Query 020231
Match_columns 329
No_of_seqs 234 out of 1079
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 08:05:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020231.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020231hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2605 OTU (ovarian tumor)-li 100.0 6.8E-37 1.5E-41 300.4 10.2 320 2-329 1-366 (371)
2 PF02338 OTU: OTU-like cystein 99.9 1.1E-25 2.3E-30 185.9 8.9 107 192-304 1-121 (121)
3 KOG2606 OTU (ovarian tumor)-li 99.9 2.9E-24 6.3E-29 203.8 10.7 141 168-311 141-299 (302)
4 KOG3288 OTU-like cysteine prot 99.6 1.1E-15 2.4E-20 143.3 6.7 123 186-311 110-234 (307)
5 PF10275 Peptidase_C65: Peptid 99.5 2.1E-13 4.7E-18 126.9 12.0 95 214-309 140-244 (244)
6 KOG3991 Uncharacterized conser 99.4 7.9E-13 1.7E-17 122.6 8.6 95 213-310 156-256 (256)
7 COG5539 Predicted cysteine pro 98.7 6.9E-09 1.5E-13 99.4 1.4 122 182-307 167-304 (306)
8 COG5539 Predicted cysteine pro 98.5 3.8E-08 8.2E-13 94.4 2.0 110 193-308 119-230 (306)
9 PF05415 Peptidase_C36: Beet n 78.3 8.9 0.00019 31.8 6.4 64 191-272 3-68 (104)
10 PRK09784 hypothetical protein; 61.7 4.5 9.8E-05 39.3 1.6 24 181-204 195-218 (417)
11 PF05412 Peptidase_C33: Equine 54.5 8.5 0.00018 32.6 1.9 83 191-311 4-87 (108)
12 COG5007 Predicted transcriptio 45.2 20 0.00043 28.9 2.5 54 175-228 4-61 (80)
13 smart00718 DM4_12 DM4/DM12 fam 36.4 97 0.0021 25.2 5.4 72 173-256 9-81 (95)
14 TIGR01078 arcA arginine deimin 31.3 69 0.0015 32.7 4.5 73 162-246 34-106 (405)
15 PRK13381 peptidase T; Provisio 29.6 60 0.0013 32.1 3.7 52 145-196 4-56 (404)
16 PF05381 Peptidase_C21: Tymovi 28.7 2.8E+02 0.0062 23.4 7.0 89 195-306 3-94 (104)
17 KOG4634 Mitochondrial F1F0-ATP 27.2 56 0.0012 27.5 2.5 24 57-80 52-75 (105)
18 PRK01388 arginine deiminase; P 25.0 1E+02 0.0022 31.5 4.5 53 162-226 41-93 (406)
19 PHA03308 transcriptional regul 23.1 1.6E+02 0.0034 33.1 5.5 17 189-205 1320-1336(1463)
20 TIGR02934 nifT_nitrog probable 21.7 12 0.00026 29.2 -2.2 34 225-258 6-41 (67)
21 KOG2605 OTU (ovarian tumor)-li 21.3 18 0.00039 36.7 -1.7 92 181-272 50-141 (371)
No 1
>KOG2605 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=6.8e-37 Score=300.42 Aligned_cols=320 Identities=32% Similarity=0.414 Sum_probs=253.6
Q ss_pred ccccCCCCceeecccccCCCCCCC----CCCCCCcccccCCCCcc-ccccccCCCccccccCCccchHHHHHHHHHHHHH
Q 020231 2 ATEDQDSGFVQWGLRFFDYDPYLH----SGYHDDIIQHDGNDIYH-GRSFRNNDDDDAESSNNVESDEIIARTLQEEFSQ 76 (329)
Q Consensus 2 ~~~~~~~~~~~w~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~d~~~~~~~q~~~~~ 76 (329)
+.++++|++++|.|+.+..+..+. .|-++.+.|.... +|. .++.+..|+. .+...|.+|++||+++|++++.
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~s~~~r~~~~-~~~~~g~~~~~~~~--~r~~~v~~~~~~~~~~~d~~~~ 77 (371)
T KOG2605|consen 1 TFREEVSGDFDWYLWDLGKTKTLGTILELGAMSHVYRRNVI-DYEPFGMGTDGYNN--KRYGEVDRDFMIARGHQDEVLT 77 (371)
T ss_pred CCccccCchHHHHhhcCCCCcccccchhhhhccccccCCCC-CcCCccceeccccC--ccccchhhhhhhhccccccccc
Confidence 357899999999999887555444 5677777666533 444 5677777777 4688999999999999999999
Q ss_pred HHHHHhccCCcccccccccccccCCC-CCCCC-------------C-----------------CCC----CCCCCCCCCC
Q 020231 77 LAIEEASQYSHAQDEHTMLETSQDHD-WNSSS-------------T-----------------RNY----SSGPSSSCSS 121 (329)
Q Consensus 77 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~-------------~-----------------~~~----~~~~~~~~s~ 121 (329)
++.+|.+...+.-...+ ..++ |..++ . +.+ ...+..+-++
T Consensus 78 ~e~~e~~~~~~~v~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~a~s~~~~~~~~~~~~~~~~~~~~~ 152 (371)
T KOG2605|consen 78 VEDAEMAAICQSVLFKV-----LYQERFKLPSDTPCNGENSPMCSFHSRRGNESFQAASFGGLEIDLEVERNSPEWLGQS 152 (371)
T ss_pred ccHHHHhhHHhhhhhhh-----hhhhcccCCCCCcccccCCCCCcccccccccccccccccccccchhhhccCchhcccc
Confidence 99999998865332211 2222 11111 0 000 0112222223
Q ss_pred CCCCCCCccchhccc-ccccchHHhhhhhccccccCCCCCCCCCCCCcccchHHHHHHHHHHhCCcEEEEecCCCChHHH
Q 020231 122 PGDGEEDPYSLEITD-ECLLDDEVGKRLNQMVAIRHVPRINGEIPSVDEATSDHERLLNRLQLYGFVEHKVQGDGNCQFR 200 (329)
Q Consensus 122 ~~~~~~~~~~~~~~~-~~~~~~~~~krl~~~~p~p~~p~~ng~iPs~dea~~d~~rL~~~L~~~GL~v~~V~GDGNCLFR 200 (329)
+++......+.+... ....+.++|.+++++.|++.+|.+++.+|+..+..++++++.+++..+|+.+++|.+||||+||
T Consensus 153 ~sd~~~~~~~~~~~~~~~~~~~~~g~~in~y~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~g~e~~Kv~edGsC~fr 232 (371)
T KOG2605|consen 153 PSDPLRSVPSMEAIHARHPEAKEVGVRINDYNPKVLVPFINGLPPSEEEPQSAHERSAKRKKHFGFEYKKVVEDGSCLFR 232 (371)
T ss_pred ccccccccccccchhhccccchhhcccccCCCccccccccccCCCchHHHHHHHHHHHHHHHHhhhhhhhcccCCchhhh
Confidence 333333333332222 1256789999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhHhcCCccHHHHHHHHHHHHhcCcccccccccccHHHHHHhhcCCCCCCchHHHHHHHH--hhCCcEEEEEcCCCc
Q 020231 201 ALSDQLYHTPEHHKSVRQQIVTQLKSHPEMYEGYVPMEYSEYLKKMSMSGEWGDHVTLQAAAD--LFHVKIVVITSFKDT 278 (329)
Q Consensus 201 ALS~qL~g~~~~H~~VR~~vV~yL~~n~d~f~~fv~~~~~eYl~~Msk~g~WGg~iELqAlA~--~y~v~I~V~ss~~~~ 278 (329)
|+|+|+|++.+.|.++|++++++++++++.|+.|+++++.+|+++|++++.||+|+|+||+|. -+..++.++++.+.+
T Consensus 233 a~aDQvy~d~e~~~~~~~~~~dq~~~e~~~~~~~vt~~~~~y~k~kr~~~~~gnhie~Qa~a~~~~~~~~~~~~~~~~~t 312 (371)
T KOG2605|consen 233 ALADQVYGDDEQHDHNRRECVDQLKKERDFYEDYVTEDFTSYIKRKRADGEPGNHIEQQAAADIYEEIEKPLNITSFKDT 312 (371)
T ss_pred ccHHHhhcCHHHHHHHHHHHHHHHhhcccccccccccchhhcccccccCCCCcchHHHhhhhhhhhhccccceeeccccc
Confidence 999999999999999999999999999999999999999999999999999999999999998 677888888899999
Q ss_pred eEEEEcCCCCCCCCeEEEEecCCCcccccccC--C-CCCCccccccccccccCC
Q 020231 279 CYIEILPNVEKIKRAICLSFWAEVHYNSIFSQ--D-DRPLGESKRKKKWWNFGN 329 (329)
Q Consensus 279 ~~i~i~P~~~~~~~~I~Lsy~~g~HYdSV~~~--~-d~~~~~~~~~~~~~~~~~ 329 (329)
+++.+.|........+++.||...||+.++.. . +......++||+||+||+
T Consensus 313 ~~~~~~~~~~~~~~~~~~n~~~~~h~~~~~~~~~~~~s~~~~~~~~r~~~~~~~ 366 (371)
T KOG2605|consen 313 CYIQTPPAIEESVKMEKYNFWVEVHYNTARHSGKSADSATLEEKTKRKSLRRGT 366 (371)
T ss_pred ceeccCcccccchhhhhhcccchhhhhhcccccccccccchhhccCCCchhhcc
Confidence 99988887777788899999999999999984 3 332344578899999985
No 2
>PF02338 OTU: OTU-like cysteine protease; InterPro: IPR003323 This is a group of proteins found primarily in viruses, eukaryotes and in the pathogenic bacterium Chlamydia pneumoniae. In viruses they are annotated as replicase or RNA-dependent RNA polymerase. The eukaryotic sequences are related to the Ovarian Tumour (OTU) gene in Drosophila, cezanne deubiquitinating peptidase and tumor necrosis factor, alpha-induced protein 3 (MEROPS peptidase family C64) and otubain 1 and otubain 2 (MEROPS peptidase family C65). None of these proteins has a known biochemical function but low sequence similarity with the polyprotein regions of arteriviruses, and conserved cysteine and histidine, and possibly the aspartate, residues suggests that those not yet recognised as peptidases could possess cysteine protease activity [].; PDB: 2VFJ_C 3DKB_F 3PHW_A 3PHU_B 3PHX_A 3BY4_A 3C0R_C 3PRM_C 3PRP_C 3ZRH_A ....
Probab=99.92 E-value=1.1e-25 Score=185.91 Aligned_cols=107 Identities=35% Similarity=0.669 Sum_probs=93.0
Q ss_pred cCCCChHHHHHHHhHh----cCCccHHHHHHHHHHHHh-cCcccccccccccHHHHHHhhcCCCCCCchHHHHHHHHhhC
Q 020231 192 QGDGNCQFRALSDQLY----HTPEHHKSVRQQIVTQLK-SHPEMYEGYVPMEYSEYLKKMSMSGEWGDHVTLQAAADLFH 266 (329)
Q Consensus 192 ~GDGNCLFRALS~qL~----g~~~~H~~VR~~vV~yL~-~n~d~f~~fv~~~~~eYl~~Msk~g~WGg~iELqAlA~~y~ 266 (329)
||||||||||||+||+ +++..|.+||+.|++||+ +|++.|..|+..+ +|+++|+|||++||+|+|++|+
T Consensus 1 pgDGnClF~Avs~~l~~~~~~~~~~~~~lR~~~~~~l~~~~~~~~~~~~~~~------~~~~~~~Wg~~~el~a~a~~~~ 74 (121)
T PF02338_consen 1 PGDGNCLFRAVSDQLYGDGGGSEDNHQELRKAVVDYLRDKNRDKFEEFLEGD------KMSKPGTWGGEIELQALANVLN 74 (121)
T ss_dssp -SSTTHHHHHHHHHHCTT-SSSTTTHHHHHHHHHHHHHTHTTTHHHHHHHHH------HHTSTTSHEEHHHHHHHHHHHT
T ss_pred CCCccHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHhccchhhhhhhhh------hhccccccCcHHHHHHHHHHhC
Confidence 7999999999999999 999999999999999999 9999999988655 9999999999999999999999
Q ss_pred CcEEEEEcCCCce--EEEEcC--CCCCCCCeEEEEecC-----CCcc
Q 020231 267 VKIVVITSFKDTC--YIEILP--NVEKIKRAICLSFWA-----EVHY 304 (329)
Q Consensus 267 v~I~V~ss~~~~~--~i~i~P--~~~~~~~~I~Lsy~~-----g~HY 304 (329)
|+|+|++...... ++.+.+ ......++|+|+|.. ++||
T Consensus 75 ~~I~v~~~~~~~~~~~~~~~~~~~~~~~~~~i~l~~~~~l~~~~~Hy 121 (121)
T PF02338_consen 75 RPIIVYSSSDGDNVVFIKFTGKYPPLESPPPICLCYHGHLYYTGNHY 121 (121)
T ss_dssp SEEEEECETTTBEEEEEEESCEESTTTTTTSEEEEEETEEEEETTEE
T ss_pred CeEEEEEcCCCCccceeeecCccccCCCCCeEEEEEcCCccCCCCCC
Confidence 9999998765543 344443 123567899999998 9998
No 3
>KOG2606 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.91 E-value=2.9e-24 Score=203.83 Aligned_cols=141 Identities=21% Similarity=0.403 Sum_probs=123.3
Q ss_pred cccchHHHHHHHHHHhCCcEEEEecCCCChHHHHHHHhHhcC---CccHHHHHHHHHHHHhcCccccccccc--------
Q 020231 168 DEATSDHERLLNRLQLYGFVEHKVQGDGNCQFRALSDQLYHT---PEHHKSVRQQIVTQLKSHPEMYEGYVP-------- 236 (329)
Q Consensus 168 dea~~d~~rL~~~L~~~GL~v~~V~GDGNCLFRALS~qL~g~---~~~H~~VR~~vV~yL~~n~d~f~~fv~-------- 236 (329)
+...++.+.|.+.|...||...+||.||+|||+||++||--. .-..+.||.++++||++|.+.|.+|+.
T Consensus 141 ~~k~~E~~k~~~il~~~~l~~~~Ip~DG~ClY~aI~hQL~~~~~~~~~v~kLR~~~a~Ymr~H~~df~pf~~~eet~d~~ 220 (302)
T KOG2606|consen 141 DAKSMEKEKLAQILEERGLKMFDIPADGHCLYAAISHQLKLRSGKLLSVQKLREETADYMREHVEDFLPFLLDEETGDSL 220 (302)
T ss_pred chhhhHHHHHHHHHHhccCccccCCCCchhhHHHHHHHHHhccCCCCcHHHHHHHHHHHHHHHHHHhhhHhcCccccccC
Confidence 345677889999999999999999999999999999998633 357899999999999999999999873
Q ss_pred --ccHHHHHHhhcCCCCCCchHHHHHHHHhhCCcEEEEEcCCCceEEEEcCCCCCCCCeEEEEecC-----CCccccccc
Q 020231 237 --MEYSEYLKKMSMSGEWGDHVTLQAAADLFHVKIVVITSFKDTCYIEILPNVEKIKRAICLSFWA-----EVHYNSIFS 309 (329)
Q Consensus 237 --~~~~eYl~~Msk~g~WGg~iELqAlA~~y~v~I~V~ss~~~~~~i~i~P~~~~~~~~I~Lsy~~-----g~HYdSV~~ 309 (329)
.+|+.||+.|+.++.|||++||.|+|.+|++||.||...++. +.|++...+ .+||.|+|++ |.||||+.+
T Consensus 221 ~~~~f~~Yc~eI~~t~~WGgelEL~AlShvL~~PI~Vy~~~~p~--~~~geey~k-d~pL~lvY~rH~y~LGeHYNS~~~ 297 (302)
T KOG2606|consen 221 GPEDFDKYCREIRNTAAWGGELELKALSHVLQVPIEVYQADGPI--LEYGEEYGK-DKPLILVYHRHAYGLGEHYNSVTP 297 (302)
T ss_pred CHHHHHHHHHHhhhhccccchHHHHHHHHhhccCeEEeecCCCc--eeechhhCC-CCCeeeehHHhHHHHHhhhccccc
Confidence 269999999999999999999999999999999999988764 456655544 6899999987 799999987
Q ss_pred CC
Q 020231 310 QD 311 (329)
Q Consensus 310 ~~ 311 (329)
..
T Consensus 298 ~~ 299 (302)
T KOG2606|consen 298 LK 299 (302)
T ss_pred cc
Confidence 54
No 4
>KOG3288 consensus OTU-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.60 E-value=1.1e-15 Score=143.34 Aligned_cols=123 Identities=19% Similarity=0.399 Sum_probs=102.7
Q ss_pred cEEEEecCCCChHHHHHHHhHhcCCc-cHHHHHHHHHHHHhcCcccccc-cccccHHHHHHhhcCCCCCCchHHHHHHHH
Q 020231 186 FVEHKVQGDGNCQFRALSDQLYHTPE-HHKSVRQQIVTQLKSHPEMYEG-YVPMEYSEYLKKMSMSGEWGDHVTLQAAAD 263 (329)
Q Consensus 186 L~v~~V~GDGNCLFRALS~qL~g~~~-~H~~VR~~vV~yL~~n~d~f~~-fv~~~~~eYl~~Msk~g~WGg~iELqAlA~ 263 (329)
|.++.||.|.+|||+||++-+++.-. .-.++|+.+.+.+.+||+.|.. ++...-.+||..+.++..|||.|||..+|+
T Consensus 110 l~~~vvp~DNSCLF~ai~yv~~k~~~~~~~elR~iiA~~Vasnp~~yn~AiLgK~n~eYc~WI~k~dsWGGaIElsILS~ 189 (307)
T KOG3288|consen 110 LSRRVVPDDNSCLFTAIAYVIFKQVSNRPYELREIIAQEVASNPDKYNDAILGKPNKEYCAWILKMDSWGGAIELSILSD 189 (307)
T ss_pred eEEEeccCCcchhhhhhhhhhcCccCCCcHHHHHHHHHHHhcChhhhhHHHhCCCcHHHHHHHccccccCceEEeeeehh
Confidence 66778999999999999999987533 3369999999999999999975 567788999999999999999999999999
Q ss_pred hhCCcEEEEEcCCCceEEEEcCCCCCCCCeEEEEecCCCcccccccCC
Q 020231 264 LFHVKIVVITSFKDTCYIEILPNVEKIKRAICLSFWAEVHYNSIFSQD 311 (329)
Q Consensus 264 ~y~v~I~V~ss~~~~~~i~i~P~~~~~~~~I~Lsy~~g~HYdSV~~~~ 311 (329)
.|+|.|+|++... ..|+-+..+......++|.| +|.|||++.-..
T Consensus 190 ~ygveI~vvDiqt--~rid~fged~~~~~rv~lly-dGIHYD~l~m~~ 234 (307)
T KOG3288|consen 190 YYGVEICVVDIQT--VRIDRFGEDKNFDNRVLLLY-DGIHYDPLAMNE 234 (307)
T ss_pred hhceeEEEEecce--eeehhcCCCCCCCceEEEEe-cccccChhhhcc
Confidence 9999999997643 23444455555667777766 899999998655
No 5
>PF10275 Peptidase_C65: Peptidase C65 Otubain; InterPro: IPR019400 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 family of proteins is a highly specific ubiquitin iso-peptidase that removes ubiquitin from proteins. The modification of cellular proteins by ubiquitin (Ub) is an important event that underlies protein stability and function in eukaryotes, as it is a dynamic and reversible process. Otubain carries several key conserved domains: (i) the OTU (ovarian tumour domain) in which there is an active cysteine protease triad (ii) a nuclear localisation signal, (iii) a Ub interaction motif (UIM)-like motif phi-xx-A-xxxs-xx-Ac (where phi indicates an aromatic amino acid, x indicates any amino acid and Ac indicates an acidic amino acid), (iv) a Ub-associated (UBA)-like domain and (v) the LxxLL motif. ; PDB: 4DDG_C 3VON_O 2ZFY_A 4DHZ_A 4DDI_C 1TFF_A 4DHJ_I 4DHI_B.
Probab=99.49 E-value=2.1e-13 Score=126.87 Aligned_cols=95 Identities=24% Similarity=0.320 Sum_probs=70.8
Q ss_pred HHHHHHHHHHHhcCccccccccc----ccHHHHHH-hhcCCCCCCchHHHHHHHHhhCCcEEEEEcCCC---c--eEEEE
Q 020231 214 KSVRQQIVTQLKSHPEMYEGYVP----MEYSEYLK-KMSMSGEWGDHVTLQAAADLFHVKIVVITSFKD---T--CYIEI 283 (329)
Q Consensus 214 ~~VR~~vV~yL~~n~d~f~~fv~----~~~~eYl~-~Msk~g~WGg~iELqAlA~~y~v~I~V~ss~~~---~--~~i~i 283 (329)
..+|..+..||+.|++.|.+|++ .++++||. .+...+.-+||+.|.|||++++++|.|+..++. . ....+
T Consensus 140 ~flRLlts~~l~~~~d~y~~fi~~~~~~tve~~C~~~Vep~~~Ead~v~i~ALa~aL~v~i~v~yld~~~~~~~~~~~~~ 219 (244)
T PF10275_consen 140 IFLRLLTSAYLKSNSDEYEPFIDGLEYLTVEEFCSQEVEPMGKEADHVQIIALAQALGVPIRVEYLDRSVEGDEVNRHEF 219 (244)
T ss_dssp HHHHHHHHHHHHHTHHHHGGGSSTT--S-HHHHHHHHTSSTT--B-HHHHHHHHHHHT--EEEEESSSSGCSTTSEEEEE
T ss_pred HHHHHHHHHHHHhhHHHHhhhhcccccCCHHHHHHhhcccccccchhHHHHHHHHHhCCeEEEEEecCCCCCCccccccC
Confidence 47899999999999999999997 67999997 577788889999999999999999999988764 1 12222
Q ss_pred cCCCCCCCCeEEEEecCCCccccccc
Q 020231 284 LPNVEKIKRAICLSFWAEVHYNSIFS 309 (329)
Q Consensus 284 ~P~~~~~~~~I~Lsy~~g~HYdSV~~ 309 (329)
.|......+.|.|.| +++|||.+||
T Consensus 220 ~~~~~~~~~~i~LLy-rpgHYdIly~ 244 (244)
T PF10275_consen 220 PPDNESQEPQITLLY-RPGHYDILYP 244 (244)
T ss_dssp S-SSTTSS-SEEEEE-ETBEEEEEEE
T ss_pred CCccCCCCCEEEEEE-cCCccccccC
Confidence 223335678899987 5679999986
No 6
>KOG3991 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.40 E-value=7.9e-13 Score=122.60 Aligned_cols=95 Identities=17% Similarity=0.284 Sum_probs=77.9
Q ss_pred HHHHHHHHHHHHhcCccccccccc--ccHHHHHHh-hcCCCCCCchHHHHHHHHhhCCcEEEEEcCCCceE-E--EEcCC
Q 020231 213 HKSVRQQIVTQLKSHPEMYEGYVP--MEYSEYLKK-MSMSGEWGDHVTLQAAADLFHVKIVVITSFKDTCY-I--EILPN 286 (329)
Q Consensus 213 H~~VR~~vV~yL~~n~d~f~~fv~--~~~~eYl~~-Msk~g~WGg~iELqAlA~~y~v~I~V~ss~~~~~~-i--~i~P~ 286 (329)
.+.+|..+..+|++|++.|++||+ +++.+||.. +....+-.|||+|.||++++++.|.|...++..+- . ...|
T Consensus 156 V~ylRLvtS~~ik~~adfy~pFI~e~~tV~~fC~~eVEPm~kesdhi~I~ALs~Al~i~irVey~dr~~~~~~~hH~fp- 234 (256)
T KOG3991|consen 156 VMYLRLVTSGFIKSNADFYQPFIDEGMTVKAFCTQEVEPMYKESDHIHITALSQALGIRIRVEYVDRGSGDTVNHHDFP- 234 (256)
T ss_pred HHHHHHHHHHHHhhChhhhhccCCCCCcHHHHHHhhcchhhhccCceeHHHHHhhhCceEEEEEecCCCCCCCCCCcCc-
Confidence 467899999999999999999996 589999985 55557779999999999999999999988875431 1 1223
Q ss_pred CCCCCCeEEEEecCCCcccccccC
Q 020231 287 VEKIKRAICLSFWAEVHYNSIFSQ 310 (329)
Q Consensus 287 ~~~~~~~I~Lsy~~g~HYdSV~~~ 310 (329)
....+.|+|.| +.+|||.||++
T Consensus 235 -e~s~P~I~LLY-rpGHYdilY~~ 256 (256)
T KOG3991|consen 235 -EASAPEIYLLY-RPGHYDILYKK 256 (256)
T ss_pred -cccCceEEEEe-cCCccccccCC
Confidence 34678899976 78999999974
No 7
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=98.66 E-value=6.9e-09 Score=99.37 Aligned_cols=122 Identities=17% Similarity=0.150 Sum_probs=87.3
Q ss_pred HhCCcEEEEecCCCChHHHHHHHhHhcC-----CccHHHHHHHHHHHHhcCccccccccc-------ccHHHHHHhhcCC
Q 020231 182 QLYGFVEHKVQGDGNCQFRALSDQLYHT-----PEHHKSVRQQIVTQLKSHPEMYEGYVP-------MEYSEYLKKMSMS 249 (329)
Q Consensus 182 ~~~GL~v~~V~GDGNCLFRALS~qL~g~-----~~~H~~VR~~vV~yL~~n~d~f~~fv~-------~~~~eYl~~Msk~ 249 (329)
..-+++-..+.|||+|+|-+||+||--. -+.-+..|-.=..|..++...|.++.- ..|++|++.|..+
T Consensus 167 y~~~i~k~d~~~dG~ieia~iS~~l~v~i~~Vdv~~~~~dr~~~~~~~q~~~i~f~g~hfD~~t~~m~~~dt~~ne~~~~ 246 (306)
T COG5539 167 YATWIVKPDSQGDGCIEIAIISDQLPVRIHVVDVDKDSEDRYNSHPYVQRISILFTGIHFDEETLAMVLWDTYVNEVLFD 246 (306)
T ss_pred HHHhhhccccCCCceEEEeEeccccceeeeeeecchhHHhhccCChhhhhhhhhhcccccchhhhhcchHHHHHhhhccc
Confidence 3445666779999999999999998521 122355555555666666667776541 3799999999999
Q ss_pred CCCCchHHHHHHHHhhCCcEEEEEcCCCceEEEEcCCCCCCCCeEEEEecC----CCccccc
Q 020231 250 GEWGDHVTLQAAADLFHVKIVVITSFKDTCYIEILPNVEKIKRAICLSFWA----EVHYNSI 307 (329)
Q Consensus 250 g~WGg~iELqAlA~~y~v~I~V~ss~~~~~~i~i~P~~~~~~~~I~Lsy~~----g~HYdSV 307 (329)
..||..+|+++||..|++|+.++...++. |...+.+.++. ..+.|+. -+|||++
T Consensus 247 a~~g~~~ei~qLas~lk~~~~~~nT~~~~--ik~n~c~~~~~--~e~~~~~Ha~a~GH~n~~ 304 (306)
T COG5539 247 ASDGITIEIQQLASLLKNPHYYTNTASPS--IKCNICGTGFV--GEKDYYAHALATGHYNFG 304 (306)
T ss_pred ccccchHHHHHHHHHhcCceEEeecCCce--EEeeccccccc--hhhHHHHHHHhhcCcccc
Confidence 99999999999999999999999876654 55444333332 3333332 2499987
No 8
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=98.51 E-value=3.8e-08 Score=94.38 Aligned_cols=110 Identities=17% Similarity=0.270 Sum_probs=90.7
Q ss_pred CCCChHHHHHHHhHhcCCccHHHHHHHHHHHHhcCccccccccc-ccHHHHHHhhcCCCCCC-chHHHHHHHHhhCCcEE
Q 020231 193 GDGNCQFRALSDQLYHTPEHHKSVRQQIVTQLKSHPEMYEGYVP-MEYSEYLKKMSMSGEWG-DHVTLQAAADLFHVKIV 270 (329)
Q Consensus 193 GDGNCLFRALS~qL~g~~~~H~~VR~~vV~yL~~n~d~f~~fv~-~~~~eYl~~Msk~g~WG-g~iELqAlA~~y~v~I~ 270 (329)
.|..|+|+|.+..++.- ...++|..+...+.+||+.|.+.+. -+.-.|+.++.+...|| |++|+.++++.|++.|+
T Consensus 119 ~d~srl~q~~~~~l~~a--sv~~lrE~vs~Ev~snPDl~n~~i~~~~~i~y~~~i~k~d~~~dG~ieia~iS~~l~v~i~ 196 (306)
T COG5539 119 DDNSRLFQAERYSLRDA--SVAKLREVVSLEVLSNPDLYNPAILEIDVIAYATWIVKPDSQGDGCIEIAIISDQLPVRIH 196 (306)
T ss_pred CchHHHHHHHHhhhhhh--hHHHHHHHHHHHHhhCccccchhhcCcchHHHHHhhhccccCCCceEEEeEeccccceeee
Confidence 57999999999998743 7789999999999999999999875 47889999999999999 99999999999999999
Q ss_pred EEEcCCCceEEEEcCCCCCCCCeEEEEecCCCcccccc
Q 020231 271 VITSFKDTCYIEILPNVEKIKRAICLSFWAEVHYNSIF 308 (329)
Q Consensus 271 V~ss~~~~~~i~i~P~~~~~~~~I~Lsy~~g~HYdSV~ 308 (329)
|+..+.+.. ..+.+. +....|++.| .|.|||..+
T Consensus 197 ~Vdv~~~~~-dr~~~~--~~~q~~~i~f-~g~hfD~~t 230 (306)
T COG5539 197 VVDVDKDSE-DRYNSH--PYVQRISILF-TGIHFDEET 230 (306)
T ss_pred eeecchhHH-hhccCC--hhhhhhhhhh-cccccchhh
Confidence 998876531 122321 2234566655 789999887
No 9
>PF05415 Peptidase_C36: Beet necrotic yellow vein furovirus-type papain-like endopeptidase; InterPro: IPR008746 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases correspond to MEROPS peptidase family C36 (clan CA). The type example is beet necrotic yellow vein furovirus-type papain-like endopeptidase (beet necrotic yellow vein virus), which is involved in processing the viral polyprotein.
Probab=78.30 E-value=8.9 Score=31.78 Aligned_cols=64 Identities=22% Similarity=0.318 Sum_probs=43.4
Q ss_pred ecCCCChHHHHHHHhHhcCCccHHHHHHHHHHHHhcCcccccccccccHHHHHHhhc--CCCCCCchHHHHHHHHhhCCc
Q 020231 191 VQGDGNCQFRALSDQLYHTPEHHKSVRQQIVTQLKSHPEMYEGYVPMEYSEYLKKMS--MSGEWGDHVTLQAAADLFHVK 268 (329)
Q Consensus 191 V~GDGNCLFRALS~qL~g~~~~H~~VR~~vV~yL~~n~d~f~~fv~~~~~eYl~~Ms--k~g~WGg~iELqAlA~~y~v~ 268 (329)
+..|.|||--|||..|.-+-+.-..+ |..|. .+.+.|+..++ .+.+|-|- ..+|+.++|.
T Consensus 3 ~sR~NNCLVVAis~~L~~T~e~l~~~-------M~An~--------~~i~~y~~W~r~~~~STW~DC---~mFA~~LkVs 64 (104)
T PF05415_consen 3 ASRPNNCLVVAISECLGVTLEKLDNL-------MQANV--------STIKKYHTWLRKKRPSTWDDC---RMFADALKVS 64 (104)
T ss_pred ccCCCCeEeehHHHHhcchHHHHHHH-------HHhhH--------HHHHHHHHHHhcCCCCcHHHH---HHHHHhheeE
Confidence 56799999999999996543322211 22221 24678888665 46788664 4689999999
Q ss_pred EEEE
Q 020231 269 IVVI 272 (329)
Q Consensus 269 I~V~ 272 (329)
|.|=
T Consensus 65 m~vk 68 (104)
T PF05415_consen 65 MQVK 68 (104)
T ss_pred EEEE
Confidence 9883
No 10
>PRK09784 hypothetical protein; Provisional
Probab=61.75 E-value=4.5 Score=39.27 Aligned_cols=24 Identities=38% Similarity=0.631 Sum_probs=21.1
Q ss_pred HHhCCcEEEEecCCCChHHHHHHH
Q 020231 181 LQLYGFVEHKVQGDGNCQFRALSD 204 (329)
Q Consensus 181 L~~~GL~v~~V~GDGNCLFRALS~ 204 (329)
=+.+||+--+|.|||-||.||+--
T Consensus 195 n~~~glkyapvdgdgycllrailv 218 (417)
T PRK09784 195 NKTYGLKYAPVDGDGYCLLRAILV 218 (417)
T ss_pred hhhhCceecccCCCchhHHHHHHH
Confidence 367999999999999999999753
No 11
>PF05412 Peptidase_C33: Equine arterivirus Nsp2-type cysteine proteinase; InterPro: IPR008743 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases corresponds to MEROPS peptidase family C33 (clan CA). The type example is equine arteritis virus Nsp2-type cysteine proteinase, which is involved in viral polyprotein processing [].; GO: 0016032 viral reproduction, 0019082 viral protein processing
Probab=54.53 E-value=8.5 Score=32.61 Aligned_cols=83 Identities=14% Similarity=0.274 Sum_probs=45.7
Q ss_pred ecCCCChHHHHHHHhHhcCCccHHHHHHHHHHHHhcCcccccccccccHH-HHHHhhcCCCCCCchHHHHHHHHhhCCcE
Q 020231 191 VQGDGNCQFRALSDQLYHTPEHHKSVRQQIVTQLKSHPEMYEGYVPMEYS-EYLKKMSMSGEWGDHVTLQAAADLFHVKI 269 (329)
Q Consensus 191 V~GDGNCLFRALS~qL~g~~~~H~~VR~~vV~yL~~n~d~f~~fv~~~~~-eYl~~Msk~g~WGg~iELqAlA~~y~v~I 269 (329)
-|+||+|.+|+||..+.+ |.. .+|. .|-+.-+....|.++-.|.-+-..++.|+
T Consensus 4 PP~DG~CG~H~i~aI~n~---------------m~~----------~~~t~~l~~~~r~~d~W~~dedl~~~iq~l~lPa 58 (108)
T PF05412_consen 4 PPGDGSCGWHCIAAIMNH---------------MMG----------GEFTTPLPQRNRPSDDWADDEDLYQVIQSLRLPA 58 (108)
T ss_pred CCCCCchHHHHHHHHHHH---------------hhc----------cCCCccccccCCChHHccChHHHHHHHHHccCce
Confidence 589999999999986642 211 1111 11122234567888877765555556665
Q ss_pred EEEEcCCCceEEEEcCCCCCCCCeEEEEecCCCcccccccCC
Q 020231 270 VVITSFKDTCYIEILPNVEKIKRAICLSFWAEVHYNSIFSQD 311 (329)
Q Consensus 270 ~V~ss~~~~~~i~i~P~~~~~~~~I~Lsy~~g~HYdSV~~~~ 311 (329)
-+.. ...-....|+.-..+.|+..-+..+
T Consensus 59 t~~~-------------~~~Cp~ArYv~~l~~qHW~V~~~~g 87 (108)
T PF05412_consen 59 TLDR-------------NGACPHARYVLKLDGQHWEVSVRKG 87 (108)
T ss_pred eccC-------------CCCCCCCEEEEEecCceEEEEEcCC
Confidence 5531 1111222333334677777666655
No 12
>COG5007 Predicted transcriptional regulator, BolA superfamily [Transcription]
Probab=45.19 E-value=20 Score=28.91 Aligned_cols=54 Identities=19% Similarity=0.265 Sum_probs=37.7
Q ss_pred HHHHHHHH-hCCcEEEEecCCCChHHH-HHHHhHhcC--CccHHHHHHHHHHHHhcCc
Q 020231 175 ERLLNRLQ-LYGFVEHKVQGDGNCQFR-ALSDQLYHT--PEHHKSVRQQIVTQLKSHP 228 (329)
Q Consensus 175 ~rL~~~L~-~~GL~v~~V~GDGNCLFR-ALS~qL~g~--~~~H~~VR~~vV~yL~~n~ 228 (329)
+.+.+.|. .+.+...+|.|||+=+|- +|++.+-|- -..|+.|-.-+.+||.+|.
T Consensus 4 e~Ik~ll~~~L~~e~v~V~Gdg~Hf~vi~Vs~~F~g~srvkrqq~vYApL~~~i~~~~ 61 (80)
T COG5007 4 EEIKSLLENALPLEEVEVEGDGSHFQVIAVSEEFAGKSRVKRQQLVYAPLMAYIADNE 61 (80)
T ss_pred HHHHHHHHhcCCccEEEEecCCceEEEEEehHhhcCccHHHHHHHHHHHHHHHhhcCc
Confidence 34444443 467889999999987765 466666543 2467778888888988764
No 13
>smart00718 DM4_12 DM4/DM12 family of domains in Drosophila melanogaster proteins of unknown function.
Probab=36.42 E-value=97 Score=25.22 Aligned_cols=72 Identities=22% Similarity=0.410 Sum_probs=44.5
Q ss_pred HHHHHHHHHHhCCcEEEEecCCC-ChHHHHHHHhHhcCCccHHHHHHHHHHHHhcCcccccccccccHHHHHHhhcCCCC
Q 020231 173 DHERLLNRLQLYGFVEHKVQGDG-NCQFRALSDQLYHTPEHHKSVRQQIVTQLKSHPEMYEGYVPMEYSEYLKKMSMSGE 251 (329)
Q Consensus 173 d~~rL~~~L~~~GL~v~~V~GDG-NCLFRALS~qL~g~~~~H~~VR~~vV~yL~~n~d~f~~fv~~~~~eYl~~Msk~g~ 251 (329)
=++.|.+.|..+|+ || .|+.|||-+.--. ...|.-|=..++..|.+-++.-+ ..--.+|.+.+. .|.
T Consensus 9 lY~~lE~~l~~~G~-------~g~~ClLR~ICE~a~~-~~~~~Gll~ell~ilftps~~~~---~~~~~~Y~~A~~-~G~ 76 (95)
T smart00718 9 LYEALENLLDQLGF-------NGRACLLRAICESAQK-LDDHRGLLGELLRIVLTPPDELE---EVLDPDYREAYR-AGR 76 (95)
T ss_pred HHHHHHHHHHHcCC-------CchhhHHHHHHHcccc-cccccchHHHHHHHhhcCCcchh---hhchHHHHHHHH-cCC
Confidence 36778888999996 77 9999999775432 23344466677777766662211 112356766654 344
Q ss_pred CCchH
Q 020231 252 WGDHV 256 (329)
Q Consensus 252 WGg~i 256 (329)
-|+++
T Consensus 77 ~g~dC 81 (95)
T smart00718 77 AGGDC 81 (95)
T ss_pred CCCCH
Confidence 46664
No 14
>TIGR01078 arcA arginine deiminase. Arginine deiminase is the first enzyme of the arginine deiminase pathway of arginine degradation.
Probab=31.30 E-value=69 Score=32.72 Aligned_cols=73 Identities=22% Similarity=0.413 Sum_probs=49.2
Q ss_pred CCCCCCcccchHHHHHHHHHHhCCcEEEEecCCCChHHHHHHHhHhcCCccHHHHHHHHHHHHhcCcccccccccccHHH
Q 020231 162 GEIPSVDEATSDHERLLNRLQLYGFVEHKVQGDGNCQFRALSDQLYHTPEHHKSVRQQIVTQLKSHPEMYEGYVPMEYSE 241 (329)
Q Consensus 162 g~iPs~dea~~d~~rL~~~L~~~GL~v~~V~GDGNCLFRALS~qL~g~~~~H~~VR~~vV~yL~~n~d~f~~fv~~~~~e 241 (329)
..+|..+.|..+|+.|.+.|+..|..+..+.. -+++.| .+..+|+..++........+..-......+
T Consensus 34 d~i~~~~~a~~EHd~f~~~Lr~~GveV~~l~d-------ll~e~l-----~~~~~r~~~l~~~~~~~~~~~~~~~~~~~~ 101 (405)
T TIGR01078 34 DDIPWVEDAQKEHDQFANTLRDNGIEVLYLED-------LLAETL-----DLPEAKEKFIDEFLSESEILGLGLKVELRD 101 (405)
T ss_pred cCCCCHHHHHHHHHHHHHHHHHCCCEEEEhHH-------HHHHHh-----CCHHHHHHHHHHHHhhccCCCHHHHHHHHH
Confidence 46888899999999999999999999887542 233333 133888888887766544433322344556
Q ss_pred HHHhh
Q 020231 242 YLKKM 246 (329)
Q Consensus 242 Yl~~M 246 (329)
|+..|
T Consensus 102 ~l~~~ 106 (405)
T TIGR01078 102 YLKSL 106 (405)
T ss_pred HHHhC
Confidence 66554
No 15
>PRK13381 peptidase T; Provisional
Probab=29.60 E-value=60 Score=32.09 Aligned_cols=52 Identities=13% Similarity=0.220 Sum_probs=36.5
Q ss_pred hhhhhccccccCCCC-CCCCCCCCcccchHHHHHHHHHHhCCcEEEEecCCCC
Q 020231 145 GKRLNQMVAIRHVPR-INGEIPSVDEATSDHERLLNRLQLYGFVEHKVQGDGN 196 (329)
Q Consensus 145 ~krl~~~~p~p~~p~-~ng~iPs~dea~~d~~rL~~~L~~~GL~v~~V~GDGN 196 (329)
-+||.+++.||.+.. ..++||+......-.+.|.++|+.+|+....+.+.+|
T Consensus 4 ~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~l~~~l~~~G~~~~~~~~~~n 56 (404)
T PRK13381 4 TDRFFRYLKVNSQSDAASGTLPSTPGQHELAKLLADELRELGLEDIVIDEHAI 56 (404)
T ss_pred HHHhHhhEEEeccCCCCCCCCcCChhHHHHHHHHHHHHHHcCCCcEEEcCCeE
Confidence 457889999988773 3467888665444456678999999995445555554
No 16
>PF05381 Peptidase_C21: Tymovirus endopeptidase; InterPro: IPR008043 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 entry is found in cysteine peptidases belong to the MEROPS peptidase family C21 (tymovirus endopeptidase family, clan CA). The type example is tymovirus endopeptidase (turnip yellow mosaic virus). The noncapsid protein expressed from ORF-206 of turnip yellow mosaic virus (TYMV) is autocatalytically processed by a papain-like protease, producing N-terminal 150kDa and C-terminal 70kDa proteins.; GO: 0003968 RNA-directed RNA polymerase activity, 0016032 viral reproduction
Probab=28.65 E-value=2.8e+02 Score=23.45 Aligned_cols=89 Identities=15% Similarity=0.178 Sum_probs=53.5
Q ss_pred CChHHHHHHHhHhcCC-ccHHHHHHHHHHHHhcCcccccccccccHHHHHHhhcCCCCCCchHHHHHHHHhhCCcEEEEE
Q 020231 195 GNCQFRALSDQLYHTP-EHHKSVRQQIVTQLKSHPEMYEGYVPMEYSEYLKKMSMSGEWGDHVTLQAAADLFHVKIVVIT 273 (329)
Q Consensus 195 GNCLFRALS~qL~g~~-~~H~~VR~~vV~yL~~n~d~f~~fv~~~~~eYl~~Msk~g~WGg~iELqAlA~~y~v~I~V~s 273 (329)
-+||--|||.|..-.+ .-+..|...+=+=+.+|++. ++-|- .--.+.|+|-.|+....|.+
T Consensus 3 ~~CLL~A~s~at~~~~~~LW~~L~~~lPDSlL~n~ei----------------~~~GL--STDhltaLa~~~~~~~~~hs 64 (104)
T PF05381_consen 3 LDCLLVAISQATSISPETLWATLCEILPDSLLDNPEI----------------RTLGL--STDHLTALAYRYHFQCTFHS 64 (104)
T ss_pred cceeHHhhhhhhCCCHHHHHHHHHHhCchhhcCchhh----------------hhcCC--cHHHHHHHHHHHheEEEEEc
Confidence 5899999999975443 23444433333333333222 12221 12236789999999999987
Q ss_pred cCCCceEEEEcCCCCCCCCeEEEEecCC--Ccccc
Q 020231 274 SFKDTCYIEILPNVEKIKRAICLSFWAE--VHYNS 306 (329)
Q Consensus 274 s~~~~~~i~i~P~~~~~~~~I~Lsy~~g--~HYdS 306 (329)
..+. ++++.. .....+.|.|..| .||..
T Consensus 65 ~~~~---~~~Gi~--~as~~~~I~ht~G~p~HFs~ 94 (104)
T PF05381_consen 65 DHGV---LHYGIK--DASTVFTITHTPGPPGHFSL 94 (104)
T ss_pred CCce---EEeecC--CCceEEEEEeCCCCCCcccc
Confidence 6543 455543 3566777777654 79988
No 17
>KOG4634 consensus Mitochondrial F1F0-ATP synthase, subunit Cf6 (coupling factor 6) [Energy production and conversion]
Probab=27.17 E-value=56 Score=27.48 Aligned_cols=24 Identities=33% Similarity=0.394 Sum_probs=20.9
Q ss_pred cCCccchHHHHHHHHHHHHHHHHH
Q 020231 57 SNNVESDEIIARTLQEEFSQLAIE 80 (329)
Q Consensus 57 ~~~~~~d~~~~~~~q~~~~~~~~~ 80 (329)
-.-||.|.-+-+.|+|||-+||-.
T Consensus 52 Gklvds~pe~e~eLk~el~rla~q 75 (105)
T KOG4634|consen 52 GKLVDSDPEYEQELKEELFRLAQQ 75 (105)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHH
Confidence 356999999999999999999843
No 18
>PRK01388 arginine deiminase; Provisional
Probab=24.96 E-value=1e+02 Score=31.53 Aligned_cols=53 Identities=19% Similarity=0.312 Sum_probs=37.6
Q ss_pred CCCCCCcccchHHHHHHHHHHhCCcEEEEecCCCChHHHHHHHhHhcCCccHHHHHHHHHHHHhc
Q 020231 162 GEIPSVDEATSDHERLLNRLQLYGFVEHKVQGDGNCQFRALSDQLYHTPEHHKSVRQQIVTQLKS 226 (329)
Q Consensus 162 g~iPs~dea~~d~~rL~~~L~~~GL~v~~V~GDGNCLFRALS~qL~g~~~~H~~VR~~vV~yL~~ 226 (329)
..+|..+.|..+|+.|.+.|+..|..+..+.. -+++.|. ...+|+.+++....
T Consensus 41 ddi~~l~~aq~EHd~f~~~Lr~~GveV~~l~d-------ll~e~l~-----~~~~r~~~l~~~~~ 93 (406)
T PRK01388 41 DDVPWVERAQKEHDAFAQTLRDRGVEVLYLED-------LLAETLA-----NPEAREWFLDRQIS 93 (406)
T ss_pred ccCCCHHHHHHHHHHHHHHHHHCCCEEEEhHH-------HHHHHhc-----CHHHHHHHHHHHhh
Confidence 46888999999999999999999999887542 2233331 23466666665543
No 19
>PHA03308 transcriptional regulator ICP4; Provisional
Probab=23.11 E-value=1.6e+02 Score=33.15 Aligned_cols=17 Identities=24% Similarity=0.442 Sum_probs=12.0
Q ss_pred EEecCCCChHHHHHHHh
Q 020231 189 HKVQGDGNCQFRALSDQ 205 (329)
Q Consensus 189 ~~V~GDGNCLFRALS~q 205 (329)
+++-|--..-||||+.+
T Consensus 1320 ~D~v~Gtsasfravaaw 1336 (1463)
T PHA03308 1320 ADIVGGTSASFRAVAAW 1336 (1463)
T ss_pred hhhhcCcchhHHHHHHh
Confidence 34555567789999875
No 20
>TIGR02934 nifT_nitrog probable nitrogen fixation protein FixT. This largely uncharacterized protein family is assigned a role in nitrogen fixation by two criteria. First, its gene occurs, generally, among genes essential for expression of active nitrogenase. Second, its phylogenetic profile closely matches that of nitrogen-fixing bacteria. However, mutational studies in Klebsiella pneumoniae failed to demonstrate any phenotype for deletion or overexpression of the protein.
Probab=21.71 E-value=12 Score=29.23 Aligned_cols=34 Identities=26% Similarity=0.501 Sum_probs=26.0
Q ss_pred hcCccc-cccccc-ccHHHHHHhhcCCCCCCchHHH
Q 020231 225 KSHPEM-YEGYVP-MEYSEYLKKMSMSGEWGDHVTL 258 (329)
Q Consensus 225 ~~n~d~-f~~fv~-~~~~eYl~~Msk~g~WGg~iEL 258 (329)
++|.+- +..||+ .|+++=+-.|.+++.|||.+.|
T Consensus 6 R~~~~g~l~~YvpKKDLEE~Vv~~e~~~~WGG~v~L 41 (67)
T TIGR02934 6 RRNRAGELSAYVPKKDLEEVIVSVEKEELWGGWVTL 41 (67)
T ss_pred EeCCCCCEEEEEECCcchhheeeeecCccccCEEEE
Confidence 445443 677886 5899999999999999997544
No 21
>KOG2605 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=21.33 E-value=18 Score=36.70 Aligned_cols=92 Identities=11% Similarity=-0.132 Sum_probs=72.4
Q ss_pred HHhCCcEEEEecCCCChHHHHHHHhHhcCCccHHHHHHHHHHHHhcCcccccccccccHHHHHHhhcCCCCCCchHHHHH
Q 020231 181 LQLYGFVEHKVQGDGNCQFRALSDQLYHTPEHHKSVRQQIVTQLKSHPEMYEGYVPMEYSEYLKKMSMSGEWGDHVTLQA 260 (329)
Q Consensus 181 L~~~GL~v~~V~GDGNCLFRALS~qL~g~~~~H~~VR~~vV~yL~~n~d~f~~fv~~~~~eYl~~Msk~g~WGg~iELqA 260 (329)
+..++..+....-+++|.+|...+++...+.-+..-+.++|-|...+.+.|..=-.....-|+..|...++|-|...++|
T Consensus 50 ~~~~~~~r~~~v~~~~~~~~~~~d~~~~~e~~e~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~a 129 (371)
T KOG2605|consen 50 TDGYNNKRYGEVDRDFMIARGHQDEVLTVEDAEMAAICQSVLFKVLYQERFKLPSDTPCNGENSPMCSFHSRRGNESFQA 129 (371)
T ss_pred eccccCccccchhhhhhhhcccccccccccHHHHhhHHhhhhhhhhhhhcccCCCCCcccccCCCCCccccccccccccc
Confidence 34566667777789999999999999999999999999999999999998876333355677778888899988888888
Q ss_pred HHHhhCCcEEEE
Q 020231 261 AADLFHVKIVVI 272 (329)
Q Consensus 261 lA~~y~v~I~V~ 272 (329)
++.--.+.+...
T Consensus 130 ~s~~~~~~~~~~ 141 (371)
T KOG2605|consen 130 ASFGGLEIDLEV 141 (371)
T ss_pred ccccccccchhh
Confidence 766554444433
Done!