Query 007298
Match_columns 609
No_of_seqs 174 out of 435
Neff 4.9
Searched_HMMs 46136
Date Thu Mar 28 21:40:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007298.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007298hhsearch_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 3E-100 6E-105 857.3 33.7 343 153-523 363-713 (713)
2 KOG2179 Nucleotide excision re 100.0 4.4E-95 9E-100 797.0 25.9 408 73-523 249-669 (669)
3 COG5535 RAD4 DNA repair protei 100.0 8E-76 1.7E-80 632.5 13.2 366 128-523 266-649 (650)
4 PF10405 BHD_3: Rad4 beta-hair 100.0 1.1E-32 2.4E-37 233.4 7.9 75 407-481 1-76 (76)
5 PF03835 Rad4: Rad4 transgluta 99.9 8.7E-24 1.9E-28 198.3 5.2 110 153-280 28-145 (145)
6 PF10403 BHD_1: Rad4 beta-hair 99.8 2.7E-20 5.9E-25 149.9 2.3 51 285-335 3-57 (57)
7 PF10404 BHD_2: Rad4 beta-hair 99.7 1.3E-17 2.9E-22 137.0 1.1 64 337-400 1-64 (64)
8 KOG0909 Peptide:N-glycanase [P 99.6 2.1E-16 4.6E-21 168.4 2.4 112 159-283 248-362 (500)
9 TIGR00598 rad14 DNA repair pro 97.4 0.0013 2.7E-08 64.5 11.0 35 573-609 137-172 (172)
10 COG5145 RAD14 DNA excision rep 94.9 0.057 1.2E-06 54.9 6.2 35 574-609 258-292 (292)
11 KOG4017 DNA excision repair pr 93.2 0.34 7.4E-06 50.1 8.1 34 574-609 241-274 (274)
12 smart00460 TGc Transglutaminas 92.8 0.27 5.8E-06 39.4 5.4 22 157-183 46-67 (68)
13 PF01841 Transglut_core: Trans 92.6 0.11 2.4E-06 45.4 3.3 65 84-182 47-113 (113)
14 COG5216 Uncharacterized conser 69.1 2 4.2E-05 35.7 0.6 26 583-608 10-37 (67)
15 PF12677 DUF3797: Domain of un 57.1 4.1 8.8E-05 32.5 0.3 15 589-605 35-49 (49)
16 COG1305 Transglutaminase-like 49.2 12 0.00026 38.0 2.3 26 158-187 238-263 (319)
17 PF05207 zf-CSL: CSL zinc fing 48.6 12 0.00025 30.4 1.7 25 583-607 6-30 (55)
18 PF09082 DUF1922: Domain of un 26.4 34 0.00074 29.2 1.2 18 592-609 17-34 (68)
19 PF14402 7TM_transglut: 7 tran 20.6 51 0.0011 35.6 1.4 28 158-190 29-56 (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=2.7e-100 Score=857.27 Aligned_cols=343 Identities=36% Similarity=0.634 Sum_probs=305.5
Q ss_pred CCCCCCCCceEEEEEeCCCCCCCceEEEeccc-ccccCcc-hhhhhHHhcCCCceEEEEEcCCC-cccchhhhHhhHHH-
Q 007298 153 GSRKVGAPLYWAEVYCSGENLTGKWVHVDAAN-AIIDGEQ-KVEAAAAACKTSLRYIVAFAGCG-AKDVTRRYCMKWYR- 228 (609)
Q Consensus 153 ~~~~~~~P~fWvEVy~~~e~~~~rWI~VDPv~-~~vd~p~-~~Ep~~~~~~~~msYVVAfd~dG-akDVTrRYa~~~~k- 228 (609)
...+++||+||+|||++. .++||||||++ ++++++. .+|+ +.++|+|||||++|| |+|||+||+.+|+.
T Consensus 363 ~~~~~~~p~~W~Ev~~~~---~~rWI~VD~~~~~~~~~~~~~~e~----~~~~m~YVvAf~~d~~~kDVT~RY~~~~~~k 435 (713)
T TIGR00605 363 IDRWITYVDFWVEVFIEQ---EEKWVCVDAVHSGVVPKGVTCFEP----ATLMMTYVFAYDRDGYVKDVTRRYCDQWSTK 435 (713)
T ss_pred ccccCCCCeeEEEEeecc---cceeEEeccccccccCCchhhccC----CCCceEEEEEEcCCCceeechhhHhhhhhhh
Confidence 345799999999999975 68999999999 8898876 4454 469999999999987 99999999999985
Q ss_pred hhhccCCHHHHHHH-HhhhhhcccCCCCCccccccccCcccccCCchHHHHHHHHhccCCCCCChhhhccCCceeehhcc
Q 007298 229 IASKRVNSAWWDAV-LAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWL 307 (609)
Q Consensus 229 ~~rkRv~~~Ww~~~-L~~l~~~~s~~~~~~~i~~~~~~~~~~~Rd~~Ed~eL~~~~~~e~iPtsi~~fKnHP~YVLer~L 307 (609)
+++.|++..||..+ |+++...-. ++. ..+|..||.||.++.++|+||+|+++|||||+|||||||
T Consensus 436 ~r~~Rv~~~w~~~~w~~~~~~~~~-------------~r~-~~~d~~Ed~el~~~~~~e~~P~si~~fKnHP~YvLer~L 501 (713)
T TIGR00605 436 VRKRRVEKADFGETWFRPIFGALH-------------KRK-RTIDDIEDQEFLRRHESEGIPKSIQDLKNHPLYVLERHL 501 (713)
T ss_pred hheeeecccchHHHHHHHHhhhhc-------------cCc-cchhhhhhhHhhhhhcccCCChhHHHhhcCceEEehhhc
Confidence 77889998888777 666542110 111 127899999999999999999999999999999999999
Q ss_pred ccccccCCC--CCcceeeccee-eeecCCccccccHHHHHHhcccccCCCcccceeccCCCCCCCCCCCCCCcccccccc
Q 007298 308 NKYQILYPK--GPILGFCSGHA-VYPRSCVQTLKTKERWLREALQVKANEVPVKVIKNSSKSKKGQDFEPEDYDEVDARG 384 (609)
Q Consensus 308 kk~EvI~P~--~~v~G~~~GEp-VY~RsdV~~LkS~e~W~r~GR~VK~gE~PlK~vk~~~~~~k~~~~~~~~~~e~~~~~ 384 (609)
++||+|||+ ++++|+++|++ ||+|+||+.|||+++|+++||+||+||+|+|+|+.+++..+. ..++. ...
T Consensus 502 ~~~Evi~P~~~~~~~g~~~g~~~VY~Rs~V~~lkS~~~W~~~GR~VK~ge~P~K~vk~r~r~~~~---~~~~~----~~~ 574 (713)
T TIGR00605 502 KKTQALKPGKKACTLGFVNGKAGVYSRKDVHDLKSAEQWYKKGRVIKLGEQPYKVVKARARTVRL---PKGEA----EEE 574 (713)
T ss_pred ccceeeccCCCCCceeccCCCCCccchhHhhhhhhHHHHHHcCCccCCCCccceEeccccccccc---ccccc----ccc
Confidence 999999994 46789999998 999999999999999999999999999999999977432211 11111 124
Q ss_pred ccccccccccccCCCCCCCCCCccCCCCCceEeecCCCCCCceeeecCccHHHHHHHcCCCeeeeeeeeeecCCeeeeee
Q 007298 385 NIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVF 464 (609)
Q Consensus 385 ~~~LYg~wQTe~y~pPpvvdG~VPkN~yGNIDlf~p~MlP~G~VHI~~~~i~kvAkkLgIDyA~AVtGFeFk~G~a~Pvi 464 (609)
.++|||+|||++|+|||++||+||||+|||||||+|+|||+|||||++++|+++|++||||||+|||||+|++|+++|||
T Consensus 575 ~~~LY~~~QTe~y~Pppv~dG~VPkN~yGNidv~~p~MiP~G~vhi~~~~~~rvak~LgIDyA~AVtGFeF~~g~~~Pv~ 654 (713)
T TIGR00605 575 DLGLYSYEQTELYIPPPAVDGIVPKNAYGNIDLFVPSMIPKGAVHLRLPGAIKAAKKLNIDYAPAVTGFDFHRGYSKPVL 654 (713)
T ss_pred ccccCCHhhCcCccCCCccCCccccCCCCCEEecCCCCCCCCcEEecCccHHHHHHHhCCCeeeeeeceeecCCceeEee
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceEEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcC
Q 007298 465 DGIVVCAEFKDTILEAYAEEEEKREAEEKKRREAQATSRWYQLLSSIVTRQRLNNCYGN 523 (609)
Q Consensus 465 dGIVV~~e~~~~l~~a~~e~~e~~~~~e~~~~e~~aL~~Wk~Ll~~L~Ir~RL~~~Yg~ 523 (609)
+|||||+||+++|++||.++++.++++++++++++||.+|++||++|||++||+++||.
T Consensus 655 ~GvVV~~e~~~~v~~a~~~~~~~~~~~e~~k~e~~aL~~Wk~ll~~LrIr~Rl~~~Yg~ 713 (713)
T TIGR00605 655 DGIIVCEEFREAIETAWEEIEQIQEEKEQEKHRKRALGNWKTLLKGLRIRERLKETYGK 713 (713)
T ss_pred ceEEEehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCc
Confidence 99999999999999999999999999999999999999999999999999999999994
No 2
>KOG2179 consensus Nucleotide excision repair complex XPC-HR23B, subunit XPC/DPB11 [Replication, recombination and repair]
Probab=100.00 E-value=4.4e-95 Score=797.01 Aligned_cols=408 Identities=42% Similarity=0.651 Sum_probs=343.8
Q ss_pred ccccCchhhhhhhhc-cCcHHHHHHHHHHHHhhhhhhcccCccCcccC--CCCCCCCcccchhhhhcccCCCCCCCCCCc
Q 007298 73 SEACHPKEKSQALKR-KGDLEFEMQLEMALSATNVATSKSNICSDVKD--LNSNSSTVLPVKRLKKIESGESSTSCLGIS 149 (609)
Q Consensus 73 ~~~~~~~~~~~~~kr-kgd~~~e~q~~ma~~a~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s 149 (609)
.|.| |..++..++ +||-.+..|.+|||..+.- ++...++.+ ..++.+ +.. .++.+..+++
T Consensus 249 ~~~~--p~~~a~i~~~~g~~d~~~q~~~~l~~~~n----~~r~~~~l~p~~~~~~~-------~~~----~s~~~~~~~s 311 (669)
T KOG2179|consen 249 LEAV--PAHRADIRPNKGDADVSSQIIHALLRTPN----NARLAPSLQPPVFSNLS-------VKD----LSDTSLYGNS 311 (669)
T ss_pred hhcC--cHHHhhhccCCCCcchHHHHHHHHhhccc----hhhcccccCCcchhhcc-------ccc----cccccccccc
Confidence 4556 455555555 9999999999999998864 222222222 122211 111 1223334444
Q ss_pred cccCCCCCCCCceEEEEEeCCCCCCCceEEEec--ccccccCcchhhhhHHhcCCCceEEEEEcCCC-cccchhhhHhhH
Q 007298 150 TAVGSRKVGAPLYWAEVYCSGENLTGKWVHVDA--ANAIIDGEQKVEAAAAACKTSLRYIVAFAGCG-AKDVTRRYCMKW 226 (609)
Q Consensus 150 t~~~~~~~~~P~fWvEVy~~~e~~~~rWI~VDP--v~~~vd~p~~~Ep~~~~~~~~msYVVAfd~dG-akDVTrRYa~~~ 226 (609)
+...+. ..|+||+|||+.. .++|||||| +.+.++..+.+...+..+.+.|.|||||+.+| ++|||+||+..|
T Consensus 312 ~~~~~~--~~p~~W~ev~~~~---e~kwV~vd~~~v~~~~~~~~~~~~~a~~~~~~~~yVva~da~~~~kDVT~RY~~~~ 386 (669)
T KOG2179|consen 312 LENIDG--AGPVFWLEVLDKF---EKKWVCVDPPSVIGKYHLFQPIGAVAEINGRHLAYVVAYDADGYVKDVTRRYCESW 386 (669)
T ss_pred hhhcCC--cccchhHHHHHhh---cceEEEecchhhcceeccccccchhhhhccccceEEEEecCCCccchhHHHHhhhh
Confidence 443333 3499999999965 589999995 34566666666665555667999999999998 999999999999
Q ss_pred HHhhh----ccCCHHHHHHHHhhhhhcccCCCCCccccccccCcccccCCchHHHHHHHHhccCCCCCChhhhccCCcee
Q 007298 227 YRIAS----KRVNSAWWDAVLAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYV 302 (609)
Q Consensus 227 ~k~~r----kRv~~~Ww~~~L~~l~~~~s~~~~~~~i~~~~~~~~~~~Rd~~Ed~eL~~~~~~e~iPtsi~~fKnHP~YV 302 (609)
+.+.+ .|++..||..+|.+|.++ ..+|+..||+++.++...++||+|+++|||||+||
T Consensus 387 ~s~~~~~~k~~~~~~w~~~~l~~~~~~------------------~~~~e~~ed~~~~~~~~~~~lP~sv~~~K~Hp~fv 448 (669)
T KOG2179|consen 387 SSILRKRSKVRFSKKWFDKVLAPLGKL------------------RKDREDTEDIELLRRHTSEGLPTSVQDLKNHPLFV 448 (669)
T ss_pred hhhhhccccccHHHHHhhhhHhhhccc------------------cchHHHHHHHHHHHHhccCCCCchHHHhccCchhh
Confidence 98766 456789999999999853 24678999999999999999999999999999999
Q ss_pred ehhccccccccCC-CCCcceeecc--eeeeecCCccccccHHHHHHhcccccCCCcccceeccCCCCCCCCCCCCCCccc
Q 007298 303 IERWLNKYQILYP-KGPILGFCSG--HAVYPRSCVQTLKTKERWLREALQVKANEVPVKVIKNSSKSKKGQDFEPEDYDE 379 (609)
Q Consensus 303 Ler~Lkk~EvI~P-~~~v~G~~~G--EpVY~RsdV~~LkS~e~W~r~GR~VK~gE~PlK~vk~~~~~~k~~~~~~~~~~e 379 (609)
|||||++||+||| +.+++|+++| |+||+|.||++|||+++||+.||+||+||||+|+||+++++.+.....+.+..+
T Consensus 449 ler~Lkk~q~l~P~k~p~~g~~kG~~E~VY~R~~V~~LkS~e~W~r~GRvIk~geqP~K~vK~~~~r~r~~r~~e~~~~~ 528 (669)
T KOG2179|consen 449 LERHLKKNQALKPCKKPTLGFTKGDVEAVYLRRDVVTLKSREQWYRKGRVIKPGEQPYKIVKRRPKRERMKRELEKDVRE 528 (669)
T ss_pred hHHHHhhcccccccccceeeeecCCceeeeehhhHHhhccHHHHHHhcccccCCCcchHHHhcCcchhhhhhhhhhhhhh
Confidence 9999999999999 6788999999 999999999999999999999999999999999999988766554332222211
Q ss_pred cccccccccccccccccCCCCCCCCCCccCCCCCceEeecCCCCCCceeeecCccHHHHHHHcCCCeeeeeeeeeecCCe
Q 007298 380 VDARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGR 459 (609)
Q Consensus 380 ~~~~~~~~LYg~wQTe~y~pPpvvdG~VPkN~yGNIDlf~p~MlP~G~VHI~~~~i~kvAkkLgIDyA~AVtGFeFk~G~ 459 (609)
...++|||+|||++|.|||+++|+||||+|||||||+|+|||.|||||++|++.+|||+||||||+|||||+|+.|.
T Consensus 529 ---~~~~~Lys~wqte~Y~pp~a~~givpkN~yGNielf~p~miP~g~vhl~~p~~~~vAk~L~id~a~av~gF~f~~~~ 605 (669)
T KOG2179|consen 529 ---EYEQELYSPWQTELYCPPPAVEGIVPKNEYGNIELFSPSMIPKGCVHLRLPNAVDVAKKLGIDYAPAVTGFDFRRGY 605 (669)
T ss_pred ---hhhhhccCcccccccCCCccccCccccccccceeeeccccCCCCeEEecCchHHHHHHHhCCcccccccceeeccCc
Confidence 25678999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeeeceEEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcC
Q 007298 460 STPVFDGIVVCAEFKDTILEAYAEEEEKREAEEKKRREAQATSRWYQLLSSIVTRQRLNNCYGN 523 (609)
Q Consensus 460 a~PvidGIVV~~e~~~~l~~a~~e~~e~~~~~e~~~~e~~aL~~Wk~Ll~~L~Ir~RL~~~Yg~ 523 (609)
++|+++|||||+++++.+..||+++++.++++|+++.+++||.+|+.||++||||+||+++||.
T Consensus 606 ~~P~~~Givv~~e~k~~i~~a~ee~~~~~e~ker~~~~~~~l~~Wk~Ll~~Lrir~Rl~~~Yg~ 669 (669)
T KOG2179|consen 606 AVPVFEGIVVCKEFKEVILLAWEEDQKIQEEKERRKKRKRALGRWKILLRGLRIRERLKKEYGN 669 (669)
T ss_pred ceecccceEeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhhcC
Confidence 9999999999999999999999999999999999999999999999999999999999999995
No 3
>COG5535 RAD4 DNA repair protein RAD4 [DNA replication, recombination, and repair]
Probab=100.00 E-value=8e-76 Score=632.48 Aligned_cols=366 Identities=28% Similarity=0.406 Sum_probs=301.8
Q ss_pred ccchhhhhcccCCCCCCCCCCcc---ccC-CCCCCCCceEEEEEeCCCCCCCceEEEecccc-cc-c-CcchhhhhHHhc
Q 007298 128 LPVKRLKKIESGESSTSCLGIST---AVG-SRKVGAPLYWAEVYCSGENLTGKWVHVDAANA-II-D-GEQKVEAAAAAC 200 (609)
Q Consensus 128 ~~~~~~~~~~~~~~~~~~~~~st---~~~-~~~~~~P~fWvEVy~~~e~~~~rWI~VDPv~~-~v-d-~p~~~Ep~~~~~ 200 (609)
.+.+-+..++++.++.-....+. ... ...+.+|.||+|||.- +.++||+|||++- +| . ....|||.+..-
T Consensus 266 v~~Rli~~l~~P~Fs~~~~~~~~~e~~~~~iD~l~~p~fw~ev~~~---~~~kwv~vdp~~l~~v~~~l~~kfepa~~~~ 342 (650)
T COG5535 266 VFARLIASLIQPVFSNNSDLDVLSEGLLEYIDSLEYPGFWGEVVDK---FEKKWVFVDPVRLYIVYSELKCKFEPAASIH 342 (650)
T ss_pred cchhhhccccCcccccccccccCccccceeccchhcchHHHHHHHH---HHhceEecccchhhhhhhhhhheechhHHHH
Confidence 34455666667666652222111 111 1236799999999974 5789999999963 32 2 456789855555
Q ss_pred CCCceEEEEEcCCC-cccchhhhHhhHHHhhhccC-----CHHHHHHHHhhhhhcccCCCCCccccccccCcccccCCch
Q 007298 201 KTSLRYIVAFAGCG-AKDVTRRYCMKWYRIASKRV-----NSAWWDAVLAPLRELESGATGDLNVESSAKDSFVADRNSL 274 (609)
Q Consensus 201 ~~~msYVVAfd~dG-akDVTrRYa~~~~k~~rkRv-----~~~Ww~~~L~~l~~~~s~~~~~~~i~~~~~~~~~~~Rd~~ 274 (609)
.+.|.||+|++.++ ++|||+||+...+...+ |+ +..|+.+.+..+.+.. .+ .+-+.+
T Consensus 343 ~n~~~~V~ayd~~~y~~DVt~RY~d~~~s~~k-ritk~~fs~qy~~r~~~~l~~~k---------------~~-~~~e~i 405 (650)
T COG5535 343 LNIMEYVGAYDACVYVKDVTLRYRDQSYSFLK-RITKHLFSVQYFVRQFPGLGKCK---------------EA-SDEEAI 405 (650)
T ss_pred HHHHHHhhhhccCccchhHHHHHHHHHhhhhh-hhhccchHHHHHHHHhcccCccc---------------cc-ccHHHH
Confidence 67899999999987 99999999976554433 33 4789999988776432 11 233556
Q ss_pred HHHHHHHHhccCCCCCChhhhccCCceeehhccccccccCCCCCc-ceeecc----eeeeecCCccccccHHHHHHhccc
Q 007298 275 EDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPI-LGFCSG----HAVYPRSCVQTLKTKERWLREALQ 349 (609)
Q Consensus 275 Ed~eL~~~~~~e~iPtsi~~fKnHP~YVLer~Lkk~EvI~P~~~v-~G~~~G----EpVY~RsdV~~LkS~e~W~r~GR~ 349 (609)
|+.++-+....++||+|++||||||+|||||||+++|+|+|++.+ .++++| |+||+|.||+.|+|+++||++||+
T Consensus 406 ~~~~~L~~~~~~~iPkSvqdlK~HP~FVle~~Lk~~q~ikp~ak~~~~~tkGk~~vE~VY~RrdVv~lkS~e~wy~~GRv 485 (650)
T COG5535 406 EDFDDLDERRSEGIPKSVQDLKRHPKFVLESHLKWNQAIKPGAKPGFTLTKGKNSVEAVYLRRDVVRLKSAEQWYRMGRV 485 (650)
T ss_pred HhHHHHhhcccccCCccHHHhccCCceeeHhhhhhhhhhccCCccceeeecCCCccchhhhhhhHHhhcCHHHHHhcCcc
Confidence 666555555578999999999999999999999999999999754 456678 999999999999999999999999
Q ss_pred ccCCCcccceeccCCCCCCCCCCCCCCccccccccccccccccccccCCCCCCCCCCccCCCCCceEeecCCCCCCceee
Q 007298 350 VKANEVPVKVIKNSSKSKKGQDFEPEDYDEVDARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVH 429 (609)
Q Consensus 350 VK~gE~PlK~vk~~~~~~k~~~~~~~~~~e~~~~~~~~LYg~wQTe~y~pPpvvdG~VPkN~yGNIDlf~p~MlP~G~VH 429 (609)
||+|+||+|+||+. ..+.+ +.+ .....+||++|||+.|.|||+++|+||||.|||||+|+|+|+|.||+|
T Consensus 486 IkpgaqP~K~vK~~--~~rv~--~~~------d~vi~~LYs~eqT~ly~pp~vv~~~i~KN~yGNid~~~psmiP~g~~~ 555 (650)
T COG5535 486 IKPGAQPLKIVKRM--RERVR--NLD------DKVIRELYSPEQTELYGPPLVVAGIIPKNMYGNIDYYVPSMIPRGCVL 555 (650)
T ss_pred cCCCCchHHHHHHH--hhhcc--ccc------chHHHhhcCHHHHHhhcCCccccccccccccCCeeeecccccCCCeEe
Confidence 99999999999972 12221 112 235667999999999999999999999999999999999999999999
Q ss_pred ecCccHHHHHHHcCCCeeeeeeeeeecCCeeeeeeceEEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 007298 430 LRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEAYAEEEEKREAEEKKRREAQATSRWYQLLS 509 (609)
Q Consensus 430 I~~~~i~kvAkkLgIDyA~AVtGFeFk~G~a~PvidGIVV~~e~~~~l~~a~~e~~e~~~~~e~~~~e~~aL~~Wk~Ll~ 509 (609)
|+.+++.+||+.||||||+|||||+|+.-+++||..||||.+++.++|..+..+.+..++++++.+-.+-+|..|+.||+
T Consensus 556 i~~~~a~~iAr~L~I~ya~aVtGFdF~r~~~kPv~~Givv~K~~~eai~~~~~e~e~iq~~ke~~e~r~~~L~~Wk~Ll~ 635 (650)
T COG5535 556 IPNRNARDIARLLGIDYADAVTGFDFGRSTVKPVLRGIVVPKKNLEAISNFLAEYERIQEEKERSEVRLGGLKRWKILLR 635 (650)
T ss_pred ccCchHHHHHHHhCCchhhhhcccccccccccccccceecchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999998899999999999999999999999999888888888888899999999999
Q ss_pred HHHHHHHHHhhhcC
Q 007298 510 SIVTRQRLNNCYGN 523 (609)
Q Consensus 510 ~L~Ir~RL~~~Yg~ 523 (609)
+||||.||+++||.
T Consensus 636 ~LRir~Ri~~eYG~ 649 (650)
T COG5535 636 KLRIRLRINEEYGL 649 (650)
T ss_pred HhHHHHHHHHHhcc
Confidence 99999999999996
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=1.1e-32 Score=233.40 Aligned_cols=75 Identities=48% Similarity=0.918 Sum_probs=62.4
Q ss_pred ccCCCCCceEeecCCCCCCceeeecCccHHHHHHHcCCCeeeeeeeeee-cCCeeeeeeceEEEccccHHHHHHHH
Q 007298 407 VPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEF-RNGRSTPVFDGIVVCAEFKDTILEAY 481 (609)
Q Consensus 407 VPkN~yGNIDlf~p~MlP~G~VHI~~~~i~kvAkkLgIDyA~AVtGFeF-k~G~a~PvidGIVV~~e~~~~l~~a~ 481 (609)
||||+|||||||+|+|+|+|||||+++++.++||+||||||+|||||+| ++|+++|+++||||++||+++|++||
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=99.89 E-value=8.7e-24 Score=198.27 Aligned_cols=110 Identities=33% Similarity=0.616 Sum_probs=79.8
Q ss_pred CCCCCCCCceEEEEEeCCCCCCCceEEEecccccccCcchhhhhHHhcCCCceEEEEEcCCC-cccchhhhHhh-HH-Hh
Q 007298 153 GSRKVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCG-AKDVTRRYCMK-WY-RI 229 (609)
Q Consensus 153 ~~~~~~~P~fWvEVy~~~e~~~~rWI~VDPv~~~vd~p~~~Ep~~~~~~~~msYVVAfd~dG-akDVTrRYa~~-~~-k~ 229 (609)
...++.+|+||+|||++. .++||||||+++.+.....+||....+.++|+|||||+++| |+|||+||+++ |. .+
T Consensus 28 ~~~~~~~~~~W~EV~~~~---~~rWI~VDp~~~~~~~~~~~ep~~~~~~~~~~YViA~d~~~~~kDVT~RY~~~~~~~~~ 104 (145)
T PF03835_consen 28 KDKDLPYPNFWVEVYSPE---EKRWIHVDPVVGKIIKVSCDEPLEENANNPMSYVIAFDNDGYAKDVTRRYASNYWNSKT 104 (145)
T ss_dssp HHHHTTTTCEEEEEEETT---TTEEEEEETTTS-EESTBTTSTCCCCCS--B-EEEEE-CTTEEEE-HHHH-T-TCCCCC
T ss_pred ccccCCCCeEEEEEEecC---CCeEEEeeeeccccccccccCchhhccCCceEEEEEEeCCCCEEEchHhhccccccccc
Confidence 344689999999999974 68999999999865567778888778899999999998877 99999999998 54 56
Q ss_pred hhccCC-----HHHHHHHHhhhhhcccCCCCCccccccccCcccccCCchHHHHHH
Q 007298 230 ASKRVN-----SAWWDAVLAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELE 280 (609)
Q Consensus 230 ~rkRv~-----~~Ww~~~L~~l~~~~s~~~~~~~i~~~~~~~~~~~Rd~~Ed~eL~ 280 (609)
.+.|+. ..||..+|+.|+.... ....||.+||.||+
T Consensus 105 ~r~R~~~~~~~~~W~~~~l~~~~~~~~---------------~~~~~d~~Ed~el~ 145 (145)
T PF03835_consen 105 RRLRVDRSYEEEDWWEKVLRPYNRPRR---------------DRTIRDKKEDEELH 145 (145)
T ss_dssp GGGSGGGSHHHHHHHHHHHHHH--S------------------H--HHHHHHHHH-
T ss_pred ccccCCccccHHHHHHHHHHHHhcccc---------------cccchHHHHHhhcC
Confidence 788888 8999999999985321 11146888999884
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=99.79 E-value=2.7e-20 Score=149.88 Aligned_cols=51 Identities=43% Similarity=0.741 Sum_probs=40.1
Q ss_pred cCCCCCChhhhccCCceeehhccccccccCCCCCcceeecc----eeeeecCCcc
Q 007298 285 TEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSG----HAVYPRSCVQ 335 (609)
Q Consensus 285 ~e~iPtsi~~fKnHP~YVLer~Lkk~EvI~P~~~v~G~~~G----EpVY~RsdV~ 335 (609)
+|+||+|+++|||||+|||||||++||+|+|+++++|+|+| |+||+|+||+
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
>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=99.66 E-value=1.3e-17 Score=136.97 Aligned_cols=64 Identities=36% Similarity=0.637 Sum_probs=30.6
Q ss_pred cccHHHHHHhcccccCCCcccceeccCCCCCCCCCCCCCCccccccccccccccccccccCCCC
Q 007298 337 LKTKERWLREALQVKANEVPVKVIKNSSKSKKGQDFEPEDYDEVDARGNIELYGKWQLEPLRLP 400 (609)
Q Consensus 337 LkS~e~W~r~GR~VK~gE~PlK~vk~~~~~~k~~~~~~~~~~e~~~~~~~~LYg~wQTe~y~pP 400 (609)
|||+++|+++||+||+||+|+|+|+.++++.+.......+..+.+....++|||+||||+|+||
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 7999999999999999999999999976533222221111111123468999999999999998
No 8
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=99.60 E-value=2.1e-16 Score=168.38 Aligned_cols=112 Identities=25% Similarity=0.386 Sum_probs=88.2
Q ss_pred CCceEEEEEeCCCCCCCceEEEecccccccCcchhhhhHHhcCCCceEEEEEcCCCcccchhhhHhhHHHh--hhccCCH
Q 007298 159 APLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRI--ASKRVNS 236 (609)
Q Consensus 159 ~P~fWvEVy~~~e~~~~rWI~VDPv~~~vd~p~~~Ep~~~~~~~~msYVVAfd~dGakDVTrRYa~~~~k~--~rkRv~~ 236 (609)
.-|+|+|||+. +.+||+|||||++.+|+|.+||.+ |+++|+|||||+.|||.|||.||+.+|.++ ++.++.+
T Consensus 248 tDHVWtEvYS~---~qqRW~HvDpcE~v~D~PllYe~G---W~KklsY~iafgkD~VvDVT~RYi~~h~e~~~~R~~~~E 321 (500)
T KOG0909|consen 248 TDHVWTEVYSN---AQQRWVHVDPCENVFDKPLLYEIG---WGKKLSYCIAFGKDGVVDVTWRYILDHKENLLPRDLCKE 321 (500)
T ss_pred CcchhHHhhhh---hhheeEeecccccccccceeeecc---cCcccceEEEeccCceEeeehhhhccchhhccchhhcch
Confidence 55899999996 469999999999999999999987 999999999999999999999999998765 4556788
Q ss_pred HHHHHHHhhhhhccc-CCCCCccccccccCcccccCCchHHHHHHHHh
Q 007298 237 AWWDAVLAPLRELES-GATGDLNVESSAKDSFVADRNSLEDMELETRA 283 (609)
Q Consensus 237 ~Ww~~~L~~l~~~~s-~~~~~~~i~~~~~~~~~~~Rd~~Ed~eL~~~~ 283 (609)
.=+..+|..++...+ +.+ ..+......||..|.+||....
T Consensus 322 ~~l~~~l~~in~~rr~~lt-------~~r~~~L~~rd~~e~~El~~~~ 362 (500)
T KOG0909|consen 322 SVLQQTLQFINKRRRYSLT-------DDRKKELAQRDEREQIELIRGK 362 (500)
T ss_pred HHHHHHHHHHHHHHHhhcC-------hHHHHHHHhhhHHHHHHHHhcc
Confidence 889999988874321 111 1112334557777888876433
No 9
>TIGR00598 rad14 DNA repair protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.43 E-value=0.0013 Score=64.45 Aligned_cols=35 Identities=23% Similarity=0.471 Sum_probs=31.8
Q ss_pred CCCccccccccccCccccccceecccC-CCceEEEeeC
Q 007298 573 SEEHEHVYLIEDQSFDEENSVTTKRCH-CGFTIQVEEL 609 (609)
Q Consensus 573 ~~~h~h~f~~~~~sfdee~~~~tkrc~-cg~~iqve~~ 609 (609)
...|+|.|.. +.+|+|+.+++|+|- |||.|.+|+|
T Consensus 137 ~~~H~H~f~~--~~~~~e~~~~~k~C~~Cg~e~~~e~m 172 (172)
T TIGR00598 137 GRVHEHEFGP--ETNGVEEDTYRRTCTTCGLEETYEKM 172 (172)
T ss_pred CCcccccCCc--ccccccCCceeeecCCCCceEEEEeC
Confidence 4679999988 678899999999997 9999999987
No 10
>COG5145 RAD14 DNA excision repair protein [DNA replication, recombination, and repair]
Probab=94.86 E-value=0.057 Score=54.94 Aligned_cols=35 Identities=34% Similarity=0.643 Sum_probs=26.6
Q ss_pred CCccccccccccCccccccceecccCCCceEEEeeC
Q 007298 574 EEHEHVYLIEDQSFDEENSVTTKRCHCGFTIQVEEL 609 (609)
Q Consensus 574 ~~h~h~f~~~~~sfdee~~~~tkrc~cg~~iqve~~ 609 (609)
+-|.|+|.++-+. -.|-.+-.-||.||+.|+-+++
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 4599999775333 2278899999999999876654
No 11
>KOG4017 consensus DNA excision repair protein XPA/XPAC/RAD14 [Replication, recombination and repair]
Probab=93.20 E-value=0.34 Score=50.11 Aligned_cols=34 Identities=32% Similarity=0.481 Sum_probs=27.3
Q ss_pred CCccccccccccCccccccceecccCCCceEEEeeC
Q 007298 574 EEHEHVYLIEDQSFDEENSVTTKRCHCGFTIQVEEL 609 (609)
Q Consensus 574 ~~h~h~f~~~~~sfdee~~~~tkrc~cg~~iqve~~ 609 (609)
.-|.|+|..|- -=||-..+.-+|.||+++..|+|
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 67999999964 44555666669999999999886
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=92.79 E-value=0.27 Score=39.44 Aligned_cols=22 Identities=45% Similarity=0.854 Sum_probs=18.8
Q ss_pred CCCCceEEEEEeCCCCCCCceEEEecc
Q 007298 157 VGAPLYWAEVYCSGENLTGKWVHVDAA 183 (609)
Q Consensus 157 ~~~P~fWvEVy~~~e~~~~rWI~VDPv 183 (609)
...+|.|+|||.. ++|+.+||.
T Consensus 46 ~~~~H~W~ev~~~-----~~W~~~D~~ 67 (68)
T smart00460 46 IWEAHAWAEVYLE-----GGWVPVDPT 67 (68)
T ss_pred CCCcEEEEEEEEC-----CCeEEEeCC
Confidence 4578999999984 589999995
No 13
>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=92.64 E-value=0.11 Score=45.43 Aligned_cols=65 Identities=23% Similarity=0.241 Sum_probs=39.6
Q ss_pred hhhccCcHHHHHHHHHHHHhhhhhhcccCcc--CcccCCCCCCCCcccchhhhhcccCCCCCCCCCCccccCCCCCCCCc
Q 007298 84 ALKRKGDLEFEMQLEMALSATNVATSKSNIC--SDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKVGAPL 161 (609)
Q Consensus 84 ~~krkgd~~~e~q~~ma~~a~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~st~~~~~~~~~P~ 161 (609)
-..++|+=. +.+..|.|.+++.+-.+.- +...... .+.. ........|
T Consensus 47 l~~~~G~C~---~~a~l~~allr~~Gipar~v~g~~~~~~------~~~~---------------------~~~~~~~~H 96 (113)
T PF01841_consen 47 LRSGRGDCE---DYASLFVALLRALGIPARVVSGYVKGPD------PDGD---------------------YSVDGNDNH 96 (113)
T ss_dssp HHCEEESHH---HHHHHHHHHHHHHT--EEEEEEEEEECS------STTC---------------------TSTSSEEEE
T ss_pred HHcCCCccH---HHHHHHHHHHhhCCCceEEEEEEcCCcc------cccc---------------------ccCCCCCCE
Confidence 346779998 8999999999999875531 1010000 0000 011223449
Q ss_pred eEEEEEeCCCCCCCceEEEec
Q 007298 162 YWAEVYCSGENLTGKWVHVDA 182 (609)
Q Consensus 162 fWvEVy~~~e~~~~rWI~VDP 182 (609)
.|+|||.+ .++|+++||
T Consensus 97 ~w~ev~~~----~~~W~~~Dp 113 (113)
T PF01841_consen 97 AWVEVYLP----GGGWIPLDP 113 (113)
T ss_dssp EEEEEEET----TTEEEEEET
T ss_pred EEEEEEEc----CCcEEEcCC
Confidence 99999994 368999998
No 14
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=69.07 E-value=2 Score=35.66 Aligned_cols=26 Identities=42% Similarity=0.829 Sum_probs=21.2
Q ss_pred cccCccccccceecccCCC--ceEEEee
Q 007298 583 EDQSFDEENSVTTKRCHCG--FTIQVEE 608 (609)
Q Consensus 583 ~~~sfdee~~~~tkrc~cg--~~iqve~ 608 (609)
||=.|+.|+...|--|+|| |.|-.|.
T Consensus 10 edftf~~e~~~ftyPCPCGDRFeIsLeD 37 (67)
T COG5216 10 EDFTFSREEKTFTYPCPCGDRFEISLED 37 (67)
T ss_pred eeeEEcCCCceEEecCCCCCEeEEEHHH
Confidence 5678999999999999999 5555554
No 15
>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=57.13 E-value=4.1 Score=32.54 Aligned_cols=15 Identities=40% Similarity=1.006 Sum_probs=10.0
Q ss_pred ccccceecccCCCceEE
Q 007298 589 EENSVTTKRCHCGFTIQ 605 (609)
Q Consensus 589 ee~~~~tkrc~cg~~iq 605 (609)
|-|+.| -|.|||.|.
T Consensus 35 edtfkR--tCkCGfnie 49 (49)
T PF12677_consen 35 EDTFKR--TCKCGFNIE 49 (49)
T ss_pred ccceee--eeccccccC
Confidence 445544 499999873
No 16
>COG1305 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]
Probab=49.24 E-value=12 Score=37.96 Aligned_cols=26 Identities=38% Similarity=0.828 Sum_probs=20.5
Q ss_pred CCCceEEEEEeCCCCCCCceEEEecccccc
Q 007298 158 GAPLYWAEVYCSGENLTGKWVHVDAANAII 187 (609)
Q Consensus 158 ~~P~fWvEVy~~~e~~~~rWI~VDPv~~~v 187 (609)
...|.|+|||.++ ..|+++||..+..
T Consensus 238 ~~~Haw~ev~~~~----~gW~~~Dpt~~~~ 263 (319)
T COG1305 238 DDAHAWAEVYLPG----RGWVPLDPTNGLL 263 (319)
T ss_pred cccceeeeeecCC----CccEeecCCCCCc
Confidence 4558999999964 2699999997644
No 17
>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=48.60 E-value=12 Score=30.38 Aligned_cols=25 Identities=36% Similarity=0.769 Sum_probs=20.4
Q ss_pred cccCccccccceecccCCCceEEEe
Q 007298 583 EDQSFDEENSVTTKRCHCGFTIQVE 607 (609)
Q Consensus 583 ~~~sfdee~~~~tkrc~cg~~iqve 607 (609)
++=.||+++.+++..|+||-...|.
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 4466888999999999999876654
No 18
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=26.44 E-value=34 Score=29.22 Aligned_cols=18 Identities=44% Similarity=0.853 Sum_probs=12.7
Q ss_pred cceecccCCCceEEEeeC
Q 007298 592 SVTTKRCHCGFTIQVEEL 609 (609)
Q Consensus 592 ~~~tkrc~cg~~iqve~~ 609 (609)
...||.|.||..+-|.+.
T Consensus 17 ~~kTkkC~CG~~l~vk~~ 34 (68)
T PF09082_consen 17 GAKTKKCVCGKTLKVKER 34 (68)
T ss_dssp T-SEEEETTTEEEE--SS
T ss_pred CcceeEecCCCeeeeeeE
Confidence 357999999999998763
No 19
>PF14402 7TM_transglut: 7 transmembrane helices usually fused to an inactive transglutaminase
Probab=20.55 E-value=51 Score=35.65 Aligned_cols=28 Identities=25% Similarity=0.414 Sum_probs=21.9
Q ss_pred CCCceEEEEEeCCCCCCCceEEEecccccccCc
Q 007298 158 GAPLYWAEVYCSGENLTGKWVHVDAANAIIDGE 190 (609)
Q Consensus 158 ~~P~fWvEVy~~~e~~~~rWI~VDPv~~~vd~p 190 (609)
..+..|.|||+. ++|+.+||..+....|
T Consensus 29 q~l~~~lev~~~-----~~W~~f~p~tg~~g~p 56 (313)
T PF14402_consen 29 QSLEPWLEVFNG-----GKWVLFNPRTGEQGLP 56 (313)
T ss_pred cCcHhHHheeeC-----CeEEEECCCCCCcCCC
Confidence 567889999984 5899999998755443
Done!