BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 001045
(1176 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1X9N|A Chain A, Crystal Structure Of Human Dna Ligase I Bound To
5'-Adenylated, Nicked Dna
Length = 688
Score = 320 bits (820), Expect = 3e-87, Method: Compositional matrix adjust.
Identities = 181/498 (36%), Positives = 275/498 (55%), Gaps = 24/498 (4%)
Query: 687 MDPTLVSLPPEKYDPIEHACWSSGQPAPYIHLARTFDLVEAERGKIKAMSMLCNMFRSLL 746
+DP+ + Y P+E ACW GQ PY+ +ARTF+ +E +++ + L N+ RS++
Sbjct: 30 LDPSGYNPAKNNYHPVEDACWKPGQKVPYLAVARTFEKIEEVSARLRXVETLSNLLRSVV 89
Query: 747 ALSPDDVLPAVYLCTNKIASNHENIELNIGGSLVTSAIEEACGTNRSKIRDMYNRLGDLG 806
ALSP D+LP +YL N + + +EL +G ++ A+ +A G +R GD+G
Sbjct: 90 ALSPPDLLPVLYLSLNHLGPPQQGLELGVGDGVLLKAVAQATGRQLESVRAEAAEKGDVG 149
Query: 807 DVAQECRQTQXXXXXXXXXXIKDVYSMLCKISVQTGSGSTARKKSLIVNLMCSCREKEMK 866
VA+ R TQ V+S I+ TGS STA+K +I L +CR E +
Sbjct: 150 LVAENSRSTQRLXLPPPPLTASGVFSKFRDIARLTGSASTAKKIDIIKGLFVACRHSEAR 209
Query: 867 FLVRTLVRNLRIGAMMRTILPALAQAVVMN-SSLEF------SHEGK-MENLKEKLQSLS 918
F+ R+L LR+G +++L AL+QAV + EF + +GK E K L+
Sbjct: 210 FIARSLSGRLRLGLAEQSVLAALSQAVSLTPPGQEFPPAXVDAGKGKTAEARKTWLEEQG 269
Query: 919 AAAVEAYNXXXXXXXXXXXXMNKGIGFSASTLSMVPGVPIKPMLAKITNGVPQVLKLFQN 978
+ + + G+ + PG+P+KP LA T G+ +VLK F+
Sbjct: 270 XILKQTFCEVPDLDRIIPVLLEHGLERLPEHCKLSPGIPLKPXLAHPTRGISEVLKRFEE 329
Query: 979 KAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDETTSRFPDLISIINEFCKPAAGTFILDA 1038
AFTCEYKYDGQRAQIH L G V+IFSRN ++ T ++PD+IS I + P+ +FILD
Sbjct: 330 AAFTCEYKYDGQRAQIHALEGGEVKIFSRNQEDNTGKYPDIISRIPKIKLPSVTSFILDT 389
Query: 1039 EVVAIDRKNGCKIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTL 1098
E VA DR+ +I FQ L++R+R D+ ++V +C++ FD+++ NGE L+ L
Sbjct: 390 EAVAWDREKK-QIQPFQVLTTRKRKEVDA----SEIQVQVCLYAFDLIYLNGESLVREPL 444
Query: 1099 RQRRKYLKDLFYDEKMGYFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIV 1158
+RR+ L++ F E G F +A + T D+ +I FLE+++ SCEG+ V
Sbjct: 445 SRRRQLLRENFV-ETEGEFVFATSLD--------TKDI--EQIAEFLEQSVKDSCEGLXV 493
Query: 1159 KSLDVDAGYSPSKRSDSW 1176
K+LDVDA Y +KRS +W
Sbjct: 494 KTLDVDATYEIAKRSHNW 511
>pdb|4B87|A Chain A, Crystal Structure Of Human Dna Cross-Link Repair 1a
Length = 367
Score = 201 bits (512), Expect = 1e-51, Method: Compositional matrix adjust.
Identities = 123/349 (35%), Positives = 190/349 (54%), Gaps = 31/349 (8%)
Query: 36 RTFPPSKHVPNTRFLIDAFRYAA-DFSVSYFLSHFHSDHYTGLSPSWSKGIIFCSEITSR 94
+T P K +P T F +DAF+Y + +YFL+HFHSDHY GLS ++ + +CSEIT
Sbjct: 26 KTCPFYKKIPGTGFTVDAFQYGVVEGCTAYFLTHFHSDHYAGLSKHFTFPV-YCSEITGN 84
Query: 95 LLSQILNINPKFIYPLPIKIPVLIDGCEVVLVGANHCPGAVQFLFKVPGRNGGFERYVHT 154
LL L++ ++I+PLP+ +++G +VVL+ ANHCPGAV LF +P NG +HT
Sbjct: 85 LLKNKLHVQEQYIHPLPLDTECIVNGVKVVLLDANHCPGAVMILFYLP--NG--TVILHT 140
Query: 155 GDFRFCKTMLLQPVMNEFAGCDAVFLDTTYCNPKFLFPLQXXXXXXXXXXXXXXXXXXXX 214
GDFR +M + ++ ++LDTTYC+P++ FP Q
Sbjct: 141 GDFRADPSMERSLLADQ--KVHMLYLDTTYCSPEYTFPSQQEVIRFAINTAFEAVT---- 194
Query: 215 XLQKRVLFLVATYVIGKEKILIEIFKKCGRKVCVDSRKMEVLRVLGYGD-SGVFTEDESE 273
L L + TY IGKEK+ + I G KV + K + L+ L + + + T D
Sbjct: 195 -LNPHALVVCGTYSIGKEKVFLAIADVLGSKVGMSQEKYKTLQCLNIPEINSLITTDMCS 253
Query: 274 TDVHVVGWNEIMVER----------GYDKVVGFVPTGWTYEVKRNKFA---VRSKDAFEI 320
+ VH++ +I + Y++++ F PTGWT+ K + A ++K I
Sbjct: 254 SLVHLLPMMQINFKGLQSHLKKCGGKYNQILAFRPTGWTHSNKFTRIADVIPQTKGNISI 313
Query: 321 HLVPYSEHSNYDELREYVKFLKPKRVIPTVGMDIEKLDSKHANKMRKYF 369
+ +PYSEHS+Y E++ +V++LKP+++IPTV + K S M KYF
Sbjct: 314 YGIPYSEHSSYLEMKRFVQWLKPQKIIPTVNVGTWKSRS----TMEKYF 358
>pdb|2HIV|A Chain A, Atp-Dependent Dna Ligase From S. Solfataricus
pdb|2HIX|A Chain A, Atp Dependent Dna Ligase From S. Solfataricus Bound To Atp
Length = 621
Score = 160 bits (406), Expect = 3e-39, Method: Compositional matrix adjust.
Identities = 137/469 (29%), Positives = 215/469 (45%), Gaps = 53/469 (11%)
Query: 718 LARTFDLVEAERGKIKAMSMLCNMFRSLLALSPDDVL-PAVYLCTNKIASNHENI-ELNI 775
+A FD +E KI + L + LL+ S ++ VY+ K+ + EL I
Sbjct: 26 IAEYFDKLE----KISSRLQLTALLADLLSKSDKTIIDKVVYIIQGKLWPDFLGYPELGI 81
Query: 776 GGSLVTSAIEEACGTNRSKIRDMYNRLGDLGDVAQECRQTQXXX--------XXXXXXXI 827
G + AI A T+ + + ++Y +GDLG+VA+ + Q +
Sbjct: 82 GEKFLIKAISIATNTDENSVENLYKTIGDLGEVARRLKSKQQSTGILGFLGTTSKESLTV 141
Query: 828 KDVYSMLCKISVQTGSGSTARKKSLIVNLMCSCREKEMKFLVRTLVRNLRIGAMMRTILP 887
+VYS L K+++ TG GS K L+ L+ E KFLVR + LR+G T+L
Sbjct: 142 DEVYSTLSKVALTTGEGSRDLKIRLLAGLLKKADPLEAKFLVRFVEGRLRVGIGDATVLD 201
Query: 888 ALAQAVVMNSSLEFSHEGKMENLKEKLQSLSAAAVEAYNXXXXXXXXXXXXMNKGIGFSA 947
A+A A QS S AYN + KGI +
Sbjct: 202 AMAIAFGGG------------------QSASEIIERAYNLRADLGNIAKIIVEKGIE-AL 242
Query: 948 STLSMVPGVPIKPMLAKITNGVPQVLKLFQNKAFTCEYKYDGQRAQIHKLVDGTVRIFSR 1007
TL G+PI+PMLA+ + ++LK A +YKYDG+RAQIHK D + IFSR
Sbjct: 243 KTLKPQVGIPIRPMLAERLSNPEEILKKMGGNAI-VDYKYDGERAQIHKKED-KIFIFSR 300
Query: 1008 NGDETTSRFPDLISIINEFCKPAAGTFILDAEVVAIDRKNGCKIMSFQELSSRERGGKDS 1067
+ TS++PD++ ++++ + FI++ E+VAID ++G ++ FQEL R+R D
Sbjct: 301 RLENITSQYPDVVDYVSKYIE--GKEFIIEGEIVAIDPESG-EMRPFQELMHRKRKS-DI 356
Query: 1068 VITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRRKYLKDLFYDEKMGYFQYAKEMTVEG 1127
IK V+ VF+FD+M+ L RRK L+ + + Y + A +
Sbjct: 357 YEAIKEYPVN--VFLFDLMYYEDVDYTTKPLEARRKLLESIV--KPNDYVKIAHHIQAN- 411
Query: 1128 DDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSLDVDAGYSPSKRSDSW 1176
++ + +F A+ EG++VK++ DA Y R W
Sbjct: 412 ---------NVEDLKSFFYRAISEGGEGVMVKAIGKDAIYQAGARGWLW 451
>pdb|3ZDK|A Chain A, Crystal Structure Of Human 5' Exonuclease Apollo
Length = 336
Score = 147 bits (370), Expect = 5e-35, Method: Compositional matrix adjust.
Identities = 98/316 (31%), Positives = 160/316 (50%), Gaps = 32/316 (10%)
Query: 44 VPNTRFLID--AFRYAADFSVSYFLSHFHSDHYTGLSPSWSKGIIFCSEITSRLLSQILN 101
+P+T +D + R A + +FLSH HSDH GLS +W++ + +CS IT+ LL + L
Sbjct: 7 IPHTPIAVDFWSLRRAGTARL-FFLSHMHSDHTVGLSSTWARPL-YCSPITAHLLHRHLQ 64
Query: 102 INPKFIYPLPIK----IPVLIDGCE---VVLVGANHCPGAVQFLFKVPGRNGGFERYVHT 154
++ ++I L + +P+ G E V L+ ANHCPG+V FLF+ G F ++T
Sbjct: 65 VSKQWIQALEVGESHVLPLDEIGQETMTVTLLDANHCPGSVMFLFE-----GYFGTILYT 119
Query: 155 GDFRFCKTMLLQPVMNEFAGCDAVFLDTTYCNPKFLFPLQXXXXXXXXXXXXXXXXXXXX 214
GDFR+ +ML +P + ++LD T CNP + P +
Sbjct: 120 GDFRYTPSMLKEPALTLGKQIHTLYLDNTNCNPALVLPSRQEAAHQIVQLIRKHPQHNIK 179
Query: 215 XLQKRVLFLVATYVIGKEKILIEIFKKCGRKVCVDSRKMEVLRVLGYGDSGVFTEDESET 274
+ Y +GKE +L ++ + V + R++E++++LG D VFT +E
Sbjct: 180 ---------IGLYSLGKESLLEQLALEFQTWVVLSPRRLELVQLLGLAD--VFTVEEKAG 228
Query: 275 DVHVVGWNEIMVERGYDKVVGFVPTGWTYEVKRNKFAVRSKDAFEIHLVPYSEHSNYDEL 334
+H V EI + ++ + T T + + S +IH++PYS+HS+Y EL
Sbjct: 229 RIHAVDHMEIC----HSNMLRWNQTHPTIAILPTSRKIHSSHP-DIHVIPYSDHSSYSEL 283
Query: 335 REYVKFLKPKRVIPTV 350
R +V LKP +V+P V
Sbjct: 284 RAFVAALKPCQVVPIV 299
>pdb|3RR5|A Chain A, Dna Ligase From The Archaeon Thermococcus Sp. 1519
Length = 570
Score = 126 bits (317), Expect = 6e-29, Method: Compositional matrix adjust.
Identities = 112/447 (25%), Positives = 191/447 (42%), Gaps = 72/447 (16%)
Query: 745 LLALSPDDVLPAV-YLCTNKIASNHENIELNIGGSLVTSAIEEACGTNRSKIRDMYNRLG 803
L +PD++L V YL K+ + + EL +G L+ A+ A G +I + G
Sbjct: 40 FLKKTPDELLEVVPYLILGKVFPDWDERELGVGEKLLIKAVSMATGVPEKEIENSIKDTG 99
Query: 804 DLGD-VAQECRQTQXXXXXXXXXXIKDVYSMLCKISVQTGSGSTARKKSLIVNLMCSCRE 862
DLG+ VA ++ + IK VYS K++ +G GS RK + NL +
Sbjct: 100 DLGESVALALKKRKQKSFFSQPLTIKRVYSTFVKVAEASGEGSQDRKMKYLANLFMDAQP 159
Query: 863 KEMKFLVRTLVRNLRIGAMMRTILPALAQAVVMNSSL---------EFSHEGKMENLKEK 913
+E K++ RT++ +R G + A+A+A + L +F + K+ L+
Sbjct: 160 EEGKYIARTVLGTMRTGVAEGILRDAIAEAFRVKPELVERAYMLTSDFGYVAKVAKLE-- 217
Query: 914 LQSLSAAAVEAYNXXXXXXXXXXXXMNKGIGFSASTLSMVPGVPIKPMLAKITNGVPQVL 973
N+G+ S +S+ G PI+PMLA+ V + L
Sbjct: 218 -------------------------GNEGL----SKVSIQIGKPIRPMLAQNAASVKEAL 248
Query: 974 KLFQNKAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDETTSRFPDLISIINEFCKPAAGT 1033
+A E KYDG R Q+H+ D + I+SR + T P+++ + KP+
Sbjct: 249 IEMGGEA-AFEIKYDGARVQVHRDGDRVI-IYSRRLENVTRSIPEIVEAVKASLKPS--K 304
Query: 1034 FILDAEVVAIDRKNGCKIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQL 1093
I++ E+VA+ + + R + D +I K+ + + +FDI++ +GE L
Sbjct: 305 VIVEGELVAVGENGRPRPFQYVLRRFRRKYNIDEMIE----KIPLELNLFDILYVDGESL 360
Query: 1094 LGYTLRQRRKYLKDLFYDEKMGYFQYAKEMTVEGDDNCLTSDVSLSK----INNFLEEAL 1149
+ +RRK L E +VE + ++ ++K F + AL
Sbjct: 361 IDTEFVERRKRL----------------EESVEESEKIKIAEQLVTKKVEEAEAFYKRAL 404
Query: 1150 HSSCEGIIVKSLDVDAGYSPSKRSDSW 1176
EG++ K L D+ Y P R W
Sbjct: 405 ELGHEGLMAKRL--DSVYEPGNRGKKW 429
>pdb|4EQ5|A Chain A, Dna Ligase From The Archaeon Thermococcus Sibiricus
Length = 571
Score = 118 bits (296), Expect = 2e-26, Method: Compositional matrix adjust.
Identities = 112/436 (25%), Positives = 188/436 (43%), Gaps = 67/436 (15%)
Query: 752 DVLPAVYLCTNKIASNHENIELNIGGSLVTSAIEEACGTNRSKIRDMYNRLGDLGD-VAQ 810
+V+P YL K+ + + EL IG L+ A+ A G N +I + GDLG+ +A
Sbjct: 51 EVIP--YLILGKVFPDWDERELGIGEKLLIKAVSMATGINSEEIENSVRDTGDLGESIAL 108
Query: 811 ECRQTQXXXXXXXXXXIKDVYSMLCKISVQTGSGSTARKKSLIVNLMCSCREKEMKFLVR 870
+ + I+ VY+ L KI+ +G+GS RK + NL E K+L R
Sbjct: 109 ALNKRKQKSFFSQPLTIERVYNTLVKIAEASGAGSQDRKLKYLANLFMDASPDEGKYLAR 168
Query: 871 TLVRNLRIGAMMRTILPALAQAVVMNSSL---------EFSHEGKMENLKEKLQSLSAAA 921
T++ +R G + ALA A + L +F K+ L E + L+
Sbjct: 169 TVLGIMRTGVAEGLLRDALADAFKVRVELVERAYMLTSDFGFVAKVAKL-EGDEGLAKVK 227
Query: 922 VEAYNXXXXXXXXXXXXMNKGIGFSASTLSMVPGVPIKPMLAKITNGVPQVLKLFQNKAF 981
++ G PIKPMLA++ V + L +A
Sbjct: 228 IQV------------------------------GKPIKPMLAQMAANVREALVEMGGEA- 256
Query: 982 TCEYKYDGQRAQIHKLVDGT-VRIFSRNGDETTSRFPDLISIINEFCKPAAGTFILDAEV 1040
E KYDG R Q+HK +G V I+SR + T P+++ + E KP I++ E+
Sbjct: 257 EFEIKYDGARVQVHK--NGNKVLIYSRRLENVTKSIPEVVERVKEALKPE--KVIVEGEL 312
Query: 1041 VAIDRKNGCKIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQ 1100
VA++ + FQ + R R + I+ + +++ +F DI++ +G+ ++ +
Sbjct: 313 VAVEETGRPR--PFQYVLRRFRRKYNIEEMIEKIPLELNLF--DILYVDGQNMIDTPFME 368
Query: 1101 RRKYLKDLFYDEKMGYFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKS 1160
RRK L+ + + ++ +N +T S + F +AL EG++ K
Sbjct: 369 RRKVLESVVNSNEW----------IKSAENLITK--SPEEAEAFYHKALDLGHEGLMAKR 416
Query: 1161 LDVDAGYSPSKRSDSW 1176
L D+ Y P R W
Sbjct: 417 L--DSTYEPGNRGKKW 430
>pdb|3GDE|A Chain A, The Closed Conformation Of Atp-Dependent Dna Ligase From
Archaeoglobus Fulgidus
Length = 558
Score = 118 bits (296), Expect = 2e-26, Method: Compositional matrix adjust.
Identities = 108/427 (25%), Positives = 187/427 (43%), Gaps = 51/427 (11%)
Query: 752 DVLPAVYLCTNKIASNHENIELNIGGSLVTSAIEEACGTNRSKIRDMYNRLGDLGDVAQE 811
D+ V T K+ + EL +G L+ A+E G RS+I M GDLG VA++
Sbjct: 41 DLYDVVLFITGKVYPPWDERELGVGIGLLYEALENVSGVKRSEIESMIREYGDLGLVAEQ 100
Query: 812 -CRQTQXXXXXXXXXXIKDVYSMLCKISVQTGSGSTARKKSLIVNLMCSCREKEMKFLVR 870
++ + ++ V +I+ TG GS RK L+ L E ++L R
Sbjct: 101 LIKKKKMTTLAFEELTVRKVRETFDEIASLTGEGSMKRKIMLLTGLYGLATPLEARYLTR 160
Query: 871 TLVRNLRIGAMMRTILPALAQAVVMNSSLEFSHEGKMENLKEKLQSLSAAAVEAYNXXXX 930
++ +R+G + A+A+A + +E L AV A
Sbjct: 161 LILNEMRLGVGEGIMRDAIARAFRADPE-------TVERAYMITNDLGRVAVVAKKEGEE 213
Query: 931 XXXXXXXXMNKGIGFSASTLSMVPGVPIKPMLAKITNGVPQVLKLFQNKAFTCEYKYDGQ 990
++ +P++ MLA++ + ++ + A E+K+DG
Sbjct: 214 GLRKMKIEIH---------------IPVRMMLAQVAESLESAVREMRTAA--VEWKFDGS 256
Query: 991 RAQIHKLVDGT-VRIFSRNGDETTSRFPDLISIINEFCKPAAGTFILDAEVVAIDRKNGC 1049
R Q+H DG+ V I+SR + T+ PD++ I + KP ILD EV+A+ K G
Sbjct: 257 RVQVH--WDGSRVTIYSRRLENVTNALPDIVEEIKKSVKPGV---ILDGEVIAV--KEG- 308
Query: 1050 KIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRRKYLKDLF 1109
K M FQ + R R D ++ K+ + FDI++ +GE + LR+RRK L+
Sbjct: 309 KPMPFQHVLRRFRRKHDVAKMVE--KIPLEAHFFDILYHDGE-CIDLPLRERRKLLESAV 365
Query: 1110 YDEKMGYFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSLDVDAGYSP 1169
+ + + AK++ + S+ ++ +EA+ + EG+++K + Y P
Sbjct: 366 NESEK--IKLAKQIVTD----------SVDEVRKMYDEAISAGHEGVMIKL--PSSPYIP 411
Query: 1170 SKRSDSW 1176
KR +W
Sbjct: 412 GKRGKNW 418
>pdb|2CFM|A Chain A, Atp-Dependent Dna Ligase From Pyrococcus Furiosus
Length = 561
Score = 115 bits (289), Expect = 1e-25, Method: Compositional matrix adjust.
Identities = 114/474 (24%), Positives = 201/474 (42%), Gaps = 70/474 (14%)
Query: 715 YIHLARTFDLVEAERGKIKAMSMLCNMFRSLLALSPDDVLPAV-YLCTNKIASNHENIEL 773
Y+ LA+ + +E K+ ++ + + + PDD L + YL ++ + EL
Sbjct: 3 YLELAQLYQKLEKTTXKLIKTRLVADFLKKV----PDDHLEFIPYLILGEVFPEWDEREL 58
Query: 774 NIGGSLVTSAIEEACGTNRSKIRDMYNRLGDLGD-VAQECRQTQXXXXXXXXXXIKDVYS 832
+G L+ A+ A G + +I + GDLG+ +A ++ + IK VY
Sbjct: 59 GVGEKLLIKAVAXATGIDAKEIEESVKDTGDLGESIALAVKKKKQKSFFSQPLTIKRVYQ 118
Query: 833 MLCKISVQTGSGSTARKKSLIVNLMCSCREKEMKFLVRTLVRNLRIGAMMRTILPALAQA 892
L K++ TG GS +K + +L E K+L RT++ R G + A+A A
Sbjct: 119 TLVKVAETTGEGSQDKKVKYLADLFXDAEPLEAKYLARTILGTXRTGVAEGLLRDAIAXA 178
Query: 893 VVMNSSL---------EFSHEGKMENLKEKLQSLSAAAVEAYNXXXXXXXXXXXXMNKGI 943
+ L +F + K+ L+ N+G+
Sbjct: 179 FHVKVELVERAYXLTSDFGYVAKIAKLE---------------------------GNEGL 211
Query: 944 GFSASTLSMVPGVPIKPMLAKITNGVPQVLKLFQNKAFTCEYKYDGQRAQIHKLVDGT-V 1002
+ + + G PIKP LA+ + L L E KYDG R Q+HK DG+ +
Sbjct: 212 ----AKVQVQLGKPIKPXLAQQAASIRDAL-LEXGGEAEFEIKYDGARVQVHK--DGSKI 264
Query: 1003 RIFSRNGDETTSRFPDLISIINEFCKPAAGTFILDAEVVAIDRKNGCKIMSFQELSSRER 1062
++SR + T P+++ + E P I++ E+VAI +NG + + FQ + R R
Sbjct: 265 IVYSRRLENVTRAIPEIVEALKEAIIPEKA--IVEGELVAIG-ENG-RPLPFQYVLRRFR 320
Query: 1063 GGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRRKYLKDLFYDEKMGYFQYAKE 1122
+ I K+ + + +FD+++ +G+ L+ RR+ L+++ +
Sbjct: 321 --RKHNIEEXXEKIPLELNLFDVLYVDGQSLIDTKFIDRRRTLEEII----------KQN 368
Query: 1123 MTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSLDVDAGYSPSKRSDSW 1176
++ +N +T V + F + AL EG+ K L DA Y P R W
Sbjct: 369 EKIKVAENLITKKV--EEAEAFYKRALEXGHEGLXAKRL--DAVYEPGNRGKKW 418
>pdb|3L2P|A Chain A, Human Dna Ligase Iii Recognizes Dna Ends By Dynamic
Switching Between Two Dna Bound States
Length = 579
Score = 75.5 bits (184), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 85/351 (24%), Positives = 149/351 (42%), Gaps = 58/351 (16%)
Query: 827 IKDVYSMLCKISVQTGSGSTARKKSLIVNLMCSCREKEMKFLVRTLVRNLRIGAMMRTIL 886
I++V L ++S T ++ + ++ C ++K ++R + +L++ + + +L
Sbjct: 120 IQEVDEFLLRLSKLTKEDE---QQQALQDIASRCTANDLKCIIRLIKHDLKMNSGAKHVL 176
Query: 887 PALAQAVVMNSSLEFSHEGKMENLKEKLQSLSAAAVEAYNXXXXXXXXXXXXMNKGIGFS 946
AL N+ F ++++ E++ +A VE + +
Sbjct: 177 DALDP----NAYEAFKASRNLQDVVERVLH-NAQEVE-----------KEPGQRRALSVQ 220
Query: 947 ASTLSMVPGVPIKPMLAKITNGVPQVLKLFQNKAFTCEYKYDGQRAQIHKLVDGTVRIFS 1006
AS ++ P++PMLA+ V +K N F+ E KYDG+R Q+HK D FS
Sbjct: 221 ASLMT-----PVQPMLAEACKSVEYAMKKCPNGMFS-EIKYDGERVQVHKNGD-HFSYFS 273
Query: 1007 RNGD----ETTSRFPDLISIINEFCKPAAGTFILDAEVVAIDRKNGCKIMSFQELSSRER 1062
R+ + F D I F P + ILD+EV+ ID K G K + F L ++
Sbjct: 274 RSLKPVLPHKVAHFKDYIP--QAF--PGGHSMILDSEVLLIDNKTG-KPLPFGTLGVHKK 328
Query: 1063 GGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRRKYLKDLFYD-EKMGYFQYAK 1121
++C+FVFD ++ N L+ L +RRK+L D + F K
Sbjct: 329 AAFQDA--------NVCLFVFDCIYFNDVSLMDRPLCERRKFLHDNMVEIPNRIMFSEMK 380
Query: 1122 EMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSLDVDAGYSPSKR 1172
+T D + + + + EG+++K DV Y P KR
Sbjct: 381 RVTKALD------------LADMITRVIQEGLEGLVLK--DVKGTYEPGKR 417
>pdb|1VS0|A Chain A, Crystal Structure Of The Ligase Domain From M. Tuberculosis
Ligd At 2.4a
pdb|1VS0|B Chain B, Crystal Structure Of The Ligase Domain From M. Tuberculosis
Ligd At 2.4a
Length = 310
Score = 50.4 bits (119), Expect = 6e-06, Method: Composition-based stats.
Identities = 60/219 (27%), Positives = 95/219 (43%), Gaps = 43/219 (19%)
Query: 958 IKPMLAKITNGVPQVLKLFQNKAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDETTSRFP 1017
+ P LA T+G LK Q + E +DG R + + G VR+ SR+G + T+ +P
Sbjct: 9 LAPXLA--THGTVAGLKASQ---WAFEGXWDGYRLLV-EADHGAVRLRSRSGRDVTAEYP 62
Query: 1018 DLISIINEFCKPAAGTFILDAEVVAIDRKNGCKIMSFQELSSRERGGKDSVITIKSVKVD 1077
L ++ + A +LD E V +D + SF + +R G+D+ +
Sbjct: 63 QLRALAEDL---ADHHVVLDGEAVVLDSSG---VPSFSQXQNR---GRDTRVEF------ 107
Query: 1078 ICVFVFDIMFANGEQLLGYTLRQRRKYLKDLFYDEKMGYFQYAKEMTVEGDDNCLTSDVS 1137
+ FD+++ +G LLG + RRK L+ L A +TV L D +
Sbjct: 108 ---WAFDLLYLDGRALLGTRYQDRRKLLETL---------ANATSLTVP---ELLPGDGA 152
Query: 1138 LSKINNFLEEALHSSCEGIIVKSLDVDAGYSPSKRSDSW 1176
+ F H EG+I K D+ Y P +R SW
Sbjct: 153 QA----FACSRKH-GWEGVIAKRR--DSRYQPGRRCASW 184
>pdb|3VNN|A Chain A, Crystal Structure Of A Sub-Domain Of The
Nucleotidyltransferase (Adenylation) Domain Of Human Dna
Ligase Iv
Length = 139
Score = 47.4 bits (111), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 44/137 (32%), Positives = 64/137 (46%), Gaps = 19/137 (13%)
Query: 981 FTCEYKYDGQRAQIHKLVDGTV-RIFSRNGDETTSRFP------DLISIINEFCKPAAGT 1033
F E K DG+R Q+HK DG V + FSRNG T +F L I+ K
Sbjct: 1 FYIETKLDGERMQMHK--DGDVYKYFSRNGYNYTDQFGASPTEGSLTPFIHNAFKADIQI 58
Query: 1034 FILDAEVVAIDRKNGCKIMSFQELSSRERGGK-DSVITIKSVKVDICVFVFDIMFANGEQ 1092
ILD E++A + N M ++G K D ++ + C VFD++ N ++
Sbjct: 59 CILDGEMMAYN-PNTQTFM--------QKGTKFDIKRMVEDSDLQTCYCVFDVLMVNNKK 109
Query: 1093 LLGYTLRQRRKYLKDLF 1109
L TLR+R + L +F
Sbjct: 110 LGHETLRKRYEILSSIF 126
>pdb|2YCB|A Chain A, Structure Of The Archaeal Beta-Casp Protein With
N-Terminal Kh Domains From Methanothermobacter
Thermautotrophicus
pdb|2YCB|B Chain B, Structure Of The Archaeal Beta-Casp Protein With
N-Terminal Kh Domains From Methanothermobacter
Thermautotrophicus
Length = 636
Score = 38.1 bits (87), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 41/184 (22%), Positives = 77/184 (41%), Gaps = 48/184 (26%)
Query: 45 PNTRFLID------------AFRY--AADFSV----SYFLSHFHSDHYTGLSPSWSK--- 83
PN+R L+D ++ Y +F++ + ++H H DH +G P
Sbjct: 201 PNSRVLLDCGVNVAGGDDKNSYPYLNVPEFTLDSLDAVIITHAHLDH-SGFLPYLYHYGY 259
Query: 84 -GIIFCSEITSRLLSQI----LNINPKFIYPLP---------IKIPVLIDGCEVV----- 124
G ++C+ T L++ + ++I + PLP +K + +D EV
Sbjct: 260 DGPVYCTAPTRDLMTLLQLDHIDIAHREDEPLPFNVKHVKKSVKHTITLDYGEVTDIAPD 319
Query: 125 ----LVGANHCPGAVQFLFKVPGRNGGFERYVHTGDFRFCKTMLLQPVMNEFAGCDAVFL 180
L A H G+ + G V+TGDF++ ++ LL+ N F + + +
Sbjct: 320 IRLTLHNAGHILGSAMAHLHI---GDGQHNMVYTGDFKYEQSRLLEAAANRFPRIETLVM 376
Query: 181 DTTY 184
++TY
Sbjct: 377 ESTY 380
>pdb|2XR1|A Chain A, Dimeric Archaeal Cleavage And Polyadenylation Specificity
Factor With N-Terminal Kh Domains (Kh-Cpsf) From
Methanosarcina Mazei
pdb|2XR1|B Chain B, Dimeric Archaeal Cleavage And Polyadenylation Specificity
Factor With N-Terminal Kh Domains (Kh-Cpsf) From
Methanosarcina Mazei
Length = 640
Score = 37.7 bits (86), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 38/156 (24%), Positives = 63/156 (40%), Gaps = 30/156 (19%)
Query: 63 SYFLSHFHSDHYTGLSPSWSK----GIIFCSEITSRLLSQI----LNINPKFIYPLP--- 111
+ ++H H DH GL P K G ++C+ T L+ + +++ K +P
Sbjct: 240 AVIVTHAHLDH-QGLVPLLFKYGYEGPVYCTPPTRDLMVLLQLDYIDVAAKEGKKIPYES 298
Query: 112 ------IKIPVLIDGCEVVLVG---------ANHCPGAVQFLFKVPGRNGGFERYVHTGD 156
+K + +D EV + A H G+ F + G V TGD
Sbjct: 299 GMVAKTLKHTIPLDYEEVTDIAPDIKLTFHNAGHILGSAISHFHI---GDGLHNVVFTGD 355
Query: 157 FRFCKTMLLQPVMNEFAGCDAVFLDTTYCNPKFLFP 192
+++ KT L P +N+F + V + TY N P
Sbjct: 356 YKYEKTRLFDPAVNKFPRVETVISEATYGNANAFQP 391
>pdb|3AF5|A Chain A, The Crystal Structure Of An Archaeal Cpsf Subunit, Ph1404
From Pyrococcus Horikoshii
pdb|3AF6|A Chain A, The Crystal Structure Of An Archaeal Cpsf Subunit, Ph1404
From Pyrococcus Horikoshii Complexed With Rna-Analog
Length = 651
Score = 33.1 bits (74), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 28/64 (43%), Gaps = 3/64 (4%)
Query: 121 CEVVLVGANHCPGAVQFLFKVPGRNGGFERYVHTGDFRFCKTMLLQPVMNEFAGCDAVFL 180
+ L A H G+ + G TGDF+F T LL+P +F + + +
Sbjct: 335 IRLTLHNAGHILGSAIVHLHI---GNGLHNIAITGDFKFIPTRLLEPANAKFPRLETLVM 391
Query: 181 DTTY 184
++TY
Sbjct: 392 ESTY 395
>pdb|2FHP|A Chain A, Crystal Structure Of Putative Methylase From Enterococcus
Faecalis
pdb|2FHP|B Chain B, Crystal Structure Of Putative Methylase From Enterococcus
Faecalis
Length = 187
Score = 33.1 bits (74), Expect = 1.0, Method: Composition-based stats.
Identities = 25/86 (29%), Positives = 40/86 (46%), Gaps = 4/86 (4%)
Query: 440 EFGSKDVTALDDEET----EKMVQEIRNCLPTWVTQNQILDLISSSGRNIVDAVSNFYEH 495
E+G + + ALD + T +K+ + I N + + LDL S SG ++AVS +
Sbjct: 10 EYGGRRLKALDGDNTRPTTDKVKESIFNXIGPYFDGGXALDLYSGSGGLAIEAVSRGXDK 69
Query: 496 ETQLYEQEYKLPTIKHSIKSTLSPSK 521
+ + L IK +I T P K
Sbjct: 70 SICIEKNFAALKVIKENIAITKEPEK 95
>pdb|1DZF|A Chain A, Rpb5 From S.Cerevisiae
pdb|1I3Q|E Chain E, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
pdb|1I50|E Chain E, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
pdb|1I6H|E Chain E, Rna Polymerase Ii Elongation Complex
pdb|1K83|E Chain E, Crystal Structure Of Yeast Rna Polymerase Ii Complexed With
The Inhibitor Alpha Amanitin
pdb|1NIK|E Chain E, Wild Type Rna Polymerase Ii
pdb|1NT9|E Chain E, Complete 12-Subunit Rna Polymerase Ii
pdb|1PQV|E Chain E, Rna Polymerase Ii-Tfiis Complex
pdb|1R5U|E Chain E, Rna Polymerase Ii Tfiib Complex
pdb|1SFO|E Chain E, Rna Polymerase Ii Strand Separated Elongation Complex
pdb|1R9S|E Chain E, Rna Polymerase Ii Strand Separated Elongation Complex,
Matched Nucleotide
pdb|1R9T|E Chain E, Rna Polymerase Ii Strand Separated Elongation Complex,
Mismatched Nucleotide
pdb|1TWA|E Chain E, Rna Polymerase Ii Complexed With Atp
pdb|1TWC|E Chain E, Rna Polymerase Ii Complexed With Gtp
pdb|1TWF|E Chain E, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
pdb|1TWG|E Chain E, Rna Polymerase Ii Complexed With Ctp
pdb|1TWH|E Chain E, Rna Polymerase Ii Complexed With 2'datp
pdb|1WCM|E Chain E, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
pdb|1Y1W|E Chain E, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|E Chain E, Complete Rna Polymerase Ii Elongation Complex With Substrate
Analogue Gmpcpp
pdb|1Y1V|E Chain E, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|E Chain E, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|2B63|E Chain E, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2B8K|E Chain E, 12-Subunit Rna Polymerase Ii
pdb|2E2H|E Chain E, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With Gtp
pdb|2E2I|E Chain E, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dgtp
pdb|2E2J|E Chain E, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
Gmpcpp
pdb|2NVQ|E Chain E, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
2'dutp
pdb|2NVT|E Chain E, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Gmpcpp
pdb|2NVX|E Chain E, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dutp
pdb|2NVY|E Chain E, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
pdb|2NVZ|E Chain E, Rna Polymerase Ii Elongation Complex With Utp, Updated
112006
pdb|2JA5|E Chain E, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex A
pdb|2JA6|E Chain E, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex B
pdb|2JA7|E Chain E, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex C
pdb|2JA7|Q Chain Q, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex C
pdb|2JA8|E Chain E, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex D
pdb|2YU9|E Chain E, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With Utp
pdb|2R7Z|E Chain E, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|E Chain E, Elongation Complex Of Rna Polymerase Ii With Artificial Rdrp
Scaffold
pdb|2R93|E Chain E, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|E Chain E, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3CQZ|E Chain E, Crystal Structure Of 10 Subunit Rna Polymerase Ii In Complex
With The Inhibitor Alpha-Amanitin
pdb|3FKI|E Chain E, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3GTG|E Chain E, Backtracked Rna Polymerase Ii Complex With 12mer Rna
pdb|3GTJ|E Chain E, Backtracked Rna Polymerase Ii Complex With 13mer Rna
pdb|3GTK|E Chain E, Backtracked Rna Polymerase Ii Complex With 18mer Rna
pdb|3GTL|E Chain E, Backtracked Rna Polymerase Ii Complex With 13mer With G<>u
Mismatch
pdb|3GTM|E Chain E, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
pdb|3GTO|E Chain E, Backtracked Rna Polymerase Ii Complex With 15mer Rna
pdb|3GTP|E Chain E, Backtracked Rna Polymerase Ii Complex With 24mer Rna
pdb|3GTQ|E Chain E, Backtracked Rna Polymerase Ii Complex Induced By Damage
pdb|3H3V|F Chain F, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|E Chain E, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOU|Q Chain Q, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOV|E Chain E, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3HOW|E Chain E, Complete Rna Polymerase Ii Elongation Complex Iii With A T-U
Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|E Chain E, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|E Chain E, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|E Chain E, Complete Rna Polymerase Ii Elongation Complex Iv With A T-U
Mismatch And A Frayed Rna 3'-Guanine
pdb|3I4M|E Chain E, 8-oxoguanine Containing Rna Polymerase Ii Elongation Complex
D
pdb|3I4N|E Chain E, 8-oxoguanine Containing Rna Polymerase Ii Elongation Complex
E
pdb|3K1F|E Chain E, Crystal Structure Of Rna Polymerase Ii In Complex With Tfiib
pdb|3K7A|E Chain E, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
pdb|3M3Y|E Chain E, Rna Polymerase Ii Elongation Complex C
pdb|3M4O|E Chain E, Rna Polymerase Ii Elongation Complex B
pdb|3PO2|E Chain E, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|E Chain E, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3QT1|E Chain E, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
pdb|3RZD|E Chain E, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
pdb|3RZO|E Chain E, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
pdb|3S14|E Chain E, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
pdb|3S15|E Chain E, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
pdb|3S16|E Chain E, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
pdb|3S17|E Chain E, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
pdb|3S1M|E Chain E, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 1)
pdb|3S1N|E Chain E, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 2)
pdb|3S1Q|E Chain E, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Atp
pdb|3S1R|E Chain E, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Gtp
pdb|3S2D|E Chain E, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
Containing A 5br- U
pdb|3S2H|E Chain E, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
Containing A 2[prime]-Iodo Atp
pdb|3J0K|E Chain E, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
pdb|4A3C|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid
pdb|4A3B|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid
pdb|4A3D|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid
pdb|4A3E|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3F|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3J|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid And Soaked With Gmpcpp
pdb|4A3K|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid
pdb|4A3L|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3M|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3G|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid
pdb|4A3I|E Chain E, Rna Polymerase Ii Binary Complex With Dna
pdb|4A93|E Chain E, Rna Polymerase Ii Elongation Complex Containing A Cpd Lesion
pdb|4BBR|E Chain E, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|E Chain E, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 215
Score = 32.0 bits (71), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 24/39 (61%), Gaps = 1/39 (2%)
Query: 1010 DETTSRFPDLISIINEFC-KPAAGTFILDAEVVAIDRKN 1047
+E+ S+FPD+ S+ EFC +P+ G + V+ I KN
Sbjct: 66 EESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKN 104
>pdb|3DI0|A Chain A, Crystal Structure Of Dihydrodipicolinate Synthase From
Staphylococcus Aureus
pdb|3DI0|B Chain B, Crystal Structure Of Dihydrodipicolinate Synthase From
Staphylococcus Aureus
pdb|3DI1|A Chain A, Crystal Structure Of The Staphylococcus Aureus
Dihydrodipicolinate Synthase-pyruvate Complex
pdb|3DI1|B Chain B, Crystal Structure Of The Staphylococcus Aureus
Dihydrodipicolinate Synthase-pyruvate Complex
Length = 295
Score = 30.8 bits (68), Expect = 4.7, Method: Composition-based stats.
Identities = 23/91 (25%), Positives = 42/91 (46%), Gaps = 3/91 (3%)
Query: 550 ITSFFNKLLPNMSQGDVVESKSEECPKDENPLQSNAIKTYGEEIDQFLKIING---NESL 606
+ + N LL N +Q +V + E P + +KT + +D+ + +I G N++
Sbjct: 26 LKTHVNFLLENNAQAIIVNGTTAESPTLTTDEKERILKTVIDLVDKRVPVIAGTGTNDTE 85
Query: 607 KGYAATLLEKTKGNVSMALDLYYDNQEGDRG 637
K A++ K G ++ L Y N+ RG
Sbjct: 86 KSIQASIQAKALGADAIMLITPYYNKTNQRG 116
>pdb|2WNS|A Chain A, Human Orotate Phosphoribosyltransferase (Oprtase) Domain Of
Uridine 5'-Monophosphate Synthase (Umps) In Complex With
Its Substrate Orotidine 5'-Monophosphate (Omp)
pdb|2WNS|B Chain B, Human Orotate Phosphoribosyltransferase (Oprtase) Domain Of
Uridine 5'-Monophosphate Synthase (Umps) In Complex With
Its Substrate Orotidine 5'-Monophosphate (Omp)
Length = 205
Score = 30.4 bits (67), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 36/133 (27%), Positives = 59/133 (44%), Gaps = 36/133 (27%)
Query: 940 NKGIGFSASTLSMVPGVPIKPM-LAKI---TNGVPQVLKLFQNKAFTCEYKYDGQRAQIH 995
N GI F V GVP + LA + TN +P +++ + K + +
Sbjct: 58 NAGISFDT-----VCGVPYTALPLATVICSTNQIPMLIRRKETKDYGTK----------- 101
Query: 996 KLVDGTVRIFSRNGDETTSRFPDLISIINEFCKPAAGTFILDAEVVAIDRKNGCKIMSFQ 1055
+LV+GT+ N ET D+++ +G+ +L E V + +K G K+
Sbjct: 102 RLVEGTI-----NPGETCLIIEDVVT---------SGSSVL--ETVEVLQKEGLKVTDAI 145
Query: 1056 ELSSRERGGKDSV 1068
L RE+GGKD +
Sbjct: 146 VLLDREQGGKDKL 158
>pdb|2I7T|A Chain A, Structure Of Human Cpsf-73
pdb|2I7V|A Chain A, Structure Of Human Cpsf-73
Length = 459
Score = 30.0 bits (66), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 33/76 (43%), Gaps = 11/76 (14%)
Query: 323 VPYSEHSNYDELREYVKFLKPKRVIPTVGMDIEKLDSKHANKMRKYFAGLVDEMASKKEF 382
+ +S H++Y + E+++ LKP VI G N+M + A L+ E E
Sbjct: 391 ISFSAHTDYQQTSEFIRALKPPHVILVHG---------EQNEMARLKAALIREYEDNDEV 441
Query: 383 LMGFH--RGTSEIDEN 396
+ H R T + N
Sbjct: 442 HIEVHNPRNTEAVTLN 457
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.317 0.134 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 32,490,427
Number of Sequences: 62578
Number of extensions: 1331966
Number of successful extensions: 3660
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 3602
Number of HSP's gapped (non-prelim): 32
length of query: 1176
length of database: 14,973,337
effective HSP length: 110
effective length of query: 1066
effective length of database: 8,089,757
effective search space: 8623680962
effective search space used: 8623680962
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 57 (26.6 bits)