Query 002340
Match_columns 934
No_of_seqs 236 out of 457
Neff 5.0
Searched_HMMs 46136
Date Thu Mar 28 21:50:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002340.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002340hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00605 rad4 DNA repair prot 100.0 1E-121 2E-126 1078.4 42.2 542 170-848 138-713 (713)
2 KOG2179 Nucleotide excision re 100.0 8.2E-98 2E-102 854.0 32.1 619 123-848 38-669 (669)
3 COG5535 RAD4 DNA repair protei 100.0 5.8E-83 1.3E-87 715.9 17.8 483 172-848 127-649 (650)
4 PF10405 BHD_3: Rad4 beta-hair 100.0 5.2E-32 1.1E-36 240.1 7.6 75 732-806 1-76 (76)
5 PF03835 Rad4: Rad4 transgluta 99.9 5.3E-23 1.1E-27 203.2 5.0 109 479-605 29-145 (145)
6 PF10403 BHD_1: Rad4 beta-hair 99.8 1.2E-19 2.5E-24 153.1 2.4 51 610-660 3-57 (57)
7 KOG0909 Peptide:N-glycanase [P 99.8 5.7E-19 1.2E-23 195.6 8.2 82 486-573 250-333 (500)
8 PF10404 BHD_2: Rad4 beta-hair 99.6 5.9E-17 1.3E-21 139.8 1.1 64 662-725 1-64 (64)
9 TIGR00605 rad4 DNA repair prot 99.2 1E-12 2.2E-17 157.4 -6.0 148 149-301 13-176 (713)
10 PF01841 Transglut_core: Trans 96.8 0.00088 1.9E-08 62.2 3.1 65 229-295 16-80 (113)
11 KOG2179 Nucleotide excision re 95.7 0.0063 1.4E-07 73.1 2.7 114 188-304 1-120 (669)
12 smart00460 TGc Transglutaminas 95.2 0.012 2.5E-07 50.2 2.2 30 262-291 2-31 (68)
13 TIGR00598 rad14 DNA repair pro 95.0 0.21 4.6E-06 51.6 10.9 35 898-934 137-172 (172)
14 COG1305 Transglutaminase-like 92.0 0.15 3.3E-06 54.9 4.1 85 196-291 133-219 (319)
15 COG5145 RAD14 DNA excision rep 87.1 1.4 2.9E-05 47.3 6.3 35 899-934 258-292 (292)
16 KOG4017 DNA excision repair pr 86.7 2.4 5.3E-05 46.2 8.0 34 899-934 241-274 (274)
17 smart00460 TGc Transglutaminas 85.8 0.68 1.5E-05 39.3 2.8 21 483-508 47-67 (68)
18 PF01841 Transglut_core: Trans 85.0 0.65 1.4E-05 43.0 2.5 20 484-507 94-113 (113)
19 PF13369 Transglut_core2: Tran 67.7 6.8 0.00015 39.5 4.3 36 256-291 54-89 (152)
20 COG5216 Uncharacterized conser 53.6 5.5 0.00012 34.7 0.6 28 907-934 9-38 (67)
21 COG5535 RAD4 DNA repair protei 53.1 3.8 8.3E-05 49.4 -0.5 162 123-300 43-228 (650)
22 PF12677 DUF3797: Domain of un 44.3 9.6 0.00021 32.0 0.6 13 915-929 36-48 (49)
23 COG1305 Transglutaminase-like 39.0 19 0.00041 38.8 2.1 25 484-512 239-263 (319)
24 PRK10941 hypothetical protein; 34.6 60 0.0013 36.2 5.1 62 230-291 58-120 (269)
25 PF05207 zf-CSL: CSL zinc fing 23.9 48 0.001 28.4 1.6 25 908-932 6-30 (55)
26 PF00797 Acetyltransf_2: N-ace 23.3 77 0.0017 33.8 3.4 24 268-291 48-71 (240)
27 PF14402 7TM_transglut: 7 tran 22.8 45 0.00098 37.9 1.6 28 484-516 30-57 (313)
No 1
>TIGR00605 rad4 DNA repair protein rad4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=9.6e-122 Score=1078.37 Aligned_cols=542 Identities=28% Similarity=0.435 Sum_probs=424.9
Q ss_pred cChHHHHHHHHHHHHHHHHHhhhhhHHHhhcCc-HHHHHHhhcccccccccccCcc---------ccccccchhhHHhhh
Q 002340 170 ASAEDKELAELVHKVHLLCLLARGRLIDSVCDD-PLIQASLLSLLPSYLLKISEVS---------KLTANALSPIVSWFH 239 (934)
Q Consensus 170 ~t~~eKelr~~vHKvHLLCLLAhg~~rN~~Cnd-~~lQa~llSlLP~~~~~~~~~~---------~~~~~~L~~lv~WF~ 239 (934)
++.++|+.|++||++||||||.|+.+||.|||| +++|+.|..+||.++....++. ....++|++|+.-|+
T Consensus 138 ~~~~eR~~R~~iH~~~ll~ll~h~~~RN~w~n~~~~~~~~L~~~~p~k~~~~l~p~~~~~~~~~s~s~~~~~~~l~~~~k 217 (713)
T TIGR00605 138 CSNEARKDRKYIHILYLLCLMVHLFTRNEWSLSAPLKSAKLSNLIPEKVRLLLHPSVRKSEELPSRSLRGLRKPLVEKLK 217 (713)
T ss_pred ccHHHHHHHHHHHHHHHHHHhhhhHhhhhhhCChHHHhHHHhhhCCHHHHHhcCccccccccccchhhhhhhHHHHHhhh
Confidence 789999999999999999999999999999999 7999999999999987665433 234688889999999
Q ss_pred cceeecccCccc---c------------chhhHHHHHHHHhcCCHHHHHHHHHHHHHhcCCceEEEEeeccccCCccccc
Q 002340 240 DNFHVRSSVSTR---R------------SFHSDLAHALESREGTPEEIAALSVALFRALKLTTRFVSILDVASLKPEADK 304 (934)
Q Consensus 240 ~~F~v~~~~~~~---~------------~~~~~L~~~l~~~~Gs~de~aqLF~aLLRaLgl~aRLV~sLqp~sLKp~~~k 304 (934)
..|+++.+-..+ . ..+.++..+..+++||++.++||||||||++|+.+||||||||+|+.....
T Consensus 218 k~~~it~~g~~~~~~~~~~~~~~~~~~~~~~~ef~~~a~~~~gsrd~~aql~~allr~~~~~~rlv~slqpl~~~~~~~- 296 (713)
T TIGR00605 218 KCMETWQKGLRKTTKGLLKLLNGGRYSRSKWEEIEKSSNRKLGGRKYRTLKRGSILENLNVPTRLVFSDFLLSVSKGHN- 296 (713)
T ss_pred hcchhcccccccCcccccccchhhHHhhhhHHHHHHhhhccccccchhhhHHHHHHhhhcccccccccccccCcccCCC-
Confidence 999998653100 0 003346677788999999999999999999999999999999988755310
Q ss_pred ccCCCCCCCCcCCCccCCCcccccCccccccCCCcccccCccccccccCCCCCCCCCCCCCCCCCccCCCCCccccccCC
Q 002340 305 NVSSNQDSSRVGGGIFNAPTLMVAKPEEVLASPVKSFSCDKKENVCETSSKGSPECKYSSPKSNNTQSKKSPVSCELSSG 384 (934)
Q Consensus 305 ~~~~~~~~s~~~~g~~~~~~p~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~s~e~~~~ 384 (934)
+.-+..+.. .+.. ++..
T Consensus 297 --------------------~~~~~~~~~--~~~~-----------------------------~~~~------------ 313 (713)
T TIGR00605 297 --------------------DPEISSEGF--VPKL-----------------------------SACN------------ 313 (713)
T ss_pred --------------------Ccccccccc--cccc-----------------------------cccc------------
Confidence 000000000 0000 0000
Q ss_pred CCCCCCccccCCccccC-CCccchhhhccCCChhHHHHHHHHhhccccccccccccccccccCCCCCccccccccccccc
Q 002340 385 NLDPSSSMACSDISEAC-HPKEKSQALKRKGDLEFEMQLEMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKKIES 463 (934)
Q Consensus 385 ~~~~~~~~~~~~~~e~~-~~~~~~~~~rr~g~~~~~~q~~~a~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~k~~~ 463 (934)
+...+..+ ..++ .+ ......++.+.|.|.. + ..+.++.+.. .
T Consensus 314 ----~~q~~~~s-~~S~~~t-sR~~l~~~l~~P~fs~----------------------------~--~~~~k~~~~~-~ 356 (713)
T TIGR00605 314 ----ANQRLIMS-CESADRT-SRFRMKKDPSLPGFSA----------------------------Y--SDMDKSPIFT-C 356 (713)
T ss_pred ----cccccccc-cCCCCcc-ccccccccCCCCCccc----------------------------c--ccCCCCCccc-h
Confidence 00000000 0000 00 0000123333332210 0 0000100000 0
Q ss_pred CCCCCccCCcccccCCccCCCCceeEEEEeccCCCCCceEEecccc-cccccchh-hhHhHHhccCCeeEEEEEcCCC-c
Q 002340 464 GESSTSCLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVHVDAAN-AIIDGEQK-VEAAAAACKTSLRYIVAFAGCG-A 540 (934)
Q Consensus 464 ~~s~~~~~~~s~~~~~~~l~~P~fWvEV~~~~e~~~~kWI~VDPv~-~~vd~p~~-~Ep~~~~~~~~msYVVAfd~DG-a 540 (934)
. ......+.+++||+||+|||++. +++||||||++ ++++++.. +|+ +.++|+|||||++|| |
T Consensus 357 ~--------~~~~~~~~~~~~p~~W~Ev~~~~---~~rWI~VD~~~~~~~~~~~~~~e~----~~~~m~YVvAf~~d~~~ 421 (713)
T TIGR00605 357 E--------EGDKFIDRWITYVDFWVEVFIEQ---EEKWVCVDAVHSGVVPKGVTCFEP----ATLMMTYVFAYDRDGYV 421 (713)
T ss_pred h--------cccccccccCCCCeeEEEEeecc---cceeEEeccccccccCCchhhccC----CCCceEEEEEEcCCCce
Confidence 0 01112456788999999999986 49999999999 88988764 443 569999999999997 9
Q ss_pred ccchhhhhhhHHH-hhcccCCHHHHHHH-HhhhhhcccCcCCCccccccccCcccccCCchHHHHHHHHHccCCCCcChh
Q 002340 541 KDVTRRYCMKWYR-IASKRVNSAWWDAV-LAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQ 618 (934)
Q Consensus 541 kDVTrRYa~~w~k-~~rkRv~~~Ww~~~-L~~~~~~~s~~~~~~~i~~~~~~~~~~~rd~~Ed~EL~~~~~~epmPtsi~ 618 (934)
+|||+||+++|++ +++.||+..||..+ |++|.+.. .++... +|..||.||.+++++||||+|++
T Consensus 422 kDVT~RY~~~~~~k~r~~Rv~~~w~~~~w~~~~~~~~-------------~~r~~~-~d~~Ed~el~~~~~~e~~P~si~ 487 (713)
T TIGR00605 422 KDVTRRYCDQWSTKVRKRRVEKADFGETWFRPIFGAL-------------HKRKRT-IDDIEDQEFLRRHESEGIPKSIQ 487 (713)
T ss_pred eechhhHhhhhhhhhheeeecccchHHHHHHHHhhhh-------------ccCccc-hhhhhhhHhhhhhcccCCChhHH
Confidence 9999999999996 67789998888887 77765321 011222 78899999999999999999999
Q ss_pred hhccCCceeeccccccccccCCC--CCcceeeccee-eeecCCccccccHHHHHHhcccccCCCcccceeccCCCCCCCC
Q 002340 619 AYKNHQLYVIERWLNKYQILYPK--GPILGFCSGHA-VYPRSCVQTLKTKERWLREALQVKANEVPVKVIKNSSKSKKGQ 695 (934)
Q Consensus 619 ~fKnHP~YvLerhL~k~EvI~P~--a~v~G~~~GEp-VY~RsdV~~LkS~e~W~r~GR~VK~gE~P~K~vk~~~~~~k~~ 695 (934)
+|||||+|||||||++||+|||+ ++++|+++|++ ||+|+||++|||+++||++||+||+||+|+|+|+.+++..+.
T Consensus 488 ~fKnHP~YvLer~L~~~Evi~P~~~~~~~g~~~g~~~VY~Rs~V~~lkS~~~W~~~GR~VK~ge~P~K~vk~r~r~~~~- 566 (713)
T TIGR00605 488 DLKNHPLYVLERHLKKTQALKPGKKACTLGFVNGKAGVYSRKDVHDLKSAEQWYKKGRVIKLGEQPYKVVKARARTVRL- 566 (713)
T ss_pred HhhcCceEEehhhcccceeeccCCCCCceeccCCCCCccchhHhhhhhhHHHHHHcCCccCCCCccceEeccccccccc-
Confidence 99999999999999999999994 46789999998 999999999999999999999999999999999987432211
Q ss_pred CCCCCCccccccccccccccccccccCCCCCCCCCCccCCCCCceEeecCCCCCCCeeeecCccHHHHHHHcCCCeeece
Q 002340 696 DFEPEDYDEVDARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAM 775 (934)
Q Consensus 696 ~~~~~~~~~~~~~~~~~LY~~wQTe~y~PPpvvdG~VPkN~yGNVdlf~psMlP~G~VHL~l~~i~rvAkkLgIDyApAV 775 (934)
..++. ...+++|||+||||+|+|||++||+||||+|||||||+|+|||+|||||++++|.+||++||||||+||
T Consensus 567 --~~~~~----~~~~~~LY~~~QTe~y~Pppv~dG~VPkN~yGNidv~~p~MiP~G~vhi~~~~~~rvak~LgIDyA~AV 640 (713)
T TIGR00605 567 --PKGEA----EEEDLGLYSYEQTELYIPPPAVDGIVPKNAYGNIDLFVPSMIPKGAVHLRLPGAIKAAKKLNIDYAPAV 640 (713)
T ss_pred --ccccc----cccccccCCHhhCcCccCCCccCCccccCCCCCEEecCCCCCCCCcEEecCccHHHHHHHhCCCeeeee
Confidence 11111 114789999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eceeecCCeeeeeEceEEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcC
Q 002340 776 VGFEFRNGRSTPVFDGIVVCAEFKDTILEAYAEEEEKREAEEKKRREAQATSRWYQLLSSIVTRQRLNNCYGN 848 (934)
Q Consensus 776 tGFeFk~G~a~PvidGIVV~eE~~e~l~~a~~e~~e~~~~~e~~kre~~aL~~Wk~Llk~LrIreRL~~~Yg~ 848 (934)
|||+|++|+++|||+|||||+||+++|++||.++++.++++++++++++||++|++||++|||++||+.+||.
T Consensus 641 tGFeF~~g~~~Pv~~GvVV~~e~~~~v~~a~~~~~~~~~~~e~~k~e~~aL~~Wk~ll~~LrIr~Rl~~~Yg~ 713 (713)
T TIGR00605 641 TGFDFHRGYSKPVLDGIIVCEEFREAIETAWEEIEQIQEEKEQEKHRKRALGNWKTLLKGLRIRERLKETYGK 713 (713)
T ss_pred eceeecCCceeEeeceEEEehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCc
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999995
No 2
>KOG2179 consensus Nucleotide excision repair complex XPC-HR23B, subunit XPC/DPB11 [Replication, recombination and repair]
Probab=100.00 E-value=8.2e-98 Score=853.96 Aligned_cols=619 Identities=35% Similarity=0.461 Sum_probs=429.3
Q ss_pred CCCCCCCcccCCCCCCCCCCCCCCCCCCceEEEEecCCccccccccccChHHHHHHHHHHHHHHHHHhhhhhHHHhhcCc
Q 002340 123 EEMYDSDWEDGSIPVACSKENHPESDIKGVTIEFDAADSVTKKPVRRASAEDKELAELVHKVHLLCLLARGRLIDSVCDD 202 (934)
Q Consensus 123 ~e~~d~dWEeV~~~~~~~~~~~~~~~~~~veIeie~~~~~kkk~~RR~t~~eKelr~~vHKvHLLCLLAhg~~rN~~Cnd 202 (934)
+++++..|++|...-..... +.....++++++..... ++..+.......++....|-.|.+|.+-+...+|.||.+
T Consensus 38 ~~~~~~~~~~~~~~~~~~~l--~~~~~~~~~~~~~~s~~--~~~~~k~~~~d~~~~~~~~~l~~~~~~~~~~~~~~~~~~ 113 (669)
T KOG2179|consen 38 DEEDDLLSSDVKWFSLDSEL--PVENVNDVRDTILVSLE--KRKANKEARDDQDLEYQFHLLDRLFMLFLLKTRNLWPDP 113 (669)
T ss_pred cccccchhhccCcccccccc--cccccchhhhHhhhhhh--hhhhhcccccHHHHHHHHHHHhhhhHHHHHHHhcccCCc
Confidence 55666666666554322211 11122334444443321 112223346788999999999999999999999999987
Q ss_pred HHHHHHhhcccccccccccCccccccccchhhHHhhhcceeecccCccccchhhHHHHHHHHhcCCHHHHHHHHHHHHHh
Q 002340 203 PLIQASLLSLLPSYLLKISEVSKLTANALSPIVSWFHDNFHVRSSVSTRRSFHSDLAHALESREGTPEEIAALSVALFRA 282 (934)
Q Consensus 203 ~~lQa~llSlLP~~~~~~~~~~~~~~~~L~~lv~WF~~~F~v~~~~~~~~~~~~~L~~~l~~~~Gs~de~aqLF~aLLRa 282 (934)
-.+-+ + +.|-..+++++...+ +...+.....+++.++-..+++.|++..+
T Consensus 114 ~r~~~-l-------------------------~~~~p~~~~~s~~p~---s~~~s~a~~~~s~r~~~~~l~~~~~~~~g- 163 (669)
T KOG2179|consen 114 VRLNA-L-------------------------VRSKPKKIRKSFKPS---SSRKSQAFKNKSRRKTLHGLVLVCLSKYG- 163 (669)
T ss_pred chhhH-h-------------------------hhccCcccccCCCcc---ccccchHhHhhhhhhhHHHHHHHHHHHhc-
Confidence 66644 3 333333344433222 22234556777778888889999988888
Q ss_pred cCCceEEEEeeccccCCcccccccCCCCCCCCcCCCccCCCcccccCccccccCCCcccccCccccccccCCCCCCCCCC
Q 002340 283 LKLTTRFVSILDVASLKPEADKNVSSNQDSSRVGGGIFNAPTLMVAKPEEVLASPVKSFSCDKKENVCETSSKGSPECKY 362 (934)
Q Consensus 283 Lgl~aRLV~sLqp~sLKp~~~k~~~~~~~~s~~~~g~~~~~~p~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 362 (934)
++.+|.+.. .-+.+|+...-..+..........+.+.+.+......+... -+++..+.-+.. +++.-
T Consensus 164 -~irt~~~~~-~~~~~k~~~~~sEse~~~~~k~~e~~~~~~~~l~~~~~~~s-~~k~~~~~~k~~--------~~~~~-- 230 (669)
T KOG2179|consen 164 -KIRTNFLRK-NYADLKNENLISESELKKVAKNQELFSGSRPLLLKGVEDAS-IRKKWKSKMKNV--------SSGTE-- 230 (669)
T ss_pred -ccccchhhh-hhhhcccccCCcchhccchhhhhhhhccCchHhhhhhhhhh-hhhhhcCCcccc--------Ccchh--
Confidence 899999853 55556553211110000000001111111111111110000 000000000000 00000
Q ss_pred CCCCCCCccCCCCCccccccCCCCCCCCccccCCccccCCCccchhhhccCCChhHHHHHHHHhhcccc---cccccccc
Q 002340 363 SSPKSNNTQSKKSPVSCELSSGNLDPSSSMACSDISEACHPKEKSQALKRKGDLEFEMQLEMALSATNV---ATSKSNIC 439 (934)
Q Consensus 363 ~~~~~~~~~s~~~~~s~e~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~rr~g~~~~~~q~~~a~~a~~~---~~~~~~~~ 439 (934)
+. +.+.+. .....++... -+.++ ..+...+.-+|+..+..|..+++..++. .++..+
T Consensus 231 ----------~~---s~~~~~--~~d~~~~~~~--~~~~p-~~~a~i~~~~g~~d~~~q~~~~l~~~~n~~r~~~~l~-- 290 (669)
T KOG2179|consen 231 ----------KL---SKELSD--GADEASKPYL--LEAVP-AHRADIRPNKGDADVSSQIIHALLRTPNNARLAPSLQ-- 290 (669)
T ss_pred ----------hh---cccccC--CCccccchhh--hhcCc-HHHhhhccCCCCcchHHHHHHHHhhccchhhcccccC--
Confidence 00 000000 0000011100 01111 0122233338898999999999866542 111111
Q ss_pred ccccccCCCCCcccccccccccccCCCCCccCCcccccCCccCCCCceeEEEEeccCCCCCceEEecc--cccccccchh
Q 002340 440 SDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVHVDA--ANAIIDGEQK 517 (934)
Q Consensus 440 ~~~~~~~~~~~~~~~~k~~~k~~~~~s~~~~~~~s~~~~~~~l~~P~fWvEV~~~~e~~~~kWI~VDP--v~~~vd~p~~ 517 (934)
+...++ ...+ ..|+++..++++...+.+ .|+||+|||+..+ ++|||||| +.+.++..+.
T Consensus 291 ---p~~~~~----~~~~-------~~s~~~~~~~s~~~~~~~--~p~~W~ev~~~~e---~kwV~vd~~~v~~~~~~~~~ 351 (669)
T KOG2179|consen 291 ---PPVFSN----LSVK-------DLSDTSLYGNSLENIDGA--GPVFWLEVLDKFE---KKWVCVDPPSVIGKYHLFQP 351 (669)
T ss_pred ---Ccchhh----cccc-------ccccccccccchhhcCCc--ccchhHHHHHhhc---ceEEEecchhhcceeccccc
Confidence 111111 0111 233344455554433333 4999999999765 89999995 4566666666
Q ss_pred hhHhHHhccCCeeEEEEEcCCC-cccchhhhhhhHHHhhc----ccCCHHHHHHHHhhhhhcccCcCCCccccccccCcc
Q 002340 518 VEAAAAACKTSLRYIVAFAGCG-AKDVTRRYCMKWYRIAS----KRVNSAWWDAVLAPLRELESGATGDLNVESSAKDSF 592 (934)
Q Consensus 518 ~Ep~~~~~~~~msYVVAfd~DG-akDVTrRYa~~w~k~~r----kRv~~~Ww~~~L~~~~~~~s~~~~~~~i~~~~~~~~ 592 (934)
+...+..+.+.|.|||||+.+| ++|||+||+..|+++.+ .|+...||..++.+|..+
T Consensus 352 ~~~~a~~~~~~~~yVva~da~~~~kDVT~RY~~~~~s~~~~~~k~~~~~~w~~~~l~~~~~~------------------ 413 (669)
T KOG2179|consen 352 IGAVAEINGRHLAYVVAYDADGYVKDVTRRYCESWSSILRKRSKVRFSKKWFDKVLAPLGKL------------------ 413 (669)
T ss_pred cchhhhhccccceEEEEecCCCccchhHHHHhhhhhhhhhccccccHHHHHhhhhHhhhccc------------------
Confidence 6555555667999999999999 99999999999998766 467789999999999742
Q ss_pred cccCCchHHHHHHHHHccCCCCcChhhhccCCceeeccccccccccCC-CCCcceeecc--eeeeecCCccccccHHHHH
Q 002340 593 VADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYP-KGPILGFCSG--HAVYPRSCVQTLKTKERWL 669 (934)
Q Consensus 593 ~~~rd~~Ed~EL~~~~~~epmPtsi~~fKnHP~YvLerhL~k~EvI~P-~a~v~G~~~G--EpVY~RsdV~~LkS~e~W~ 669 (934)
..+++..||+++..+...++||+|+++|||||+|||||||++||+||| +++++||++| |+||+|.||++|||+++||
T Consensus 414 ~~~~e~~ed~~~~~~~~~~~lP~sv~~~K~Hp~fvler~Lkk~q~l~P~k~p~~g~~kG~~E~VY~R~~V~~LkS~e~W~ 493 (669)
T KOG2179|consen 414 RKDREDTEDIELLRRHTSEGLPTSVQDLKNHPLFVLERHLKKNQALKPCKKPTLGFTKGDVEAVYLRRDVVTLKSREQWY 493 (669)
T ss_pred cchHHHHHHHHHHHHhccCCCCchHHHhccCchhhhHHHHhhcccccccccceeeeecCCceeeeehhhHHhhccHHHHH
Confidence 346788999999999999999999999999999999999999999999 5788999999 9999999999999999999
Q ss_pred HhcccccCCCcccceeccCCCCCCCCCCCCCCccccccccccccccccccccCCCCCCCCCCccCCCCCceEeecCCCCC
Q 002340 670 REALQVKANEVPVKVIKNSSKSKKGQDFEPEDYDEVDARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLP 749 (934)
Q Consensus 670 r~GR~VK~gE~P~K~vk~~~~~~k~~~~~~~~~~~~~~~~~~~LY~~wQTe~y~PPpvvdG~VPkN~yGNVdlf~psMlP 749 (934)
++||+||+||+|+|+||+++++.+.....+.+..+ ...++|||+|||++|+|||+++|+||||+|||||||+|+|||
T Consensus 494 r~GRvIk~geqP~K~vK~~~~r~r~~r~~e~~~~~---~~~~~Lys~wqte~Y~pp~a~~givpkN~yGNielf~p~miP 570 (669)
T KOG2179|consen 494 RKGRVIKPGEQPYKIVKRRPKRERMKRELEKDVRE---EYEQELYSPWQTELYCPPPAVEGIVPKNEYGNIELFSPSMIP 570 (669)
T ss_pred HhcccccCCCcchHHHhcCcchhhhhhhhhhhhhh---hhhhhccCcccccccCCCccccCccccccccceeeeccccCC
Confidence 99999999999999999988754332221111111 156789999999999999999999999999999999999999
Q ss_pred CCeeeecCccHHHHHHHcCCCeeeceeceeecCCeeeeeEceEEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002340 750 PGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEAYAEEEEKREAEEKKRREAQATSRW 829 (934)
Q Consensus 750 ~G~VHL~l~~i~rvAkkLgIDyApAVtGFeFk~G~a~PvidGIVV~eE~~e~l~~a~~e~~e~~~~~e~~kre~~aL~~W 829 (934)
.|||||++|++.+|||+||||||+|||||+|+.|+++|+++|||||++++++|..||+++++.++++|+++.+++||.+|
T Consensus 571 ~g~vhl~~p~~~~vAk~L~id~a~av~gF~f~~~~~~P~~~Givv~~e~k~~i~~a~ee~~~~~e~ker~~~~~~~l~~W 650 (669)
T KOG2179|consen 571 KGCVHLRLPNAVDVAKKLGIDYAPAVTGFDFRRGYAVPVFEGIVVCKEFKEVILLAWEEDQKIQEEKERRKKRKRALGRW 650 (669)
T ss_pred CCeEEecCchHHHHHHHhCCcccccccceeeccCcceecccceEeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhhcC
Q 002340 830 YQLLSSIVTRQRLNNCYGN 848 (934)
Q Consensus 830 k~Llk~LrIreRL~~~Yg~ 848 (934)
+.||++||||+||+.+||.
T Consensus 651 k~Ll~~Lrir~Rl~~~Yg~ 669 (669)
T KOG2179|consen 651 KILLRGLRIRERLKKEYGN 669 (669)
T ss_pred HHHHHHhHHHHHHHHhhcC
Confidence 9999999999999999995
No 3
>COG5535 RAD4 DNA repair protein RAD4 [DNA replication, recombination, and repair]
Probab=100.00 E-value=5.8e-83 Score=715.87 Aligned_cols=483 Identities=26% Similarity=0.354 Sum_probs=380.3
Q ss_pred hHHHHHHHHHHHHHHHHHhhhhhHHHhhcCcHHHHHHhhcccccccccccCcc-------ccccccchhhHHhhhcceee
Q 002340 172 AEDKELAELVHKVHLLCLLARGRLIDSVCDDPLIQASLLSLLPSYLLKISEVS-------KLTANALSPIVSWFHDNFHV 244 (934)
Q Consensus 172 ~~eKelr~~vHKvHLLCLLAhg~~rN~~Cnd~~lQa~llSlLP~~~~~~~~~~-------~~~~~~L~~lv~WF~~~F~v 244 (934)
..++.+|...|++|++|||.||++||.|-++..+-..|+-+++.+...+.... .....-|.++-.||..-|..
T Consensus 127 ~~d~s~rks~him~~tcll~~g~irn~W~rsk~lsngLr~~~~ekq~~~l~~q~~ss~~~~~~~KlL~glr~y~nk~fk~ 206 (650)
T COG5535 127 FKDWSVRKSAHIMDSTCLLLLGFIRNLWFRSKMLSNGLRFNRLEKQIKYLDNQNESSISESTYKKLLEGLRFYGNKPFKN 206 (650)
T ss_pred ccCcchhhhHHHHHHHHHHHHHHHHHHHHHhhhhhcccchhhHHHhHHhhccccccccchhHHHHHHHhHHHHhhhhhHH
Confidence 37899999999999999999999999999999888888888777665443311 12245566777999999984
Q ss_pred cccCcccc------------chhh-------HHHHHHHHhcCCHHHHHHHHHHHHHhcCCceEEEEeeccccCCcccccc
Q 002340 245 RSSVSTRR------------SFHS-------DLAHALESREGTPEEIAALSVALFRALKLTTRFVSILDVASLKPEADKN 305 (934)
Q Consensus 245 ~~~~~~~~------------~~~~-------~L~~~l~~~~Gs~de~aqLF~aLLRaLgl~aRLV~sLqp~sLKp~~~k~ 305 (934)
+.....+. .++. .....+.+..|.+|.-++=|.|++|++.+.+||..+|||..
T Consensus 207 i~~~dnrkl~~rt~kq~~~s~f~~~i~en~s~~~~~~~~~~~~~D~~vrgf~a~~r~~~v~~Rli~~l~~P~-------- 278 (650)
T COG5535 207 IGVEDNRKLAKRTMKQMESSDFWEEIFENYSLEVVPLKSADGRRDADVRGFEAEHRILNVFARLIASLIQPV-------- 278 (650)
T ss_pred hhhcccHHHHHHHHHHHHhccchHHHHhhcchHHhhHhhccCCCcchhHHHHHHHHHhccchhhhccccCcc--------
Confidence 32111110 0110 11334456679999999999999999999999997544421
Q ss_pred cCCCCCCCCcCCCccCCCcccccCccccccCCCcccccCccccccccCCCCCCCCCCCCCCCCCccCCCCCccccccCCC
Q 002340 306 VSSNQDSSRVGGGIFNAPTLMVAKPEEVLASPVKSFSCDKKENVCETSSKGSPECKYSSPKSNNTQSKKSPVSCELSSGN 385 (934)
Q Consensus 306 ~~~~~~~s~~~~g~~~~~~p~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~s~e~~~~~ 385 (934)
|.+. ++
T Consensus 279 --------------Fs~~------------------------------------------------------------~~ 284 (650)
T COG5535 279 --------------FSNN------------------------------------------------------------SD 284 (650)
T ss_pred --------------cccc------------------------------------------------------------cc
Confidence 1110 00
Q ss_pred CCCCCccccCCccccCCCccchhhhccCCChhHHHHHHHHhhccccccccccccccccccCCCCCcccccccccccccCC
Q 002340 386 LDPSSSMACSDISEACHPKEKSQALKRKGDLEFEMQLEMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKKIESGE 465 (934)
Q Consensus 386 ~~~~~~~~~~~~~e~~~~~~~~~~~rr~g~~~~~~q~~~a~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~k~~~~~ 465 (934)
.+.+ ++. .. .
T Consensus 285 ~~~~--------~e~-~~-------------~------------------------------------------------ 294 (650)
T COG5535 285 LDVL--------SEG-LL-------------E------------------------------------------------ 294 (650)
T ss_pred cccC--------ccc-cc-------------e------------------------------------------------
Confidence 0000 000 00 0
Q ss_pred CCCccCCcccccCCccCCCCceeEEEEeccCCCCCceEEeccccc--ccc-cchhhhHhHHhccCCeeEEEEEcCCC-cc
Q 002340 466 SSTSCLGISTAVGSRKVGAPLYWAEVYCSGENLTGKWVHVDAANA--IID-GEQKVEAAAAACKTSLRYIVAFAGCG-AK 541 (934)
Q Consensus 466 s~~~~~~~s~~~~~~~l~~P~fWvEV~~~~e~~~~kWI~VDPv~~--~vd-~p~~~Ep~~~~~~~~msYVVAfd~DG-ak 541 (934)
-...+.+|.||+|||+-. .++||+|||++- ++. -...|||.+..--+.|.||+|++.++ ++
T Consensus 295 ------------~iD~l~~p~fw~ev~~~~---~~kwv~vdp~~l~~v~~~l~~kfepa~~~~~n~~~~V~ayd~~~y~~ 359 (650)
T COG5535 295 ------------YIDSLEYPGFWGEVVDKF---EKKWVFVDPVRLYIVYSELKCKFEPAASIHLNIMEYVGAYDACVYVK 359 (650)
T ss_pred ------------eccchhcchHHHHHHHHH---HhceEecccchhhhhhhhhhheechhHHHHHHHHHHhhhhccCccch
Confidence 001234899999999864 589999999952 333 45678885555567999999999997 99
Q ss_pred cchhhhhhhHHHhhcccC-----CHHHHHHHHhhhhhcccCcCCCccccccccCcccccCCchHHHHHHHHHccCCCCcC
Q 002340 542 DVTRRYCMKWYRIASKRV-----NSAWWDAVLAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTN 616 (934)
Q Consensus 542 DVTrRYa~~w~k~~rkRv-----~~~Ww~~~L~~~~~~~s~~~~~~~i~~~~~~~~~~~rd~~Ed~EL~~~~~~epmPts 616 (934)
|||.||+-..+...+ |+ ...||...+..+.... .+ .+.+.+|+.++-+....++||+|
T Consensus 360 DVt~RY~d~~~s~~k-ritk~~fs~qy~~r~~~~l~~~k---------------~~-~~~e~i~~~~~L~~~~~~~iPkS 422 (650)
T COG5535 360 DVTLRYRDQSYSFLK-RITKHLFSVQYFVRQFPGLGKCK---------------EA-SDEEAIEDFDDLDERRSEGIPKS 422 (650)
T ss_pred hHHHHHHHHHhhhhh-hhhccchHHHHHHHHhcccCccc---------------cc-ccHHHHHhHHHHhhcccccCCcc
Confidence 999999985554433 33 4689999998776431 11 34455566555555556899999
Q ss_pred hhhhccCCceeeccccccccccCCCCCc-ceeecc----eeeeecCCccccccHHHHHHhcccccCCCcccceeccCCCC
Q 002340 617 QQAYKNHQLYVIERWLNKYQILYPKGPI-LGFCSG----HAVYPRSCVQTLKTKERWLREALQVKANEVPVKVIKNSSKS 691 (934)
Q Consensus 617 i~~fKnHP~YvLerhL~k~EvI~P~a~v-~G~~~G----EpVY~RsdV~~LkS~e~W~r~GR~VK~gE~P~K~vk~~~~~ 691 (934)
+++|||||+|||||||+++|+|+|++.+ .++++| |+||+|.||..|+|+++||++||+||+|+||+|+||+- .
T Consensus 423 vqdlK~HP~FVle~~Lk~~q~ikp~ak~~~~~tkGk~~vE~VY~RrdVv~lkS~e~wy~~GRvIkpgaqP~K~vK~~--~ 500 (650)
T COG5535 423 VQDLKRHPKFVLESHLKWNQAIKPGAKPGFTLTKGKNSVEAVYLRRDVVRLKSAEQWYRMGRVIKPGAQPLKIVKRM--R 500 (650)
T ss_pred HHHhccCCceeeHhhhhhhhhhccCCccceeeecCCCccchhhhhhhHHhhcCHHHHHhcCcccCCCCchHHHHHHH--h
Confidence 9999999999999999999999999754 456678 99999999999999999999999999999999999972 1
Q ss_pred CCCCCCCCCCccccccccccccccccccccCCCCCCCCCCccCCCCCceEeecCCCCCCCeeeecCccHHHHHHHcCCCe
Q 002340 692 KKGQDFEPEDYDEVDARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDS 771 (934)
Q Consensus 692 ~k~~~~~~~~~~~~~~~~~~~LY~~wQTe~y~PPpvvdG~VPkN~yGNVdlf~psMlP~G~VHL~l~~i~rvAkkLgIDy 771 (934)
.+.+ +.++ ....+||++|||+.|.||||++|+||||.|||||+|+|+|||.||+||+.+++.+||+.|||||
T Consensus 501 ~rv~--~~~d------~vi~~LYs~eqT~ly~pp~vv~~~i~KN~yGNid~~~psmiP~g~~~i~~~~a~~iAr~L~I~y 572 (650)
T COG5535 501 ERVR--NLDD------KVIRELYSPEQTELYGPPLVVAGIIPKNMYGNIDYYVPSMIPRGCVLIPNRNARDIARLLGIDY 572 (650)
T ss_pred hhcc--cccc------hHHHhhcCHHHHHhhcCCccccccccccccCCeeeecccccCCCeEeccCchHHHHHHHhCCch
Confidence 2222 2222 2456799999999999999999999999999999999999999999999999999999999999
Q ss_pred eeceeceeecCCeeeeeEceEEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcC
Q 002340 772 APAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEAYAEEEEKREAEEKKRREAQATSRWYQLLSSIVTRQRLNNCYGN 848 (934)
Q Consensus 772 ApAVtGFeFk~G~a~PvidGIVV~eE~~e~l~~a~~e~~e~~~~~e~~kre~~aL~~Wk~Llk~LrIreRL~~~Yg~ 848 (934)
|+|||||+|+.-++.||..||||.+++.++|..+..+.+..++++++.+-.+.+|..|+.||++||||.||+.+||.
T Consensus 573 a~aVtGFdF~r~~~kPv~~Givv~K~~~eai~~~~~e~e~iq~~ke~~e~r~~~L~~Wk~Ll~~LRir~Ri~~eYG~ 649 (650)
T COG5535 573 ADAVTGFDFGRSTVKPVLRGIVVPKKNLEAISNFLAEYERIQEEKERSEVRLGGLKRWKILLRKLRIRLRINEEYGL 649 (650)
T ss_pred hhhhcccccccccccccccceecchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHhcc
Confidence 99999999999899999999999999999999999988888888888777889999999999999999999999996
No 4
>PF10405 BHD_3: Rad4 beta-hairpin domain 3; InterPro: IPR018328 Mutations in the nucleotide excision repair (NER) pathway can cause the xeroderma pigmentosum skin cancer predisposition syndrome. NER lesions are limited to one DNA strand, but otherwise they are chemically and structurally diverse, being caused by a wide variety of genotoxic chemicals and ultraviolet radiation. The xeroderma pigmentosum C (XPC) protein has a central role in initiating global-genome NER by recognising the lesion and recruiting downstream factors. In NER in eukaryotes, DNA is incised on both sides of the lesion, resulting in the removal of a fragment ~25-30 nucleotides long. This is followed by repair synthesis and ligation. This reaction, in yeast, requires the damage binding factors Rad14, RPA, and the Rad4-Rad23 complex, the transcription factor TFIIH which contains the two DNA helicases Rad3 and Rad25, essential for creating a bubble structure, and the two endonucleases, the Rad1-Rad10 complex and Rad2, which incise the damaged DNA strand on the 5'- and 3'-side of the lesion, respectively []. The crystal structure of the yeast XPC orthologue Rad4 bound to DNA containing a cyclobutane pyrimidine dimer lesion has been determined. The structure shows that Rad4 inserts a beta-hairpin through the DNA duplex, causing the two damaged base pairs to flip out of the double helix. The expelled nucleotides of the undamaged strand are recognised by Rad4, whereas the two cyclobutane pyrimidine dimer-linked nucleotides become disordered. This indicates that the lesions recognised by Rad4/XPC thermodynamically destabilise the double helix in a manner that facilitates the flipping-out of two base pairs []. Homologues of all the above mentioned yeast genes, except for RAD7, RAD16, and MMS19, have been identified in humans, and mutations in these human genes affect NER in a similar fashion as they do in yeast, with the exception of XPC, the human counterpart of yeast RAD4. Deletion of RAD4 causes the same high level of UV sensitivity as do mutations in the other class 1 genes, and rad4 mutants are completely defective in incision. By contrast, XPC is required for the repair of nontranscribed regions of the genome but not for the repair of the transcribed DNA strand. This entry represents the DNA-binding domain of Rad4, which has a beta-hairpin structure []. Rad4 inserts a beta-hairpin through the DNA duplex, causing the two damaged base pairs to flip out of the double helix. ; GO: 0003684 damaged DNA binding, 0006289 nucleotide-excision repair, 0005634 nucleus; PDB: 2QSG_A 2QSF_A 2QSH_A.
Probab=99.97 E-value=5.2e-32 Score=240.07 Aligned_cols=75 Identities=48% Similarity=0.918 Sum_probs=62.5
Q ss_pred ccCCCCCceEeecCCCCCCCeeeecCccHHHHHHHcCCCeeeceeceee-cCCeeeeeEceEEEccccHHHHHHHH
Q 002340 732 VPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEF-RNGRSTPVFDGIVVCAEFKDTILEAY 806 (934)
Q Consensus 732 VPkN~yGNVdlf~psMlP~G~VHL~l~~i~rvAkkLgIDyApAVtGFeF-k~G~a~PvidGIVV~eE~~e~l~~a~ 806 (934)
||||+|||||||+|+|+|.|||||+++++.++|++||||||+|||||+| ++|+++|+++|||||+||+++|++||
T Consensus 1 vPkN~~GNiei~~~~m~P~G~vhi~~~~~~~~a~~l~Idya~AV~GF~f~~~g~~~Pv~~GiVV~~e~~~~v~~a~ 76 (76)
T PF10405_consen 1 VPKNEYGNIEIFVPSMLPEGCVHIKLPGIEKVAKKLGIDYAPAVVGFDFQKGGRAVPVIDGIVVAEEDEEAVQDAW 76 (76)
T ss_dssp ----TTS-EE-SSGGGS-TTEEEEE-TTHHHHHHHTT---EEEEEEEEE-STT-EEEEEEEEEEEGGGHHHHHHHH
T ss_pred CCCCCCCCEEEeCCCCCCCceEEEecccHHHHHHHcCCcEEeeecceeEccCCCCeEEECeEEEEhhHHHHHHhhC
Confidence 7999999999999999999999999999999999999999999999999 99999999999999999999999998
No 5
>PF03835 Rad4: Rad4 transglutaminase-like domain; InterPro: IPR018325 RAD4/Xp-C proteins contain an ancient transglutaminase fold that is also found in peptide-N-glycanases (PNGases), which remove glycans from glycoproteins during their degradation. The PNGases retain the catalytic triad that is typical of this fold and are predicted to have a reaction mechanism similar to that involved in transglutamination. In contrast, the RAD4/Xp-C proteins are predicted to be inactive and are likely to only possess the interaction function in DNA repair []. ; GO: 0003684 damaged DNA binding, 0006289 nucleotide-excision repair, 0005634 nucleus; PDB: 2QSG_A 2QSF_A 2QSH_A 1X3W_A 1X3Z_A 3ESW_A.
Probab=99.87 E-value=5.3e-23 Score=203.17 Aligned_cols=109 Identities=33% Similarity=0.625 Sum_probs=79.4
Q ss_pred CccCCCCceeEEEEeccCCCCCceEEecccccccccchhhhHhHHhccCCeeEEEEEcCCC-cccchhhhhhh-HH-Hhh
Q 002340 479 SRKVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCG-AKDVTRRYCMK-WY-RIA 555 (934)
Q Consensus 479 ~~~l~~P~fWvEV~~~~e~~~~kWI~VDPv~~~vd~p~~~Ep~~~~~~~~msYVVAfd~DG-akDVTrRYa~~-w~-k~~ 555 (934)
..++.+|+||+|||++. .++||||||+++.+.....+||....+.++|+|||||+++| |+|||+||+++ |+ .+.
T Consensus 29 ~~~~~~~~~W~EV~~~~---~~rWI~VDp~~~~~~~~~~~ep~~~~~~~~~~YViA~d~~~~~kDVT~RY~~~~~~~~~~ 105 (145)
T PF03835_consen 29 DKDLPYPNFWVEVYSPE---EKRWIHVDPVVGKIIKVSCDEPLEENANNPMSYVIAFDNDGYAKDVTRRYASNYWNSKTR 105 (145)
T ss_dssp HHHTTTTCEEEEEEETT---TTEEEEEETTTS-EESTBTTSTCCCCCS--B-EEEEE-CTTEEEE-HHHH-T-TCCCCCG
T ss_pred cccCCCCeEEEEEEecC---CCeEEEeeeeccccccccccCchhhccCCceEEEEEEeCCCCEEEchHhhcccccccccc
Confidence 45678999999999975 48999999998755567778888778899999999999888 99999999998 55 456
Q ss_pred cccCC-----HHHHHHHHhhhhhcccCcCCCccccccccCcccccCCchHHHHHH
Q 002340 556 SKRVN-----SAWWDAVLAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELE 605 (934)
Q Consensus 556 rkRv~-----~~Ww~~~L~~~~~~~s~~~~~~~i~~~~~~~~~~~rd~~Ed~EL~ 605 (934)
+.|+. ..||..+|++|++.. .....+|.+||.||+
T Consensus 106 r~R~~~~~~~~~W~~~~l~~~~~~~---------------~~~~~~d~~Ed~el~ 145 (145)
T PF03835_consen 106 RLRVDRSYEEEDWWEKVLRPYNRPR---------------RDRTIRDKKEDEELH 145 (145)
T ss_dssp GGSGGGSHHHHHHHHHHHHHH--S------------------H--HHHHHHHHH-
T ss_pred cccCCccccHHHHHHHHHHHHhccc---------------ccccchHHHHHhhcC
Confidence 78888 899999999998532 111246888999885
No 6
>PF10403 BHD_1: Rad4 beta-hairpin domain 1; InterPro: IPR018326 Mutations in the nucleotide excision repair (NER) pathway can cause the xeroderma pigmentosum skin cancer predisposition syndrome. NER lesions are limited to one DNA strand, but otherwise they are chemically and structurally diverse, being caused by a wide variety of genotoxic chemicals and ultraviolet radiation. The xeroderma pigmentosum C (XPC) protein has a central role in initiating global-genome NER by recognising the lesion and recruiting downstream factors. In NER in eukaryotes, DNA is incised on both sides of the lesion, resulting in the removal of a fragment ~25-30 nucleotides long. This is followed by repair synthesis and ligation. This reaction, in yeast, requires the damage binding factors Rad14, RPA, and the Rad4-Rad23 complex, the transcription factor TFIIH which contains the two DNA helicases Rad3 and Rad25, essential for creating a bubble structure, and the two endonucleases, the Rad1-Rad10 complex and Rad2, which incise the damaged DNA strand on the 5'- and 3'-side of the lesion, respectively []. The crystal structure of the yeast XPC orthologue Rad4 bound to DNA containing a cyclobutane pyrimidine dimer lesion has been determined. The structure shows that Rad4 inserts a beta-hairpin through the DNA duplex, causing the two damaged base pairs to flip out of the double helix. The expelled nucleotides of the undamaged strand are recognised by Rad4, whereas the two cyclobutane pyrimidine dimer-linked nucleotides become disordered. This indicates that the lesions recognised by Rad4/XPC thermodynamically destabilise the double helix in a manner that facilitates the flipping-out of two base pairs []. Homologues of all the above mentioned yeast genes, except for RAD7, RAD16, and MMS19, have been identified in humans, and mutations in these human genes affect NER in a similar fashion as they do in yeast, with the exception of XPC, the human counterpart of yeast RAD4. Deletion of RAD4 causes the same high level of UV sensitivity as do mutations in the other class 1 genes, and rad4 mutants are completely defective in incision. By contrast, XPC is required for the repair of nontranscribed regions of the genome but not for the repair of the transcribed DNA strand. This entry represents the DNA-binding domain of Rad4, which has a beta-hairpin structure []. Rad4 inserts a beta-hairpin through the DNA duplex, causing the two damaged base pairs to flip out of the double helix. ; GO: 0003684 damaged DNA binding, 0006289 nucleotide-excision repair, 0005634 nucleus; PDB: 2QSG_A 2QSF_A 2QSH_A.
Probab=99.76 E-value=1.2e-19 Score=153.12 Aligned_cols=51 Identities=43% Similarity=0.741 Sum_probs=40.2
Q ss_pred cCCCCcChhhhccCCceeeccccccccccCCCCCcceeecc----eeeeecCCcc
Q 002340 610 TEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSG----HAVYPRSCVQ 660 (934)
Q Consensus 610 ~epmPtsi~~fKnHP~YvLerhL~k~EvI~P~a~v~G~~~G----EpVY~RsdV~ 660 (934)
+|+||+|+++|||||+|||||||++||+|+|+++++|+|+| ||||+|+||+
T Consensus 3 ~e~~P~s~~~~K~hP~yvLe~~L~~~E~i~P~a~~vg~~~~~~~~e~VY~R~~V~ 57 (57)
T PF10403_consen 3 NEPLPKSIQDFKNHPNYVLERHLKRNEVIYPGAKPVGTFKGKGKKEPVYLRSDVI 57 (57)
T ss_dssp HH-S-SSCGGGTT-SSEEEGGGS-TTEEE-TT---SEEEE-TSTEEEEEEGGGE-
T ss_pred cCCCCccHHHHhCCChhhhhhhcCcceeECCCCceeEEEeCCCcceeeEeHhhCC
Confidence 68999999999999999999999999999999999999999 9999999996
No 7
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=99.76 E-value=5.7e-19 Score=195.59 Aligned_cols=82 Identities=27% Similarity=0.454 Sum_probs=73.1
Q ss_pred ceeEEEEeccCCCCCceEEecccccccccchhhhHhHHhccCCeeEEEEEcCCCcccchhhhhhhHHHh--hcccCCHHH
Q 002340 486 LYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRI--ASKRVNSAW 563 (934)
Q Consensus 486 ~fWvEV~~~~e~~~~kWI~VDPv~~~vd~p~~~Ep~~~~~~~~msYVVAfd~DGakDVTrRYa~~w~k~--~rkRv~~~W 563 (934)
|+|+|||+.. .+||+|||||.+++|+|.+||.. |.+.|+|||||+.||++|||.||+.+|.+. +|.++.+.=
T Consensus 250 HVWtEvYS~~---qqRW~HvDpcE~v~D~PllYe~G---W~KklsY~iafgkD~VvDVT~RYi~~h~e~~~~R~~~~E~~ 323 (500)
T KOG0909|consen 250 HVWTEVYSNA---QQRWVHVDPCENVFDKPLLYEIG---WGKKLSYCIAFGKDGVVDVTWRYILDHKENLLPRDLCKESV 323 (500)
T ss_pred chhHHhhhhh---hheeEeecccccccccceeeecc---cCcccceEEEeccCceEeeehhhhccchhhccchhhcchHH
Confidence 5999999975 49999999999999999999876 899999999999999999999999988875 456678888
Q ss_pred HHHHHhhhhh
Q 002340 564 WDAVLAPLRE 573 (934)
Q Consensus 564 w~~~L~~~~~ 573 (934)
+..+|..++.
T Consensus 324 l~~~l~~in~ 333 (500)
T KOG0909|consen 324 LQQTLQFINK 333 (500)
T ss_pred HHHHHHHHHH
Confidence 8888887764
No 8
>PF10404 BHD_2: Rad4 beta-hairpin domain 2; InterPro: IPR018327 Mutations in the nucleotide excision repair (NER) pathway can cause the xeroderma pigmentosum skin cancer predisposition syndrome. NER lesions are limited to one DNA strand, but otherwise they are chemically and structurally diverse, being caused by a wide variety of genotoxic chemicals and ultraviolet radiation. The xeroderma pigmentosum C (XPC) protein has a central role in initiating global-genome NER by recognising the lesion and recruiting downstream factors. In NER in eukaryotes, DNA is incised on both sides of the lesion, resulting in the removal of a fragment ~25-30 nucleotides long. This is followed by repair synthesis and ligation. This reaction, in yeast, requires the damage binding factors Rad14, RPA, and the Rad4-Rad23 complex, the transcription factor TFIIH which contains the two DNA helicases Rad3 and Rad25, essential for creating a bubble structure, and the two endonucleases, the Rad1-Rad10 complex and Rad2, which incise the damaged DNA strand on the 5'- and 3'-side of the lesion, respectively []. The crystal structure of the yeast XPC orthologue Rad4 bound to DNA containing a cyclobutane pyrimidine dimer lesion has been determined. The structure shows that Rad4 inserts a beta-hairpin through the DNA duplex, causing the two damaged base pairs to flip out of the double helix. The expelled nucleotides of the undamaged strand are recognised by Rad4, whereas the two cyclobutane pyrimidine dimer-linked nucleotides become disordered. This indicates that the lesions recognised by Rad4/XPC thermodynamically destabilise the double helix in a manner that facilitates the flipping-out of two base pairs []. Homologues of all the above mentioned yeast genes, except for RAD7, RAD16, and MMS19, have been identified in humans, and mutations in these human genes affect NER in a similar fashion as they do in yeast, with the exception of XPC, the human counterpart of yeast RAD4. Deletion of RAD4 causes the same high level of UV sensitivity as do mutations in the other class 1 genes, and rad4 mutants are completely defective in incision. By contrast, XPC is required for the repair of nontranscribed regions of the genome but not for the repair of the transcribed DNA strand. This entry represents the DNA-binding domain of Rad4, which has a beta-hairpin structure []. Rad4 inserts a beta-hairpin through the DNA duplex, causing the two damaged base pairs to flip out of the double helix. ; GO: 0003684 damaged DNA binding, 0006289 nucleotide-excision repair, 0005634 nucleus; PDB: 2QSG_A 2QSF_A 2QSH_A.
Probab=99.63 E-value=5.9e-17 Score=139.78 Aligned_cols=64 Identities=36% Similarity=0.637 Sum_probs=30.6
Q ss_pred cccHHHHHHhcccccCCCcccceeccCCCCCCCCCCCCCCccccccccccccccccccccCCCC
Q 002340 662 LKTKERWLREALQVKANEVPVKVIKNSSKSKKGQDFEPEDYDEVDARGNIELYGKWQLEPLRLP 725 (934)
Q Consensus 662 LkS~e~W~r~GR~VK~gE~P~K~vk~~~~~~k~~~~~~~~~~~~~~~~~~~LY~~wQTe~y~PP 725 (934)
|||+++|+++||+||+||+|+|+|+.++++.+.......+..+.+....++|||+||||+|+||
T Consensus 1 LkS~e~W~r~GR~Vk~gE~P~K~vk~r~~~~~~~~~~~~~~~~~~~~~~~~LYg~wQTe~y~PP 64 (64)
T PF10404_consen 1 LKSAEKWYREGRVVKPGEQPYKVVKSRARTINRKREDEADENEDGEDETVPLYGEWQTEPYIPP 64 (64)
T ss_dssp -BEHHHHHTTTEEE-TT---SEEEE-----------------------EEEEB-GGGEEE----
T ss_pred CCCHHHHHHcCCccCCCCceeeEEecccccccccccccccccccccccCccCCCHHHCccccCC
Confidence 7999999999999999999999999987632211111111111122368999999999999998
No 9
>TIGR00605 rad4 DNA repair protein rad4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.15 E-value=1e-12 Score=157.36 Aligned_cols=148 Identities=23% Similarity=0.163 Sum_probs=118.5
Q ss_pred CCceEEEEecCCcccccc----------c-cccChHHHHHHHHHHHHHHHHHhhhhhHHHhhcCcHHHHHHhhccccccc
Q 002340 149 IKGVTIEFDAADSVTKKP----------V-RRASAEDKELAELVHKVHLLCLLARGRLIDSVCDDPLIQASLLSLLPSYL 217 (934)
Q Consensus 149 ~~~veIeie~~~~~kkk~----------~-RR~t~~eKelr~~vHKvHLLCLLAhg~~rN~~Cnd~~lQa~llSlLP~~~ 217 (934)
.++|+||++++++.+++. + |||+++.|++++++|||||||+|+++...|+.|+++++.+.. +++|+.+
T Consensus 13 ~~~~~~e~~~~~~~~~r~~~~~~~~~~~~~~~~~r~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~d~~~~~-~~~~~~~ 91 (713)
T TIGR00605 13 IRKVENEKEAEKQPKSRRRKVRRENEPSLRRRKKRFKTGLNELPHEVVLMCNLDSTHSDDRVVSVPDSLSVS-EEIPSRE 91 (713)
T ss_pred HHHHHhhhhcchhhhhhcchhhhhhhhhHhhhhhhhhccccccCcceEEEEEeccccccccccccccccccc-ccCCccc
Confidence 567999999986633221 3 456689999999999999999999999999999999888777 9999998
Q ss_pred ccccCccccccccchhhHHhhhcceeecccCccccchhhHHHHHHHHhcCCH-----HHHHHHHHHHHHhcCCceEEEEe
Q 002340 218 LKISEVSKLTANALSPIVSWFHDNFHVRSSVSTRRSFHSDLAHALESREGTP-----EEIAALSVALFRALKLTTRFVSI 292 (934)
Q Consensus 218 ~~~~~~~~~~~~~L~~lv~WF~~~F~v~~~~~~~~~~~~~L~~~l~~~~Gs~-----de~aqLF~aLLRaLgl~aRLV~s 292 (934)
.... ...+...+|++++.||.++|.+++..+.. -..++...++++..+. ...+|+|..||+.+++.+|++.+
T Consensus 92 ~~~~-~~~~e~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~r~~~~~~eR~~R~~iH~~~ll~ll~h~~~RN~w~ 168 (713)
T TIGR00605 92 EDYD-SREFEDVYLSNLVAEFETISVEIKPSSKA--ESDDDAETLSRNVCSNEARKDRKYIHILYLLCLMVHLFTRNEWS 168 (713)
T ss_pred cccc-hhhhhhhhhcccccccCcccccccccchh--hhhhHHHHHHHhhccHHHHHHHHHHHHHHHHHHhhhhHhhhhhh
Confidence 7654 47888999999999999999998543222 2233455666655544 45999999999999999999999
Q ss_pred eccccCCcc
Q 002340 293 LDVASLKPE 301 (934)
Q Consensus 293 Lqp~sLKp~ 301 (934)
+|| ++.+.
T Consensus 169 n~~-~~~~~ 176 (713)
T TIGR00605 169 LSA-PLKSA 176 (713)
T ss_pred CCh-HHHhH
Confidence 998 55554
No 10
>PF01841 Transglut_core: Transglutaminase-like superfamily; InterPro: IPR002931 This domain is found in many proteins known to have transglutaminase activity, i.e. which cross-link proteins through an acyl-transfer reaction between the gamma-carboxamide group of peptide-bound glutamine and the epsilon-amino group of peptide-bound lysine, resulting in a epsilon-(gamma-glutamyl)lysine isopeptide bond. Tranglutaminases have been found in a diverse range of species, from bacteria through to mammals. The enzymes require calcium binding and their activity leads to post-translational modification of proteins through acyl-transfer reactions, involving peptidyl glutamine residues as acyl donors and a variety of primary amines as acyl acceptors, with the generation of proteinase resistant isopeptide bonds []. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterised transglutaminase, the human blood clotting factor XIIIa' []. On the basis of the experimentally demonstrated activity of the Methanobacterium phage psiM2 pseudomurein endoisopeptidase [], it is proposed that many, if not all, microbial homologs of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease []. A subunit of plasma Factor XIII revealed that each Factor XIIIA subunit is composed of four domains (termed N-terminal beta-sandwich, core domain (containing the catalytic and the regulatory sites), and C-terminal beta-barrels 1 and 2) and that two monomers assemble into the native dimer through the surfaces in domains 1 and 2, in opposite orientation. This organisation in four domains is highly conserved during evolution among transglutaminase isoforms [].; PDB: 2F4M_A 2F4O_A 1GGY_B 1FIE_B 1GGU_B 1GGT_B 1F13_A 1QRK_B 1EVU_A 1EX0_B ....
Probab=96.81 E-value=0.00088 Score=62.24 Aligned_cols=65 Identities=29% Similarity=0.334 Sum_probs=46.6
Q ss_pred ccchhhHHhhhcceeecccCccccchhhHHHHHHHHhcCCHHHHHHHHHHHHHhcCCceEEEEeecc
Q 002340 229 NALSPIVSWFHDNFHVRSSVSTRRSFHSDLAHALESREGTPEEIAALSVALFRALKLTTRFVSILDV 295 (934)
Q Consensus 229 ~~L~~lv~WF~~~F~v~~~~~~~~~~~~~L~~~l~~~~Gs~de~aqLF~aLLRaLgl~aRLV~sLqp 295 (934)
..+..+..|++++|......... ...+...+|++..|+-.+.+.||++|||++||+||+|.....
T Consensus 16 ~~~~~i~~~v~~~~~y~~~~~~~--~~~~~~~~l~~~~G~C~~~a~l~~allr~~Gipar~v~g~~~ 80 (113)
T PF01841_consen 16 EKAKAIYDWVRSNIRYDDPNYSP--GPRDASEVLRSGRGDCEDYASLFVALLRALGIPARVVSGYVK 80 (113)
T ss_dssp CCCCCCCCCCCCCCCEC-TCCCC--CCTTHHHHHHCEEESHHHHHHHHHHHHHHHT--EEEEEEEEE
T ss_pred HHHHHHHHHHHhCcEEeCCCCCC--CCCCHHHHHHcCCCccHHHHHHHHHHHhhCCCceEEEEEEcC
Confidence 55667889999999887211111 112356788888899999999999999999999999974433
No 11
>KOG2179 consensus Nucleotide excision repair complex XPC-HR23B, subunit XPC/DPB11 [Replication, recombination and repair]
Probab=95.66 E-value=0.0063 Score=73.10 Aligned_cols=114 Identities=18% Similarity=0.103 Sum_probs=90.3
Q ss_pred HHhhhhhHHHhhcCcHH-HHHHhhcccccccccccCccccccccchhhHHhhhcceeecccCccccchhhHHHHHHHHh-
Q 002340 188 CLLARGRLIDSVCDDPL-IQASLLSLLPSYLLKISEVSKLTANALSPIVSWFHDNFHVRSSVSTRRSFHSDLAHALESR- 265 (934)
Q Consensus 188 CLLAhg~~rN~~Cnd~~-lQa~llSlLP~~~~~~~~~~~~~~~~L~~lv~WF~~~F~v~~~~~~~~~~~~~L~~~l~~~- 265 (934)
|.+|+....|+.|.-.+ ...+.+.++|....... ++.....+|...++||...+++....+... +......++.+
T Consensus 1 c~~a~~d~~n~~~s~~~~~~~~~l~l~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--~~~~~~s~~~~~ 77 (669)
T KOG2179|consen 1 CESANNDKANRKNSKIDKEVSLYLELLPDRSFRSV-VRDEEDDLLSSDVKWFSLDSELPVENVNDV--RDTILVSLEKRK 77 (669)
T ss_pred CccchhhhhccccchhhHhHhcccccCCCcccccc-cccccccchhhccCcccccccccccccchh--hhHhhhhhhhhh
Confidence 78999999999999888 88889999998765332 245667899999999999999986543331 22333444333
Q ss_pred ----cCCHHHHHHHHHHHHHhcCCceEEEEeeccccCCccccc
Q 002340 266 ----EGTPEEIAALSVALFRALKLTTRFVSILDVASLKPEADK 304 (934)
Q Consensus 266 ----~Gs~de~aqLF~aLLRaLgl~aRLV~sLqp~sLKp~~~k 304 (934)
.++.+.+..+|.+|+|.+++.+++|.+|+|.|+++-+.+
T Consensus 78 ~~k~~~~d~~~~~~~~~l~~~~~~~~~~~~~~~~~~~r~~~l~ 120 (669)
T KOG2179|consen 78 ANKEARDDQDLEYQFHLLDRLFMLFLLKTRNLWPDPVRLNALV 120 (669)
T ss_pred hhcccccHHHHHHHHHHHhhhhHHHHHHHhcccCCcchhhHhh
Confidence 358889999999999999999999999999999997644
No 12
>smart00460 TGc Transglutaminase/protease-like homologues. Transglutaminases are enzymes that establish covalent links between proteins. A subset of transglutaminase homologues appear to catalyse the reverse reaction, the hydrolysis of peptide bonds. Proteins with this domain are both extracellular and intracellular, and it is likely that the eukaryotic intracellular proteins are involved in signalling events.
Probab=95.22 E-value=0.012 Score=50.20 Aligned_cols=30 Identities=50% Similarity=0.633 Sum_probs=26.8
Q ss_pred HHHhcCCHHHHHHHHHHHHHhcCCceEEEE
Q 002340 262 LESREGTPEEIAALSVALFRALKLTTRFVS 291 (934)
Q Consensus 262 l~~~~Gs~de~aqLF~aLLRaLgl~aRLV~ 291 (934)
|+.+.|+-.+.+.||++|||++|++||+|.
T Consensus 2 ~~~~~G~C~~~a~l~~~llr~~GIpar~v~ 31 (68)
T smart00460 2 LKTKYGTCGEFAALFVALLRSLGIPARVVS 31 (68)
T ss_pred CcccceeeHHHHHHHHHHHHHCCCCeEEEe
Confidence 455678888999999999999999999996
No 13
>TIGR00598 rad14 DNA repair protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=95.02 E-value=0.21 Score=51.65 Aligned_cols=35 Identities=26% Similarity=0.489 Sum_probs=30.1
Q ss_pred CCCccccccccccCcccccceeecccC-CCceEEEeeC
Q 002340 898 SEEHEHVYLIEDQSFDEENSVTTKRCH-CGFTIQVEEL 934 (934)
Q Consensus 898 ~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~ 934 (934)
...|+|.|-.+ .+|+|+.+-+|+|- |||.|..|+|
T Consensus 137 ~~~H~H~f~~~--~~~~e~~~~~k~C~~Cg~e~~~e~m 172 (172)
T TIGR00598 137 GRVHEHEFGPE--TNGVEEDTYRRTCTTCGLEETYEKM 172 (172)
T ss_pred CCcccccCCcc--cccccCCceeeecCCCCceEEEEeC
Confidence 36799999664 46789999999997 9999999987
No 14
>COG1305 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]
Probab=92.04 E-value=0.15 Score=54.94 Aligned_cols=85 Identities=16% Similarity=0.226 Sum_probs=56.4
Q ss_pred HHhhcC--cHHHHHHhhcccccccccccCccccccccchhhHHhhhcceeecccCccccchhhHHHHHHHHhcCCHHHHH
Q 002340 196 IDSVCD--DPLIQASLLSLLPSYLLKISEVSKLTANALSPIVSWFHDNFHVRSSVSTRRSFHSDLAHALESREGTPEEIA 273 (934)
Q Consensus 196 rN~~Cn--d~~lQa~llSlLP~~~~~~~~~~~~~~~~L~~lv~WF~~~F~v~~~~~~~~~~~~~L~~~l~~~~Gs~de~a 273 (934)
....|+ ++.+++++..+.-.. ......+..+..|+...|.-+.... . ....-..+|+...|+=...+
T Consensus 133 ~~~~~~~~~~~~~~la~~~~~~~--------~~~~~~~~~~~~~~~~~~~y~~~~~-~--~~~~~~~~l~~~~G~C~d~a 201 (319)
T COG1305 133 VSPDTPIKKPRVAELAARETGGA--------TTPREKAAALFDYVNSKIRYSPGPT-P--VTGSASDALRLGRGVCRDFA 201 (319)
T ss_pred CCCCCCcccHHHHHHHHHhhccc--------CCHHHHHHHHHHHHhhcceeecCCC-C--CCCCHHHHHHhCCcccccHH
Confidence 344554 577777776633311 1122445567888887777664421 1 11223467777789888999
Q ss_pred HHHHHHHHhcCCceEEEE
Q 002340 274 ALSVALFRALKLTTRFVS 291 (934)
Q Consensus 274 qLF~aLLRaLgl~aRLV~ 291 (934)
+||++|||++||+||+|.
T Consensus 202 ~l~val~Ra~GIpAR~V~ 219 (319)
T COG1305 202 HLLVALLRAAGIPARYVS 219 (319)
T ss_pred HHHHHHHHHcCCcceeee
Confidence 999999999999999994
No 15
>COG5145 RAD14 DNA excision repair protein [DNA replication, recombination, and repair]
Probab=87.13 E-value=1.4 Score=47.29 Aligned_cols=35 Identities=34% Similarity=0.643 Sum_probs=26.2
Q ss_pred CCccccccccccCcccccceeecccCCCceEEEeeC
Q 002340 899 EEHEHVYLIEDQSFDEENSVTTKRCHCGFTIQVEEL 934 (934)
Q Consensus 899 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 934 (934)
+.|.|+|-++-+. --|..|-..||.||..|.-+|+
T Consensus 258 ~kHvH~f~e~vdg-~~e~g~~iqRC~CGlevEq~ei 292 (292)
T COG5145 258 EKHVHVFDEFVDG-PNEPGVIIQRCSCGLEVEQEEI 292 (292)
T ss_pred hcceeeccccccC-CCCCCeEEEecccccchhhccC
Confidence 4599999766444 2278899999999998765553
No 16
>KOG4017 consensus DNA excision repair protein XPA/XPAC/RAD14 [Replication, recombination and repair]
Probab=86.73 E-value=2.4 Score=46.16 Aligned_cols=34 Identities=32% Similarity=0.481 Sum_probs=26.8
Q ss_pred CCccccccccccCcccccceeecccCCCceEEEeeC
Q 002340 899 EEHEHVYLIEDQSFDEENSVTTKRCHCGFTIQVEEL 934 (934)
Q Consensus 899 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 934 (934)
.-|+|+|-.|- --+|..++..+|.||+++.-|+|
T Consensus 241 ~~H~Hef~~e~--~~eEd~y~~tc~~Cg~e~e~ekl 274 (274)
T KOG4017|consen 241 EKHVHEFGPET--GIEEDGYRITCCTCGLEEEQEKL 274 (274)
T ss_pred cccceecCCCC--CCCCCcceeEeecccchhhhhcC
Confidence 56999999885 44556666669999999887765
No 17
>smart00460 TGc Transglutaminase/protease-like homologues. Transglutaminases are enzymes that establish covalent links between proteins. A subset of transglutaminase homologues appear to catalyse the reverse reaction, the hydrolysis of peptide bonds. Proteins with this domain are both extracellular and intracellular, and it is likely that the eukaryotic intracellular proteins are involved in signalling events.
Probab=85.76 E-value=0.68 Score=39.29 Aligned_cols=21 Identities=48% Similarity=0.846 Sum_probs=18.2
Q ss_pred CCCceeEEEEeccCCCCCceEEeccc
Q 002340 483 GAPLYWAEVYCSGENLTGKWVHVDAA 508 (934)
Q Consensus 483 ~~P~fWvEV~~~~e~~~~kWI~VDPv 508 (934)
..+|.|+|||+. ++|+.+||.
T Consensus 47 ~~~H~W~ev~~~-----~~W~~~D~~ 67 (68)
T smart00460 47 WEAHAWAEVYLE-----GGWVPVDPT 67 (68)
T ss_pred CCcEEEEEEEEC-----CCeEEEeCC
Confidence 368999999984 699999995
No 18
>PF01841 Transglut_core: Transglutaminase-like superfamily; InterPro: IPR002931 This domain is found in many proteins known to have transglutaminase activity, i.e. which cross-link proteins through an acyl-transfer reaction between the gamma-carboxamide group of peptide-bound glutamine and the epsilon-amino group of peptide-bound lysine, resulting in a epsilon-(gamma-glutamyl)lysine isopeptide bond. Tranglutaminases have been found in a diverse range of species, from bacteria through to mammals. The enzymes require calcium binding and their activity leads to post-translational modification of proteins through acyl-transfer reactions, involving peptidyl glutamine residues as acyl donors and a variety of primary amines as acyl acceptors, with the generation of proteinase resistant isopeptide bonds []. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterised transglutaminase, the human blood clotting factor XIIIa' []. On the basis of the experimentally demonstrated activity of the Methanobacterium phage psiM2 pseudomurein endoisopeptidase [], it is proposed that many, if not all, microbial homologs of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease []. A subunit of plasma Factor XIII revealed that each Factor XIIIA subunit is composed of four domains (termed N-terminal beta-sandwich, core domain (containing the catalytic and the regulatory sites), and C-terminal beta-barrels 1 and 2) and that two monomers assemble into the native dimer through the surfaces in domains 1 and 2, in opposite orientation. This organisation in four domains is highly conserved during evolution among transglutaminase isoforms [].; PDB: 2F4M_A 2F4O_A 1GGY_B 1FIE_B 1GGU_B 1GGT_B 1F13_A 1QRK_B 1EVU_A 1EX0_B ....
Probab=85.00 E-value=0.65 Score=43.05 Aligned_cols=20 Identities=40% Similarity=0.963 Sum_probs=17.1
Q ss_pred CCceeEEEEeccCCCCCceEEecc
Q 002340 484 APLYWAEVYCSGENLTGKWVHVDA 507 (934)
Q Consensus 484 ~P~fWvEV~~~~e~~~~kWI~VDP 507 (934)
..|.|+|||.++ ++||++||
T Consensus 94 ~~H~w~ev~~~~----~~W~~~Dp 113 (113)
T PF01841_consen 94 DNHAWVEVYLPG----GGWIPLDP 113 (113)
T ss_dssp EEEEEEEEEETT----TEEEEEET
T ss_pred CCEEEEEEEEcC----CcEEEcCC
Confidence 459999999953 79999998
No 19
>PF13369 Transglut_core2: Transglutaminase-like superfamily
Probab=67.72 E-value=6.8 Score=39.48 Aligned_cols=36 Identities=36% Similarity=0.423 Sum_probs=33.2
Q ss_pred hHHHHHHHHhcCCHHHHHHHHHHHHHhcCCceEEEE
Q 002340 256 SDLAHALESREGTPEEIAALSVALFRALKLTTRFVS 291 (934)
Q Consensus 256 ~~L~~~l~~~~Gs~de~aqLF~aLLRaLgl~aRLV~ 291 (934)
..|..+|+++.|.+-.++.||++++|.|||++..|.
T Consensus 54 ~~l~~vL~~r~G~Pi~L~ily~~va~rlGl~~~~v~ 89 (152)
T PF13369_consen 54 SFLHKVLERRRGIPISLAILYLEVARRLGLPAEPVN 89 (152)
T ss_pred hhHHHHHhcCCCCcHHHHHHHHHHHHHcCCeEEEEe
Confidence 346789999999999999999999999999999995
No 20
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=53.64 E-value=5.5 Score=34.67 Aligned_cols=28 Identities=46% Similarity=0.865 Sum_probs=22.3
Q ss_pred ccccCcccccceeecccCCC--ceEEEeeC
Q 002340 907 IEDQSFDEENSVTTKRCHCG--FTIQVEEL 934 (934)
Q Consensus 907 ~~~~~~~~~~~~~~~~~~~~--~~~~~~~~ 934 (934)
.||-.|+.|+-.-|--|+|| |.|.+|.|
T Consensus 9 iedftf~~e~~~ftyPCPCGDRFeIsLeDl 38 (67)
T COG5216 9 IEDFTFSREEKTFTYPCPCGDRFEISLEDL 38 (67)
T ss_pred eeeeEEcCCCceEEecCCCCCEeEEEHHHh
Confidence 35678999999999999999 66665543
No 21
>COG5535 RAD4 DNA repair protein RAD4 [DNA replication, recombination, and repair]
Probab=53.13 E-value=3.8 Score=49.38 Aligned_cols=162 Identities=12% Similarity=0.009 Sum_probs=101.1
Q ss_pred CCCCCCCcccCCCCCCCCCCCCCCCCCCceEEEEecCCccccccccccChHHHHHHHHHHHHHHHHHhhh-hhHHHhhcC
Q 002340 123 EEMYDSDWEDGSIPVACSKENHPESDIKGVTIEFDAADSVTKKPVRRASAEDKELAELVHKVHLLCLLAR-GRLIDSVCD 201 (934)
Q Consensus 123 ~e~~d~dWEeV~~~~~~~~~~~~~~~~~~veIeie~~~~~kkk~~RR~t~~eKelr~~vHKvHLLCLLAh-g~~rN~~Cn 201 (934)
+++.+++||.++++. ++++++.... +.+..--.+..+....+..|..||+|+=-+ ..-||.||+
T Consensus 43 ~~ek~i~e~~~el~g-------------d~~vtvn~~~--rdrs~v~k~sdd~neklqssq~hl~~~~f~~l~s~nk~~d 107 (650)
T COG5535 43 DEEKDIDEEPVELDG-------------DLTVTVNNIR--RDRSKVSKYSDDHNEKLQSSQLHLIMIPFMLLKSRNKWID 107 (650)
T ss_pred hhccccccCCccCCC-------------cceeeecccc--ccccccccccchhhHHhccchhhhhcchhhhhcCcCeecc
Confidence 556669998776652 2555555431 111111124566777788999999999888 555999999
Q ss_pred cHHHHHHhhcccccccccccCccc-------cccccch--h--hHHhhhcceeecccCc-cccch-----------hhHH
Q 002340 202 DPLIQASLLSLLPSYLLKISEVSK-------LTANALS--P--IVSWFHDNFHVRSSVS-TRRSF-----------HSDL 258 (934)
Q Consensus 202 d~~lQa~llSlLP~~~~~~~~~~~-------~~~~~L~--~--lv~WF~~~F~v~~~~~-~~~~~-----------~~~L 258 (934)
|.+|--.+....|........... ++.-.|- . +..||+.+...+. +. ..... ...+
T Consensus 108 derLn~~~k~s~pk~~~~s~~d~s~rks~him~~tcll~~g~irn~W~rsk~lsng-Lr~~~~ekq~~~l~~q~~ss~~~ 186 (650)
T COG5535 108 DERLNRRLKRSVPKLGGKSFKDWSVRKSAHIMDSTCLLLLGFIRNLWFRSKMLSNG-LRFNRLEKQIKYLDNQNESSISE 186 (650)
T ss_pred chhhceeeeccCcccccccccCcchhhhHHHHHHHHHHHHHHHHHHHHHhhhhhcc-cchhhHHHhHHhhccccccccch
Confidence 999988888888854332221111 1111111 1 4679998443221 00 00000 0023
Q ss_pred HHHHHHhcCCHHHHHHHHHHHHHhcCCceEEEEeeccccCCc
Q 002340 259 AHALESREGTPEEIAALSVALFRALKLTTRFVSILDVASLKP 300 (934)
Q Consensus 259 ~~~l~~~~Gs~de~aqLF~aLLRaLgl~aRLV~sLqp~sLKp 300 (934)
....+-+.|.++-+.+.|..+.+-.+...+++..+|..+.-.
T Consensus 187 ~~~~KlL~glr~y~nk~fk~i~~~dnrkl~~rt~kq~~~s~f 228 (650)
T COG5535 187 STYKKLLEGLRFYGNKPFKNIGVEDNRKLAKRTMKQMESSDF 228 (650)
T ss_pred hHHHHHHHhHHHHhhhhhHHhhhcccHHHHHHHHHHHHhccc
Confidence 455566789999999999999999999999998777765544
No 22
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=44.26 E-value=9.6 Score=32.03 Aligned_cols=13 Identities=38% Similarity=1.025 Sum_probs=9.0
Q ss_pred ccceeecccCCCceE
Q 002340 915 ENSVTTKRCHCGFTI 929 (934)
Q Consensus 915 ~~~~~~~~~~~~~~~ 929 (934)
.|+-| -|.|||.|
T Consensus 36 dtfkR--tCkCGfni 48 (49)
T PF12677_consen 36 DTFKR--TCKCGFNI 48 (49)
T ss_pred cceee--eecccccc
Confidence 34444 49999987
No 23
>COG1305 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]
Probab=38.97 E-value=19 Score=38.80 Aligned_cols=25 Identities=40% Similarity=0.860 Sum_probs=20.1
Q ss_pred CCceeEEEEeccCCCCCceEEeccccccc
Q 002340 484 APLYWAEVYCSGENLTGKWVHVDAANAII 512 (934)
Q Consensus 484 ~P~fWvEV~~~~e~~~~kWI~VDPv~~~v 512 (934)
..|.|+|||..+ ..|+++||..+..
T Consensus 239 ~~Haw~ev~~~~----~gW~~~Dpt~~~~ 263 (319)
T COG1305 239 DAHAWAEVYLPG----RGWVPLDPTNGLL 263 (319)
T ss_pred ccceeeeeecCC----CccEeecCCCCCc
Confidence 468999999964 2699999987643
No 24
>PRK10941 hypothetical protein; Provisional
Probab=34.60 E-value=60 Score=36.20 Aligned_cols=62 Identities=18% Similarity=0.194 Sum_probs=44.1
Q ss_pred cchhhHHhhhcceeecccCccc-cchhhHHHHHHHHhcCCHHHHHHHHHHHHHhcCCceEEEE
Q 002340 230 ALSPIVSWFHDNFHVRSSVSTR-RSFHSDLAHALESREGTPEEIAALSVALFRALKLTTRFVS 291 (934)
Q Consensus 230 ~L~~lv~WF~~~F~v~~~~~~~-~~~~~~L~~~l~~~~Gs~de~aqLF~aLLRaLgl~aRLV~ 291 (934)
.|..|..||-+..--..+...- .+-.+-|-.+|++|.|.+-.++.||+.|+|.|||++.-|.
T Consensus 58 ~l~~L~~~fy~~lgF~Gn~~~Y~~p~ns~L~~VL~~R~G~PisL~il~l~iA~~lglp~~gV~ 120 (269)
T PRK10941 58 QLEKLIALFYGEWGFGGASGVYRLSDALWLDKVLKTRQGSAVSLGAILLWIANRLDLPLMPVI 120 (269)
T ss_pred HHHHHHHHHHHHhCCCCCccccCCchhhHHHHHHHccCCCcHHHHHHHHHHHHHcCCCeeeee
Confidence 4666777776654332211111 1112347799999999999999999999999999999994
No 25
>PF05207 zf-CSL: CSL zinc finger; InterPro: IPR007872 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 a probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ IPR001623 from INTERPRO domain. Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death []. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [, ]. The function of this motif is unknown. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2L6L_A 1WGE_A 2JR7_A 1YOP_A 1YWS_A.
Probab=23.86 E-value=48 Score=28.37 Aligned_cols=25 Identities=36% Similarity=0.769 Sum_probs=20.2
Q ss_pred cccCcccccceeecccCCCceEEEe
Q 002340 908 EDQSFDEENSVTTKRCHCGFTIQVE 932 (934)
Q Consensus 908 ~~~~~~~~~~~~~~~~~~~~~~~~~ 932 (934)
++-.||++..+-+..|+||-...|.
T Consensus 6 ~d~~~~~~~~~~~y~CRCG~~f~i~ 30 (55)
T PF05207_consen 6 DDMEFDEEEGVYSYPCRCGGEFEIS 30 (55)
T ss_dssp TTSEEETTTTEEEEEETTSSEEEEE
T ss_pred hhceecCCCCEEEEcCCCCCEEEEc
Confidence 4466788888999999999877664
No 26
>PF00797 Acetyltransf_2: N-acetyltransferase; InterPro: IPR001447 Arylamine N-acetyltransferase (NAT) is a cytosolic enzyme of approximately 30 kDa. It facilitates the transfer of an acetyl group from acetyl coenzyme A on to a wide range of arylamine, N-hydroxyarylamines and hydrazines. Acetylation of these compounds generally results in inactivation. NAT is found in many species from Mycobacteria (Mycobacterium tuberculosis, Mycobacterium smegmatis etc) to Homo sapiens (Human). It was the first enzyme to be observed to have polymorphic activity amongst human individuals. NAT is responsible for the inactivation of Isoniazid (a drug used to treat tuberculosis) in humans. The NAT protein has also been shown to be involved in the breakdown of folic acid. NAT catalyses the reaction: Acetyl-coA + arylamine = coA + N-acetylarylamine NAT is the target of a common genetic polymorphism of clinical relevance in humans. The N-acetylation polymorphism is determined by low or high NAT activity in liver. NAT has been implicated in the action and toxicity of amine-containing drugs, and in the susceptibility to cancer and systematic lupus erythematosus. Two highly similar human genes for NAT, termed NAT1 and NAT2, encode genetically invariant and variant NAT proteins, respectively. ; GO: 0016407 acetyltransferase activity, 0008152 metabolic process; PDB: 1W6F_A 1W5R_A 1GX3_D 2PQT_A 2IJA_A 1W4T_A 2BSZ_B 3D9W_B 3LTW_A 3LNB_A ....
Probab=23.28 E-value=77 Score=33.79 Aligned_cols=24 Identities=29% Similarity=0.240 Sum_probs=19.9
Q ss_pred CHHHHHHHHHHHHHhcCCceEEEE
Q 002340 268 TPEEIAALSVALFRALKLTTRFVS 291 (934)
Q Consensus 268 s~de~aqLF~aLLRaLgl~aRLV~ 291 (934)
-=-++..||..||++||+.+++|.
T Consensus 48 ~C~elN~lf~~lL~~lGf~v~~~~ 71 (240)
T PF00797_consen 48 YCFELNGLFYWLLRELGFDVTLVS 71 (240)
T ss_dssp -HHHHHHHHHHHHHHCT-EEEEEE
T ss_pred EhHHHHHHHHHHHHHCCCeEEEEE
Confidence 334899999999999999999995
No 27
>PF14402 7TM_transglut: 7 transmembrane helices usually fused to an inactive transglutaminase
Probab=22.77 E-value=45 Score=37.90 Aligned_cols=28 Identities=25% Similarity=0.446 Sum_probs=22.4
Q ss_pred CCceeEEEEeccCCCCCceEEecccccccccch
Q 002340 484 APLYWAEVYCSGENLTGKWVHVDAANAIIDGEQ 516 (934)
Q Consensus 484 ~P~fWvEV~~~~e~~~~kWI~VDPv~~~vd~p~ 516 (934)
.+..|+|||+. ++|+.+||..+....|.
T Consensus 30 ~l~~~lev~~~-----~~W~~f~p~tg~~g~p~ 57 (313)
T PF14402_consen 30 SLEPWLEVFNG-----GKWVLFNPRTGEQGLPE 57 (313)
T ss_pred CcHhHHheeeC-----CeEEEECCCCCCcCCCC
Confidence 57899999985 68999999987555443
Done!