Query 036608
Match_columns 565
No_of_seqs 395 out of 1495
Neff 8.3
Searched_HMMs 46136
Date Fri Mar 29 03:46:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036608.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036608hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03097 FHY3 Protein FAR-RED 100.0 4.6E-40 1E-44 365.2 18.5 255 1-272 326-621 (846)
2 PF02338 OTU: OTU-like cystein 99.7 1.9E-17 4.1E-22 145.7 6.1 107 384-507 1-121 (121)
3 KOG2606 OTU (ovarian tumor)-li 99.6 1.5E-16 3.2E-21 152.8 5.5 135 368-514 149-299 (302)
4 PF10551 MULE: MULE transposas 99.4 1.9E-13 4.2E-18 114.3 5.0 58 1-60 36-93 (93)
5 PF00872 Transposase_mut: Tran 99.2 5E-12 1.1E-16 132.8 -0.2 135 1-144 207-352 (381)
6 smart00575 ZnF_PMZ plant mutat 98.6 1.6E-08 3.6E-13 63.9 0.7 25 218-242 1-25 (28)
7 KOG2605 OTU (ovarian tumor)-li 98.5 3.3E-08 7.1E-13 101.3 2.7 131 371-513 211-344 (371)
8 KOG3288 OTU-like cysteine prot 98.2 1.6E-05 3.5E-10 75.3 11.2 124 378-518 110-238 (307)
9 PF10275 Peptidase_C65: Peptid 98.1 5.3E-06 1.1E-10 82.1 7.0 98 407-511 141-243 (244)
10 COG3328 Transposase and inacti 98.0 1.1E-05 2.4E-10 83.7 6.8 132 5-145 190-332 (379)
11 PF04434 SWIM: SWIM zinc finge 97.6 1.8E-05 3.9E-10 54.8 0.8 28 214-241 11-38 (40)
12 KOG3991 Uncharacterized conser 97.5 0.00052 1.1E-08 64.5 9.0 92 409-512 160-255 (256)
13 COG5539 Predicted cysteine pro 97.4 2.3E-05 5E-10 76.0 -1.6 137 360-510 153-304 (306)
14 PF06782 UPF0236: Uncharacteri 90.9 1.5 3.1E-05 47.8 10.2 60 5-65 239-299 (470)
15 PF05412 Peptidase_C33: Equine 89.6 0.22 4.8E-06 41.4 2.0 59 381-472 2-60 (108)
16 PF01610 DDE_Tnp_ISL3: Transpo 89.6 0.17 3.7E-06 50.0 1.6 45 21-65 54-98 (249)
17 COG5539 Predicted cysteine pro 88.5 1.2 2.6E-05 44.0 6.4 112 385-513 119-232 (306)
18 PRK09784 hypothetical protein; 50.7 10 0.00022 36.4 2.0 37 374-411 196-232 (417)
19 PF13610 DDE_Tnp_IS240: DDE do 49.0 15 0.00032 32.8 2.7 25 22-46 57-81 (140)
20 KOG4825 Component of synaptic 44.7 52 0.0011 34.9 6.0 31 299-329 284-314 (666)
21 KOG4345 NF-kappa B regulator A 42.9 18 0.00039 40.2 2.6 52 458-511 225-290 (774)
22 COG4279 Uncharacterized conser 38.5 12 0.00026 36.5 0.4 23 217-242 124-146 (266)
23 COG5431 Uncharacterized metal- 37.7 13 0.00028 31.0 0.4 25 217-241 49-78 (117)
24 PF02178 AT_hook: AT hook moti 36.7 16 0.00034 18.7 0.5 8 302-309 2-9 (13)
25 TIGR03277 methan_mark_9 putati 30.6 43 0.00092 28.1 2.3 32 388-419 77-109 (109)
26 PF03412 Peptidase_C39: Peptid 29.1 2.4E+02 0.0052 24.0 7.3 85 385-513 9-93 (131)
27 COG3464 Transposase and inacti 27.7 2.2E+02 0.0047 30.4 7.8 35 23-57 204-238 (402)
28 PF05381 Peptidase_C21: Tymovi 25.5 1.6E+02 0.0034 24.9 4.8 89 387-509 3-94 (104)
29 PF04545 Sigma70_r4: Sigma-70, 25.3 58 0.0012 23.0 2.1 32 386-417 18-49 (50)
30 PF09607 BrkDBD: Brinker DNA-b 24.3 67 0.0015 24.0 2.2 25 378-402 12-39 (58)
31 COG3316 Transposase and inacti 23.7 91 0.002 30.0 3.6 36 10-48 116-151 (215)
32 smart00384 AT_hook DNA binding 22.2 51 0.0011 20.3 1.0 8 302-309 2-9 (26)
33 PF05379 Peptidase_C23: Carlav 21.6 63 0.0014 26.5 1.8 15 388-402 4-18 (89)
34 COG3160 Rsd Regulator of sigma 21.5 1.1E+02 0.0024 27.1 3.4 37 390-426 4-49 (162)
35 TIGR00334 5S_RNA_mat_M5 ribonu 20.6 1.1E+02 0.0024 28.5 3.3 40 10-51 37-79 (174)
No 1
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=100.00 E-value=4.6e-40 Score=365.22 Aligned_cols=255 Identities=19% Similarity=0.324 Sum_probs=210.3
Q ss_pred CCchhhHHHHHHHHHHHccCCCCCcEEEeeccHHHHHHHHHhCcccchhhhHHHHHHhHHhhhhhhhcchhHHHHHHHhH
Q 036608 1 SEREDNYIWALERLKTIMQDDILPTMIVTDRELALMNAIEKIFPSATNLLCRWHISRNVLANCKKLFETNERWEAFNSSW 80 (565)
Q Consensus 1 ~E~~es~~W~l~~l~~~~~~~~~P~~iiTD~~~al~~AI~~vFP~a~h~lC~~Hi~kn~~~~~~~~~~~~~~~~~~~~~~ 80 (565)
||+.|+|.|+|++|+++| ++..|.+||||++.||.+||++|||++.|++|+|||.+|+.+++...+... +.|...|
T Consensus 326 dEt~eSf~WLf~tfl~aM-~gk~P~tIiTDqd~am~~AI~~VfP~t~Hr~C~wHI~~~~~e~L~~~~~~~---~~f~~~f 401 (846)
T PLN03097 326 DESAATYSWLMQTWLRAM-GGQAPKVIITDQDKAMKSVISEVFPNAHHCFFLWHILGKVSENLGQVIKQH---ENFMAKF 401 (846)
T ss_pred cCchhhHHHHHHHHHHHh-CCCCCceEEecCCHHHHHHHHHHCCCceehhhHHHHHHHHHHHhhHHhhhh---hHHHHHH
Confidence 799999999999999999 589999999999999999999999999999999999999999999876543 4566555
Q ss_pred -HHHhhcccHHHHHHHHHH---HH--hhhccch---hhhhHHHHHHhccccccCccccccccchhhhhhhhhccCCCcHH
Q 036608 81 -NVLVFSATEQEYIQHLTL---VY--VKQTWLD---KYKEKFIAAWTDFIMHFGNMTTNRAETAHSKLKRQLCSSQGNFV 151 (565)
Q Consensus 81 -~~i~~a~t~~efe~~~~~---~y--~~~~WL~---~~ke~W~~a~~~~~~~~g~~TTnr~ES~n~~lK~~l~~~~~~l~ 151 (565)
++|..+.|++||+..|.. .| ..+.||. +.|++||++|++..|++|+.||+++||+|+.||++++.. .+|.
T Consensus 402 ~~cv~~s~t~eEFE~~W~~mi~ky~L~~n~WL~~LY~~RekWapaY~k~~F~agm~sTqRSES~Ns~fk~yv~~~-tsL~ 480 (846)
T PLN03097 402 EKCIYRSWTEEEFGKRWWKILDRFELKEDEWMQSLYEDRKQWVPTYMRDAFLAGMSTVQRSESINAFFDKYVHKK-TTVQ 480 (846)
T ss_pred HHHHhCCCCHHHHHHHHHHHHHhhcccccHHHHHHHHhHhhhhHHHhcccccCCcccccccccHHHHHHHHhCcC-CCHH
Confidence 578889999999999988 44 4688987 679999999999999999999999999999999999876 6899
Q ss_pred HHHHHHHHHHHH-HHHHHHHHHHhhhh------------hhhcccCHHHHHHHHhHHHHHHHHHHHh---hc--------
Q 036608 152 TLWTKLYSLVEL-QHTEIKASFEKSLT------------TVQHSFTPSVFKELRGLVARNALDMILS---ES-------- 207 (565)
Q Consensus 152 ~~~~~i~~~v~~-~~~e~~~~~~~~~~------------~~~~~~t~~~~~~l~~~is~~a~~~v~~---q~-------- 207 (565)
.|++++..++.. +.+|.++++..++. .+..+||+.+|++|+.++.....+.+.. ..
T Consensus 481 ~Fv~qye~~l~~~~ekE~~aD~~s~~~~P~l~t~~piEkQAs~iYT~~iF~kFQ~El~~~~~~~~~~~~~dg~~~~y~V~ 560 (846)
T PLN03097 481 EFVKQYETILQDRYEEEAKADSDTWNKQPALKSPSPLEKSVSGVYTHAVFKKFQVEVLGAVACHPKMESQDETSITFRVQ 560 (846)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhcccCCcccccccHHHHHHHHHhHHHHHHHHHHHHHHhhheEEeeeccCCceEEEEEE
Confidence 999999999875 67778888765432 2467899999999999986543322211 00
Q ss_pred ----cceeec--c--ccccccCccccccccccchhhhhccccccccccccccCCCCCCChhhHHHHhhhcCCC
Q 036608 208 ----KRANLI--G--IDISACGCVVRHTHGLPCAHEIGEYKREDLVCTSYEKSAELSCTPKMEMIIKSFEDSD 272 (565)
Q Consensus 208 ----~~~~~v--~--~~~~~CsC~~~~~~GiPC~H~lavl~~~df~~~~~~~~~~~~~~p~~~~i~~r~~~~~ 272 (565)
.+.+.| + ....+|+|++|+..||||+|+|+||... .+.-.|+ .+|.+||.+-+
T Consensus 561 ~~~~~~~~~V~~d~~~~~v~CsC~kFE~~GILCrHaLkVL~~~-----------~v~~IP~-~YILkRWTKdA 621 (846)
T PLN03097 561 DFEKNQDFTVTWNQTKLEVSCICRLFEYKGYLCRHALVVLQMC-----------QLSAIPS-QYILKRWTKDA 621 (846)
T ss_pred EecCCCcEEEEEecCCCeEEeeccCeecCccchhhHHHHHhhc-----------CcccCch-hhhhhhchhhh
Confidence 111222 2 2356999999999999999999999888 4455566 78888887754
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=99.69 E-value=1.9e-17 Score=145.73 Aligned_cols=107 Identities=24% Similarity=0.386 Sum_probs=86.7
Q ss_pred CCCCCchHHHHHHHhh----cCcchHHHHHHHHHHHHH-hcccchhhhhcchhhHHHHHhhccccCCCCCcCCcccCCCc
Q 036608 384 VADGNCGFRAVANLIG----IGEDSWAQVRKDLVIELQ-SHFNDYKRVFEYAGRAEEVLHSLLYFENNPGREYWMTMPEI 458 (565)
Q Consensus 384 ~gdG~C~fraia~~l~----~~~~~~~~vR~~~~~~l~-~~~~~y~~~~~~~~~~~~~~~~l~~~~~~~~~~~W~~~~~~ 458 (565)
+|||||+|||||++|+ ++++.|..||++++++|+ .+++.|.+++.++ .| ...+.|++.+++
T Consensus 1 pgDGnClF~Avs~~l~~~~~~~~~~~~~lR~~~~~~l~~~~~~~~~~~~~~~--------~~------~~~~~Wg~~~el 66 (121)
T PF02338_consen 1 PGDGNCLFRAVSDQLYGDGGGSEDNHQELRKAVVDYLRDKNRDKFEEFLEGD--------KM------SKPGTWGGEIEL 66 (121)
T ss_dssp -SSTTHHHHHHHHHHCTT-SSSTTTHHHHHHHHHHHHHTHTTTHHHHHHHHH--------HH------TSTTSHEEHHHH
T ss_pred CCCccHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHhccchhhhhhhhh--------hh------ccccccCcHHHH
Confidence 6999999999999999 999999999999999999 9999999988654 55 566899998888
Q ss_pred hhhhccccceeEEEEeCCcc--ccccCCcC--CCCCCCCCceEEEEEec-----CCce
Q 036608 459 GHIIASKYNVVLLHISDVLN--LTFLPLRS--IPLSRSSHKIIAIGFVN-----RNHF 507 (565)
Q Consensus 459 g~~iA~~y~~pi~~~s~~~~--~t~~p~~~--~p~~~~~~~~i~l~~~~-----~~Hf 507 (565)
+++|+.|+|+|++++.... ..+++..+ +|... .++|+|+|.. ++||
T Consensus 67 -~a~a~~~~~~I~v~~~~~~~~~~~~~~~~~~~~~~~--~~~i~l~~~~~l~~~~~Hy 121 (121)
T PF02338_consen 67 -QALANVLNRPIIVYSSSDGDNVVFIKFTGKYPPLES--PPPICLCYHGHLYYTGNHY 121 (121)
T ss_dssp -HHHHHHHTSEEEEECETTTBEEEEEEESCEESTTTT--TTSEEEEEETEEEEETTEE
T ss_pred -HHHHHHhCCeEEEEEcCCCCccceeeecCccccCCC--CCeEEEEEcCCccCCCCCC
Confidence 7999999999999875333 23332221 23333 5889999997 8998
No 3
>KOG2606 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.64 E-value=1.5e-16 Score=152.84 Aligned_cols=135 Identities=13% Similarity=0.127 Sum_probs=112.6
Q ss_pred ccCcccccccccccccCCCCCchHHHHHHHhhcCc---chHHHHHHHHHHHHHhcccchhhhhcc--------hhhHHHH
Q 036608 368 SFPFGLRPYICGVSDVVADGNCGFRAVANLIGIGE---DSWAQVRKDLVIELQSHFNDYKRVFEY--------AGRAEEV 436 (565)
Q Consensus 368 ~~~~~l~~~~~~~~~v~gdG~C~fraia~~l~~~~---~~~~~vR~~~~~~l~~~~~~y~~~~~~--------~~~~~~~ 436 (565)
.+-..|.+-.+.++|+++||||.|+||++||.... -+-..+|.+..+||++|.++|.+|+-+ .++|+.|
T Consensus 149 k~~~il~~~~l~~~~Ip~DG~ClY~aI~hQL~~~~~~~~~v~kLR~~~a~Ymr~H~~df~pf~~~eet~d~~~~~~f~~Y 228 (302)
T KOG2606|consen 149 KLAQILEERGLKMFDIPADGHCLYAAISHQLKLRSGKLLSVQKLREETADYMREHVEDFLPFLLDEETGDSLGPEDFDKY 228 (302)
T ss_pred HHHHHHHhccCccccCCCCchhhHHHHHHHHHhccCCCCcHHHHHHHHHHHHHHHHHHhhhHhcCccccccCCHHHHHHH
Confidence 45677888999999999999999999999998874 358999999999999999999999833 3479999
Q ss_pred HhhccccCCCCCcCCcccCCCchhhhccccceeEEEEeCCccccccCCcCCCCCCCCCceEEEEEe-----cCCceEeee
Q 036608 437 LHSLLYFENNPGREYWMTMPEIGHIIASKYNVVLLHISDVLNLTFLPLRSIPLSRSSHKIIAIGFV-----NRNHFIEVF 511 (565)
Q Consensus 437 ~~~l~~~~~~~~~~~W~~~~~~g~~iA~~y~~pi~~~s~~~~~t~~p~~~~p~~~~~~~~i~l~~~-----~~~Hf~sl~ 511 (565)
++.+ +.++.|++-+..+ +|+++|++||.+|..+++.. ..++...+ -+||+|+|+ .|.||||+.
T Consensus 229 c~eI------~~t~~WGgelEL~-AlShvL~~PI~Vy~~~~p~~----~~geey~k-d~pL~lvY~rH~y~LGeHYNS~~ 296 (302)
T KOG2606|consen 229 CREI------RNTAAWGGELELK-ALSHVLQVPIEVYQADGPIL----EYGEEYGK-DKPLILVYHRHAYGLGEHYNSVT 296 (302)
T ss_pred HHHh------hhhccccchHHHH-HHHHhhccCeEEeecCCCce----eechhhCC-CCCeeeehHHhHHHHHhhhcccc
Confidence 9999 7889999999984 99999999999998765532 23344442 278999987 689999998
Q ss_pred cCC
Q 036608 512 MLP 514 (565)
Q Consensus 512 ~~~ 514 (565)
...
T Consensus 297 ~~~ 299 (302)
T KOG2606|consen 297 PLK 299 (302)
T ss_pred ccc
Confidence 643
No 4
>PF10551 MULE: MULE transposase domain; InterPro: IPR018289 This entry represents a domain found in Mutator-like elements (MULE)-encoded tranposases, some of which also contain a zinc-finger motif [, ]. This domain is also found in a transposase for the insertion sequence element IS256 in transposon Tn4001 [].
Probab=99.41 E-value=1.9e-13 Score=114.26 Aligned_cols=58 Identities=47% Similarity=0.834 Sum_probs=54.7
Q ss_pred CCchhhHHHHHHHHHHHccCCCCCcEEEeeccHHHHHHHHHhCcccchhhhHHHHHHhHH
Q 036608 1 SEREDNYIWALERLKTIMQDDILPTMIVTDRELALMNAIEKIFPSATNLLCRWHISRNVL 60 (565)
Q Consensus 1 ~E~~es~~W~l~~l~~~~~~~~~P~~iiTD~~~al~~AI~~vFP~a~h~lC~~Hi~kn~~ 60 (565)
+|+.++|.|+|+.|++.+. .. |.+||||++.|+.+||+++||++.|++|.||+.+|++
T Consensus 36 ~e~~~~~~~~l~~~~~~~~-~~-p~~ii~D~~~~~~~Ai~~vfP~~~~~~C~~H~~~n~k 93 (93)
T PF10551_consen 36 SESEESYEWFLEKLKEAMP-QK-PKVIISDFDKALINAIKEVFPDARHQLCLFHILRNIK 93 (93)
T ss_pred CCChhhhHHHHHHhhhccc-cC-ceeeeccccHHHHHHHHHHCCCceEehhHHHHHHhhC
Confidence 5899999999999999995 35 9999999999999999999999999999999999974
No 5
>PF00872 Transposase_mut: Transposase, Mutator family; InterPro: IPR001207 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. The mutator family of transposases consists of a number of elements that include, mutator from maize, IsT2 from Thiobacillus ferrooxidans, Is256 from Staphylococcus aureus, Is1201 from Lactobacillus helveticus, Is1081 from Mycobacterium bovis, IsRm3 from Rhizobium meliloti and others. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=99.15 E-value=5e-12 Score=132.85 Aligned_cols=135 Identities=22% Similarity=0.280 Sum_probs=100.5
Q ss_pred CCchhhHHHHHHHHHHHccCCCCCcEEEeeccHHHHHHHHHhCcccchhhhHHHHHHhHHhhhhhhhcchhHHHHHHHhH
Q 036608 1 SEREDNYIWALERLKTIMQDDILPTMIVTDRELALMNAIEKIFPSATNLLCRWHISRNVLANCKKLFETNERWEAFNSSW 80 (565)
Q Consensus 1 ~E~~es~~W~l~~l~~~~~~~~~P~~iiTD~~~al~~AI~~vFP~a~h~lC~~Hi~kn~~~~~~~~~~~~~~~~~~~~~~ 80 (565)
.|+.++|.-+|+.|++. |...|..|++|..+||..||.++||++.++.|.+|+++|+.+++... ..+.+....
T Consensus 207 ~Es~~~W~~~l~~L~~R--Gl~~~~lvv~Dg~~gl~~ai~~~fp~a~~QrC~vH~~RNv~~~v~~k-----~~~~v~~~L 279 (381)
T PF00872_consen 207 RESAASWREFLQDLKER--GLKDILLVVSDGHKGLKEAIREVFPGAKWQRCVVHLMRNVLRKVPKK-----DRKEVKADL 279 (381)
T ss_pred CCccCEeeecchhhhhc--cccccceeeccccccccccccccccchhhhhheechhhhhccccccc-----cchhhhhhc
Confidence 47889999999999997 77889999999999999999999999999999999999999998643 346778888
Q ss_pred HHHhhcccHHHHHHHHHHHHhhhccchhhh---hHHHHHH--------hccccccCccccccccchhhhhhhhhc
Q 036608 81 NVLVFSATEQEYIQHLTLVYVKQTWLDKYK---EKFIAAW--------TDFIMHFGNMTTNRAETAHSKLKRQLC 144 (565)
Q Consensus 81 ~~i~~a~t~~efe~~~~~~y~~~~WL~~~k---e~W~~a~--------~~~~~~~g~~TTnr~ES~n~~lK~~l~ 144 (565)
+.|..+.+.++....++. +...|-..++ +.|-..| +....+--.+|||.+|++|+.+|+...
T Consensus 280 k~I~~a~~~e~a~~~l~~--f~~~~~~kyp~~~~~l~~~~~~~~tf~~fP~~~~~~i~TTN~iEsln~~irrr~~ 352 (381)
T PF00872_consen 280 KAIYQAPDKEEAREALEE--FAEKWEKKYPKAAKSLEENWDELLTFLDFPPEHRRSIRTTNAIESLNKEIRRRTK 352 (381)
T ss_pred cccccccccchhhhhhhh--cccccccccchhhhhhhhccccccceeeecchhccccchhhhccccccchhhhcc
Confidence 888888888777666654 1111211110 1111111 111222235799999999999998554
No 6
>smart00575 ZnF_PMZ plant mutator transposase zinc finger.
Probab=98.56 E-value=1.6e-08 Score=63.88 Aligned_cols=25 Identities=24% Similarity=0.636 Sum_probs=22.8
Q ss_pred cccCccccccccccchhhhhccccc
Q 036608 218 SACGCVVRHTHGLPCAHEIGEYKRE 242 (565)
Q Consensus 218 ~~CsC~~~~~~GiPC~H~lavl~~~ 242 (565)
.+|||+.|+..||||+|+|+|+...
T Consensus 1 ~~CsC~~~~~~gipC~H~i~v~~~~ 25 (28)
T smart00575 1 KTCSCRKFQLSGIPCRHALAAAIHI 25 (28)
T ss_pred CcccCCCcccCCccHHHHHHHHHHh
Confidence 3799999999999999999998765
No 7
>KOG2605 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=98.54 E-value=3.3e-08 Score=101.33 Aligned_cols=131 Identities=17% Similarity=0.115 Sum_probs=98.2
Q ss_pred cccccccccccccCCCCCchHHHHHHHhhcCcchHHHHHHHHHHHHHhcccchhhhhcchhhHHHHHhhccccCCCCCcC
Q 036608 371 FGLRPYICGVSDVVADGNCGFRAVANLIGIGEDSWAQVRKDLVIELQSHFNDYKRVFEYAGRAEEVLHSLLYFENNPGRE 450 (565)
Q Consensus 371 ~~l~~~~~~~~~v~gdG~C~fraia~~l~~~~~~~~~vR~~~~~~l~~~~~~y~~~~~~~~~~~~~~~~l~~~~~~~~~~ 450 (565)
..+.-|+..+.-|.+||+|.|||+|+|+.++.|.|..+|++..++++.++++|..++.. .|..|++.... .+
T Consensus 211 ~~~~~~g~e~~Kv~edGsC~fra~aDQvy~d~e~~~~~~~~~~dq~~~e~~~~~~~vt~--~~~~y~k~kr~------~~ 282 (371)
T KOG2605|consen 211 KRKKHFGFEYKKVVEDGSCLFRALADQVYGDDEQHDHNRRECVDQLKKERDFYEDYVTE--DFTSYIKRKRA------DG 282 (371)
T ss_pred HHHHHhhhhhhhcccCCchhhhccHHHhhcCHHHHHHHHHHHHHHHhhccccccccccc--chhhccccccc------CC
Confidence 34577889999999999999999999999999999999999999999999999888854 68999988844 45
Q ss_pred CcccCCCchhhhcc---ccceeEEEEeCCccccccCCcCCCCCCCCCceEEEEEecCCceEeeecC
Q 036608 451 YWMTMPEIGHIIAS---KYNVVLLHISDVLNLTFLPLRSIPLSRSSHKIIAIGFVNRNHFIEVFML 513 (565)
Q Consensus 451 ~W~~~~~~g~~iA~---~y~~pi~~~s~~~~~t~~p~~~~p~~~~~~~~i~l~~~~~~Hf~sl~~~ 513 (565)
.|++...+ |++|. -..+|++..+.+ ...|- ..+|....+...+++.++...||+.++..
T Consensus 283 ~~gnhie~-Qa~a~~~~~~~~~~~~~~~~-~t~~~--~~~~~~~~~~~~~~~n~~~~~h~~~~~~~ 344 (371)
T KOG2605|consen 283 EPGNHIEQ-QAAADIYEEIEKPLNITSFK-DTCYI--QTPPAIEESVKMEKYNFWVEVHYNTARHS 344 (371)
T ss_pred CCcchHHH-hhhhhhhhhccccceeeccc-cccee--ccCcccccchhhhhhcccchhhhhhcccc
Confidence 66666665 67885 334555444432 21111 11234444456688899889999988863
No 8
>KOG3288 consensus OTU-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=98.18 E-value=1.6e-05 Score=75.29 Aligned_cols=124 Identities=16% Similarity=0.162 Sum_probs=89.2
Q ss_pred ccccccCCCCCchHHHHHHHhhcCcchH-HHHHHHHHHHHHhcccchhhhh-cc-hhhHHHHHhhccccCCCCCcCCccc
Q 036608 378 CGVSDVVADGNCGFRAVANLIGIGEDSW-AQVRKDLVIELQSHFNDYKRVF-EY-AGRAEEVLHSLLYFENNPGREYWMT 454 (565)
Q Consensus 378 ~~~~~v~gdG~C~fraia~~l~~~~~~~-~~vR~~~~~~l~~~~~~y~~~~-~~-~~~~~~~~~~l~~~~~~~~~~~W~~ 454 (565)
...+=|+.|--|+|+||+.-+....+.- .++|+-+.+++-++++.|..-+ |. ..+|..++.++ +.|++
T Consensus 110 l~~~vvp~DNSCLF~ai~yv~~k~~~~~~~elR~iiA~~Vasnp~~yn~AiLgK~n~eYc~WI~k~---------dsWGG 180 (307)
T KOG3288|consen 110 LSRRVVPDDNSCLFTAIAYVIFKQVSNRPYELREIIAQEVASNPDKYNDAILGKPNKEYCAWILKM---------DSWGG 180 (307)
T ss_pred eEEEeccCCcchhhhhhhhhhcCccCCCcHHHHHHHHHHHhcChhhhhHHHhCCCcHHHHHHHccc---------cccCc
Confidence 3445678899999999998886653322 6899999999999999997655 32 34566666555 89998
Q ss_pred CCCchhhhccccceeEEEEeCC--ccccccCCcCCCCCCCCCceEEEEEecCCceEeeecCCCCCC
Q 036608 455 MPEIGHIIASKYNVVLLHISDV--LNLTFLPLRSIPLSRSSHKIIAIGFVNRNHFIEVFMLPASPI 518 (565)
Q Consensus 455 ~~~~g~~iA~~y~~pi~~~s~~--~~~t~~p~~~~p~~~~~~~~i~l~~~~~~Hf~sl~~~~~~p~ 518 (565)
-.+.+ ||++.|++-|+++..+ ....|=+- +... ++ ++|.| +|-||.+|.+....|.
T Consensus 181 aIEls-ILS~~ygveI~vvDiqt~rid~fged---~~~~--~r-v~lly-dGIHYD~l~m~~~~~~ 238 (307)
T KOG3288|consen 181 AIELS-ILSDYYGVEICVVDIQTVRIDRFGED---KNFD--NR-VLLLY-DGIHYDPLAMNEFKPT 238 (307)
T ss_pred eEEee-eehhhhceeEEEEecceeeehhcCCC---CCCC--ce-EEEEe-cccccChhhhccCCcc
Confidence 88886 9999999999999753 33333222 1122 33 55665 5999999999765443
No 9
>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=98.11 E-value=5.3e-06 Score=82.11 Aligned_cols=98 Identities=12% Similarity=-0.036 Sum_probs=50.3
Q ss_pred HHHHHHHHHHHhcccchhhhhcch--hhHHHHHhhccccCCCCCcCCcccCCCchhhhccccceeEEEEeCCcc---ccc
Q 036608 407 QVRKDLVIELQSHFNDYKRVFEYA--GRAEEVLHSLLYFENNPGREYWMTMPEIGHIIASKYNVVLLHISDVLN---LTF 481 (565)
Q Consensus 407 ~vR~~~~~~l~~~~~~y~~~~~~~--~~~~~~~~~l~~~~~~~~~~~W~~~~~~g~~iA~~y~~pi~~~s~~~~---~t~ 481 (565)
-+|-....+|+.|.+.|.+++.+. ..++++|..= +.......++ . ...+||++++++|.++-...+ ..+
T Consensus 141 flRLlts~~l~~~~d~y~~fi~~~~~~tve~~C~~~-Vep~~~Ead~----v-~i~ALa~aL~v~i~v~yld~~~~~~~~ 214 (244)
T PF10275_consen 141 FLRLLTSAYLKSNSDEYEPFIDGLEYLTVEEFCSQE-VEPMGKEADH----V-QIIALAQALGVPIRVEYLDRSVEGDEV 214 (244)
T ss_dssp HHHHHHHHHHHHTHHHHGGGSSTT--S-HHHHHHHH-TSSTT--B-H----H-HHHHHHHHHT--EEEEESSSSGCSTTS
T ss_pred HHHHHHHHHHHhhHHHHhhhhcccccCCHHHHHHhh-cccccccchh----H-HHHHHHHHhCCeEEEEEecCCCCCCcc
Confidence 345556666777777777777654 5667776433 1111111111 1 124699999999966642221 111
Q ss_pred cCCcCCCCCCCCCceEEEEEecCCceEeee
Q 036608 482 LPLRSIPLSRSSHKIIAIGFVNRNHFIEVF 511 (565)
Q Consensus 482 ~p~~~~p~~~~~~~~i~l~~~~~~Hf~sl~ 511 (565)
-...-+|.+....|.|.|.|-. .||+.|+
T Consensus 215 ~~~~~~~~~~~~~~~i~LLyrp-gHYdIly 243 (244)
T PF10275_consen 215 NRHEFPPDNESQEPQITLLYRP-GHYDILY 243 (244)
T ss_dssp EEEEES-SSTTSS-SEEEEEET-BEEEEEE
T ss_pred ccccCCCccCCCCCEEEEEEcC-Ccccccc
Confidence 1111112222336889999985 5999886
No 10
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=97.99 E-value=1.1e-05 Score=83.70 Aligned_cols=132 Identities=20% Similarity=0.221 Sum_probs=91.5
Q ss_pred hhHHHHHHHHHHHccCCCCCcEEEeeccHHHHHHHHHhCcccchhhhHHHHHHhHHhhhhhhhcchhHHHHHHHhHHHHh
Q 036608 5 DNYIWALERLKTIMQDDILPTMIVTDRELALMNAIEKIFPSATNLLCRWHISRNVLANCKKLFETNERWEAFNSSWNVLV 84 (565)
Q Consensus 5 es~~W~l~~l~~~~~~~~~P~~iiTD~~~al~~AI~~vFP~a~h~lC~~Hi~kn~~~~~~~~~~~~~~~~~~~~~~~~i~ 84 (565)
..|.-+|..|+.. +......+++|...++.+||..+||.+.+++|..|+.+|+.++.... .++.+....+.+.
T Consensus 190 ~~w~~~l~~l~~r--gl~~v~l~v~Dg~~gl~~aI~~v~p~a~~Q~C~vH~~Rnll~~v~~k-----~~d~i~~~~~~I~ 262 (379)
T COG3328 190 KFWLSFLLDLKNR--GLSDVLLVVVDGLKGLPEAISAVFPQAAVQRCIVHLVRNLLDKVPRK-----DQDAVLSDLRSIY 262 (379)
T ss_pred hhHHHHHHHHHhc--cccceeEEecchhhhhHHHHHHhccHhhhhhhhhHHHhhhhhhhhhh-----hhHHHHhhhhhhh
Confidence 4677777777776 56667788889999999999999999999999999999999998643 4456777777778
Q ss_pred hcccHHHHHHHHHHHHhhhccchh---hhhHHHHHHhcc----cccc----Cccccccccchhhhhhhhhcc
Q 036608 85 FSATEQEYIQHLTLVYVKQTWLDK---YKEKFIAAWTDF----IMHF----GNMTTNRAETAHSKLKRQLCS 145 (565)
Q Consensus 85 ~a~t~~efe~~~~~~y~~~~WL~~---~ke~W~~a~~~~----~~~~----g~~TTnr~ES~n~~lK~~l~~ 145 (565)
.+++.++....|..-- ..|-.. .-..|-.+|... .+.. -..|||..|++|..+++....
T Consensus 263 ~a~~~e~~~~~~~~~~--~~w~~~yP~i~~~~~~~~~~~~~F~~fp~~~r~~i~ttN~IE~~n~~ir~~~~~ 332 (379)
T COG3328 263 IAPDAEEALLALLAFS--ELWGKRYPAILKSWRNALEELLPFFAFPSEIRKIIYTTNAIESLNKLIRRRTKV 332 (379)
T ss_pred ccCCcHHHHHHHHHHH--HhhhhhcchHHHHHHHHHHHhcccccCcHHHHhHhhcchHHHHHHHHHHHHHhh
Confidence 8887777666655400 022211 011222222211 1112 246999999999988875543
No 11
>PF04434 SWIM: SWIM zinc finger; InterPro: IPR007527 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the SWIM (SWI2/SNF2 and MuDR) zinc-binding domain, which is found in a variety of prokaryotic and eukaryotic proteins, such as mitogen-activated protein kinase kinase kinase 1 (or MEKK1). It is also found in the related protein MEX (MEKK1-related protein X), a testis-expressed protein that acts as an E3 ubiquitin ligase through the action of E2 ubiquitin-conjugating enzymes in the proteasome degradation pathway; the SWIM domain is critical for MEX ubiquitination []. SWIM domains are also found in the homologous recombination protein Sws1 [], as well as in several hypothetical proteins. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=97.62 E-value=1.8e-05 Score=54.79 Aligned_cols=28 Identities=25% Similarity=0.566 Sum_probs=24.9
Q ss_pred cccccccCccccccccccchhhhhcccc
Q 036608 214 GIDISACGCVVRHTHGLPCAHEIGEYKR 241 (565)
Q Consensus 214 ~~~~~~CsC~~~~~~GiPC~H~lavl~~ 241 (565)
+.....|||..|+..|.||+|++|++..
T Consensus 11 ~~~~~~CsC~~~~~~~~~CkHi~av~~~ 38 (40)
T PF04434_consen 11 SIEQASCSCPYFQFRGGPCKHIVAVLLA 38 (40)
T ss_pred cccccEeeCCCccccCCcchhHHHHHHh
Confidence 4567899999999999999999999864
No 12
>KOG3991 consensus Uncharacterized conserved protein [Function unknown]
Probab=97.50 E-value=0.00052 Score=64.46 Aligned_cols=92 Identities=11% Similarity=0.002 Sum_probs=56.5
Q ss_pred HHHHHHHHHhcccchhhhhcchhhHHHHHhhccccCCCCCcCCcccCCCchhh--hccccceeE--EEEeCCccccccCC
Q 036608 409 RKDLVIELQSHFNDYKRVFEYAGRAEEVLHSLLYFENNPGREYWMTMPEIGHI--IASKYNVVL--LHISDVLNLTFLPL 484 (565)
Q Consensus 409 R~~~~~~l~~~~~~y~~~~~~~~~~~~~~~~l~~~~~~~~~~~W~~~~~~g~~--iA~~y~~pi--~~~s~~~~~t~~p~ 484 (565)
|--.-.+|+++.|.|.+|+.++..+++++..- +. |.. .-.+|-+| |+++.++-| .+++-+..-++-+.
T Consensus 160 RLvtS~~ik~~adfy~pFI~e~~tV~~fC~~e-VE----Pm~---kesdhi~I~ALs~Al~i~irVey~dr~~~~~~~hH 231 (256)
T KOG3991|consen 160 RLVTSGFIKSNADFYQPFIDEGMTVKAFCTQE-VE----PMY---KESDHIHITALSQALGIRIRVEYVDRGSGDTVNHH 231 (256)
T ss_pred HHHHHHHHhhChhhhhccCCCCCcHHHHHHhh-cc----hhh---hccCceeHHHHHhhhCceEEEEEecCCCCCCCCCC
Confidence 44444578899999999998888899988765 21 111 12234444 788888655 44442222233332
Q ss_pred cCCCCCCCCCceEEEEEecCCceEeeec
Q 036608 485 RSIPLSRSSHKIIAIGFVNRNHFIEVFM 512 (565)
Q Consensus 485 ~~~p~~~~~~~~i~l~~~~~~Hf~sl~~ 512 (565)
.- | ..+.|.|.|.|- +-||..|+.
T Consensus 232 ~f-p--e~s~P~I~LLYr-pGHYdilY~ 255 (256)
T KOG3991|consen 232 DF-P--EASAPEIYLLYR-PGHYDILYK 255 (256)
T ss_pred cC-c--cccCceEEEEec-CCccccccC
Confidence 21 2 223588999998 469998875
No 13
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=97.38 E-value=2.3e-05 Score=75.99 Aligned_cols=137 Identities=9% Similarity=-0.139 Sum_probs=87.2
Q ss_pred CCCCCcccccCcccccccccccccCCCCCchHHHHHHHhhcCc-----chHHHHHHHHHHHHHhcccchhhhhcch----
Q 036608 360 PKHASYIDSFPFGLRPYICGVSDVVADGNCGFRAVANLIGIGE-----DSWAQVRKDLVIELQSHFNDYKRVFEYA---- 430 (565)
Q Consensus 360 ~~~~~~~~~~~~~l~~~~~~~~~v~gdG~C~fraia~~l~~~~-----~~~~~vR~~~~~~l~~~~~~y~~~~~~~---- 430 (565)
....++|-.+|.....--..-.+..|||||.|.+|+++|+..- +.=...|..-..+...+...|.++.-++
T Consensus 153 Dl~n~~i~~~~~i~y~~~i~k~d~~~dG~ieia~iS~~l~v~i~~Vdv~~~~~dr~~~~~~~q~~~i~f~g~hfD~~t~~ 232 (306)
T COG5539 153 DLYNPAILEIDVIAYATWIVKPDSQGDGCIEIAIISDQLPVRIHVVDVDKDSEDRYNSHPYVQRISILFTGIHFDEETLA 232 (306)
T ss_pred cccchhhcCcchHHHHHhhhccccCCCceEEEeEeccccceeeeeeecchhHHhhccCChhhhhhhhhhcccccchhhhh
Confidence 3344555566665555555557889999999999999999853 2124455555556666666776654332
Q ss_pred -hhHHHHHhhccccCCCCCcCCcccCCCchhhhccccceeEEEEeCCccccccCCcCCCCCCCCCceEEEEEe-----cC
Q 036608 431 -GRAEEVLHSLLYFENNPGREYWMTMPEIGHIIASKYNVVLLHISDVLNLTFLPLRSIPLSRSSHKIIAIGFV-----NR 504 (565)
Q Consensus 431 -~~~~~~~~~l~~~~~~~~~~~W~~~~~~g~~iA~~y~~pi~~~s~~~~~t~~p~~~~p~~~~~~~~i~l~~~-----~~ 504 (565)
..++.+++.+ -..+.|+..+.. +.||+.+..|+-++..+....-+- +-.. +...++.|+ .|
T Consensus 233 m~~~dt~~ne~------~~~a~~g~~~ei-~qLas~lk~~~~~~nT~~~~ik~n----~c~~--~~~~e~~~~~Ha~a~G 299 (306)
T COG5539 233 MVLWDTYVNEV------LFDASDGITIEI-QQLASLLKNPHYYTNTASPSIKCN----ICGT--GFVGEKDYYAHALATG 299 (306)
T ss_pred cchHHHHHhhh------cccccccchHHH-HHHHHHhcCceEEeecCCceEEee----cccc--ccchhhHHHHHHHhhc
Confidence 4588888888 555788755444 679999999998876543222221 2222 344555554 46
Q ss_pred CceEee
Q 036608 505 NHFIEV 510 (565)
Q Consensus 505 ~Hf~sl 510 (565)
||+++
T Consensus 300 -H~n~~ 304 (306)
T COG5539 300 -HYNFG 304 (306)
T ss_pred -Ccccc
Confidence 99875
No 14
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=90.89 E-value=1.5 Score=47.80 Aligned_cols=60 Identities=18% Similarity=0.251 Sum_probs=44.8
Q ss_pred hhHHHHHHHHHHHccCCCC-CcEEEeeccHHHHHHHHHhCcccchhhhHHHHHHhHHhhhhh
Q 036608 5 DNYIWALERLKTIMQDDIL-PTMIVTDRELALMNAIEKIFPSATNLLCRWHISRNVLANCKK 65 (565)
Q Consensus 5 es~~W~l~~l~~~~~~~~~-P~~iiTD~~~al~~AI~~vFP~a~h~lC~~Hi~kn~~~~~~~ 65 (565)
+-|.-+.+.+-+...-... -.++..|+..-+.+++. .||.+.|.+..||+.+.+.+.++.
T Consensus 239 ~~~~~v~~~i~~~Y~~~~~~~iiingDGa~WIk~~~~-~~~~~~~~LD~FHl~k~i~~~~~~ 299 (470)
T PF06782_consen 239 EFWEEVLDYIYNHYDLDKTTKIIINGDGASWIKEGAE-FFPKAEYFLDRFHLNKKIKQALSH 299 (470)
T ss_pred HHHHHHHHHHHHhcCcccceEEEEeCCCcHHHHHHHH-hhcCceEEecHHHHHHHHHHHhhh
Confidence 4466666666666531222 34678899999988776 999999999999999999988764
No 15
>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=89.65 E-value=0.22 Score=41.36 Aligned_cols=59 Identities=17% Similarity=0.308 Sum_probs=36.9
Q ss_pred cccCCCCCchHHHHHHHhhcCcchHHHHHHHHHHHHHhcccchhhhhcchhhHHHHHhhccccCCCCCcCCcccCCCchh
Q 036608 381 SDVVADGNCGFRAVANLIGIGEDSWAQVRKDLVIELQSHFNDYKRVFEYAGRAEEVLHSLLYFENNPGREYWMTMPEIGH 460 (565)
Q Consensus 381 ~~v~gdG~C~fraia~~l~~~~~~~~~vR~~~~~~l~~~~~~y~~~~~~~~~~~~~~~~l~~~~~~~~~~~W~~~~~~g~ 460 (565)
+.+++||+||+++||.-+.. +++++ |.. .| +.-+-+.+.|++--++++
T Consensus 2 ysPP~DG~CG~H~i~aI~n~-------------------------m~~~~--~t~---~l--~~~~r~~d~W~~dedl~~ 49 (108)
T PF05412_consen 2 YSPPGDGSCGWHCIAAIMNH-------------------------MMGGE--FTT---PL--PQRNRPSDDWADDEDLYQ 49 (108)
T ss_pred CCCCCCCchHHHHHHHHHHH-------------------------hhccC--CCc---cc--cccCCChHHccChHHHHH
Confidence 35799999999999876632 22210 000 00 111357789999999988
Q ss_pred hhccccceeEEE
Q 036608 461 IIASKYNVVLLH 472 (565)
Q Consensus 461 ~iA~~y~~pi~~ 472 (565)
+|-.. +.|+-+
T Consensus 50 ~iq~l-~lPat~ 60 (108)
T PF05412_consen 50 VIQSL-RLPATL 60 (108)
T ss_pred HHHHc-cCceec
Confidence 87654 566644
No 16
>PF01610 DDE_Tnp_ISL3: Transposase; InterPro: IPR002560 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. This family includes the IS204 [], IS1001 [], IS1096 [] and IS1165 [] transposases. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=89.56 E-value=0.17 Score=49.97 Aligned_cols=45 Identities=20% Similarity=0.229 Sum_probs=41.0
Q ss_pred CCCCcEEEeeccHHHHHHHHHhCcccchhhhHHHHHHhHHhhhhh
Q 036608 21 DILPTMIVTDRELALMNAIEKIFPSATNLLCRWHISRNVLANCKK 65 (565)
Q Consensus 21 ~~~P~~iiTD~~~al~~AI~~vFP~a~h~lC~~Hi~kn~~~~~~~ 65 (565)
.....+|++|...+...||++.||+|.+....|||++++.+.+..
T Consensus 54 ~~~v~~V~~Dm~~~y~~~~~~~~P~A~iv~DrFHvvk~~~~al~~ 98 (249)
T PF01610_consen 54 RKNVKVVSMDMSPPYRSAIREYFPNAQIVADRFHVVKLANRALDK 98 (249)
T ss_pred ccceEEEEcCCCccccccccccccccccccccchhhhhhhhcchh
Confidence 356789999999999999999999999999999999999987654
No 17
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=88.54 E-value=1.2 Score=44.02 Aligned_cols=112 Identities=17% Similarity=0.036 Sum_probs=76.6
Q ss_pred CCCCchHHHHHHHhhcCcchHHHHHHHHHHHHHhcccchhhhhcchhhHHHHHhhccccCCCCCcCCcccCCCchhhhcc
Q 036608 385 ADGNCGFRAVANLIGIGEDSWAQVRKDLVIELQSHFNDYKRVFEYAGRAEEVLHSLLYFENNPGREYWMTMPEIGHIIAS 464 (565)
Q Consensus 385 gdG~C~fraia~~l~~~~~~~~~vR~~~~~~l~~~~~~y~~~~~~~~~~~~~~~~l~~~~~~~~~~~W~~~~~~g~~iA~ 464 (565)
.|--|.|+|.+..++-- +-..+|+.+..|+.+++|.|.+.+.+. +--.++..| ..++-|.+--..-.+|.+
T Consensus 119 ~d~srl~q~~~~~l~~a--sv~~lrE~vs~Ev~snPDl~n~~i~~~-~~i~y~~~i------~k~d~~~dG~ieia~iS~ 189 (306)
T COG5539 119 DDNSRLFQAERYSLRDA--SVAKLREVVSLEVLSNPDLYNPAILEI-DVIAYATWI------VKPDSQGDGCIEIAIISD 189 (306)
T ss_pred CchHHHHHHHHhhhhhh--hHHHHHHHHHHHHhhCccccchhhcCc-chHHHHHhh------hccccCCCceEEEeEecc
Confidence 45789999998888764 688999999999999999998877543 334444455 556777643333347999
Q ss_pred ccceeEEEEeCC-cc-ccccCCcCCCCCCCCCceEEEEEecCCceEeeecC
Q 036608 465 KYNVVLLHISDV-LN-LTFLPLRSIPLSRSSHKIIAIGFVNRNHFIEVFML 513 (565)
Q Consensus 465 ~y~~pi~~~s~~-~~-~t~~p~~~~p~~~~~~~~i~l~~~~~~Hf~sl~~~ 513 (565)
.+++-|.++... .+ ..|.+ .|.. --|++.|. |-||.++++.
T Consensus 190 ~l~v~i~~Vdv~~~~~dr~~~---~~~~----q~~~i~f~-g~hfD~~t~~ 232 (306)
T COG5539 190 QLPVRIHVVDVDKDSEDRYNS---HPYV----QRISILFT-GIHFDEETLA 232 (306)
T ss_pred ccceeeeeeecchhHHhhccC---Chhh----hhhhhhhc-ccccchhhhh
Confidence 999999877643 21 12221 1222 23677776 7899888753
No 18
>PRK09784 hypothetical protein; Provisional
Probab=50.68 E-value=10 Score=36.45 Aligned_cols=37 Identities=30% Similarity=0.388 Sum_probs=26.0
Q ss_pred ccccccccccCCCCCchHHHHHHHhhcCcchHHHHHHH
Q 036608 374 RPYICGVSDVVADGNCGFRAVANLIGIGEDSWAQVRKD 411 (565)
Q Consensus 374 ~~~~~~~~~v~gdG~C~fraia~~l~~~~~~~~~vR~~ 411 (565)
+.|+++---|.|||-|+.|||-..- ..+-+|..+-..
T Consensus 196 ~~~glkyapvdgdgycllrailvlk-~h~yswal~s~k 232 (417)
T PRK09784 196 KTYGLKYAPVDGDGYCLLRAILVLK-QHDYSWALGSHK 232 (417)
T ss_pred hhhCceecccCCCchhHHHHHHHhh-hcccchhhccch
Confidence 3567777789999999999997543 333556655433
No 19
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=49.00 E-value=15 Score=32.75 Aligned_cols=25 Identities=36% Similarity=0.406 Sum_probs=23.4
Q ss_pred CCCcEEEeeccHHHHHHHHHhCccc
Q 036608 22 ILPTMIVTDRELALMNAIEKIFPSA 46 (565)
Q Consensus 22 ~~P~~iiTD~~~al~~AI~~vFP~a 46 (565)
..|.+|+||+..+...|++++++..
T Consensus 57 ~~p~~ivtDk~~aY~~A~~~l~~~~ 81 (140)
T PF13610_consen 57 GEPRVIVTDKLPAYPAAIKELNPEG 81 (140)
T ss_pred cccceeecccCCccchhhhhccccc
Confidence 7899999999999999999999974
No 20
>KOG4825 consensus Component of synaptic membrane glycine-, glutamate- and thienylcyclohexylpiperidine-binding glycoprotein (43kDa) [Signal transduction mechanisms]
Probab=44.68 E-value=52 Score=34.91 Aligned_cols=31 Identities=23% Similarity=0.284 Sum_probs=25.2
Q ss_pred cccCCCCCCCCCCCCCCCCCCCccccccccc
Q 036608 299 IKDKTRGRPSQKLDKSTRRDPSRFEYVVSAQ 329 (565)
Q Consensus 299 ~k~~tkGRPk~~~~~st~r~~s~~e~~~~~~ 329 (565)
...-++|||..-..-+++|.||.||.-..+.
T Consensus 284 pqleepgrenqfaepflqekpsswelpIrPq 314 (666)
T KOG4825|consen 284 PQLEEPGRENQFAEPFLQEKPSSWELPIRPQ 314 (666)
T ss_pred ccccCCCCccccccchhhcCCCcceeecccc
Confidence 3456799998888899999999999876654
No 21
>KOG4345 consensus NF-kappa B regulator AP20/Cezanne [Signal transduction mechanisms]
Probab=42.88 E-value=18 Score=40.23 Aligned_cols=52 Identities=15% Similarity=0.224 Sum_probs=34.5
Q ss_pred chhhhccccceeEEEEeC-----Cccc---------cccCCcCCCCCCCCCceEEEEEecCCceEeee
Q 036608 458 IGHIIASKYNVVLLHISD-----VLNL---------TFLPLRSIPLSRSSHKIIAIGFVNRNHFIEVF 511 (565)
Q Consensus 458 ~g~~iA~~y~~pi~~~s~-----~~~~---------t~~p~~~~p~~~~~~~~i~l~~~~~~Hf~sl~ 511 (565)
+..++|+...|||+++++ ..+. .|+||..++.-.. --||+|+|- .-||..+.
T Consensus 225 hifvl~~ilRrpivvvsd~mlR~s~~~sfap~~~ggiylpLe~p~~~c~-r~pLvl~yd-~~hf~~lv 290 (774)
T KOG4345|consen 225 HIFVLAHILRRPIVVVSDTMLRDSGGESFAPIPVGGIYLPLEVPAQECH-RSPLVLAYD-QAHFSALV 290 (774)
T ss_pred HHHHHHHHhhCCeeEecccccccCCCcccccCccCceEEeccCchhhcc-cchhhhhhH-hhhhhhhh
Confidence 556699999999999973 2233 4556655433332 257888886 47888873
No 22
>COG4279 Uncharacterized conserved protein [Function unknown]
Probab=38.54 E-value=12 Score=36.46 Aligned_cols=23 Identities=26% Similarity=0.498 Sum_probs=18.5
Q ss_pred ccccCccccccccccchhhhhccccc
Q 036608 217 ISACGCVVRHTHGLPCAHEIGEYKRE 242 (565)
Q Consensus 217 ~~~CsC~~~~~~GiPC~H~lavl~~~ 242 (565)
...|||..+ ..||.|+-||+..-
T Consensus 124 ~~dCSCPD~---anPCKHi~AvyY~l 146 (266)
T COG4279 124 STDCSCPDY---ANPCKHIAAVYYLL 146 (266)
T ss_pred ccccCCCCc---ccchHHHHHHHHHH
Confidence 358999874 68999999998654
No 23
>COG5431 Uncharacterized metal-binding protein [Function unknown]
Probab=37.75 E-value=13 Score=31.04 Aligned_cols=25 Identities=32% Similarity=0.397 Sum_probs=18.2
Q ss_pred ccccCcccccc-----ccccchhhhhcccc
Q 036608 217 ISACGCVVRHT-----HGLPCAHEIGEYKR 241 (565)
Q Consensus 217 ~~~CsC~~~~~-----~GiPC~H~lavl~~ 241 (565)
..-|||..+.. -.-||.|++..-..
T Consensus 49 ~gfCSCp~~~~svvl~Gk~~C~Hi~glk~A 78 (117)
T COG5431 49 GGFCSCPDFLGSVVLKGKSPCAHIIGLKVA 78 (117)
T ss_pred cCcccCHHHHhHhhhcCcccchhhhheeee
Confidence 45899998872 24579999986543
No 24
>PF02178 AT_hook: AT hook motif; InterPro: IPR017956 AT hooks are DNA-binding motifs with a preference for A/T rich regions. These motifs are found in a variety of proteins, including the high mobility group (HMG) proteins [], in DNA-binding proteins from plants [] and in hBRG1 protein, a central ATPase of the human switching/sucrose non-fermenting (SWI/SNF) remodeling complex []. High mobility group (HMG) proteins are a family of relatively low molecular weight non-histone components in chromatin []. HMG-I and HMG-Y (HMGA) are proteins of about 100 amino acid residues which are produced by the alternative splicing of a single gene. HMG-I/Y proteins bind preferentially to the minor groove of AT-rich regions in double-stranded DNA in a non-sequence specific manner [, ]. It is suggested that these proteins could function in nucleosome phasing and in the 3' end processing of mRNA transcripts. They are also involved in the transcription regulation of genes containing, or in close proximity to, AT-rich regions. ; GO: 0003677 DNA binding; PDB: 2EZE_A 2EZD_A 2EZF_A 2EZG_A.
Probab=36.72 E-value=16 Score=18.71 Aligned_cols=8 Identities=50% Similarity=1.153 Sum_probs=3.2
Q ss_pred CCCCCCCC
Q 036608 302 KTRGRPSQ 309 (565)
Q Consensus 302 ~tkGRPk~ 309 (565)
+.+|||++
T Consensus 2 r~RGRP~k 9 (13)
T PF02178_consen 2 RKRGRPRK 9 (13)
T ss_dssp --SS--TT
T ss_pred CcCCCCcc
Confidence 46899986
No 25
>TIGR03277 methan_mark_9 putative methanogenesis marker domain 9. A gene for a protein that contains a copy of this domain, to date, is found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it. A 69-amino acid core region of this 110-amino acid domain contains eight invariant Cys residues, including two copies of a motif [WFY]CCxxKPC. These motifs could be consistent with predicted metal-binding transcription factor as was suggested for the COG4008 family. Some members of this family have an additional N-terminal domain of about 250 amino acids from the nifR3 family of predicted TIM-barrel proteins.
Probab=30.61 E-value=43 Score=28.15 Aligned_cols=32 Identities=25% Similarity=0.537 Sum_probs=28.0
Q ss_pred CchHH-HHHHHhhcCcchHHHHHHHHHHHHHhc
Q 036608 388 NCGFR-AVANLIGIGEDSWAQVRKDLVIELQSH 419 (565)
Q Consensus 388 ~C~fr-aia~~l~~~~~~~~~vR~~~~~~l~~~ 419 (565)
.|-|| ....++|++.+.+..+.+++.+||-.+
T Consensus 77 PCplrd~aL~~igls~~EYm~lKkelae~i~~~ 109 (109)
T TIGR03277 77 PCPLRDSALQRIGMSPEEYMELKKKLAEELLKK 109 (109)
T ss_pred CCcCchHHHHHcCCCHHHHHHHHHHHHHHHhcC
Confidence 47788 688899999999999999999998653
No 26
>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=29.05 E-value=2.4e+02 Score=24.02 Aligned_cols=85 Identities=19% Similarity=0.240 Sum_probs=42.8
Q ss_pred CCCCchHHHHHHHhhcCcchHHHHHHHHHHHHHhcccchhhhhcchhhHHHHHhhccccCCCCCcCCcccCCCchhhhcc
Q 036608 385 ADGNCGFRAVANLIGIGEDSWAQVRKDLVIELQSHFNDYKRVFEYAGRAEEVLHSLLYFENNPGREYWMTMPEIGHIIAS 464 (565)
Q Consensus 385 gdG~C~fraia~~l~~~~~~~~~vR~~~~~~l~~~~~~y~~~~~~~~~~~~~~~~l~~~~~~~~~~~W~~~~~~g~~iA~ 464 (565)
.+-.||..|+|..+..- +-.-..+++.+.+..+ ..-.++.++. .+|.
T Consensus 9 ~~~dcg~acl~~l~~~~--------------------------g~~~s~~~l~~~~~~~------~~g~s~~~L~-~~~~ 55 (131)
T PF03412_consen 9 DSNDCGLACLAMLLKYY--------------------------GIPVSEEELRRQLGTS------EEGTSLADLK-RAAR 55 (131)
T ss_dssp STT-HHHHHHHHHHHHT--------------------------T----HHHHHCCTT-B------TTB--CCCHH-HHHH
T ss_pred CCCCHHHHHHHHHHHHh--------------------------CCCchHHHHHHHhcCC------ccCCCHHHHH-HHHH
Confidence 45679999998777431 2222344555444221 2223444443 5788
Q ss_pred ccceeEEEEeCCccccccCCcCCCCCCCCCceEEEEEecCCceEeeecC
Q 036608 465 KYNVVLLHISDVLNLTFLPLRSIPLSRSSHKIIAIGFVNRNHFIEVFML 513 (565)
Q Consensus 465 ~y~~pi~~~s~~~~~t~~p~~~~p~~~~~~~~i~l~~~~~~Hf~sl~~~ 513 (565)
.|+...-.+..... -|. ... -| +|+++..+||+.|.-.
T Consensus 56 ~~gl~~~~~~~~~~--~l~-----~~~--~P--~I~~~~~~h~vVi~~~ 93 (131)
T PF03412_consen 56 KYGLKAKAVKLNFE--KLK-----RLP--LP--AIAHLKDGHFVVIYKI 93 (131)
T ss_dssp HTTEEEEEEE--GG--GCT-----CGG--SS--EEEEECCCEEEEEEEE
T ss_pred hcccceeeeecchh--hhh-----hcc--cc--EEEEecCcceEEEEeE
Confidence 89987766653222 120 111 13 3455578899988864
No 27
>COG3464 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=27.72 E-value=2.2e+02 Score=30.36 Aligned_cols=35 Identities=20% Similarity=0.319 Sum_probs=32.4
Q ss_pred CCcEEEeeccHHHHHHHHHhCcccchhhhHHHHHH
Q 036608 23 LPTMIVTDRELALMNAIEKIFPSATNLLCRWHISR 57 (565)
Q Consensus 23 ~P~~iiTD~~~al~~AI~~vFP~a~h~lC~~Hi~k 57 (565)
....|.-|...+..+++.+.||++.+.+=.||+.+
T Consensus 204 ~v~~V~~D~~~~y~~~v~e~~pna~i~~d~fh~~~ 238 (402)
T COG3464 204 QVKSVSMDMFGPYASAVQELFPNALIIADRFHVVQ 238 (402)
T ss_pred ceeEEEccccHHHHHHHHHhCCChheeeeeeeeee
Confidence 56789999999999999999999999999999877
No 28
>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=25.47 E-value=1.6e+02 Score=24.90 Aligned_cols=89 Identities=17% Similarity=0.102 Sum_probs=53.7
Q ss_pred CCchHHHHHHHhhcCcc-hHHHHHHHHHHHHHhcccchhhhhcchhhHHHHHhhccccCCCCCcCCcccCCCchhhhccc
Q 036608 387 GNCGFRAVANLIGIGED-SWAQVRKDLVIELQSHFNDYKRVFEYAGRAEEVLHSLLYFENNPGREYWMTMPEIGHIIASK 465 (565)
Q Consensus 387 G~C~fraia~~l~~~~~-~~~~vR~~~~~~l~~~~~~y~~~~~~~~~~~~~~~~l~~~~~~~~~~~W~~~~~~g~~iA~~ 465 (565)
-+|+--||+.+++.+++ =|..+...+=+-+-.+.+ ...-+--.++--+||-.
T Consensus 3 ~~CLL~A~s~at~~~~~~LW~~L~~~lPDSlL~n~e---------------------------i~~~GLSTDhltaLa~~ 55 (104)
T PF05381_consen 3 LDCLLVAISQATSISPETLWATLCEILPDSLLDNPE---------------------------IRTLGLSTDHLTALAYR 55 (104)
T ss_pred cceeHHhhhhhhCCCHHHHHHHHHHhCchhhcCchh---------------------------hhhcCCcHHHHHHHHHH
Confidence 58999999999999864 366555443333222211 01111112355789999
Q ss_pred cceeEEEEeCCccccccCCcCCCCCCCCCceEEEEEecC--CceEe
Q 036608 466 YNVVLLHISDVLNLTFLPLRSIPLSRSSHKIIAIGFVNR--NHFIE 509 (565)
Q Consensus 466 y~~pi~~~s~~~~~t~~p~~~~p~~~~~~~~i~l~~~~~--~Hf~s 509 (565)
|+--+.+.+...... .|..+. +..+.|-|-.| -||-.
T Consensus 56 ~~~~~~~hs~~~~~~-----~Gi~~a--s~~~~I~ht~G~p~HFs~ 94 (104)
T PF05381_consen 56 YHFQCTFHSDHGVLH-----YGIKDA--STVFTITHTPGPPGHFSL 94 (104)
T ss_pred HheEEEEEcCCceEE-----eecCCC--ceEEEEEeCCCCCCcccc
Confidence 998888888755422 233443 45677777654 68876
No 29
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=25.28 E-value=58 Score=23.03 Aligned_cols=32 Identities=16% Similarity=0.237 Sum_probs=24.6
Q ss_pred CCCchHHHHHHHhhcCcchHHHHHHHHHHHHH
Q 036608 386 DGNCGFRAVANLIGIGEDSWAQVRKDLVIELQ 417 (565)
Q Consensus 386 dG~C~fraia~~l~~~~~~~~~vR~~~~~~l~ 417 (565)
..+.-+.-||..||.+...-..+....++.|+
T Consensus 18 ~~~~t~~eIa~~lg~s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 18 FEGLTLEEIAERLGISRSTVRRILKRALKKLR 49 (50)
T ss_dssp TST-SHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCcHHHHHHHHHHHHHHhc
Confidence 45567899999999998777777777777665
No 30
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=24.35 E-value=67 Score=24.02 Aligned_cols=25 Identities=28% Similarity=0.413 Sum_probs=17.7
Q ss_pred ccccccC-CCCCch--HHHHHHHhhcCc
Q 036608 378 CGVSDVV-ADGNCG--FRAVANLIGIGE 402 (565)
Q Consensus 378 ~~~~~v~-gdG~C~--fraia~~l~~~~ 402 (565)
+.|++.. -||||- +||.|...|.++
T Consensus 12 L~Vv~~a~~~~nc~~~~RAaarkf~V~r 39 (58)
T PF09607_consen 12 LKVVEYAEKDNNCKGNQRAAARKFNVSR 39 (58)
T ss_dssp HHHHHHHHH-TTTTT-HHHHHHHTTS-H
T ss_pred HHHHHHHHHccchhhhHHHHHHHhCccH
Confidence 3444443 789998 999999999975
No 31
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=23.73 E-value=91 Score=30.01 Aligned_cols=36 Identities=22% Similarity=0.261 Sum_probs=28.1
Q ss_pred HHHHHHHHccCCCCCcEEEeeccHHHHHHHHHhCcccch
Q 036608 10 ALERLKTIMQDDILPTMIVTDRELALMNAIEKIFPSATN 48 (565)
Q Consensus 10 ~l~~l~~~~~~~~~P~~iiTD~~~al~~AI~~vFP~a~h 48 (565)
||..+++. ...|.+|+||+.+....|+.++-+...|
T Consensus 116 Fl~kllk~---~g~p~v~vtDka~s~~~A~~~l~~~~eh 151 (215)
T COG3316 116 FLKKLLKK---HGEPRVFVTDKAPSYTAALRKLGSEVEH 151 (215)
T ss_pred HHHHHHHh---cCCCceEEecCccchHHHHHhcCcchhe
Confidence 45555554 2689999999999999999998885554
No 32
>smart00384 AT_hook DNA binding domain with preference for A/T rich regions. Small DNA-binding motif first described in the high mobility group non-histone chromosomal protein HMG-I(Y).
Probab=22.20 E-value=51 Score=20.29 Aligned_cols=8 Identities=50% Similarity=1.153 Sum_probs=6.5
Q ss_pred CCCCCCCC
Q 036608 302 KTRGRPSQ 309 (565)
Q Consensus 302 ~tkGRPk~ 309 (565)
+.+|||+|
T Consensus 2 RkRGRPrK 9 (26)
T smart00384 2 RKRGRPRK 9 (26)
T ss_pred CCCCCCCC
Confidence 57899986
No 33
>PF05379 Peptidase_C23: Carlavirus endopeptidase ; InterPro: IPR008041 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C23 (clan CA). The type example is Carlavirus (apple stem pitting virus) endopeptidase, this thought to play a role in the post-translational cleavage of the high molecular weight primary translation products of the virus.; GO: 0003968 RNA-directed RNA polymerase activity, 0016817 hydrolase activity, acting on acid anhydrides
Probab=21.58 E-value=63 Score=26.48 Aligned_cols=15 Identities=40% Similarity=0.700 Sum_probs=14.0
Q ss_pred CchHHHHHHHhhcCc
Q 036608 388 NCGFRAVANLIGIGE 402 (565)
Q Consensus 388 ~C~fraia~~l~~~~ 402 (565)
.|-.+|||..||+++
T Consensus 4 ~Cvi~AiA~aL~R~~ 18 (89)
T PF05379_consen 4 GCVIRAIAEALGRRE 18 (89)
T ss_pred cchhHHHHHHhCCCH
Confidence 699999999999996
No 34
>COG3160 Rsd Regulator of sigma D [Transcription]
Probab=21.49 E-value=1.1e+02 Score=27.11 Aligned_cols=37 Identities=22% Similarity=0.512 Sum_probs=26.9
Q ss_pred hHHHHHHHhhcCc---chHHHHHHHHHHH------HHhcccchhhh
Q 036608 390 GFRAVANLIGIGE---DSWAQVRKDLVIE------LQSHFNDYKRV 426 (565)
Q Consensus 390 ~fraia~~l~~~~---~~~~~vR~~~~~~------l~~~~~~y~~~ 426 (565)
.|+.+..+.|++. |.|..+|++++-+ |+-.++.|.++
T Consensus 4 ~~~n~~er~GGs~~lID~WLh~Rk~llvayc~l~gikp~ke~~~pl 49 (162)
T COG3160 4 QLENLTERVGGSNKLIDRWLHVRKHLLVAYCNLVGIKPGKESYMPL 49 (162)
T ss_pred HHHhHHHHhcchHHHHHHHHHHHHHHHHHHHHHhccCccccccCCC
Confidence 3667788888876 7899999999877 33344556554
No 35
>TIGR00334 5S_RNA_mat_M5 ribonuclease M5. This family of orthologous proteins shows a weak but significant similarity to the central region of the DnaG-type DNA primase. The region of similarity is termed the Toprim (topoisomerase-primase) domain and is also shared by RecR, OLD family nucleases, and type IA and II topoisomerases.
Probab=20.58 E-value=1.1e+02 Score=28.45 Aligned_cols=40 Identities=20% Similarity=0.333 Sum_probs=31.8
Q ss_pred HHHHHHHHccCCCCCcEEEeeccH---HHHHHHHHhCcccchhhh
Q 036608 10 ALERLKTIMQDDILPTMIVTDREL---ALMNAIEKIFPSATNLLC 51 (565)
Q Consensus 10 ~l~~l~~~~~~~~~P~~iiTD~~~---al~~AI~~vFP~a~h~lC 51 (565)
.++.++.+. ......|+||.|. -+.+-|.+.+|++.|.+=
T Consensus 37 ~i~~i~~~~--~~rgVIIfTDpD~~GekIRk~i~~~vp~~khafi 79 (174)
T TIGR00334 37 TINLIKKAQ--KKQGVIILTDPDFPGEKIRKKIEQHLPGYENCFI 79 (174)
T ss_pred HHHHHHHHh--hcCCEEEEeCCCCchHHHHHHHHHHCCCCeEEee
Confidence 356666664 4678899999996 588999999999999763
Done!