~~~~~~~~i~~~l~~~l~-~~~~~~~~~~v~~~~~pqQ~n 166 (228)
||+|||. ..||+|+|+|.+.+.|.|||||++.....++.+.+++..... ..+......... -+||||.|
T Consensus 456 I~iPIni---------~~HW~l~II~~~~~~i~~~DSLan~~~~v~~~L~~Y~ldE~k~~~~k~~~~~~~~-~~vPqQ~N 525 (578)
T COG5160 456 IFIPINI---------SYHWFLAIIDNPKKNILYFDSLANTHDPVLEFLRSYLLDEYKIQHDKDPQIKMKH-CKVPQQRN 525 (578)
T ss_pred EEEEecc---------cceEEEEEeecCcceeEEecccccCcHHHHHHHHHHHHHHHhcccCCchhhhhhc-CCCCCCCC
Confidence 9999998 799999999999999999999998775444444444332211 111112233333 78999999
Q ss_pred CCccHHHHHHHHHHHHHHhhcccCcccccchhhhhccccChHHHHHHHHHHHHHHHHhh
Q 027072 167 GYDCGVYVIAIARAICCWYESSEHKDAEGMWFSFVKEQVTSTVVSQMRKEILQLIKGLM 225 (228)
Q Consensus 167 ~~DCGvfvl~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~R~~i~~~i~~l~ 225 (228)
|+|||||||+++++++.+.+ ..++.+++.++|+.|.+.|..++
T Consensus 526 g~DCGV~vc~~~~~~~~~~p----------------~~f~~nd~~r~Rk~m~h~i~~~q 568 (578)
T COG5160 526 GSDCGVFVCMFIRYFLENPP----------------EQFSKNDRPRARKNMAHTIKDLQ 568 (578)
T ss_pred CCccceEEEEeeeecccCCh----------------hhcCccchHHHHHHHHHHHHHHH
Confidence 99999999999999888432 34557778899999999887654
No 5
>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=99.97 E-value=2.5e-29 Score=205.74 Aligned_cols=176 Identities=22% Similarity=0.290 Sum_probs=119.9
Q ss_pred CccChHHHHHHHHHHhhh-----ccCCCeeeeChhhhHHHh-cCC------------------ChHHHHHhhccC---CC
Q 027072 30 YFLNDRIIEFYFSYLSSC-----LVSQDILLVPPSIAFWIL-NCP------------------DATYLKEFIEPL---KL 82 (228)
Q Consensus 30 ~wLnD~iI~~~~~~L~~~-----~~~~~i~~~~p~~~~~~~-~~~------------------~~~~~~~~~~~~---~~ 82 (228)
+||||.|||+|+++|.+. ...+++.+++|.....+. ... ....+.+|.++. .+
T Consensus 1 ~wLnd~iId~y~~~l~~~~~~~~~~~~~~~~~~~~f~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l 80 (216)
T PF02902_consen 1 EWLNDSIIDFYLEYLRHRLESENKNSKRVHFFSSFFYQKLTECFKQFKKDKERSKFKWNESKDFYNGVQRWFRKKNKKNL 80 (216)
T ss_dssp --EEHHHHHHHHHHHHHHTCCTHHTSTTEEEE-THHHHHHH----HHHCCH--S-----HHHHCHHHCGGGGTTCCTSTG
T ss_pred CcCCHHHHHHHHHHHHHhhccCccCCCcEEEECceeeeccccccccccccccccccchhhhhHhhhhhhhhhhccccccc
Confidence 699999999999999832 335789999887544443 000 123345566655 78
Q ss_pred CCCcEEEEeeecCCCcCcCCCCceeEEEEEEcCCCeEEEEeCCCCCCH-----HHHHHHHHHHHHhhcC----cCCCCCC
Q 027072 83 PEKKLVIFPVNDNDDMSLAEGGSHWSLIVYERNGNVFVHHDSNHRMNK-----IKARKLFSAVVGFMGD----STSASNG 153 (228)
Q Consensus 83 ~~~~~I~iPin~n~~~~~~~~~~HW~Llvv~~~~~~i~~~DSl~~~~~-----~~~~~i~~~l~~~l~~----~~~~~~~ 153 (228)
+++++|++|||. +++||+|+||+.+.+++++||||++.+. .....+...+...... .....++
T Consensus 81 ~~~~~i~iPin~--------~~~HW~l~vi~~~~~~i~~~DSl~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~ 152 (216)
T PF02902_consen 81 FDKDYIFIPINI--------NNNHWVLLVIDLPKKRIYVYDSLGSSNNDKRYKRVIENIIPFLKREYKKKEGRDPDKSPF 152 (216)
T ss_dssp GGSSEEEEEEEE--------TTTEEEEEEEETTTTEEEEE-TTSTSSH-HHHHHHHHHHHHHHHHHHHHHHSSCT-TTTC
T ss_pred cccCEEEEEEec--------hhhccceeEEcccccEEEEEeccccccccccchhhhhhhhhhhhhcccccccccccccee
Confidence 899999999998 3899999999999999999999998876 2223333333332211 1113466
Q ss_pred eeecCCCCCCCCCCCccHHHHHHHHHHHHHHhhcccCcccccchhhhhccccChHHHHHHHHHHHHHHHHhh
Q 027072 154 KYLDCVDSPQQTNGYDCGVYVIAIARAICCWYESSEHKDAEGMWFSFVKEQVTSTVVSQMRKEILQLIKGLM 225 (228)
Q Consensus 154 ~~v~~~~~pqQ~n~~DCGvfvl~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~R~~i~~~i~~l~ 225 (228)
..+.+..+|||+|++|||+|||+||++++.+..... ...++++.+..+|+++...+.+..
T Consensus 153 ~~~~~~~~pqQ~n~~dCGv~vl~~~~~~~~~~~~~~------------~~~l~~~~i~~~r~~~a~~~~e~~ 212 (216)
T PF02902_consen 153 KIVRPPNVPQQPNGYDCGVYVLKFMECLLEGPSFDF------------SQELTEEDIKNFRKKLAVDLYEEL 212 (216)
T ss_dssp EEEEECTS-SSSSSSCHHHHHHHHHHHHHCTHHSTG------------CCSBTGHHHHHHHHHHHH------
T ss_pred eecccccccCCCCCCCcHHHHHHHHHHHHhCCCCcc------------cccCCHHHHHHHHHHHHhhccccc
Confidence 666667999999999999999999999999754411 011789999999999998877654
No 6
>KOG0779 consensus Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]
Probab=99.28 E-value=4.7e-12 Score=117.58 Aligned_cols=194 Identities=21% Similarity=0.271 Sum_probs=124.2
Q ss_pred CeEEehhhhhccCCCCccChHHHHHHHHHHhhhc-c----CCCeeeeChhhhHHHhcCC--------C------hHHHHH
Q 027072 15 DVVLRRSDLDILSGPYFLNDRIIEFYFSYLSSCL-V----SQDILLVPPSIAFWILNCP--------D------ATYLKE 75 (228)
Q Consensus 15 ~~~l~~~Dl~~L~~~~wLnD~iI~~~~~~L~~~~-~----~~~i~~~~p~~~~~~~~~~--------~------~~~~~~ 75 (228)
.+.++.+|+.+|..+..|||.+++||+.++...- + +++.+++ .++++.... + ...+++
T Consensus 352 ~~~v~~~Dl~cl~~~e~L~d~i~dfyl~~i~~~~l~~~~~s~~~h~f---~tffyk~l~~~~~~~~~d~~~~~~~~~~~~ 428 (595)
T KOG0779|consen 352 SHQVNNNDLVCLEEGEFLNDTIKDFYLEYIRQYLLSQKELSNDRHIF---STFFYKRLCRKLRQKSNDQIQDNRAVRLRT 428 (595)
T ss_pred ccceeccchhhccccchhhhhhhhhhhHHHHHhhhcccccCcchhhh---hhHHHhhhhhhhhhhhhhhhhccccCceee
Confidence 4478999999999999999999999999998632 2 2444544 345544321 1 124567
Q ss_pred hhccCCCCCCcEEEEeeecCCCcCcCCCCceeEEEEEEcCCC------eEEEEeCCCCCCH-HHHHHHHHHHHHhhcCcC
Q 027072 76 FIEPLKLPEKKLVIFPVNDNDDMSLAEGGSHWSLIVYERNGN------VFVHHDSNHRMNK-IKARKLFSAVVGFMGDST 148 (228)
Q Consensus 76 ~~~~~~~~~~~~I~iPin~n~~~~~~~~~~HW~Llvv~~~~~------~i~~~DSl~~~~~-~~~~~i~~~l~~~l~~~~ 148 (228)
|.+..+++.+++|++|+|. ..||.+.+++.... ....++++.-... .....+...++.......
T Consensus 429 ~~~~~d~~~k~yi~~P~~E---------~~hw~laiic~p~~e~es~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 499 (595)
T KOG0779|consen 429 WTRHFDLFNKDYVFVPTHE---------RFHWKLAIICNPDLETETPRPRLELLILKLSADFPIVENILDFMKVASIYNN 499 (595)
T ss_pred eeeccccccceeEEecCch---------HhhhhccccccCccccCccccchhhhhhccccccchhhhhhhhhhhcccccC
Confidence 8888899999999999998 69999999998642 3344444432211 111222222222111000
Q ss_pred ------------C-CCCC--eeecCCCCCCCCCCCccHHHHHHHHHHHHHHhhcc----cCcccccchhhhhccccChHH
Q 027072 149 ------------S-ASNG--KYLDCVDSPQQTNGYDCGVYVIAIARAICCWYESS----EHKDAEGMWFSFVKEQVTSTV 209 (228)
Q Consensus 149 ------------~-~~~~--~~v~~~~~pqQ~n~~DCGvfvl~~~~~l~~~~~~~----~~~~~~~~~~~~~~~~~~~~~ 209 (228)
. +.+. .+.+-...|||.|.+|||+|++.|++.+....... .....+..| +.+..
T Consensus 500 ~~~~~~~~~~~~~~~~~~~~~~s~~v~~p~q~n~~dcG~~~~~~v~~f~e~~~e~~~~~~~~~~~l~~-------~~~~~ 572 (595)
T KOG0779|consen 500 ELIVTEDLELEEELPRRLPRGKSETVREPQQNNDVDCGSFVLEFVERFIEDAPERFNIEDEGTINLEW-------FPPKE 572 (595)
T ss_pred cccccccccccccccccCcccccccccccCccCcccchhhHHHHHHHhhhChhhhccccccccccccc-------CCchH
Confidence 0 0000 00111123999999999999999999999875441 111111113 45778
Q ss_pred HHHHHHHHHHHHHHhhhc
Q 027072 210 VSQMRKEILQLIKGLMEK 227 (228)
Q Consensus 210 i~~~R~~i~~~i~~l~~~ 227 (228)
+.++|..+.+++..|.+.
T Consensus 573 ~~~~r~~~r~~~~~l~~~ 590 (595)
T KOG0779|consen 573 ILKFRDEIRNLGRKLFTS 590 (595)
T ss_pred Hhhhhhhhhccccccccc
Confidence 899999999999998765
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=97.87 E-value=4.6e-05 Score=66.13 Aligned_cols=95 Identities=18% Similarity=0.225 Sum_probs=64.3
Q ss_pred CCCCCcEEEEeeecCCCcCcCCCCceeEEEEEEcCCCeEEEEeCCCCCCHH---------------------H------H
Q 027072 81 KLPEKKLVIFPVNDNDDMSLAEGGSHWSLIVYERNGNVFVHHDSNHRMNKI---------------------K------A 133 (228)
Q Consensus 81 ~~~~~~~I~iPin~n~~~~~~~~~~HW~Llvv~~~~~~i~~~DSl~~~~~~---------------------~------~ 133 (228)
.-.+++++.+|++- .+||..+|+|.+++.+.+|||-|..... . .
T Consensus 227 k~~~~RyvmFgfcY---------~~Hwkc~IfDk~~~~v~FydSgG~~P~efhhy~nfyFysfs~gfn~n~~~~s~l~n~ 297 (423)
T PF03290_consen 227 KNSKKRYVMFGFCY---------MSHWKCCIFDKEKKIVYFYDSGGNIPEEFHHYKNFYFYSFSDGFNRNNKSTSNLDNE 297 (423)
T ss_pred hhccccEEEeeeee---------hhcceEEEEeccccEEEEEcCCCCCHHHcCcCCceEEEEccCccccCCCcccccccc
Confidence 34778999999998 6999999999999999999999863110 0 0
Q ss_pred HHHHHHHHHhhcCcCCCCCCeeecCCCCCCCCCCCccHHHHHHHHHHHHHHhhc
Q 027072 134 RKLFSAVVGFMGDSTSASNGKYLDCVDSPQQTNGYDCGVYVIAIARAICCWYES 187 (228)
Q Consensus 134 ~~i~~~l~~~l~~~~~~~~~~~v~~~~~pqQ~n~~DCGvfvl~~~~~l~~~~~~ 187 (228)
..=++.|.+++.... +.+.--...--.|-...+||+|++.||.......+.
T Consensus 298 n~dIDVLfrfF~d~f---~~~~gciNvevnQl~eseCGMF~~iFm~~c~~~ppk 348 (423)
T PF03290_consen 298 NCDIDVLFRFFEDSF---GVKYGCINVEVNQLLESECGMFISIFMILCTLTPPK 348 (423)
T ss_pred cCchHHHHHHHHhhc---ccceeEEEhhhhhhcccccchHHHHHHHHHHccCch
Confidence 011234444444321 112211112367999999999999999887775554
No 8
>PRK11836 deubiquitinase; Provisional
Probab=97.87 E-value=0.00029 Score=59.22 Aligned_cols=143 Identities=20% Similarity=0.277 Sum_probs=85.5
Q ss_pred CCCccChHHHHHHHHHHhhhcc----CCCeeeeChhhhHHHhcCCChHHHHHhhccCCCCCCcEEEEeeecCCCcCcCCC
Q 027072 28 GPYFLNDRIIEFYFSYLSSCLV----SQDILLVPPSIAFWILNCPDATYLKEFIEPLKLPEKKLVIFPVNDNDDMSLAEG 103 (228)
Q Consensus 28 ~~~wLnD~iI~~~~~~L~~~~~----~~~i~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~iPin~n~~~~~~~~ 103 (228)
+.+.|+..=|+.|..-+....+ +.-+.++.|.+. ..+++ ..+..-++.-+.+-++.-+||||.
T Consensus 162 ~nRmltsDEia~~~q~~~~~~~n~~VNyPiGLi~P~t~--~~~L~--~~L~E~i~~~~~~~k~~elFpINt--------- 228 (403)
T PRK11836 162 KNRQLTTDEIACYLQKIAANAKNTQVNYPTGLYVPYST--RTHLE--DALNENIKSDPSWPKEVQLFPINT--------- 228 (403)
T ss_pred ccccccHHHHHHHhcccccCCccceecCCceeeecCcc--cchhH--HHHHHhhhcCCCCcccceEEEecC---------
Confidence 4566777778887766665443 223445555421 11121 233333444467788899999996
Q ss_pred CceeEEEEEEc--------CCCeEEEEeCCCCC--CH-HHHHHHHHHHHH-hhcCcC--------CCCCCeeecCCCCCC
Q 027072 104 GSHWSLIVYER--------NGNVFVHHDSNHRM--NK-IKARKLFSAVVG-FMGDST--------SASNGKYLDCVDSPQ 163 (228)
Q Consensus 104 ~~HW~Llvv~~--------~~~~i~~~DSl~~~--~~-~~~~~i~~~l~~-~l~~~~--------~~~~~~~v~~~~~pq 163 (228)
|+||.|+++.. +..+..+|.|+..- +. ...+.+.+.+.. ++|+-. ...+..|++ .+ -|
T Consensus 229 g~HWil~~l~Ki~~~~~~~ekiKC~IFNs~~~l~~d~~~t~q~ii~a~~~~~~~~~~~~~ik~~~~e~ei~fie-~d-LQ 306 (403)
T PRK11836 229 GGHWILVSLQKIVNEKNNTQQIKCVIFNSLRALGHDKENSLKRVINSFNSELMGEMSNNNIKVHLTEPEIIFLH-AD-LQ 306 (403)
T ss_pred CCcEEEEEeHHhhhcccccceeEEEEEecHhhhccchhhHHHHHHHhhhhhhhhhcchhhhcccccCCceEEEe-ch-hh
Confidence 89999999864 24578889998753 21 234455554432 333211 123455554 33 45
Q ss_pred CCCCCccHHHHHHHHHHHHHHh
Q 027072 164 QTNGYDCGVYVIAIARAICCWY 185 (228)
Q Consensus 164 Q~n~~DCGvfvl~~~~~l~~~~ 185 (228)
|.=...||.|||+.+..++.+.
T Consensus 307 q~vpngCGlFv~~a~Qe~i~q~ 328 (403)
T PRK11836 307 QYLSQSCGAFVCMAAQEVIEQR 328 (403)
T ss_pred hcCCCccceehHHHHHHHHHHh
Confidence 5556789999999999777754
No 9
>PRK14848 deubiquitinase SseL; Provisional
Probab=97.83 E-value=0.00021 Score=58.87 Aligned_cols=138 Identities=17% Similarity=0.212 Sum_probs=79.0
Q ss_pred CCCccChHHHHHHHHHHhhhcc----CCCeeeeChhhhHHHhcCCChHHHHHhhccCCCCCCcEEEEeeecCCCcCcCCC
Q 027072 28 GPYFLNDRIIEFYFSYLSSCLV----SQDILLVPPSIAFWILNCPDATYLKEFIEPLKLPEKKLVIFPVNDNDDMSLAEG 103 (228)
Q Consensus 28 ~~~wLnD~iI~~~~~~L~~~~~----~~~i~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~iPin~n~~~~~~~~ 103 (228)
+.+.|+..=|+.+..-+....+ +.-+.++.|.+. ..+++ ..+..-++. -+.+..-+||||.
T Consensus 133 ~~Rmlt~DEi~~~~q~~~~~~~~~~VNyP~GL~~P~s~--~~~L~--~~L~E~i~~--s~~~~nevF~INt--------- 197 (317)
T PRK14848 133 GARMLSSDELAAATQGLVQESPLLSVNYPIGLIHPTTK--ENILS--TQLLEKIAQ--SGLSHNEVFLINT--------- 197 (317)
T ss_pred ccccccHHHHHHHhhccccCCccceecCCceeeecCcc--chhHH--HHHHhhhhh--cCCCcceEEEecC---------
Confidence 4577888888888776665443 223445555421 11121 122111221 1233344699996
Q ss_pred CceeEEEEEEc--CCCeEEEEeCCCCCCHHHHHHHHHHHHHhhcCcCCCCCCeeecCCCCCCCCCCCccHHHHHHHHHHH
Q 027072 104 GSHWSLIVYER--NGNVFVHHDSNHRMNKIKARKLFSAVVGFMGDSTSASNGKYLDCVDSPQQTNGYDCGVYVIAIARAI 181 (228)
Q Consensus 104 ~~HW~Llvv~~--~~~~i~~~DSl~~~~~~~~~~i~~~l~~~l~~~~~~~~~~~v~~~~~pqQ~n~~DCGvfvl~~~~~l 181 (228)
|+||.|+++.. ...+..+|.|+..-+....+.+.+. ....+.. ...+..|++ .+ -||.=...||.|||.+++.+
T Consensus 198 g~HWil~~~~Ki~~kiKC~iFNs~~~l~eNs~~~ii~~-ak~ag~~-~e~di~fIe-~n-LQqnVpngCGlFv~~aIq~l 273 (317)
T PRK14848 198 GDHWLLCLFYKLAEKIKCLIFNTYYDLNENTKQEIIEA-AKIAGIS-ENEDVNFIE-TN-LQNNVPNGCGLFCYHTIQLL 273 (317)
T ss_pred CCcEEEEEhHHhhhhceEEEeecHhhhhhhHHHHHHHH-HHhhCcc-cCCceEEee-hh-hhhhCCCcchHHHHHHHHHH
Confidence 89999999875 3457888999976544334555443 1222321 124556654 33 34444678999999999966
Q ss_pred HHH
Q 027072 182 CCW 184 (228)
Q Consensus 182 ~~~ 184 (228)
-..
T Consensus 274 ~~~ 276 (317)
T PRK14848 274 SNA 276 (317)
T ss_pred Hhc
Confidence 553
No 10
>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=97.01 E-value=0.0019 Score=50.41 Aligned_cols=94 Identities=14% Similarity=0.270 Sum_probs=48.4
Q ss_pred EEeeecCCCcCcCCCCceeEEEEEEcCCCeEEEEeCCCCCCHHHHHHHHH-----HHHH-hhcCcCCCCCCeeecCCCCC
Q 027072 89 IFPVNDNDDMSLAEGGSHWSLIVYERNGNVFVHHDSNHRMNKIKARKLFS-----AVVG-FMGDSTSASNGKYLDCVDSP 162 (228)
Q Consensus 89 ~iPin~n~~~~~~~~~~HW~Llvv~~~~~~i~~~DSl~~~~~~~~~~i~~-----~l~~-~l~~~~~~~~~~~v~~~~~p 162 (228)
--.||.. ....||.||.-+..++..++++.||+.+=++.+ ++++-+ .|++ .+.. ...+=.+.+.-...-
T Consensus 21 cAIVNT~---~retGGvHWlA~Aw~P~s~t~YmFDPfGfsd~~-L~qiY~FeYe~llrRSAL~~-~~dRCv~LvkstqtV 95 (183)
T PF00770_consen 21 CAIVNTG---GRETGGVHWLAFAWDPRSRTFYMFDPFGFSDQK-LKQIYQFEYEGLLRRSALSS-TPDRCVTLVKSTQTV 95 (183)
T ss_dssp EEEEESS----TTT--S-EEEEEEETTTTEEEEE-TT---HHH-HHHHH----HHHHHHHHHHH--TTSEEEEEEE-EE-
T ss_pred eEEEecC---CcccCceeEEEEEecCCcceEEEeCCCCCCHHH-HHHHHhhhHHHHHHHHhhcC-CCCceEEEEecccee
Confidence 3346652 223479999999999999999999999865432 222221 1211 1220 011223333323445
Q ss_pred CCCCCCccHHHHHHHHHHHHHHhhc
Q 027072 163 QQTNGYDCGVYVIAIARAICCWYES 187 (228)
Q Consensus 163 qQ~n~~DCGvfvl~~~~~l~~~~~~ 187 (228)
|=+++-.||+|.|+|+.++.++..+
T Consensus 96 Q~p~SaaCGLFC~lFL~aF~~~p~~ 120 (183)
T PF00770_consen 96 QCPCSAACGLFCCLFLHAFVHYPDN 120 (183)
T ss_dssp S-TT---HHHHHHHHHHHHHH-TTS
T ss_pred eccCchhHHHHHHHHHHHHHhCCCC
Confidence 5568999999999999999998755
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=94.78 E-value=1.7 Score=34.65 Aligned_cols=87 Identities=11% Similarity=0.156 Sum_probs=51.1
Q ss_pred cEEEEeeecCCCcCcCCCCceeEEEEEE-cC--CCeEEEEeCCCCCCHHH-HHHHHHHHHHhhcCcCCCCCCeeecCCCC
Q 027072 86 KLVIFPVNDNDDMSLAEGGSHWSLIVYE-RN--GNVFVHHDSNHRMNKIK-ARKLFSAVVGFMGDSTSASNGKYLDCVDS 161 (228)
Q Consensus 86 ~~I~iPin~n~~~~~~~~~~HW~Llvv~-~~--~~~i~~~DSl~~~~~~~-~~~i~~~l~~~l~~~~~~~~~~~v~~~~~ 161 (228)
-..++|+.. ++.|...+=|. .. ...++.++|-.-.+... .....+.+....... .....+ .+...
T Consensus 72 ~R~Iv~~~~--------~~~H~~a~Dvr~~~~~k~SlI~~Epa~~~~~~~~l~~~~~~~~~~~~~~--~~~~~~-~~ie~ 140 (177)
T PF03421_consen 72 WRAIVNLGG--------DGIHHVALDVRHTPNGKPSLIVFEPASFYGMKPALAGYTKLAEEARQKL--LPNAKF-AVIEM 140 (177)
T ss_pred eEEEEeCCC--------CCCcEEEEEEeecCCCCceEEEEccccccCCcchhhhHHHHHHHHHhcc--CCCcEE-EEEec
Confidence 345666554 36676654444 22 35799999986433211 111112222222100 134554 34678
Q ss_pred CCCCCCCccHHHHHHHHHHHHH
Q 027072 162 PQQTNGYDCGVYVIAIARAICC 183 (228)
Q Consensus 162 pqQ~n~~DCGvfvl~~~~~l~~ 183 (228)
.-|+..+|||+|.|.+|....+
T Consensus 141 diQkS~~dC~IFsLs~AkK~~~ 162 (177)
T PF03421_consen 141 DIQKSPSDCGIFSLSLAKKMYK 162 (177)
T ss_pred ccccCcCcchhhHHHHHHHHhh
Confidence 9999999999999999998876
No 12
>PRK15371 effector protein YopJ; Provisional
Probab=92.45 E-value=6.3 Score=33.80 Aligned_cols=79 Identities=16% Similarity=0.264 Sum_probs=45.7
Q ss_pred CceeEEEEEEcC--CCeEEEEeCCCCCCHHHHHHHHHHHHHhhcCcCCCCCCeeecCCCCCCCCCCCccHHHHHHHHHHH
Q 027072 104 GSHWSLIVYERN--GNVFVHHDSNHRMNKIKARKLFSAVVGFMGDSTSASNGKYLDCVDSPQQTNGYDCGVYVIAIARAI 181 (228)
Q Consensus 104 ~~HW~Llvv~~~--~~~i~~~DSl~~~~~~~~~~i~~~l~~~l~~~~~~~~~~~v~~~~~pqQ~n~~DCGvfvl~~~~~l 181 (228)
+.|...+=+... ...|+.++|-...+...+ .+.-.++..+... ......+ .+...--|+-.+|||+|.|.+|...
T Consensus 107 ~~H~vavDvr~~~Gk~SIIvlEPa~~~~~~~a-~l~~rl~~~le~~-~l~~~~~-avie~d~QkS~~dC~mFSL~~AkK~ 183 (287)
T PRK15371 107 GIHFSVIDYKHIDGKTSLILFEPANFNSMGPA-MLAIRTKTALERE-QLPDCHF-SMVEMDIQRSSSECGIFSLALAKKL 183 (287)
T ss_pred cceEEEEEEeccCCCeEEEEECCccccccchH-HHHHHHHHHHHhc-cCCCceE-EEEecccccCcccchhhhHHHHHHH
Confidence 567655544443 347999999865321110 0111122222110 0134444 2355789999999999999999988
Q ss_pred HHHh
Q 027072 182 CCWY 185 (228)
Q Consensus 182 ~~~~ 185 (228)
.+.-
T Consensus 184 ~~e~ 187 (287)
T PRK15371 184 YLER 187 (287)
T ss_pred hhhh
Confidence 7753
No 13
>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=85.88 E-value=6.4 Score=39.45 Aligned_cols=77 Identities=16% Similarity=0.289 Sum_probs=44.2
Q ss_pred EEeeecCCCcCcCCCCceeEEEEEEcCCCeEEEEeCCCCCCHHHHHHHHHHHHHhhcCcCCCCCCeeecCCCCCCCCCCC
Q 027072 89 IFPVNDNDDMSLAEGGSHWSLIVYERNGNVFVHHDSNHRMNKIKARKLFSAVVGFMGDSTSASNGKYLDCVDSPQQTNGY 168 (228)
Q Consensus 89 ~iPin~n~~~~~~~~~~HW~Llvv~~~~~~i~~~DSl~~~~~~~~~~i~~~l~~~l~~~~~~~~~~~v~~~~~pqQ~n~~ 168 (228)
|+||-..-++ .....||..++ ..+.+..++||+|+....+..+.+ +..-+.. ....+. .+-----|-.
T Consensus 49 fmpvltgv~p--~~~sghwimli-kg~gn~y~lfdplg~~sg~~y~ni---l~~~lp~---~~~lsv---ipn~~~ln~g 116 (1439)
T PF12252_consen 49 FMPVLTGVSP--RQDSGHWIMLI-KGQGNQYYLFDPLGKTSGEGYQNI---LARQLPQ---GSTLSV---IPNGPGLNMG 116 (1439)
T ss_pred CceeecCcCC--CCcCceeEEEE-EcCCCceEEeccccccccccHHHH---HHHhCCC---CCeeee---CCCCCCcCcc
Confidence 7888764222 22578998765 566778999999997654333333 2222331 122222 2122233556
Q ss_pred ccHHHHHHH
Q 027072 169 DCGVYVIAI 177 (228)
Q Consensus 169 DCGvfvl~~ 177 (228)
-||+||--.
T Consensus 117 lcgywvas~ 125 (1439)
T PF12252_consen 117 LCGYWVASV 125 (1439)
T ss_pred chhhhhhhh
Confidence 799999754
No 14
>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=42.06 E-value=17 Score=26.55 Aligned_cols=24 Identities=21% Similarity=0.369 Sum_probs=14.8
Q ss_pred CCCCCCCCCccHHHHHHHHHHHHH
Q 027072 160 DSPQQTNGYDCGVYVIAIARAICC 183 (228)
Q Consensus 160 ~~pqQ~n~~DCGvfvl~~~~~l~~ 183 (228)
++-.|.+..|||+-.++++-....
T Consensus 3 ~~v~Q~~~~dcg~acl~~l~~~~g 26 (131)
T PF03412_consen 3 PVVKQSDSNDCGLACLAMLLKYYG 26 (131)
T ss_dssp -----SSTT-HHHHHHHHHHHHTT
T ss_pred CeEEeCCCCCHHHHHHHHHHHHhC
Confidence 456799999999999988766543
No 15
>KOG3315 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=37.80 E-value=34 Score=27.05 Aligned_cols=27 Identities=19% Similarity=0.442 Sum_probs=24.4
Q ss_pred CCCCCCCCCCCccHHHHHHHHHHHHHH
Q 027072 158 CVDSPQQTNGYDCGVYVIAIARAICCW 184 (228)
Q Consensus 158 ~~~~pqQ~n~~DCGvfvl~~~~~l~~~ 184 (228)
...+|.-.|+.+|+.||+-+++.++.+
T Consensus 130 fISVPke~~~lnc~~fvaGIiea~L~~ 156 (191)
T KOG3315|consen 130 FISVPKENGTLNCAAFVAGIIEAVLDN 156 (191)
T ss_pred ceecccccCcccHHHHHHHHHHHHHHh
Confidence 356899999999999999999999885
No 16
>PF13529 Peptidase_C39_2: Peptidase_C39 like family; PDB: 3ERV_A.
Probab=27.77 E-value=57 Score=23.50 Aligned_cols=21 Identities=29% Similarity=0.681 Sum_probs=14.0
Q ss_pred CCceeEEEE-EEcCCCeEEEEeC
Q 027072 103 GGSHWSLIV-YERNGNVFVHHDS 124 (228)
Q Consensus 103 ~~~HW~Llv-v~~~~~~i~~~DS 124 (228)
.+.||.+++ ++... .+++.||
T Consensus 122 ~~~H~vvi~Gy~~~~-~~~v~DP 143 (144)
T PF13529_consen 122 YGGHYVVIIGYDEDG-YVYVNDP 143 (144)
T ss_dssp TTEEEEEEEEE-SSE--EEEE-T
T ss_pred cCCEEEEEEEEeCCC-EEEEeCC
Confidence 589999988 44443 7999997
No 17
>KOG4110 consensus NADH:ubiquinone oxidoreductase, NDUFS5/15kDa [Energy production and conversion]
Probab=27.37 E-value=65 Score=23.42 Aligned_cols=72 Identities=22% Similarity=0.213 Sum_probs=40.3
Q ss_pred CCeeecCCCCCCCCCCCccHHHHHHHHHHHHHH-hhcccC-cccccchhhh-hccccChHHHHHHHHHHHHHHHH
Q 027072 152 NGKYLDCVDSPQQTNGYDCGVYVIAIARAICCW-YESSEH-KDAEGMWFSF-VKEQVTSTVVSQMRKEILQLIKG 223 (228)
Q Consensus 152 ~~~~v~~~~~pqQ~n~~DCGvfvl~~~~~l~~~-~~~~~~-~~~~~~~~~~-~~~~~~~~~i~~~R~~i~~~i~~ 223 (228)
.|..+....+|--.-+.|||.|-..+++|.-.+ ...++. +-..-+.|.. +.-+-.-.-..++|++-.++|.+
T Consensus 18 r~p~tds~~~p~~~q~r~cg~FE~e~~eC~eayG~~~g~keC~ie~~dFqECv~~qKqmrra~aiR~qr~Kl~le 92 (120)
T KOG4110|consen 18 RWPTTDSTEQPYKHQGRDCGKFEKEWMECAEAYGLERGEKECAIEYDDFQECVLMQKQMRRAHAIRKQRYKLILE 92 (120)
T ss_pred hccccccccCccccccccccHHHHHHHHHHHHHhhHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 455555566777777899999999999988543 322221 1100111221 11111223345788888888764
No 18
>COG3840 ThiQ ABC-type thiamine transport system, ATPase component [Coenzyme metabolism]
Probab=26.71 E-value=73 Score=25.97 Aligned_cols=42 Identities=19% Similarity=0.309 Sum_probs=27.9
Q ss_pred HHHHHHHHHHhhcccCcccccchhhhhccccChHHHHHHHHHHHHHHHHhhhcC
Q 027072 175 IAIARAICCWYESSEHKDAEGMWFSFVKEQVTSTVVSQMRKEILQLIKGLMEKK 228 (228)
Q Consensus 175 l~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~R~~i~~~i~~l~~~~ 228 (228)
.+.|+|+.+..+- ...|..++...| .+|.+++.++.+|+.|+
T Consensus 138 vALARclvR~~Pi--------lLLDEPFsALdP----~LR~eMl~Lv~~l~~E~ 179 (231)
T COG3840 138 VALARCLVREQPI--------LLLDEPFSALDP----ALRAEMLALVSQLCDER 179 (231)
T ss_pred HHHHHHHhccCCe--------EEecCchhhcCH----HHHHHHHHHHHHHHHhh
Confidence 5678888884221 113333445554 78999999999998874
No 19
>cd00542 Ntn_PVA Penicillin V acylase (PVA), also known as conjugated bile salt acid hydrolase (CBAH), catalyzes the hydrolysis of penicillin V to yield 6-amino penicillanic acid (6-APA), an important key intermediate of semisynthetic penicillins. PVA has an N-terminal nucleophilic cysteine, as do other members of the Ntn hydrolase family to which PVA belongs. This nucleophilic cysteine is exposed by post-translational prossessing of the PVA precursor. PVA forms a homotetramer.
Probab=25.90 E-value=1.2e+02 Score=26.07 Aligned_cols=55 Identities=16% Similarity=0.242 Sum_probs=34.8
Q ss_pred hHHHhcCCChHHHHHhhccCCCCCCcEEEEeeecCCCcCcCCCCceeEE-------EEEEcCCCeEEEEeC
Q 027072 61 AFWILNCPDATYLKEFIEPLKLPEKKLVIFPVNDNDDMSLAEGGSHWSL-------IVYERNGNVFVHHDS 124 (228)
Q Consensus 61 ~~~~~~~~~~~~~~~~~~~~~~~~~~~I~iPin~n~~~~~~~~~~HW~L-------lvv~~~~~~i~~~DS 124 (228)
.+.+.++.+-+++.+.++++.+.....-..|.. ..-||.+ +||.+.++.+.+||.
T Consensus 106 ~~iL~n~~TV~Ev~~~l~~i~i~~~~~~~~~~~---------~~lH~~i~D~sG~s~VIE~~~g~l~i~~n 167 (303)
T cd00542 106 TWVLGNFASVEEVKEALKNINVVDDPINLLGPV---------PPLHWIISDKSGRSIVVEPTKGGLKVYDN 167 (303)
T ss_pred HHHHHcCCCHHHHHHHhcCceEEcccccCCCCC---------cceEEEEEcCCCCEEEEEEeCCeeEEEeC
Confidence 455667777788877777654332221111122 2579986 788888888888886
No 20
>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=24.87 E-value=55 Score=23.83 Aligned_cols=20 Identities=35% Similarity=0.474 Sum_probs=15.2
Q ss_pred CCCCCCCccHHHHHHHHHHH
Q 027072 162 PQQTNGYDCGVYVIAIARAI 181 (228)
Q Consensus 162 pqQ~n~~DCGvfvl~~~~~l 181 (228)
-.|.+..|||+..+.++-..
T Consensus 4 ~~q~~~~dcgla~l~~i~~~ 23 (129)
T cd02424 4 IKQTDLNDCGIAVIQMLYNH 23 (129)
T ss_pred EEecCccchHHHHHHHHHHH
Confidence 35667789999988876654
No 21
>COG1551 CsrA RNA-binding global regulator CsrA [Signal transduction mechanisms]
Probab=24.76 E-value=75 Score=21.28 Aligned_cols=20 Identities=35% Similarity=0.250 Sum_probs=16.7
Q ss_pred hHHHHHHHHHHHHHHHHhhh
Q 027072 207 STVVSQMRKEILQLIKGLME 226 (228)
Q Consensus 207 ~~~i~~~R~~i~~~i~~l~~ 226 (228)
|+.++=+|++|++.|.+=..
T Consensus 37 Pk~v~I~R~Eiy~~Iq~En~ 56 (73)
T COG1551 37 PKEVSIHREEIYQRIQEENS 56 (73)
T ss_pred ChhhhHHHHHHHHHHHHhhh
Confidence 78889999999999986443
No 22
>PF03206 NifW: Nitrogen fixation protein NifW; InterPro: IPR004893 Nitrogenase is a complex metalloenzyme composed of two proteins designated the Fe-protein and the MoFe-protein. Apart from these two proteins, a number of accessory proteins are essential for the maturation and assembly of nitrogenase. Even though experimental evidence suggests that these accessory proteins are required for nitrogenase activity, the exact roles played by many of these proteins in the functions of nitrogenase are unclear []. Using yeast two-hybrid screening it has been shown that NifW can interact with itself as well as NifZ. ; GO: 0009399 nitrogen fixation
Probab=23.25 E-value=93 Score=22.52 Aligned_cols=31 Identities=23% Similarity=0.288 Sum_probs=26.0
Q ss_pred cchhhhhccccChHHHHHHHHHHHHHHHHhh
Q 027072 195 GMWFSFVKEQVTSTVVSQMRKEILQLIKGLM 225 (228)
Q Consensus 195 ~~~~~~~~~~~~~~~i~~~R~~i~~~i~~l~ 225 (228)
|++|+.+.-.+.|..+.--|.+|++.+.+..
T Consensus 15 EdFf~fF~V~YDp~vv~V~RLHILkrF~~yL 45 (105)
T PF03206_consen 15 EDFFDFFGVPYDPKVVNVNRLHILKRFGQYL 45 (105)
T ss_pred HHHHHHhCCCcchhHHHHhhHHHHHHHHHHH
Confidence 5677777778899999999999999887754
No 23
>PHA02130 hypothetical protein
Probab=23.07 E-value=43 Score=21.97 Aligned_cols=37 Identities=16% Similarity=0.432 Sum_probs=28.2
Q ss_pred hHHHHHhhc-cCCCCCCcEEEEeeecCCCcCcCCCCceeEEEEEEcC
Q 027072 70 ATYLKEFIE-PLKLPEKKLVIFPVNDNDDMSLAEGGSHWSLIVYERN 115 (228)
Q Consensus 70 ~~~~~~~~~-~~~~~~~~~I~iPin~n~~~~~~~~~~HW~Llvv~~~ 115 (228)
-++++.|+. +.+-++.+++=||.-. ..||.|+.++-.
T Consensus 16 ~~sl~~wl~~~~dswdddil~ipfks---------tv~w~lcp~~qd 53 (81)
T PHA02130 16 WESLREWLDERFDSWDDDILSIPFKS---------TVYWDLCPYAQD 53 (81)
T ss_pred HHHHHHHHHhcccccccchhcccccc---------eeeeccCcchhh
Confidence 467788874 3466778888899985 799999887653
No 24
>PF15644 Tox-PL: Papain fold toxin 1; PDB: 3B21_A.
Probab=20.91 E-value=1.6e+02 Score=21.07 Aligned_cols=22 Identities=18% Similarity=0.141 Sum_probs=16.5
Q ss_pred ceeEEEEEEcCCCeEEEEeCCCCC
Q 027072 105 SHWSLIVYERNGNVFVHHDSNHRM 128 (228)
Q Consensus 105 ~HW~Llvv~~~~~~i~~~DSl~~~ 128 (228)
.|+..++ .+++.|.++|...+.
T Consensus 88 gHa~nvv--~~~G~i~~~D~Q~G~ 109 (111)
T PF15644_consen 88 GHAFNVV--NQNGKIVFLDPQSGK 109 (111)
T ss_dssp TTEEEEE--EE-SSEEEEBTTTTB
T ss_pred ceEEEEE--eCCCeEEEEeCCCCC
Confidence 8988888 555569999987653
No 25
>PRK00810 nifW nitrogenase stabilizing/protective protein; Provisional
Probab=20.81 E-value=1.1e+02 Score=22.53 Aligned_cols=30 Identities=20% Similarity=0.270 Sum_probs=25.7
Q ss_pred cchhhhhccccChHHHHHHHHHHHHHHHHh
Q 027072 195 GMWFSFVKEQVTSTVVSQMRKEILQLIKGL 224 (228)
Q Consensus 195 ~~~~~~~~~~~~~~~i~~~R~~i~~~i~~l 224 (228)
|++|+.+.-.+.|..+.--|.+|++.+.+.
T Consensus 19 Edff~ff~V~YDp~vvnV~RLHILKrF~~y 48 (113)
T PRK00810 19 EEFFQLLGVPYDPKVVNVARLHILKRMGQY 48 (113)
T ss_pred HHHHHHhCCCCCHHHHHHhHHHHHHHHHHH
Confidence 567777778899999999999999988765
No 26
>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=20.34 E-value=89 Score=22.33 Aligned_cols=22 Identities=18% Similarity=0.302 Sum_probs=15.8
Q ss_pred CCCCCCCccHHHHHHHHHHHHH
Q 027072 162 PQQTNGYDCGVYVIAIARAICC 183 (228)
Q Consensus 162 pqQ~n~~DCGvfvl~~~~~l~~ 183 (228)
-.|++..|||+..+.++-....
T Consensus 4 ~~q~~~~~~~l~~l~~~~~~~g 25 (129)
T cd02423 4 VRQSYDFSCGPAALATLLRYYG 25 (129)
T ss_pred eecCCCCChHHHHHHHHHHhcC
Confidence 3566777999998887655554
No 27
>COG0851 MinE Septum formation topological specificity factor [Cell division and chromosome partitioning]
Probab=20.04 E-value=1.2e+02 Score=21.16 Aligned_cols=21 Identities=33% Similarity=0.534 Sum_probs=17.6
Q ss_pred ccChHHHHHHHHHHHHHHHHh
Q 027072 204 QVTSTVVSQMRKEILQLIKGL 224 (228)
Q Consensus 204 ~~~~~~i~~~R~~i~~~i~~l 224 (228)
...|+++..+|++|+..|.+-
T Consensus 33 ~~~pd~l~~Lr~eIl~VI~KY 53 (88)
T COG0851 33 GLQPDYLEQLRKEILEVISKY 53 (88)
T ss_pred CCCcchHHHHHHHHHHHHHHH
Confidence 445889999999999999763
Done!