Query 005629
Match_columns 687
No_of_seqs 236 out of 484
Neff 5.3
Searched_HMMs 46136
Date Thu Mar 28 11:19:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005629.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005629hhsearch_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 7.3E-76 1.6E-80 670.3 23.9 430 121-687 90-559 (713)
2 KOG2179 Nucleotide excision re 100.0 1.1E-50 2.4E-55 452.4 19.7 436 123-687 38-511 (669)
3 COG5535 RAD4 DNA repair protei 100.0 2.1E-48 4.5E-53 425.2 5.4 368 124-686 90-497 (650)
4 PF03835 Rad4: Rad4 transgluta 99.9 1.9E-24 4.1E-29 206.4 5.6 109 479-605 29-145 (145)
5 PF10403 BHD_1: Rad4 beta-hair 99.8 9.3E-21 2E-25 154.1 0.8 52 609-660 2-57 (57)
6 KOG0909 Peptide:N-glycanase [P 99.8 1.1E-18 2.3E-23 187.6 9.1 109 487-607 251-361 (500)
7 TIGR00605 rad4 DNA repair prot 98.8 1.8E-10 4E-15 133.9 -6.3 147 149-300 13-175 (713)
8 PF10404 BHD_2: Rad4 beta-hair 98.3 1.9E-07 4.1E-12 78.0 0.8 26 662-687 1-26 (64)
9 KOG2179 Nucleotide excision re 97.3 0.00019 4.1E-09 82.9 4.1 129 171-300 141-296 (669)
10 PF01841 Transglut_core: Trans 96.5 0.00065 1.4E-08 60.9 0.2 62 228-291 15-76 (113)
11 COG5535 RAD4 DNA repair protei 95.7 0.0045 9.8E-08 70.6 1.8 162 123-301 43-229 (650)
12 smart00460 TGc Transglutaminas 95.7 0.0066 1.4E-07 49.8 2.2 30 262-291 2-31 (68)
13 COG1305 Transglutaminase-like 93.0 0.11 2.4E-06 53.9 4.6 61 228-291 159-219 (319)
14 smart00460 TGc Transglutaminas 87.1 0.66 1.4E-05 37.8 3.3 21 483-508 47-67 (68)
15 PF01841 Transglut_core: Trans 86.9 0.55 1.2E-05 41.9 2.9 20 484-507 94-113 (113)
16 PF13369 Transglut_core2: Tran 67.6 6.7 0.00014 38.0 4.0 36 256-291 54-89 (152)
17 COG1305 Transglutaminase-like 40.6 19 0.00041 37.4 2.3 25 484-512 239-263 (319)
18 PF00797 Acetyltransf_2: N-ace 33.1 42 0.0009 34.4 3.4 23 269-291 49-71 (240)
19 PF11702 DUF3295: Protein of u 32.9 19 0.0004 41.8 0.8 11 122-132 307-317 (507)
20 PRK10941 hypothetical protein; 28.0 69 0.0015 34.3 4.1 63 229-291 57-120 (269)
21 PF14402 7TM_transglut: 7 tran 22.1 50 0.0011 36.1 1.7 28 483-515 29-56 (313)
22 TIGR01544 HAD-SF-IE haloacid d 20.3 1.7E+02 0.0038 31.6 5.3 100 188-291 44-144 (277)
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=7.3e-76 Score=670.31 Aligned_cols=430 Identities=23% Similarity=0.327 Sum_probs=306.4
Q ss_pred CCCCCCCCCccccCCCCCCCCCCCCCCCCCCeEEEEecCCcc------ccccccccCHHHHHHHHHHHHHHHHHHHHhhH
Q 005629 121 GGEEMYDSDWEDGSIPVACSKENHPESDIKGVTIEFDAADSV------TKKPVRRASAEDKELAELVHKVHLLCLLARGR 194 (687)
Q Consensus 121 ~~deddd~dWEdV~~~~~~~~~~~p~~~~~~leI~l~~~~~~------kK~~~RR~s~~eKe~r~~~HKvHLLCLLah~~ 194 (687)
++++.+.+++|+|.+..... .-++..++|.+.... .+...+-++.++|+.|+.||++||||||.|+.
T Consensus 90 ~~~~~~~~~~e~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~eR~~R~~iH~~~ll~ll~h~~ 162 (713)
T TIGR00605 90 REEDYDSREFEDVYLSNLVA-------EFETISVEIKPSSKAESDDDAETLSRNVCSNEARKDRKYIHILYLLCLMVHLF 162 (713)
T ss_pred cccccchhhhhhhhhccccc-------ccCcccccccccchhhhhhHHHHHHHhhccHHHHHHHHHHHHHHHHHHhhhhH
Confidence 34555677999987643111 122233333322111 11112237899999999999999999999999
Q ss_pred HHHhhcCc-HHHHHHHhhcCchhhhcccCcc---------hhhHhhhhHHHHHhhhceeeccCCCcc-------------
Q 005629 195 LIDSVCDD-PLIQASLLSLLPSYLLKISEVS---------KLTANALSPIVSWFHDNFHVRSSVSTR------------- 251 (687)
Q Consensus 195 ~RN~wcnd-~~lqa~llSlLP~~~~~~~~~~---------~~~~~~L~~L~~Wf~~~F~vt~~~~~~------------- 251 (687)
+||.|||| +++|+.|..+||.++...+++. ..+..+|+.|+.-|+..|+|+.+....
T Consensus 163 ~RN~w~n~~~~~~~~L~~~~p~k~~~~l~p~~~~~~~~~s~s~~~~~~~l~~~~kk~~~it~~g~~~~~~~~~~~~~~~~ 242 (713)
T TIGR00605 163 TRNEWSLSAPLKSAKLSNLIPEKVRLLLHPSVRKSEELPSRSLRGLRKPLVEKLKKCMETWQKGLRKTTKGLLKLLNGGR 242 (713)
T ss_pred hhhhhhCChHHHhHHHhhhCCHHHHHhcCccccccccccchhhhhhhHHHHHhhhhcchhcccccccCcccccccchhhH
Confidence 99999999 7999999999999998776542 235789999999999999999864111
Q ss_pred cch--HHHHHHHHHHhcCCHHHHHHHHHHHHHhcCCceeEEEeeccccCCcccccccCCCCCCCCCCCCccCCCCccccC
Q 005629 252 RSF--HSDLAHALESREGTPEEIAALSVALFRALKLTTRFVSILDVASLKPEADKNVSSNQDSSRVGGGIFNAPTLMVAK 329 (687)
Q Consensus 252 ~~~--~~~l~~~l~~~~GSrD~gAqLF~ALLRALgL~aRLV~SLqpl~lk~~~~k~~~~~~~~~~~~~~~~~~~~~~~~k 329 (687)
..| ..+|+.++.+++||||.||||||||||++|++|||||||||+||.+..+-. ..+ ...+ +++
T Consensus 243 ~~~~~~~ef~~~a~~~~gsrd~~aql~~allr~~~~~~rlv~slqpl~~~~~~~~~-----~~~---~~~~------~~~ 308 (713)
T TIGR00605 243 YSRSKWEEIEKSSNRKLGGRKYRTLKRGSILENLNVPTRLVFSDFLLSVSKGHNDP-----EIS---SEGF------VPK 308 (713)
T ss_pred HhhhhHHHHHHhhhccccccchhhhHHHHHHhhhcccccccccccccCcccCCCCc-----ccc---cccc------ccc
Confidence 011 467889999999999999999999999999999999999999998731100 000 0000 000
Q ss_pred ccccccCCCCcccccccccccccCCCCCCCCCCCCCCCCCCCCCCCCccccccCCCCCCCCccccCCCcccC-CCcchhh
Q 005629 330 PEEVLASPVKSFSCDKKENVCETSSKGSPECKYSSPKSNNTQSKKSPVSCELSSGNLDPSSSMACSDISEAC-HPKEKSQ 408 (687)
Q Consensus 330 ~~~~~~~p~k~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~s~~~~~s~~~~~~~~~~~~~~~~~s~~e~~-~s~~~~~ 408 (687)
. . .+. +...+..+ ..+. .+ ....
T Consensus 309 ~----------~-------~~~-------------------------------------~~q~~~~s-~~S~~~t-sR~~ 332 (713)
T TIGR00605 309 L----------S-------ACN-------------------------------------ANQRLIMS-CESADRT-SRFR 332 (713)
T ss_pred c----------c-------ccc-------------------------------------cccccccc-cCCCCcc-cccc
Confidence 0 0 000 00000000 0000 00 0000
Q ss_pred hhhccCChHHHHHHHHHhhhccccccCCcccccccccCCCCCCccccccccccccCCCCccccCcccccCCCCCCCCceE
Q 005629 409 ALKRKGDLEFEMQLEMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKVGAPLYW 488 (687)
Q Consensus 409 ~~rR~g~~~fe~q~~~al~~t~~~~~~s~~~~~~~~~~~~~~~~~~~k~~kk~~~~~s~~~~~~~s~~~~~~~~~~P~fW 488 (687)
..++.+.|.|. +++.+.+..+.. ........+.+++||+||
T Consensus 333 l~~~l~~P~fs------------------------------~~~~~~k~~~~~---------~~~~~~~~~~~~~~p~~W 373 (713)
T TIGR00605 333 MKKDPSLPGFS------------------------------AYSDMDKSPIFT---------CEEGDKFIDRWITYVDFW 373 (713)
T ss_pred ccccCCCCCcc------------------------------ccccCCCCCccc---------hhcccccccccCCCCeeE
Confidence 11222222110 000000111000 000111356789999999
Q ss_pred EEEEeCcCCCCCceEEEeccc-Cccccch-hhHHhHhhcCCCeeEEEEEcCCC-cccchhhhhhhhhh-hccccCCHHHH
Q 005629 489 AEVYCSGENLTGKWVHVDAAN-AIIDGEQ-KVEAAAAACKTSLRYIVAFAGCG-AKDVTRRYCMKWYR-IASKRVNSAWW 564 (687)
Q Consensus 489 ~EV~~~~~~~~~kWI~VDpv~-~~V~~~~-~~Ep~~~~~~~~m~YVVAfd~dG-akDVT~RY~~~~~~-~~r~Rv~~~Ww 564 (687)
+|||++. +++||||||++ ++++++. .||| +.++|+|||||++|| |+|||+||+++|+. +++.|++..||
T Consensus 374 ~Ev~~~~---~~rWI~VD~~~~~~~~~~~~~~e~----~~~~m~YVvAf~~d~~~kDVT~RY~~~~~~k~r~~Rv~~~w~ 446 (713)
T TIGR00605 374 VEVFIEQ---EEKWVCVDAVHSGVVPKGVTCFEP----ATLMMTYVFAYDRDGYVKDVTRRYCDQWSTKVRKRRVEKADF 446 (713)
T ss_pred EEEeecc---cceeEEeccccccccCCchhhccC----CCCceEEEEEEcCCCceeechhhHhhhhhhhhheeeecccch
Confidence 9999987 48999999999 8888875 4554 459999999999998 99999999999996 56689998888
Q ss_pred HHH-HHHhhccccCCCCCCcccccccCccccccChhHHHHHHHHhccCCCCCChhhhhcCchhHhhhhhhcccccCCC--
Q 005629 565 DAV-LAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPK-- 641 (687)
Q Consensus 565 ~~~-L~~~~~~~~~~~~~~~i~a~~~~~~~~~rD~~Ed~eL~~~~~~epmP~ti~~fKnHP~YvLeRhL~r~E~I~P~-- 641 (687)
..+ |++|.+... +.. ..+|..||.||.++.++||||+|+++|||||+|||||||++||+|||+
T Consensus 447 ~~~w~~~~~~~~~-------------~r~-~~~d~~Ed~el~~~~~~e~~P~si~~fKnHP~YvLer~L~~~Evi~P~~~ 512 (713)
T TIGR00605 447 GETWFRPIFGALH-------------KRK-RTIDDIEDQEFLRRHESEGIPKSIQDLKNHPLYVLERHLKKTQALKPGKK 512 (713)
T ss_pred HHHHHHHHhhhhc-------------cCc-cchhhhhhhHhhhhhcccCCChhHHHhhcCceEEehhhcccceeeccCCC
Confidence 887 777764321 111 227899999999999999999999999999999999999999999995
Q ss_pred CCcceeeccee-eeecCCccccccHHHHHHhccccCCCCeeeccccC
Q 005629 642 GPILGFCSGHA-VYPRSCVQTLKTKERWLREALQVKANEVPVKVCSG 687 (687)
Q Consensus 642 a~~~G~~~gE~-VY~R~dV~~LkS~e~W~k~GR~VK~gE~P~K~Vkg 687 (687)
++++|+++||+ ||+|+||++|||+++||++||+||+||+|||+|++
T Consensus 513 ~~~~g~~~g~~~VY~Rs~V~~lkS~~~W~~~GR~VK~ge~P~K~vk~ 559 (713)
T TIGR00605 513 ACTLGFVNGKAGVYSRKDVHDLKSAEQWYKKGRVIKLGEQPYKVVKA 559 (713)
T ss_pred CCceeccCCCCCccchhHhhhhhhHHHHHHcCCccCCCCccceEecc
Confidence 45789999998 99999999999999999999999999999999983
No 2
>KOG2179 consensus Nucleotide excision repair complex XPC-HR23B, subunit XPC/DPB11 [Replication, recombination and repair]
Probab=100.00 E-value=1.1e-50 Score=452.41 Aligned_cols=436 Identities=30% Similarity=0.344 Sum_probs=286.3
Q ss_pred CCCCCCCccccCCCCCCCCCCCCCCCCCCeEEEEecCC--ccccccccccCHHHHHHHHHHHHHHHHHHHHhhHHHHhhc
Q 005629 123 EEMYDSDWEDGSIPVACSKENHPESDIKGVTIEFDAAD--SVTKKPVRRASAEDKELAELVHKVHLLCLLARGRLIDSVC 200 (687)
Q Consensus 123 deddd~dWEdV~~~~~~~~~~~p~~~~~~leI~l~~~~--~~kK~~~RR~s~~eKe~r~~~HKvHLLCLLah~~~RN~wc 200 (687)
+++++-.|++|..+.... ..|.....+.+++|.... +...+ .....+.+....|-+|.+|.+.+-..||.||
T Consensus 38 ~~~~~~~~~~~~~~~~~~--~l~~~~~~~~~~~~~~s~~~~~~~k----~~~~d~~~~~~~~~l~~~~~~~~~~~~~~~~ 111 (669)
T KOG2179|consen 38 DEEDDLLSSDVKWFSLDS--ELPVENVNDVRDTILVSLEKRKANK----EARDDQDLEYQFHLLDRLFMLFLLKTRNLWP 111 (669)
T ss_pred cccccchhhccCcccccc--cccccccchhhhHhhhhhhhhhhhc----ccccHHHHHHHHHHHhhhhHHHHHHHhcccC
Confidence 344555666665543222 122222334445554432 11211 1357888999999999999999999999999
Q ss_pred CcHHHHHHHhhcCchhhhcccCcc----------hhhHhhhhHHHHHhhhcee-eccCCCcc------------cchHHH
Q 005629 201 DDPLIQASLLSLLPSYLLKISEVS----------KLTANALSPIVSWFHDNFH-VRSSVSTR------------RSFHSD 257 (687)
Q Consensus 201 nd~~lqa~llSlLP~~~~~~~~~~----------~~~~~~L~~L~~Wf~~~F~-vt~~~~~~------------~~~~~~ 257 (687)
.+-.+-+ ++...|..+.....+. +-...++..|+.||...+. |+.+.... ++-...
T Consensus 112 ~~~r~~~-l~~~~p~~~~~s~~p~s~~~s~a~~~~s~r~~~~~l~~~~~~~~g~irt~~~~~~~~~~k~~~~~sEse~~~ 190 (669)
T KOG2179|consen 112 DPVRLNA-LVRSKPKKIRKSFKPSSSRKSQAFKNKSRRKTLHGLVLVCLSKYGKIRTNFLRKNYADLKNENLISESELKK 190 (669)
T ss_pred CcchhhH-hhhccCcccccCCCccccccchHhHhhhhhhhHHHHHHHHHHHhcccccchhhhhhhhcccccCCcchhccc
Confidence 9888765 7777887765443322 1124677789999988887 66542210 010112
Q ss_pred HHHHHHHhcCCHHHHHHHHHH--HHHhcCCceeEEEe-eccccCCcccccccCCCCCCCCCCCCccCCCCccccCccccc
Q 005629 258 LAHALESREGTPEEIAALSVA--LFRALKLTTRFVSI-LDVASLKPEADKNVSSNQDSSRVGGGIFNAPTLMVAKPEEVL 334 (687)
Q Consensus 258 l~~~l~~~~GSrD~gAqLF~A--LLRALgL~aRLV~S-Lqpl~lk~~~~k~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~ 334 (687)
.+..-+...|+|+-|.+++.+ +.+-.+...+.|.+ ++-+++... .+.
T Consensus 191 ~~k~~e~~~~~~~~l~~~~~~~s~~k~~~~~~k~~~~~~~~~s~~~~--------------------~~~---------- 240 (669)
T KOG2179|consen 191 VAKNQELFSGSRPLLLKGVEDASIRKKWKSKMKNVSSGTEKLSKELS--------------------DGA---------- 240 (669)
T ss_pred hhhhhhhhccCchHhhhhhhhhhhhhhhcCCccccCcchhhhccccc--------------------CCC----------
Confidence 344455667899999999987 44444444444432 111111000 000
Q ss_pred cCCCCcccccccccccccCCCCCCCCCCCCCCCCCCCCCCCCccccccCCCCCCCCccccCCCcccCCCcchhhhhhccC
Q 005629 335 ASPVKSFSCDKKENVCETSSKGSPECKYSSPKSNNTQSKKSPVSCELSSGNLDPSSSMACSDISEACHPKEKSQALKRKG 414 (687)
Q Consensus 335 ~~p~k~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~s~~~~~s~~~~~~~~~~~~~~~~~s~~e~~~s~~~~~~~rR~g 414 (687)
++. .+.... +.+ +-.+...+.-+|
T Consensus 241 ---------------------------------------d~~-------------~~~~~~---~~~-p~~~a~i~~~~g 264 (669)
T KOG2179|consen 241 ---------------------------------------DEA-------------SKPYLL---EAV-PAHRADIRPNKG 264 (669)
T ss_pred ---------------------------------------ccc-------------cchhhh---hcC-cHHHhhhccCCC
Confidence 000 000000 000 000112222378
Q ss_pred ChHHHHHHHHHhhhccccccCCcccccccccCCCCCCccccccccccccCCCCccccCcccccCCCCCCCCceEEEEEeC
Q 005629 415 DLEFEMQLEMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKVGAPLYWAEVYCS 494 (687)
Q Consensus 415 ~~~fe~q~~~al~~t~~~~~~s~~~~~~~~~~~~~~~~~~~k~~kk~~~~~s~~~~~~~s~~~~~~~~~~P~fW~EV~~~ 494 (687)
+.++..|.++++..++-.......... +.. +.... .+.|.++..++++...+ ..+|+||+|||+.
T Consensus 265 ~~d~~~q~~~~l~~~~n~~r~~~~l~p-~~~-----~~~~~-------~~~s~~~~~~~s~~~~~--~~~p~~W~ev~~~ 329 (669)
T KOG2179|consen 265 DADVSSQIIHALLRTPNNARLAPSLQP-PVF-----SNLSV-------KDLSDTSLYGNSLENID--GAGPVFWLEVLDK 329 (669)
T ss_pred CcchHHHHHHHHhhccchhhcccccCC-cch-----hhccc-------cccccccccccchhhcC--CcccchhHHHHHh
Confidence 888999999998877431111111110 000 00001 12344445555544333 3459999999998
Q ss_pred cCCCCCceEEEec--ccCccccchhhHHhHhhcCCCeeEEEEEcCCC-cccchhhhhhhhhhhcc----ccCCHHHHHHH
Q 005629 495 GENLTGKWVHVDA--ANAIIDGEQKVEAAAAACKTSLRYIVAFAGCG-AKDVTRRYCMKWYRIAS----KRVNSAWWDAV 567 (687)
Q Consensus 495 ~~~~~~kWI~VDp--v~~~V~~~~~~Ep~~~~~~~~m~YVVAfd~dG-akDVT~RY~~~~~~~~r----~Rv~~~Ww~~~ 567 (687)
.+ ++|||||| +.+.++..+.+...+..+...|.|||||+.+| ++|||+||+..|+++.+ .|+...||..+
T Consensus 330 ~e---~kwV~vd~~~v~~~~~~~~~~~~~a~~~~~~~~yVva~da~~~~kDVT~RY~~~~~s~~~~~~k~~~~~~w~~~~ 406 (669)
T KOG2179|consen 330 FE---KKWVCVDPPSVIGKYHLFQPIGAVAEINGRHLAYVVAYDADGYVKDVTRRYCESWSSILRKRSKVRFSKKWFDKV 406 (669)
T ss_pred hc---ceEEEecchhhcceeccccccchhhhhccccceEEEEecCCCccchhHHHHhhhhhhhhhccccccHHHHHhhhh
Confidence 64 89999996 33444443333333334556999999999999 99999999999997655 57788999999
Q ss_pred HHHhhccccCCCCCCcccccccCccccccChhHHHHHHHHhccCCCCCChhhhhcCchhHhhhhhhcccccCCCC-Ccce
Q 005629 568 LAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKG-PILG 646 (687)
Q Consensus 568 L~~~~~~~~~~~~~~~i~a~~~~~~~~~rD~~Ed~eL~~~~~~epmP~ti~~fKnHP~YvLeRhL~r~E~I~P~a-~~~G 646 (687)
+.+|..+ ..+++..||.++..+..+++||+|+++|||||+|||||||++||+|||.+ +..|
T Consensus 407 l~~~~~~------------------~~~~e~~ed~~~~~~~~~~~lP~sv~~~K~Hp~fvler~Lkk~q~l~P~k~p~~g 468 (669)
T KOG2179|consen 407 LAPLGKL------------------RKDREDTEDIELLRRHTSEGLPTSVQDLKNHPLFVLERHLKKNQALKPCKKPTLG 468 (669)
T ss_pred Hhhhccc------------------cchHHHHHHHHHHHHhccCCCCchHHHhccCchhhhHHHHhhcccccccccceee
Confidence 9999853 35788999999999999999999999999999999999999999999964 6679
Q ss_pred eecc--eeeeecCCccccccHHHHHHhccccCCCCeeeccccC
Q 005629 647 FCSG--HAVYPRSCVQTLKTKERWLREALQVKANEVPVKVCSG 687 (687)
Q Consensus 647 ~~~g--E~VY~R~dV~~LkS~e~W~k~GR~VK~gE~P~K~Vkg 687 (687)
+++| |+||+|.||++|||+|+||+.||+||+||+|+|+||+
T Consensus 469 ~~kG~~E~VY~R~~V~~LkS~e~W~r~GRvIk~geqP~K~vK~ 511 (669)
T KOG2179|consen 469 FTKGDVEAVYLRRDVVTLKSREQWYRKGRVIKPGEQPYKIVKR 511 (669)
T ss_pred eecCCceeeeehhhHHhhccHHHHHHhcccccCCCcchHHHhc
Confidence 9999 9999999999999999999999999999999999985
No 3
>COG5535 RAD4 DNA repair protein RAD4 [DNA replication, recombination, and repair]
Probab=100.00 E-value=2.1e-48 Score=425.20 Aligned_cols=368 Identities=23% Similarity=0.251 Sum_probs=273.7
Q ss_pred CCCCCCccccCCCCCCCCCCCCCCCCCCeEEEEecCCccccccccccCHHHHHHHHHHHHHHHHHHHHhhHHHHhhcCcH
Q 005629 124 EMYDSDWEDGSIPVACSKENHPESDIKGVTIEFDAADSVTKKPVRRASAEDKELAELVHKVHLLCLLARGRLIDSVCDDP 203 (687)
Q Consensus 124 eddd~dWEdV~~~~~~~~~~~p~~~~~~leI~l~~~~~~kK~~~RR~s~~eKe~r~~~HKvHLLCLLah~~~RN~wcnd~ 203 (687)
+..+++|+++-.+. . ..+.++|.+.|..-. +|+..+ +..++.+|...|+||.+|||.||++||.|.++.
T Consensus 90 hl~~~~f~~l~s~n------k-~~dderLn~~~k~s~--pk~~~~--s~~d~s~rks~him~~tcll~~g~irn~W~rsk 158 (650)
T COG5535 90 HLIMIPFMLLKSRN------K-WIDDERLNRRLKRSV--PKLGGK--SFKDWSVRKSAHIMDSTCLLLLGFIRNLWFRSK 158 (650)
T ss_pred hhhcchhhhhcCcC------e-eccchhhceeeeccC--cccccc--cccCcchhhhHHHHHHHHHHHHHHHHHHHHHhh
Confidence 34556777643221 0 124567888877642 232222 468999999999999999999999999999999
Q ss_pred HHHHHHhhcCchhhhcccCc-------chhhHhhhhHHHHHhhhceeeccCCCcc--------c----chH-------HH
Q 005629 204 LIQASLLSLLPSYLLKISEV-------SKLTANALSPIVSWFHDNFHVRSSVSTR--------R----SFH-------SD 257 (687)
Q Consensus 204 ~lqa~llSlLP~~~~~~~~~-------~~~~~~~L~~L~~Wf~~~F~vt~~~~~~--------~----~~~-------~~ 257 (687)
.+-..|+-+++....+.+.. .....+.|.+|-.||.+-|.++..-..+ + .|. ..
T Consensus 159 ~lsngLr~~~~ekq~~~l~~q~~ss~~~~~~~KlL~glr~y~nk~fk~i~~~dnrkl~~rt~kq~~~s~f~~~i~en~s~ 238 (650)
T COG5535 159 MLSNGLRFNRLEKQIKYLDNQNESSISESTYKKLLEGLRFYGNKPFKNIGVEDNRKLAKRTMKQMESSDFWEEIFENYSL 238 (650)
T ss_pred hhhcccchhhHHHhHHhhccccccccchhHHHHHHHhHHHHhhhhhHHhhhcccHHHHHHHHHHHHhccchHHHHhhcch
Confidence 99888998888887665542 1234788888999999999955311100 0 111 12
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHHHhcCCceeEEEeeccccCCcccccccCCCCCCCCCCCCccCCCCccccCccccccCC
Q 005629 258 LAHALESREGTPEEIAALSVALFRALKLTTRFVSILDVASLKPEADKNVSSNQDSSRVGGGIFNAPTLMVAKPEEVLASP 337 (687)
Q Consensus 258 l~~~l~~~~GSrD~gAqLF~ALLRALgL~aRLV~SLqpl~lk~~~~k~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~p 337 (687)
+...+.+..|+||-.+|-|+|++|+|.+.+||.++|||..|--.
T Consensus 239 ~~~~~~~~~~~~D~~vrgf~a~~r~~~v~~Rli~~l~~P~Fs~~------------------------------------ 282 (650)
T COG5535 239 EVVPLKSADGRRDADVRGFEAEHRILNVFARLIASLIQPVFSNN------------------------------------ 282 (650)
T ss_pred HHhhHhhccCCCcchhHHHHHHHHHhccchhhhccccCcccccc------------------------------------
Confidence 34556678899999999999999999999999998888655310
Q ss_pred CCcccccccccccccCCCCCCCCCCCCCCCCCCCCCCCCccccccCCCCCCCCccccCCCcccCCCcchhhhhhccCChH
Q 005629 338 VKSFSCDKKENVCETSSKGSPECKYSSPKSNNTQSKKSPVSCELSSGNLDPSSSMACSDISEACHPKEKSQALKRKGDLE 417 (687)
Q Consensus 338 ~k~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~s~~~~~s~~~~~~~~~~~~~~~~~s~~e~~~s~~~~~~~rR~g~~~ 417 (687)
+. .+.+ ++ +
T Consensus 283 ----------------------------------~~------------~~~~--------~e-~---------------- 291 (650)
T COG5535 283 ----------------------------------SD------------LDVL--------SE-G---------------- 291 (650)
T ss_pred ----------------------------------cc------------cccC--------cc-c----------------
Confidence 00 0000 00 0
Q ss_pred HHHHHHHHhhhccccccCCcccccccccCCCCCCccccccccccccCCCCccccCcccccCCCCCCCCceEEEEEeCcCC
Q 005629 418 FEMQLEMALSATNVATSKSNICSDVKDLNSNSSTVLPVKRLKKIESGESSTSCLGISTAVGSRKVGAPLYWAEVYCSGEN 497 (687)
Q Consensus 418 fe~q~~~al~~t~~~~~~s~~~~~~~~~~~~~~~~~~~k~~kk~~~~~s~~~~~~~s~~~~~~~~~~P~fW~EV~~~~~~ 497 (687)
.. .+..++.||.||+|||+-.
T Consensus 292 ---------------------------------------~~------------------~~iD~l~~p~fw~ev~~~~-- 312 (650)
T COG5535 292 ---------------------------------------LL------------------EYIDSLEYPGFWGEVVDKF-- 312 (650)
T ss_pred ---------------------------------------cc------------------eeccchhcchHHHHHHHHH--
Confidence 00 0123456999999999865
Q ss_pred CCCceEEEecccC-cc-c-cchhhHHhHhhcCCCeeEEEEEcCCC-cccchhhhhhhhhhhccccC-----CHHHHHHHH
Q 005629 498 LTGKWVHVDAANA-II-D-GEQKVEAAAAACKTSLRYIVAFAGCG-AKDVTRRYCMKWYRIASKRV-----NSAWWDAVL 568 (687)
Q Consensus 498 ~~~kWI~VDpv~~-~V-~-~~~~~Ep~~~~~~~~m~YVVAfd~dG-akDVT~RY~~~~~~~~r~Rv-----~~~Ww~~~L 568 (687)
.++||+|||++- +| . -...|||.+..-.+.|.||+||+.++ ++|||.||+-..+...+ |+ ...||...+
T Consensus 313 -~~kwv~vdp~~l~~v~~~l~~kfepa~~~~~n~~~~V~ayd~~~y~~DVt~RY~d~~~s~~k-ritk~~fs~qy~~r~~ 390 (650)
T COG5535 313 -EKKWVFVDPVRLYIVYSELKCKFEPAASIHLNIMEYVGAYDACVYVKDVTLRYRDQSYSFLK-RITKHLFSVQYFVRQF 390 (650)
T ss_pred -HhceEecccchhhhhhhhhhheechhHHHHHHHHHHhhhhccCccchhHHHHHHHHHhhhhh-hhhccchHHHHHHHHh
Confidence 589999999973 32 2 35679995444567899999999998 99999999985444323 32 368999999
Q ss_pred HHhhccccCCCCCCcccccccCccccccChhHHHHHHHHhccCCCCCChhhhhcCchhHhhhhhhcccccCCCCCcc-ee
Q 005629 569 APLRELESGATGDLNVESSAKDSFVADRNSLEDMELETRALTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPIL-GF 647 (687)
Q Consensus 569 ~~~~~~~~~~~~~~~i~a~~~~~~~~~rD~~Ed~eL~~~~~~epmP~ti~~fKnHP~YvLeRhL~r~E~I~P~a~~~-G~ 647 (687)
..+.... .+ .+.+.+|+..+-+....+++|+|+++||+||+|||||||+++|||+|+++++ ++
T Consensus 391 ~~l~~~k---------------~~-~~~e~i~~~~~L~~~~~~~iPkSvqdlK~HP~FVle~~Lk~~q~ikp~ak~~~~~ 454 (650)
T COG5535 391 PGLGKCK---------------EA-SDEEAIEDFDDLDERRSEGIPKSVQDLKRHPKFVLESHLKWNQAIKPGAKPGFTL 454 (650)
T ss_pred cccCccc---------------cc-ccHHHHHhHHHHhhcccccCCccHHHhccCCceeeHhhhhhhhhhccCCccceee
Confidence 8887652 11 4456677776555666899999999999999999999999999999998765 56
Q ss_pred ecc----eeeeecCCccccccHHHHHHhccccCCCCeeecccc
Q 005629 648 CSG----HAVYPRSCVQTLKTKERWLREALQVKANEVPVKVCS 686 (687)
Q Consensus 648 ~~g----E~VY~R~dV~~LkS~e~W~k~GR~VK~gE~P~K~Vk 686 (687)
++| |+||+|.||+.|+|+++||++||+|++|+||+|+||
T Consensus 455 tkGk~~vE~VY~RrdVv~lkS~e~wy~~GRvIkpgaqP~K~vK 497 (650)
T COG5535 455 TKGKNSVEAVYLRRDVVRLKSAEQWYRMGRVIKPGAQPLKIVK 497 (650)
T ss_pred ecCCCccchhhhhhhHHhhcCHHHHHhcCcccCCCCchHHHHH
Confidence 678 999999999999999999999999999999999997
No 4
>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=99.90 E-value=1.9e-24 Score=206.45 Aligned_cols=109 Identities=33% Similarity=0.616 Sum_probs=81.0
Q ss_pred CCCCCCCceEEEEEeCcCCCCCceEEEecccCccccchhhHHhHhhcCCCeeEEEEEcCCC-cccchhhhhhh-hhh-hc
Q 005629 479 SRKVGAPLYWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCG-AKDVTRRYCMK-WYR-IA 555 (687)
Q Consensus 479 ~~~~~~P~fW~EV~~~~~~~~~kWI~VDpv~~~V~~~~~~Ep~~~~~~~~m~YVVAfd~dG-akDVT~RY~~~-~~~-~~ 555 (687)
+.++.+|+||+|||++. .++||||||+++.+.....+||+...+.++|+|||||+++| |+|||+||+++ |+. +.
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 56788999999999986 48999999999855577788998778899999999999988 99999999999 554 46
Q ss_pred cccCC-----HHHHHHHHHHhhccccCCCCCCcccccccCccccccChhHHHHHH
Q 005629 556 SKRVN-----SAWWDAVLAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELE 605 (687)
Q Consensus 556 r~Rv~-----~~Ww~~~L~~~~~~~~~~~~~~~i~a~~~~~~~~~rD~~Ed~eL~ 605 (687)
++|+. ..||..+|++|+++.. ..+.+|.+||.||+
T Consensus 106 r~R~~~~~~~~~W~~~~l~~~~~~~~---------------~~~~~d~~Ed~el~ 145 (145)
T PF03835_consen 106 RLRVDRSYEEEDWWEKVLRPYNRPRR---------------DRTIRDKKEDEELH 145 (145)
T ss_dssp GGSGGGSHHHHHHHHHHHHHH--S------------------H--HHHHHHHHH-
T ss_pred cccCCccccHHHHHHHHHHHHhcccc---------------cccchHHHHHhhcC
Confidence 68998 8999999999997632 12257899999985
No 5
>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=9.3e-21 Score=154.13 Aligned_cols=52 Identities=42% Similarity=0.714 Sum_probs=40.7
Q ss_pred ccCCCCCChhhhhcCchhHhhhhhhcccccCCCCCcceeecc----eeeeecCCcc
Q 005629 609 LTEPLPTNQQAYKNHQLYVIERWLNKYQILYPKGPILGFCSG----HAVYPRSCVQ 660 (687)
Q Consensus 609 ~~epmP~ti~~fKnHP~YvLeRhL~r~E~I~P~a~~~G~~~g----E~VY~R~dV~ 660 (687)
.+|+||+|+++|||||+|||||||++||+|+|+++++|+|+| |+||+|+||+
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 378999999999999999999999999999999999999999 9999999996
No 6
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=99.76 E-value=1.1e-18 Score=187.57 Aligned_cols=109 Identities=25% Similarity=0.384 Sum_probs=83.0
Q ss_pred eEEEEEeCcCCCCCceEEEecccCccccchhhHHhHhhcCCCeeEEEEEcCCCcccchhhhhhhhhhh--ccccCCHHHH
Q 005629 487 YWAEVYCSGENLTGKWVHVDAANAIIDGEQKVEAAAAACKTSLRYIVAFAGCGAKDVTRRYCMKWYRI--ASKRVNSAWW 564 (687)
Q Consensus 487 fW~EV~~~~~~~~~kWI~VDpv~~~V~~~~~~Ep~~~~~~~~m~YVVAfd~dGakDVT~RY~~~~~~~--~r~Rv~~~Ww 564 (687)
+|+|||++.+ ++|+||||+.+++|+|.+||. +|.+.|.|||||+.||+.|||-||+.+|... .|.++.+.-+
T Consensus 251 VWtEvYS~~q---qRW~HvDpcE~v~D~PllYe~---GW~KklsY~iafgkD~VvDVT~RYi~~h~e~~~~R~~~~E~~l 324 (500)
T KOG0909|consen 251 VWTEVYSNAQ---QRWVHVDPCENVFDKPLLYEI---GWGKKLSYCIAFGKDGVVDVTWRYILDHKENLLPRDLCKESVL 324 (500)
T ss_pred hhHHhhhhhh---heeEeecccccccccceeeec---ccCcccceEEEeccCceEeeehhhhccchhhccchhhcchHHH
Confidence 8999999865 899999999999999999875 6899999999999999999999999998864 3456777888
Q ss_pred HHHHHHhhccccCCCCCCcccccccCccccccChhHHHHHHHH
Q 005629 565 DAVLAPLRELESGATGDLNVESSAKDSFVADRNSLEDMELETR 607 (687)
Q Consensus 565 ~~~L~~~~~~~~~~~~~~~i~a~~~~~~~~~rD~~Ed~eL~~~ 607 (687)
..+|..++...+.. -+ . ..+..+..||..|..||...
T Consensus 325 ~~~l~~in~~rr~~--lt---~-~r~~~L~~rd~~e~~El~~~ 361 (500)
T KOG0909|consen 325 QQTLQFINKRRRYS--LT---D-DRKKELAQRDEREQIELIRG 361 (500)
T ss_pred HHHHHHHHHHHHhh--cC---h-HHHHHHHhhhHHHHHHHHhc
Confidence 88888877542100 00 0 01223445566677776543
No 7
>TIGR00605 rad4 DNA repair protein rad4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.78 E-value=1.8e-10 Score=133.89 Aligned_cols=147 Identities=23% Similarity=0.173 Sum_probs=114.4
Q ss_pred CCCeEEEEecCCcccccc----------c-cccCHHHHHHHHHHHHHHHHHHHHhhHHHHhhcCcHHHHHHHhhcCchhh
Q 005629 149 IKGVTIEFDAADSVTKKP----------V-RRASAEDKELAELVHKVHLLCLLARGRLIDSVCDDPLIQASLLSLLPSYL 217 (687)
Q Consensus 149 ~~~leI~l~~~~~~kK~~----------~-RR~s~~eKe~r~~~HKvHLLCLLah~~~RN~wcnd~~lqa~llSlLP~~~ 217 (687)
.++++||++++++.+|+. + |++.++.+.+..++|+|||+|+|+.+..+|+.|+++++.+.. +++|..+
T Consensus 13 ~~~~~~e~~~~~~~~~r~~~~~~~~~~~~~~~~~r~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~d~~~~~-~~~~~~~ 91 (713)
T TIGR00605 13 IRKVENEKEAEKQPKSRRRKVRRENEPSLRRRKKRFKTGLNELPHEVVLMCNLDSTHSDDRVVSVPDSLSVS-EEIPSRE 91 (713)
T ss_pred HHHHHhhhhcchhhhhhcchhhhhhhhhHhhhhhhhhccccccCcceEEEEEeccccccccccccccccccc-ccCCccc
Confidence 467889998887743332 2 335578888999999999999999999999999999888776 9999998
Q ss_pred hcccCcchhhHhhhhHHHHHhhhceeeccCCCcccchHHHHHHHHHHhcCCH-----HHHHHHHHHHHHhcCCceeEEEe
Q 005629 218 LKISEVSKLTANALSPIVSWFHDNFHVRSSVSTRRSFHSDLAHALESREGTP-----EEIAALSVALFRALKLTTRFVSI 292 (687)
Q Consensus 218 ~~~~~~~~~~~~~L~~L~~Wf~~~F~vt~~~~~~~~~~~~l~~~l~~~~GSr-----D~gAqLF~ALLRALgL~aRLV~S 292 (687)
.... ...+...+|..++.||...|.+++...... ..++...+++...+. ....|+|..||+.+++.+|++.+
T Consensus 92 ~~~~-~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~r~~~~~~eR~~R~~iH~~~ll~ll~h~~~RN~w~ 168 (713)
T TIGR00605 92 EDYD-SREFEDVYLSNLVAEFETISVEIKPSSKAE--SDDDAETLSRNVCSNEARKDRKYIHILYLLCLMVHLFTRNEWS 168 (713)
T ss_pred cccc-hhhhhhhhhcccccccCcccccccccchhh--hhhHHHHHHHhhccHHHHHHHHHHHHHHHHHHhhhhHhhhhhh
Confidence 7553 256778889999999999999986443222 233445555555543 45899999999999999999999
Q ss_pred eccccCCc
Q 005629 293 LDVASLKP 300 (687)
Q Consensus 293 Lqpl~lk~ 300 (687)
+|| +...
T Consensus 169 n~~-~~~~ 175 (713)
T TIGR00605 169 LSA-PLKS 175 (713)
T ss_pred CCh-HHHh
Confidence 997 4443
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=98.29 E-value=1.9e-07 Score=78.00 Aligned_cols=26 Identities=46% Similarity=0.730 Sum_probs=19.6
Q ss_pred cccHHHHHHhccccCCCCeeeccccC
Q 005629 662 LKTKERWLREALQVKANEVPVKVCSG 687 (687)
Q Consensus 662 LkS~e~W~k~GR~VK~gE~P~K~Vkg 687 (687)
|||+++|+++||+||+||+|+|+|+.
T Consensus 1 LkS~e~W~r~GR~Vk~gE~P~K~vk~ 26 (64)
T PF10404_consen 1 LKSAEKWYREGRVVKPGEQPYKVVKS 26 (64)
T ss_dssp -BEHHHHHTTTEEE-TT---SEEEE-
T ss_pred CCCHHHHHHcCCccCCCCceeeEEec
Confidence 79999999999999999999999973
No 9
>KOG2179 consensus Nucleotide excision repair complex XPC-HR23B, subunit XPC/DPB11 [Replication, recombination and repair]
Probab=97.29 E-value=0.00019 Score=82.92 Aligned_cols=129 Identities=15% Similarity=0.197 Sum_probs=91.9
Q ss_pred CHHHHHHHHHHHHHHHHHHHHhhHHHHhhcCcHHHHHHHhhcCchh-hhcccCcc-------hhhHhhhhH--HHHHhhh
Q 005629 171 SAEDKELAELVHKVHLLCLLARGRLIDSVCDDPLIQASLLSLLPSY-LLKISEVS-------KLTANALSP--IVSWFHD 240 (687)
Q Consensus 171 s~~eKe~r~~~HKvHLLCLLah~~~RN~wcnd~~lqa~llSlLP~~-~~~~~~~~-------~~~~~~L~~--L~~Wf~~ 240 (687)
+..++.+|...|-+|++|++.||.+||+|.+....--.+.++++++ ...+.+.. .....+++. +-+||..
T Consensus 141 a~~~~s~r~~~~~l~~~~~~~~g~irt~~~~~~~~~~k~~~~~sEse~~~~~k~~e~~~~~~~~l~~~~~~~s~~k~~~~ 220 (669)
T KOG2179|consen 141 AFKNKSRRKTLHGLVLVCLSKYGKIRTNFLRKNYADLKNENLISESELKKVAKNQELFSGSRPLLLKGVEDASIRKKWKS 220 (669)
T ss_pred HhHhhhhhhhHHHHHHHHHHHhcccccchhhhhhhhcccccCCcchhccchhhhhhhhccCchHhhhhhhhhhhhhhhcC
Confidence 4788999999999999999999999999999866666667777776 22222211 122455544 7789999
Q ss_pred ceeeccCCC----------ccc--ch--HH---HHHHHHHHhcCCHHHHHHHHHHHHHhcCCceeEEEeeccccCCc
Q 005629 241 NFHVRSSVS----------TRR--SF--HS---DLAHALESREGTPEEIAALSVALFRALKLTTRFVSILDVASLKP 300 (687)
Q Consensus 241 ~F~vt~~~~----------~~~--~~--~~---~l~~~l~~~~GSrD~gAqLF~ALLRALgL~aRLV~SLqpl~lk~ 300 (687)
.+++.+..- .+. ++ .+ ..+..+..-.|+.|+.+|+|.+|+|+.+ .+|+..+|||..+--
T Consensus 221 ~~k~~~~~~~~~s~~~~~~~d~~~~~~~~~~~p~~~a~i~~~~g~~d~~~q~~~~l~~~~n-~~r~~~~l~p~~~~~ 296 (669)
T KOG2179|consen 221 KMKNVSSGTEKLSKELSDGADEASKPYLLEAVPAHRADIRPNKGDADVSSQIIHALLRTPN-NARLAPSLQPPVFSN 296 (669)
T ss_pred CccccCcchhhhcccccCCCccccchhhhhcCcHHHhhhccCCCCcchHHHHHHHHhhccc-hhhcccccCCcchhh
Confidence 998876411 011 11 00 1122333337899999999999999999 999999999987764
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=96.54 E-value=0.00065 Score=60.85 Aligned_cols=62 Identities=31% Similarity=0.415 Sum_probs=44.0
Q ss_pred HhhhhHHHHHhhhceeeccCCCcccchHHHHHHHHHHhcCCHHHHHHHHHHHHHhcCCceeEEE
Q 005629 228 ANALSPIVSWFHDNFHVRSSVSTRRSFHSDLAHALESREGTPEEIAALSVALFRALKLTTRFVS 291 (687)
Q Consensus 228 ~~~L~~L~~Wf~~~F~vt~~~~~~~~~~~~l~~~l~~~~GSrD~gAqLF~ALLRALgL~aRLV~ 291 (687)
...++.|..|++.+|+......... ......++++..|+=...|.||++|||++||+||+|.
T Consensus 15 ~~~~~~i~~~v~~~~~y~~~~~~~~--~~~~~~~l~~~~G~C~~~a~l~~allr~~Gipar~v~ 76 (113)
T PF01841_consen 15 LEKAKAIYDWVRSNIRYDDPNYSPG--PRDASEVLRSGRGDCEDYASLFVALLRALGIPARVVS 76 (113)
T ss_dssp HCCCCCCCCCCCCCCCEC-TCCCCC--CTTHHHHHHCEEESHHHHHHHHHHHHHHHT--EEEEE
T ss_pred HHHHHHHHHHHHhCcEEeCCCCCCC--CCCHHHHHHcCCCccHHHHHHHHHHHhhCCCceEEEE
Confidence 3455668889999998882111111 1124567778889999999999999999999999996
No 11
>COG5535 RAD4 DNA repair protein RAD4 [DNA replication, recombination, and repair]
Probab=95.73 E-value=0.0045 Score=70.59 Aligned_cols=162 Identities=13% Similarity=0.006 Sum_probs=104.8
Q ss_pred CCCCCCCccccCCCCCCCCCCCCCCCCCCeEEEEecCCccccccccccCHHHHHHHHHHHHHHHHHHHHh-hHHHHhhcC
Q 005629 123 EEMYDSDWEDGSIPVACSKENHPESDIKGVTIEFDAADSVTKKPVRRASAEDKELAELVHKVHLLCLLAR-GRLIDSVCD 201 (687)
Q Consensus 123 deddd~dWEdV~~~~~~~~~~~p~~~~~~leI~l~~~~~~kK~~~RR~s~~eKe~r~~~HKvHLLCLLah-~~~RN~wcn 201 (687)
+++.+++||.+.++ ++++.|++.... .+..+ -....+...++..|..|++|+=.| ..-||.||+
T Consensus 43 ~~ek~i~e~~~el~-------------gd~~vtvn~~~r-drs~v-~k~sdd~neklqssq~hl~~~~f~~l~s~nk~~d 107 (650)
T COG5535 43 DEEKDIDEEPVELD-------------GDLTVTVNNIRR-DRSKV-SKYSDDHNEKLQSSQLHLIMIPFMLLKSRNKWID 107 (650)
T ss_pred hhccccccCCccCC-------------Ccceeeeccccc-ccccc-ccccchhhHHhccchhhhhcchhhhhcCcCeecc
Confidence 34455899876654 457777776521 11111 013577788889999999999999 555999999
Q ss_pred cHHHHHHHhhcCchhhhcccCcc-----h--hhHhhhh----HHHHHhhhceeeccCCCcc----cch---------HHH
Q 005629 202 DPLIQASLLSLLPSYLLKISEVS-----K--LTANALS----PIVSWFHDNFHVRSSVSTR----RSF---------HSD 257 (687)
Q Consensus 202 d~~lqa~llSlLP~~~~~~~~~~-----~--~~~~~L~----~L~~Wf~~~F~vt~~~~~~----~~~---------~~~ 257 (687)
|..|.-.+....|........-. . ++.-.|- -+..||+. +++++.... .-+ ...
T Consensus 108 derLn~~~k~s~pk~~~~s~~d~s~rks~him~~tcll~~g~irn~W~rs--k~lsngLr~~~~ekq~~~l~~q~~ss~~ 185 (650)
T COG5535 108 DERLNRRLKRSVPKLGGKSFKDWSVRKSAHIMDSTCLLLLGFIRNLWFRS--KMLSNGLRFNRLEKQIKYLDNQNESSIS 185 (650)
T ss_pred chhhceeeeccCcccccccccCcchhhhHHHHHHHHHHHHHHHHHHHHHh--hhhhcccchhhHHHhHHhhccccccccc
Confidence 99998777777774433222111 1 1111111 24678888 555432110 000 012
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHHHhcCCceeEEEeeccccCCcc
Q 005629 258 LAHALESREGTPEEIAALSVALFRALKLTTRFVSILDVASLKPE 301 (687)
Q Consensus 258 l~~~l~~~~GSrD~gAqLF~ALLRALgL~aRLV~SLqpl~lk~~ 301 (687)
++...+-+.|.|+-|.+.|..+.+-..-..+++..+|.+++...
T Consensus 186 ~~~~~KlL~glr~y~nk~fk~i~~~dnrkl~~rt~kq~~~s~f~ 229 (650)
T COG5535 186 ESTYKKLLEGLRFYGNKPFKNIGVEDNRKLAKRTMKQMESSDFW 229 (650)
T ss_pred hhHHHHHHHhHHHHhhhhhHHhhhcccHHHHHHHHHHHHhccch
Confidence 44555566899999999999999999999999988888876653
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=95.69 E-value=0.0066 Score=49.75 Aligned_cols=30 Identities=50% Similarity=0.633 Sum_probs=26.7
Q ss_pred HHHhcCCHHHHHHHHHHHHHhcCCceeEEE
Q 005629 262 LESREGTPEEIAALSVALFRALKLTTRFVS 291 (687)
Q Consensus 262 l~~~~GSrD~gAqLF~ALLRALgL~aRLV~ 291 (687)
++...|+-.+.|.||++|||++|++||+|.
T Consensus 2 ~~~~~G~C~~~a~l~~~llr~~GIpar~v~ 31 (68)
T smart00460 2 LKTKYGTCGEFAALFVALLRSLGIPARVVS 31 (68)
T ss_pred CcccceeeHHHHHHHHHHHHHCCCCeEEEe
Confidence 345678888999999999999999999996
No 13
>COG1305 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]
Probab=93.05 E-value=0.11 Score=53.95 Aligned_cols=61 Identities=21% Similarity=0.334 Sum_probs=45.0
Q ss_pred HhhhhHHHHHhhhceeeccCCCcccchHHHHHHHHHHhcCCHHHHHHHHHHHHHhcCCceeEEE
Q 005629 228 ANALSPIVSWFHDNFHVRSSVSTRRSFHSDLAHALESREGTPEEIAALSVALFRALKLTTRFVS 291 (687)
Q Consensus 228 ~~~L~~L~~Wf~~~F~vt~~~~~~~~~~~~l~~~l~~~~GSrD~gAqLF~ALLRALgL~aRLV~ 291 (687)
...+..+..|+...|.-+....... ..-..+++...|+=..-|+||++|||++||.||+|.
T Consensus 159 ~~~~~~~~~~~~~~~~y~~~~~~~~---~~~~~~l~~~~G~C~d~a~l~val~Ra~GIpAR~V~ 219 (319)
T COG1305 159 REKAAALFDYVNSKIRYSPGPTPVT---GSASDALRLGRGVCRDFAHLLVALLRAAGIPARYVS 219 (319)
T ss_pred HHHHHHHHHHHhhcceeecCCCCCC---CCHHHHHHhCCcccccHHHHHHHHHHHcCCcceeee
Confidence 4555678889988887775431111 122355666689888999999999999999999995
No 14
>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=87.13 E-value=0.66 Score=37.81 Aligned_cols=21 Identities=48% Similarity=0.846 Sum_probs=18.2
Q ss_pred CCCceEEEEEeCcCCCCCceEEEecc
Q 005629 483 GAPLYWAEVYCSGENLTGKWVHVDAA 508 (687)
Q Consensus 483 ~~P~fW~EV~~~~~~~~~kWI~VDpv 508 (687)
..++.|+|||.. ++|+.+||.
T Consensus 47 ~~~H~W~ev~~~-----~~W~~~D~~ 67 (68)
T smart00460 47 WEAHAWAEVYLE-----GGWVPVDPT 67 (68)
T ss_pred CCcEEEEEEEEC-----CCeEEEeCC
Confidence 478999999985 699999995
No 15
>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=86.85 E-value=0.55 Score=41.86 Aligned_cols=20 Identities=40% Similarity=0.963 Sum_probs=17.2
Q ss_pred CCceEEEEEeCcCCCCCceEEEec
Q 005629 484 APLYWAEVYCSGENLTGKWVHVDA 507 (687)
Q Consensus 484 ~P~fW~EV~~~~~~~~~kWI~VDp 507 (687)
..+.|+|||.+. ++||++||
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 458999999953 79999998
No 16
>PF13369 Transglut_core2: Transglutaminase-like superfamily
Probab=67.61 E-value=6.7 Score=37.98 Aligned_cols=36 Identities=36% Similarity=0.423 Sum_probs=33.1
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHHHHhcCCceeEEE
Q 005629 256 SDLAHALESREGTPEEIAALSVALFRALKLTTRFVS 291 (687)
Q Consensus 256 ~~l~~~l~~~~GSrD~gAqLF~ALLRALgL~aRLV~ 291 (687)
..+-.+|+++.|..-.++.||++++|.|||++..|.
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 17
>COG1305 Transglutaminase-like enzymes, putative cysteine proteases [Amino acid transport and metabolism]
Probab=40.62 E-value=19 Score=37.35 Aligned_cols=25 Identities=40% Similarity=0.860 Sum_probs=20.5
Q ss_pred CCceEEEEEeCcCCCCCceEEEecccCcc
Q 005629 484 APLYWAEVYCSGENLTGKWVHVDAANAII 512 (687)
Q Consensus 484 ~P~fW~EV~~~~~~~~~kWI~VDpv~~~V 512 (687)
..+.|+|||.++ ..|+++||-.+..
T Consensus 239 ~~Haw~ev~~~~----~gW~~~Dpt~~~~ 263 (319)
T COG1305 239 DAHAWAEVYLPG----RGWVPLDPTNGLL 263 (319)
T ss_pred ccceeeeeecCC----CccEeecCCCCCc
Confidence 568999999984 2699999998643
No 18
>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=33.05 E-value=42 Score=34.40 Aligned_cols=23 Identities=30% Similarity=0.278 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHHhcCCceeEEE
Q 005629 269 PEEIAALSVALFRALKLTTRFVS 291 (687)
Q Consensus 269 rD~gAqLF~ALLRALgL~aRLV~ 291 (687)
==++..||.+||++||+++++|.
T Consensus 49 C~elN~lf~~lL~~lGf~v~~~~ 71 (240)
T PF00797_consen 49 CFELNGLFYWLLRELGFDVTLVS 71 (240)
T ss_dssp HHHHHHHHHHHHHHCT-EEEEEE
T ss_pred hHHHHHHHHHHHHHCCCeEEEEE
Confidence 35788999999999999999996
No 19
>PF11702 DUF3295: Protein of unknown function (DUF3295); InterPro: IPR021711 This family is conserved in fungi but the function is not known.
Probab=32.91 E-value=19 Score=41.79 Aligned_cols=11 Identities=45% Similarity=0.897 Sum_probs=8.7
Q ss_pred CCCCCCCCccc
Q 005629 122 GEEMYDSDWED 132 (687)
Q Consensus 122 ~deddd~dWEd 132 (687)
||||||+||||
T Consensus 307 dDDDDssDWED 317 (507)
T PF11702_consen 307 DDDDDSSDWED 317 (507)
T ss_pred cCCccchhhhh
Confidence 46778889987
No 20
>PRK10941 hypothetical protein; Provisional
Probab=27.96 E-value=69 Score=34.34 Aligned_cols=63 Identities=17% Similarity=0.218 Sum_probs=44.9
Q ss_pred hhhhHHHHHhhhceeeccCCCcccch-HHHHHHHHHHhcCCHHHHHHHHHHHHHhcCCceeEEE
Q 005629 229 NALSPIVSWFHDNFHVRSSVSTRRSF-HSDLAHALESREGTPEEIAALSVALFRALKLTTRFVS 291 (687)
Q Consensus 229 ~~L~~L~~Wf~~~F~vt~~~~~~~~~-~~~l~~~l~~~~GSrD~gAqLF~ALLRALgL~aRLV~ 291 (687)
..|..|..||-+...-..+...=... ..-+-.+++++.|..-.++.||+.|+|.|||+..-|.
T Consensus 57 ~~l~~L~~~fy~~lgF~Gn~~~Y~~p~ns~L~~VL~~R~G~PisL~il~l~iA~~lglp~~gV~ 120 (269)
T PRK10941 57 EQLEKLIALFYGEWGFGGASGVYRLSDALWLDKVLKTRQGSAVSLGAILLWIANRLDLPLMPVI 120 (269)
T ss_pred HHHHHHHHHHHHHhCCCCCccccCCchhhHHHHHHHccCCCcHHHHHHHHHHHHHcCCCeeeee
Confidence 34667777776655444221110011 2346789999999999999999999999999999984
No 21
>PF14402 7TM_transglut: 7 transmembrane helices usually fused to an inactive transglutaminase
Probab=22.11 E-value=50 Score=36.15 Aligned_cols=28 Identities=25% Similarity=0.414 Sum_probs=22.1
Q ss_pred CCCceEEEEEeCcCCCCCceEEEecccCccccc
Q 005629 483 GAPLYWAEVYCSGENLTGKWVHVDAANAIIDGE 515 (687)
Q Consensus 483 ~~P~fW~EV~~~~~~~~~kWI~VDpv~~~V~~~ 515 (687)
..+..|+|||+. ++|+.+||..+....|
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 367899999985 5899999998754433
No 22
>TIGR01544 HAD-SF-IE haloacid dehalogenase superfamily, subfamily IE hydrolase, TIGR01544. This group of sequences was found during searches for members of the haloacid dehalogenase (HAD) superfamily. All of the conserved catalytic motifs are found. The placement of the variable domain between motifs 1 and 2 indicates membership in subfamily I of the superfamily, but these sequences are sufficiently different from any of the branches (IA, TIGR01493, TIGR01509, TIGR01549; IB, TIGR01488; IC, TIGR01494; ID, TIGR01658; IF TIGR01545) of that subfamily as to constitute a separate branch to now be called IE. Considering that the closest identifiable hit outside of the noise range is to a phosphoserine phosphatase, this group may be considered to be most closely allied to subfamily IB.
Probab=20.31 E-value=1.7e+02 Score=31.56 Aligned_cols=100 Identities=11% Similarity=0.112 Sum_probs=63.7
Q ss_pred HHHHhhHHHHhhcCcHHHHHHHhhcCchhhhcccCcchhh-HhhhhHHHHHhhhceeeccCCCcccchHHHHHHHHHHhc
Q 005629 188 CLLARGRLIDSVCDDPLIQASLLSLLPSYLLKISEVSKLT-ANALSPIVSWFHDNFHVRSSVSTRRSFHSDLAHALESRE 266 (687)
Q Consensus 188 CLLah~~~RN~wcnd~~lqa~llSlLP~~~~~~~~~~~~~-~~~L~~L~~Wf~~~F~vt~~~~~~~~~~~~l~~~l~~~~ 266 (687)
|.-.||.+.|...-.++..+.+..|.-.+.---.. +.+. ..-+..++.||...-.+....... .+.+..+++...
T Consensus 44 ~~s~~~~~~~~~~~~~~~~~~~~~l~~~Y~PiE~d-~~~~~~eK~~~m~eWw~k~~~l~~~~~~~---~e~i~~~v~~~~ 119 (277)
T TIGR01544 44 CPTCHGIFDNCKLLTDECRKKLLQLKEKYYPIEVD-PVLTVEEKYPYMVEWWTKSHGLLVQQAFP---KAKIKEIVAESD 119 (277)
T ss_pred CcchHhHHhhCCCCCHHHHHHHHHHHhhccceecC-CCCChHHhhhHHHHHHHHHHHHHhcCCCC---HHHHHHHHhhcC
Confidence 56689999998777788877777665433110000 1221 244567899999987766433322 234555554333
Q ss_pred CCHHHHHHHHHHHHHhcCCceeEEE
Q 005629 267 GTPEEIAALSVALFRALKLTTRFVS 291 (687)
Q Consensus 267 GSrD~gAqLF~ALLRALgL~aRLV~ 291 (687)
=.-..|+.=|+..|+..|++.=+|.
T Consensus 120 l~l~pG~~efl~~L~~~GIpv~IvS 144 (277)
T TIGR01544 120 VMLKDGYENFFDKLQQHSIPVFIFS 144 (277)
T ss_pred CccCcCHHHHHHHHHHCCCcEEEEe
Confidence 3456788889999999999988875
Done!