Query 006346
Match_columns 649
No_of_seqs 203 out of 430
Neff 4.8
Searched_HMMs 46136
Date Thu Mar 28 21:57:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006346.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006346hhsearch_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-100 2E-105 865.5 33.1 343 153-563 363-713 (713)
2 KOG2179 Nucleotide excision re 100.0 1.8E-95 4E-100 804.9 25.8 409 73-563 249-669 (669)
3 COG5535 RAD4 DNA repair protei 100.0 2.8E-76 6.2E-81 640.0 12.5 366 129-563 267-649 (650)
4 PF10405 BHD_3: Rad4 beta-hair 100.0 1.2E-32 2.7E-37 234.9 8.0 75 447-521 1-76 (76)
5 PF03835 Rad4: Rad4 transgluta 99.9 1.4E-23 3E-28 198.2 5.0 93 153-248 28-128 (145)
6 PF10403 BHD_1: Rad4 beta-hair 99.8 2.3E-20 4.9E-25 151.5 1.1 52 324-375 2-57 (57)
7 PF10404 BHD_2: Rad4 beta-hair 99.7 9.1E-18 2E-22 139.0 1.2 64 377-440 1-64 (64)
8 KOG0909 Peptide:N-glycanase [P 99.5 4E-15 8.7E-20 159.8 3.7 85 158-248 247-333 (500)
9 TIGR00598 rad14 DNA repair pro 97.4 0.0017 3.7E-08 64.1 11.0 35 613-649 137-172 (172)
10 COG5145 RAD14 DNA excision rep 94.5 0.076 1.6E-06 54.5 6.2 33 614-649 258-292 (292)
11 KOG4017 DNA excision repair pr 93.3 0.32 7E-06 50.7 8.0 34 614-649 241-274 (274)
12 smart00460 TGc Transglutaminas 91.6 0.45 9.7E-06 38.4 5.5 23 156-183 45-67 (68)
13 PF01841 Transglut_core: Trans 89.4 0.3 6.5E-06 43.0 2.9 27 83-112 46-72 (113)
14 COG5216 Uncharacterized conser 67.6 2.2 4.8E-05 35.7 0.6 26 623-648 10-37 (67)
15 PF12677 DUF3797: Domain of un 54.8 4.7 0.0001 32.5 0.3 15 629-645 35-49 (49)
16 PF05207 zf-CSL: CSL zinc fing 46.5 13 0.00028 30.4 1.7 25 623-647 6-30 (55)
17 COG1305 Transglutaminase-like 46.1 14 0.00031 37.7 2.4 26 158-187 238-263 (319)
18 PF09082 DUF1922: Domain of un 25.2 37 0.0008 29.3 1.1 18 632-649 17-34 (68)
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=1.2e-100 Score=865.49 Aligned_cols=343 Identities=36% Similarity=0.634 Sum_probs=306.0
Q ss_pred CCCCCCCCceEEEEEeCCCCCCCceEEEeccc-Ccccccc-hhhhhHhhcCCCeeEEEEEcCCC-cccchhhhHhHHHH-
Q 006346 153 GSRKVGAPLYWAEVYCSGENLTGKWVHVDAAN-AIIDGEQ-KVEAAAAACKTSLRYIVAFAGCG-AKDVTRRYCMKWYR- 228 (649)
Q Consensus 153 ~~~~~~~P~fWvEV~~~~~~~~~rWI~VDPi~-~~Vd~~~-~~Ep~~~~~~~~msYVVAfd~dG-akDVTrRYa~~~~~- 228 (649)
..++++||+||+|||++. .++||||||++ ++++++. .+|| +.++|+|||||++|| |+|||+||+++|+.
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 346789999999999974 58999999999 8898876 4554 569999999999997 99999999999996
Q ss_pred hhhccCCHHHHHHH-HHhhhhcccCcCCCCcchhhhccchhhhHHHhhhccccccCCCCCcccccCCCCccccccccCcc
Q 006346 229 IASKRVNSAWWDAV-LAPLRELESGATGGMTQMEKRHVNASNILEALKTSNYLYRDSFPNHVSLYGDSDLNVESSAKDSF 307 (649)
Q Consensus 229 ~~rkRv~~~Ww~~~-L~~l~~~~sga~~g~~~~~kr~~~~~~i~~~~~~~~~~~~d~f~~~v~~~g~~~~~~~~~~~~~~ 307 (649)
+++.|++..||..+ |+++.... . ...
T Consensus 436 ~r~~Rv~~~w~~~~w~~~~~~~~------------------------~-----------------------------~r~ 462 (713)
T TIGR00605 436 VRKRRVEKADFGETWFRPIFGAL------------------------H-----------------------------KRK 462 (713)
T ss_pred hheeeecccchHHHHHHHHhhhh------------------------c-----------------------------cCc
Confidence 66789999999988 76653200 0 000
Q ss_pred cccCCchHHHHHHHHhccCCCCcChHhhhcCCchhhhhhhccccccCCC--CCcceeeccee-eeecCCccccccHHHHH
Q 006346 308 VADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPK--GPILGFCSGHA-VYPRSCVQTLKTKERWL 384 (649)
Q Consensus 308 ~~~rd~~Ed~EL~~~~~~E~mPtsi~~fKnHP~YvLEr~Lkk~EvI~P~--~~~~G~~~GEp-VY~RsdV~~LkS~e~W~ 384 (649)
..+|..||.||.+++++|+||+|+++|||||+|||||||++||+|||+ ++++|+++|++ ||+|+||++|||+++||
T Consensus 463 -~~~d~~Ed~el~~~~~~e~~P~si~~fKnHP~YvLer~L~~~Evi~P~~~~~~~g~~~g~~~VY~Rs~V~~lkS~~~W~ 541 (713)
T TIGR00605 463 -RTIDDIEDQEFLRRHESEGIPKSIQDLKNHPLYVLERHLKKTQALKPGKKACTLGFVNGKAGVYSRKDVHDLKSAEQWY 541 (713)
T ss_pred -cchhhhhhhHhhhhhcccCCChhHHHhhcCceEEehhhcccceeeccCCCCCceeccCCCCCccchhHhhhhhhHHHHH
Confidence 125789999999999999999999999999999999999999999994 46789999998 99999999999999999
Q ss_pred HhcccccCCCcccceeccCCCCCCCCCCCCCCccccccccccccccccccccCCCCCCCCCcccCCCCCceEeecCCCCC
Q 006346 385 REALQVKANEVPVKVIKNSSKSKKGQDFEPEDYDEVDARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLP 464 (649)
Q Consensus 385 r~GR~VK~gEqPlK~Vk~~~~~~k~~~~e~~d~~~~~~~~~~~LYg~wQTe~y~pPp~vdG~VPkN~yGNIDlf~psMlP 464 (649)
++||+||+||+|+|+|+.+++..+. ..++. ..+.++|||+|||++|+|||++||+||||+|||||||+|+|||
T Consensus 542 ~~GR~VK~ge~P~K~vk~r~r~~~~---~~~~~----~~~~~~LY~~~QTe~y~Pppv~dG~VPkN~yGNidv~~p~MiP 614 (713)
T TIGR00605 542 KKGRVIKLGEQPYKVVKARARTVRL---PKGEA----EEEDLGLYSYEQTELYIPPPAVDGIVPKNAYGNIDLFVPSMIP 614 (713)
T ss_pred HcCCccCCCCccceEeccccccccc---ccccc----cccccccCCHhhCcCccCCCccCCccccCCCCCEEecCCCCCC
Confidence 9999999999999999987543221 11111 1247999999999999999999999999999999999999999
Q ss_pred CceEEecCccHHHHHHHcCCCEeeeeeeeeecCCeeeeeEceEEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 006346 465 PGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEAYAEEEEKREAEEKKRREAQATSRW 544 (649)
Q Consensus 465 ~G~VHL~~~~~~kvAkkLgIDyA~AVtGFeFk~G~a~PvidGIVV~~E~~e~l~~a~~e~~e~~~~~e~~kre~~aL~~W 544 (649)
+|||||++++++++|++||||||+|||||+|++|+++|||+|||||+||+++|++||.++++.++++++++++++||++|
T Consensus 615 ~G~vhi~~~~~~rvak~LgIDyA~AVtGFeF~~g~~~Pv~~GvVV~~e~~~~v~~a~~~~~~~~~~~e~~k~e~~aL~~W 694 (713)
T TIGR00605 615 KGAVHLRLPGAIKAAKKLNIDYAPAVTGFDFHRGYSKPVLDGIIVCEEFREAIETAWEEIEQIQEEKEQEKHRKRALGNW 694 (713)
T ss_pred CCcEEecCccHHHHHHHhCCCeeeeeeceeecCCceeEeeceEEEehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhhcC
Q 006346 545 YQLLSSIVTRQRLNNCYGN 563 (649)
Q Consensus 545 k~Llk~LrIreRL~~~Yg~ 563 (649)
++||++|||++||+++||.
T Consensus 695 k~ll~~LrIr~Rl~~~Yg~ 713 (713)
T TIGR00605 695 KTLLKGLRIRERLKETYGK 713 (713)
T ss_pred HHHHHHHHHHHHHHHHhCc
Confidence 9999999999999999994
No 2
>KOG2179 consensus Nucleotide excision repair complex XPC-HR23B, subunit XPC/DPB11 [Replication, recombination and repair]
Probab=100.00 E-value=1.8e-95 Score=804.92 Aligned_cols=409 Identities=41% Similarity=0.645 Sum_probs=342.0
Q ss_pred cccccchhhhhhhhccCcHHHHHHHHHHHHhhhhhhcccCccCccCC--CCCCCCCcccchhhhhcccCCCCCCcCCccc
Q 006346 73 SEACHPKEKSQALKRKGDLEFEMQLEMALSATNVATSKSNICSDVKD--LNSNSSTVLPVKRLKKIESGESSTSCLGIST 150 (649)
Q Consensus 73 ~~~~~~~~~~~~~krkgd~~~e~q~~ma~~a~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~st 150 (649)
.|+++- -+.+++-.+||-.+..|.+|||..+.- ++...++.+ ..+|.+ + ...++++..++++
T Consensus 249 ~~~~p~-~~a~i~~~~g~~d~~~q~~~~l~~~~n----~~r~~~~l~p~~~~~~~----------~-~~~s~~~~~~~s~ 312 (669)
T KOG2179|consen 249 LEAVPA-HRADIRPNKGDADVSSQIIHALLRTPN----NARLAPSLQPPVFSNLS----------V-KDLSDTSLYGNSL 312 (669)
T ss_pred hhcCcH-HHhhhccCCCCcchHHHHHHHHhhccc----hhhcccccCCcchhhcc----------c-cccccccccccch
Confidence 566763 334444449999999999999998864 222222222 122211 1 1122333344554
Q ss_pred ccCCCCCCCCceEEEEEeCCCCCCCceEEEec--ccCcccccchhhhhHhhcCCCeeEEEEEcCCC-cccchhhhHhHHH
Q 006346 151 AVGSRKVGAPLYWAEVYCSGENLTGKWVHVDA--ANAIIDGEQKVEAAAAACKTSLRYIVAFAGCG-AKDVTRRYCMKWY 227 (649)
Q Consensus 151 ~~~~~~~~~P~fWvEV~~~~~~~~~rWI~VDP--i~~~Vd~~~~~Ep~~~~~~~~msYVVAfd~dG-akDVTrRYa~~~~ 227 (649)
...+.+ .|+||+|||+.. .++|||||| +.+.++....+...+....+.|.|||||+.+| ++|||+||+..|+
T Consensus 313 ~~~~~~--~p~~W~ev~~~~---e~kwV~vd~~~v~~~~~~~~~~~~~a~~~~~~~~yVva~da~~~~kDVT~RY~~~~~ 387 (669)
T KOG2179|consen 313 ENIDGA--GPVFWLEVLDKF---EKKWVCVDPPSVIGKYHLFQPIGAVAEINGRHLAYVVAYDADGYVKDVTRRYCESWS 387 (669)
T ss_pred hhcCCc--ccchhHHHHHhh---cceEEEecchhhcceeccccccchhhhhccccceEEEEecCCCccchhHHHHhhhhh
Confidence 444443 499999999864 589999996 33455666666655555667999999999998 9999999999999
Q ss_pred Hhhh----ccCCHHHHHHHHHhhhhcccCcCCCCcchhhhccchhhhHHHhhhccccccCCCCCcccccCCCCccccccc
Q 006346 228 RIAS----KRVNSAWWDAVLAPLRELESGATGGMTQMEKRHVNASNILEALKTSNYLYRDSFPNHVSLYGDSDLNVESSA 303 (649)
Q Consensus 228 ~~~r----kRv~~~Ww~~~L~~l~~~~sga~~g~~~~~kr~~~~~~i~~~~~~~~~~~~d~f~~~v~~~g~~~~~~~~~~ 303 (649)
++.+ .|++..||..++++|...
T Consensus 388 s~~~~~~k~~~~~~w~~~~l~~~~~~------------------------------------------------------ 413 (669)
T KOG2179|consen 388 SILRKRSKVRFSKKWFDKVLAPLGKL------------------------------------------------------ 413 (669)
T ss_pred hhhhccccccHHHHHhhhhHhhhccc------------------------------------------------------
Confidence 7765 567899999999998531
Q ss_pred cCcccccCCchHHHHHHHHhccCCCCcChHhhhcCCchhhhhhhccccccCC-CCCcceeecc--eeeeecCCccccccH
Q 006346 304 KDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYP-KGPILGFCSG--HAVYPRSCVQTLKTK 380 (649)
Q Consensus 304 ~~~~~~~rd~~Ed~EL~~~~~~E~mPtsi~~fKnHP~YvLEr~Lkk~EvI~P-~~~~~G~~~G--EpVY~RsdV~~LkS~ 380 (649)
..+++..||+++.++..+++||+|+++|||||+|||||||++||+||| +.++.||++| |+||+|.||++|||+
T Consensus 414 ----~~~~e~~ed~~~~~~~~~~~lP~sv~~~K~Hp~fvler~Lkk~q~l~P~k~p~~g~~kG~~E~VY~R~~V~~LkS~ 489 (669)
T KOG2179|consen 414 ----RKDREDTEDIELLRRHTSEGLPTSVQDLKNHPLFVLERHLKKNQALKPCKKPTLGFTKGDVEAVYLRRDVVTLKSR 489 (669)
T ss_pred ----cchHHHHHHHHHHHHhccCCCCchHHHhccCchhhhHHHHhhcccccccccceeeeecCCceeeeehhhHHhhccH
Confidence 124678999999999999999999999999999999999999999999 5788999999 999999999999999
Q ss_pred HHHHHhcccccCCCcccceeccCCCCCCCCCCCCCCccccccccccccccccccccCCCCCCCCCcccCCCCCceEeecC
Q 006346 381 ERWLREALQVKANEVPVKVIKNSSKSKKGQDFEPEDYDEVDARGNIELYGKWQLEPLRLPSAVNGIVPRNERGQVDVWSE 460 (649)
Q Consensus 381 e~W~r~GR~VK~gEqPlK~Vk~~~~~~k~~~~e~~d~~~~~~~~~~~LYg~wQTe~y~pPp~vdG~VPkN~yGNIDlf~p 460 (649)
++||++||+||+||||+|+||+++++.+.....+.+..+ ...++|||+|||++|.|||+++|+||||+|||||||+|
T Consensus 490 e~W~r~GRvIk~geqP~K~vK~~~~r~r~~r~~e~~~~~---~~~~~Lys~wqte~Y~pp~a~~givpkN~yGNielf~p 566 (669)
T KOG2179|consen 490 EQWYRKGRVIKPGEQPYKIVKRRPKRERMKRELEKDVRE---EYEQELYSPWQTELYCPPPAVEGIVPKNEYGNIELFSP 566 (669)
T ss_pred HHHHHhcccccCCCcchHHHhcCcchhhhhhhhhhhhhh---hhhhhccCcccccccCCCccccCccccccccceeeecc
Confidence 999999999999999999999988765544332222211 14678999999999999999999999999999999999
Q ss_pred CCCCCceEEecCccHHHHHHHcCCCEeeeeeeeeecCCeeeeeEceEEEccccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 006346 461 KCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCAEFKDTILEAYAEEEEKREAEEKKRREAQA 540 (649)
Q Consensus 461 sMlP~G~VHL~~~~~~kvAkkLgIDyA~AVtGFeFk~G~a~PvidGIVV~~E~~e~l~~a~~e~~e~~~~~e~~kre~~a 540 (649)
+|||.|||||++|++.+|||+||||||+|||||+|+.|.++|+++|||||+++++++..||+++++.++++|+++.+++|
T Consensus 567 ~miP~g~vhl~~p~~~~vAk~L~id~a~av~gF~f~~~~~~P~~~Givv~~e~k~~i~~a~ee~~~~~e~ker~~~~~~~ 646 (669)
T KOG2179|consen 567 SMIPKGCVHLRLPNAVDVAKKLGIDYAPAVTGFDFRRGYAVPVFEGIVVCKEFKEVILLAWEEDQKIQEEKERRKKRKRA 646 (669)
T ss_pred ccCCCCeEEecCchHHHHHHHhCCcccccccceeeccCcceecccceEeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHhhhcC
Q 006346 541 TSRWYQLLSSIVTRQRLNNCYGN 563 (649)
Q Consensus 541 L~~Wk~Llk~LrIreRL~~~Yg~ 563 (649)
|.+|+.||++||||+||+++||.
T Consensus 647 l~~Wk~Ll~~Lrir~Rl~~~Yg~ 669 (669)
T KOG2179|consen 647 LGRWKILLRGLRIRERLKKEYGN 669 (669)
T ss_pred HHHHHHHHHHhHHHHHHHHhhcC
Confidence 99999999999999999999994
No 3
>COG5535 RAD4 DNA repair protein RAD4 [DNA replication, recombination, and repair]
Probab=100.00 E-value=2.8e-76 Score=639.96 Aligned_cols=366 Identities=28% Similarity=0.406 Sum_probs=300.0
Q ss_pred cchhhhhcccCCCCCCcCCcccccCC----CCCCCCceEEEEEeCCCCCCCceEEEecccC-c-cc-ccchhhhhHhhcC
Q 006346 129 PVKRLKKIESGESSTSCLGISTAVGS----RKVGAPLYWAEVYCSGENLTGKWVHVDAANA-I-ID-GEQKVEAAAAACK 201 (649)
Q Consensus 129 ~~~~~~~~~~~~~~~~~~~~st~~~~----~~~~~P~fWvEV~~~~~~~~~rWI~VDPi~~-~-Vd-~~~~~Ep~~~~~~ 201 (649)
+.+-+..+.++.++.-....+..-+. ..+.+|.||+|||. ++.++||+|||++- + .. ....|||.+..-.
T Consensus 267 ~~Rli~~l~~P~Fs~~~~~~~~~e~~~~~iD~l~~p~fw~ev~~---~~~~kwv~vdp~~l~~v~~~l~~kfepa~~~~~ 343 (650)
T COG5535 267 FARLIASLIQPVFSNNSDLDVLSEGLLEYIDSLEYPGFWGEVVD---KFEKKWVFVDPVRLYIVYSELKCKFEPAASIHL 343 (650)
T ss_pred chhhhccccCcccccccccccCccccceeccchhcchHHHHHHH---HHHhceEecccchhhhhhhhhhheechhHHHHH
Confidence 34445555565555422221111121 23569999999997 46799999999963 2 22 4567899666667
Q ss_pred CCeeEEEEEcCCC-cccchhhhHhHHHHhhh----ccCCHHHHHHHHHhhhhcccCcCCCCcchhhhccchhhhHHHhhh
Q 006346 202 TSLRYIVAFAGCG-AKDVTRRYCMKWYRIAS----KRVNSAWWDAVLAPLRELESGATGGMTQMEKRHVNASNILEALKT 276 (649)
Q Consensus 202 ~~msYVVAfd~dG-akDVTrRYa~~~~~~~r----kRv~~~Ww~~~L~~l~~~~sga~~g~~~~~kr~~~~~~i~~~~~~ 276 (649)
|.|.||+|++.++ ++|||+||+-..+...+ .-...+|+.+.+.-+.+. +
T Consensus 344 n~~~~V~ayd~~~y~~DVt~RY~d~~~s~~kritk~~fs~qy~~r~~~~l~~~-------------------------k- 397 (650)
T COG5535 344 NIMEYVGAYDACVYVKDVTLRYRDQSYSFLKRITKHLFSVQYFVRQFPGLGKC-------------------------K- 397 (650)
T ss_pred HHHHHhhhhccCccchhHHHHHHHHHhhhhhhhhccchHHHHHHHHhcccCcc-------------------------c-
Confidence 8999999999987 99999999976554333 123578999887654321 0
Q ss_pred ccccccCCCCCcccccCCCCccccccccCcccccCCchHHHHHHHHhccCCCCcChHhhhcCCchhhhhhhccccccCCC
Q 006346 277 SNYLYRDSFPNHVSLYGDSDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPK 356 (649)
Q Consensus 277 ~~~~~~d~f~~~v~~~g~~~~~~~~~~~~~~~~~rd~~Ed~EL~~~~~~E~mPtsi~~fKnHP~YvLEr~Lkk~EvI~P~ 356 (649)
.+ .+.+.+++.++-+....++||+|++||||||+|||||||+++|+|+|+
T Consensus 398 -----------------------------~~-~~~e~i~~~~~L~~~~~~~iPkSvqdlK~HP~FVle~~Lk~~q~ikp~ 447 (650)
T COG5535 398 -----------------------------EA-SDEEAIEDFDDLDERRSEGIPKSVQDLKRHPKFVLESHLKWNQAIKPG 447 (650)
T ss_pred -----------------------------cc-ccHHHHHhHHHHhhcccccCCccHHHhccCCceeeHhhhhhhhhhccC
Confidence 00 133556776666666689999999999999999999999999999999
Q ss_pred CCc-ceeecc----eeeeecCCccccccHHHHHHhcccccCCCcccceeccCCCCCCCCCCCCCCccccccccccccccc
Q 006346 357 GPI-LGFCSG----HAVYPRSCVQTLKTKERWLREALQVKANEVPVKVIKNSSKSKKGQDFEPEDYDEVDARGNIELYGK 431 (649)
Q Consensus 357 ~~~-~G~~~G----EpVY~RsdV~~LkS~e~W~r~GR~VK~gEqPlK~Vk~~~~~~k~~~~e~~d~~~~~~~~~~~LYg~ 431 (649)
+.+ .++++| |+||+|.||..|+|+++||++||+||+|+||+|+||+- ..+.++. + .....+||++
T Consensus 448 ak~~~~~tkGk~~vE~VY~RrdVv~lkS~e~wy~~GRvIkpgaqP~K~vK~~--~~rv~~~--~------d~vi~~LYs~ 517 (650)
T COG5535 448 AKPGFTLTKGKNSVEAVYLRRDVVRLKSAEQWYRMGRVIKPGAQPLKIVKRM--RERVRNL--D------DKVIRELYSP 517 (650)
T ss_pred CccceeeecCCCccchhhhhhhHHhhcCHHHHHhcCcccCCCCchHHHHHHH--hhhcccc--c------chHHHhhcCH
Confidence 654 356678 99999999999999999999999999999999999972 1222221 1 2345679999
Q ss_pred cccccCCCCCCCCCcccCCCCCceEeecCCCCCCceEEecCccHHHHHHHcCCCEeeeeeeeeecCCeeeeeEceEEEcc
Q 006346 432 WQLEPLRLPSAVNGIVPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEFRNGRSTPVFDGIVVCA 511 (649)
Q Consensus 432 wQTe~y~pPp~vdG~VPkN~yGNIDlf~psMlP~G~VHL~~~~~~kvAkkLgIDyA~AVtGFeFk~G~a~PvidGIVV~~ 511 (649)
|||+.|.|||+++|+||||.|||||+|+|+|||.||+||+.+++.++|+.||||||+|||||+|+..+++||..||||.+
T Consensus 518 eqT~ly~pp~vv~~~i~KN~yGNid~~~psmiP~g~~~i~~~~a~~iAr~L~I~ya~aVtGFdF~r~~~kPv~~Givv~K 597 (650)
T COG5535 518 EQTELYGPPLVVAGIIPKNMYGNIDYYVPSMIPRGCVLIPNRNARDIARLLGIDYADAVTGFDFGRSTVKPVLRGIVVPK 597 (650)
T ss_pred HHHHhhcCCccccccccccccCCeeeecccccCCCeEeccCchHHHHHHHhCCchhhhhcccccccccccccccceecch
Confidence 99999999999999999999999999999999999999999999999999999999999999999989999999999999
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcC
Q 006346 512 EFKDTILEAYAEEEEKREAEEKKRREAQATSRWYQLLSSIVTRQRLNNCYGN 563 (649)
Q Consensus 512 E~~e~l~~a~~e~~e~~~~~e~~kre~~aL~~Wk~Llk~LrIreRL~~~Yg~ 563 (649)
++.++|..+..+.+..++++++.+-.+.+|..|+.||++||||.||+++||.
T Consensus 598 ~~~eai~~~~~e~e~iq~~ke~~e~r~~~L~~Wk~Ll~~LRir~Ri~~eYG~ 649 (650)
T COG5535 598 KNLEAISNFLAEYERIQEEKERSEVRLGGLKRWKILLRKLRIRLRINEEYGL 649 (650)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHhcc
Confidence 9999999999999988888888888889999999999999999999999995
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=1.2e-32 Score=234.88 Aligned_cols=75 Identities=48% Similarity=0.918 Sum_probs=62.5
Q ss_pred ccCCCCCceEeecCCCCCCceEEecCccHHHHHHHcCCCEeeeeeeeee-cCCeeeeeEceEEEccccHHHHHHHH
Q 006346 447 VPRNERGQVDVWSEKCLPPGTVHLRLPRVYSVAKRLEIDSAPAMVGFEF-RNGRSTPVFDGIVVCAEFKDTILEAY 521 (649)
Q Consensus 447 VPkN~yGNIDlf~psMlP~G~VHL~~~~~~kvAkkLgIDyA~AVtGFeF-k~G~a~PvidGIVV~~E~~e~l~~a~ 521 (649)
||||+|||||||+|+|||+|||||+++++.++||+||||||+|||||+| ++|+++|+++||||++||+++|++||
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=99.88 E-value=1.4e-23 Score=198.23 Aligned_cols=93 Identities=33% Similarity=0.702 Sum_probs=71.9
Q ss_pred CCCCCCCCceEEEEEeCCCCCCCceEEEecccCcccccchhhhhHhhcCCCeeEEEEEcCCC-cccchhhhHhH-HH-Hh
Q 006346 153 GSRKVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCG-AKDVTRRYCMK-WY-RI 229 (649)
Q Consensus 153 ~~~~~~~P~fWvEV~~~~~~~~~rWI~VDPi~~~Vd~~~~~Ep~~~~~~~~msYVVAfd~dG-akDVTrRYa~~-~~-~~ 229 (649)
...++.+|+||+|||++. .++||||||+++.+.....+||...++.++|+|||||+++| |+|||+||+++ |+ .+
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 345689999999999964 58999999999865577788888888999999999999887 99999999998 55 45
Q ss_pred hhccCC-----HHHHHHHHHhhhh
Q 006346 230 ASKRVN-----SAWWDAVLAPLRE 248 (649)
Q Consensus 230 ~rkRv~-----~~Ww~~~L~~l~~ 248 (649)
.+.|++ ..||..+|++|+.
T Consensus 105 ~r~R~~~~~~~~~W~~~~l~~~~~ 128 (145)
T PF03835_consen 105 RRLRVDRSYEEEDWWEKVLRPYNR 128 (145)
T ss_dssp GGGSGGGSHHHHHHHHHHHHHH--
T ss_pred ccccCCccccHHHHHHHHHHHHhc
Confidence 678998 8999999999874
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=99.78 E-value=2.3e-20 Score=151.52 Aligned_cols=52 Identities=42% Similarity=0.714 Sum_probs=40.5
Q ss_pred ccCCCCcChHhhhcCCchhhhhhhccccccCCCCCcceeecc----eeeeecCCcc
Q 006346 324 LTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSG----HAVYPRSCVQ 375 (649)
Q Consensus 324 ~~E~mPtsi~~fKnHP~YvLEr~Lkk~EvI~P~~~~~G~~~G----EpVY~RsdV~ 375 (649)
.+|+||+|+++|||||+|||||||++||+|+|+++++|+|+| |+||+|+||+
T Consensus 2 ~~e~~P~s~~~~K~hP~yvLe~~L~~~E~i~P~a~~vg~~~~~~~~e~VY~R~~V~ 57 (57)
T PF10403_consen 2 SNEPLPKSIQDFKNHPNYVLERHLKRNEVIYPGAKPVGTFKGKGKKEPVYLRSDVI 57 (57)
T ss_dssp HHH-S-SSCGGGTT-SSEEEGGGS-TTEEE-TT---SEEEE-TSTEEEEEEGGGE-
T ss_pred CcCCCCccHHHHhCCChhhhhhhcCcceeECCCCceeEEEeCCCcceeeEeHhhCC
Confidence 367999999999999999999999999999999999999999 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=99.67 E-value=9.1e-18 Score=138.97 Aligned_cols=64 Identities=36% Similarity=0.637 Sum_probs=30.6
Q ss_pred cccHHHHHHhcccccCCCcccceeccCCCCCCCCCCCCCCccccccccccccccccccccCCCC
Q 006346 377 LKTKERWLREALQVKANEVPVKVIKNSSKSKKGQDFEPEDYDEVDARGNIELYGKWQLEPLRLP 440 (649)
Q Consensus 377 LkS~e~W~r~GR~VK~gEqPlK~Vk~~~~~~k~~~~e~~d~~~~~~~~~~~LYg~wQTe~y~pP 440 (649)
|||+++|+++||+||+||+|+|+|++++++.+.......+..+.+....++|||+||||+|+||
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 7999999999999999999999999987643322222111111123468999999999999998
No 8
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=99.52 E-value=4e-15 Score=159.81 Aligned_cols=85 Identities=26% Similarity=0.427 Sum_probs=74.5
Q ss_pred CCCceEEEEEeCCCCCCCceEEEecccCcccccchhhhhHhhcCCCeeEEEEEcCCCcccchhhhHhHHHHh--hhccCC
Q 006346 158 GAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRI--ASKRVN 235 (649)
Q Consensus 158 ~~P~fWvEV~~~~~~~~~rWI~VDPi~~~Vd~~~~~Ep~~~~~~~~msYVVAfd~dGakDVTrRYa~~~~~~--~rkRv~ 235 (649)
..+|+|+|||+. +.+||+|||||++.+|+|.+||. +|++.|+|||||+.||+.|||.||+.++... .|.++.
T Consensus 247 ~tDHVWtEvYS~---~qqRW~HvDpcE~v~D~PllYe~---GW~KklsY~iafgkD~VvDVT~RYi~~h~e~~~~R~~~~ 320 (500)
T KOG0909|consen 247 RTDHVWTEVYSN---AQQRWVHVDPCENVFDKPLLYEI---GWGKKLSYCIAFGKDGVVDVTWRYILDHKENLLPRDLCK 320 (500)
T ss_pred cCcchhHHhhhh---hhheeEeecccccccccceeeec---ccCcccceEEEeccCceEeeehhhhccchhhccchhhcc
Confidence 467999999986 46999999999999999999986 8999999999999999999999999988754 456788
Q ss_pred HHHHHHHHHhhhh
Q 006346 236 SAWWDAVLAPLRE 248 (649)
Q Consensus 236 ~~Ww~~~L~~l~~ 248 (649)
+.=+..+|..|+.
T Consensus 321 E~~l~~~l~~in~ 333 (500)
T KOG0909|consen 321 ESVLQQTLQFINK 333 (500)
T ss_pred hHHHHHHHHHHHH
Confidence 8778888887763
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=97.35 E-value=0.0017 Score=64.06 Aligned_cols=35 Identities=23% Similarity=0.471 Sum_probs=31.8
Q ss_pred CCCccccccccccCccccccceecccC-CCceEEEeeC
Q 006346 613 SEEHEHVYLIEDQSFDEENSVTTKRCH-CGFTIQVEEL 649 (649)
Q Consensus 613 ~~~h~h~f~~~~~sfdeet~~~tkrc~-cg~~iqve~~ 649 (649)
...|+|.|.. +.+|+|+.+++|+|- |||.|.+|+|
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=94.54 E-value=0.076 Score=54.50 Aligned_cols=33 Identities=39% Similarity=0.736 Sum_probs=26.6
Q ss_pred CCccccccccccCccc--cccceecccCCCceEEEeeC
Q 006346 614 EEHEHVYLIEDQSFDE--ENSVTTKRCHCGFTIQVEEL 649 (649)
Q Consensus 614 ~~h~h~f~~~~~sfde--et~~~tkrc~cg~~iqve~~ 649 (649)
+-|.|+|-++ ||- |-.+-.-||.||+.|+-+|+
T Consensus 258 ~kHvH~f~e~---vdg~~e~g~~iqRC~CGlevEq~ei 292 (292)
T COG5145 258 EKHVHVFDEF---VDGPNEPGVIIQRCSCGLEVEQEEI 292 (292)
T ss_pred hcceeecccc---ccCCCCCCeEEEecccccchhhccC
Confidence 4599999775 554 78899999999999876654
No 11
>KOG4017 consensus DNA excision repair protein XPA/XPAC/RAD14 [Replication, recombination and repair]
Probab=93.26 E-value=0.32 Score=50.71 Aligned_cols=34 Identities=32% Similarity=0.481 Sum_probs=27.3
Q ss_pred CCccccccccccCccccccceecccCCCceEEEeeC
Q 006346 614 EEHEHVYLIEDQSFDEENSVTTKRCHCGFTIQVEEL 649 (649)
Q Consensus 614 ~~h~h~f~~~~~sfdeet~~~tkrc~cg~~iqve~~ 649 (649)
.-|.|+|..|- -=||-..+.-+|.||+++..|+|
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=91.64 E-value=0.45 Score=38.44 Aligned_cols=23 Identities=43% Similarity=0.819 Sum_probs=19.1
Q ss_pred CCCCCceEEEEEeCCCCCCCceEEEecc
Q 006346 156 KVGAPLYWAEVYCSGENLTGKWVHVDAA 183 (649)
Q Consensus 156 ~~~~P~fWvEV~~~~~~~~~rWI~VDPi 183 (649)
....+|.|+|||.. ++|+.+||.
T Consensus 45 ~~~~~H~W~ev~~~-----~~W~~~D~~ 67 (68)
T smart00460 45 SIWEAHAWAEVYLE-----GGWVPVDPT 67 (68)
T ss_pred cCCCcEEEEEEEEC-----CCeEEEeCC
Confidence 34578999999984 689999995
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=89.44 E-value=0.3 Score=42.97 Aligned_cols=27 Identities=19% Similarity=0.067 Sum_probs=20.1
Q ss_pred hhhhccCcHHHHHHHHHHHHhhhhhhcccC
Q 006346 83 QALKRKGDLEFEMQLEMALSATNVATSKSN 112 (649)
Q Consensus 83 ~~~krkgd~~~e~q~~ma~~a~~~~~~~~~ 112 (649)
--..++|+=+ +.+..|.|.+++.+-.+
T Consensus 46 ~l~~~~G~C~---~~a~l~~allr~~Gipa 72 (113)
T PF01841_consen 46 VLRSGRGDCE---DYASLFVALLRALGIPA 72 (113)
T ss_dssp HHHCEEESHH---HHHHHHHHHHHHHT--E
T ss_pred HHHcCCCccH---HHHHHHHHHHhhCCCce
Confidence 3346779998 88999999999998444
No 14
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=67.55 E-value=2.2 Score=35.74 Aligned_cols=26 Identities=42% Similarity=0.829 Sum_probs=21.2
Q ss_pred cccCccccccceecccCCC--ceEEEee
Q 006346 623 EDQSFDEENSVTTKRCHCG--FTIQVEE 648 (649)
Q Consensus 623 ~~~sfdeet~~~tkrc~cg--~~iqve~ 648 (649)
||=.|+.|+...|--|+|| |.|-.|.
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=54.77 E-value=4.7 Score=32.53 Aligned_cols=15 Identities=40% Similarity=1.006 Sum_probs=10.0
Q ss_pred ccccceecccCCCceEE
Q 006346 629 EENSVTTKRCHCGFTIQ 645 (649)
Q Consensus 629 eet~~~tkrc~cg~~iq 645 (649)
|-|+.| -|.|||.|.
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
>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=46.52 E-value=13 Score=30.41 Aligned_cols=25 Identities=36% Similarity=0.769 Sum_probs=20.4
Q ss_pred cccCccccccceecccCCCceEEEe
Q 006346 623 EDQSFDEENSVTTKRCHCGFTIQVE 647 (649)
Q Consensus 623 ~~~sfdeet~~~tkrc~cg~~iqve 647 (649)
+|=.||++..+++..|+||-...|.
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 4466888999999999999876664
No 17
>COG1305 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]
Probab=46.14 E-value=14 Score=37.65 Aligned_cols=26 Identities=38% Similarity=0.828 Sum_probs=20.2
Q ss_pred CCCceEEEEEeCCCCCCCceEEEecccCcc
Q 006346 158 GAPLYWAEVYCSGENLTGKWVHVDAANAII 187 (649)
Q Consensus 158 ~~P~fWvEV~~~~~~~~~rWI~VDPi~~~V 187 (649)
...|.|+|||.++ ..|+++||..+..
T Consensus 238 ~~~Haw~ev~~~~----~gW~~~Dpt~~~~ 263 (319)
T COG1305 238 DDAHAWAEVYLPG----RGWVPLDPTNGLL 263 (319)
T ss_pred cccceeeeeecCC----CccEeecCCCCCc
Confidence 3458999999864 2699999987643
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=25.15 E-value=37 Score=29.32 Aligned_cols=18 Identities=44% Similarity=0.853 Sum_probs=12.7
Q ss_pred cceecccCCCceEEEeeC
Q 006346 632 SVTTKRCHCGFTIQVEEL 649 (649)
Q Consensus 632 ~~~tkrc~cg~~iqve~~ 649 (649)
...||.|.||-.+-|++.
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
Done!