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= psy11420
(315 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3CVU|A Chain A, Drosophila Melanogaster (6-4) Photolyase Bound To Ds Dna
With A T-T (6-4) Photolesion
pdb|3CVY|A Chain A, Drosophila Melanogaster (6-4) Photolyase Bound To Repaired
Ds Dna
pdb|2WB2|A Chain A, Drosophila Melanogaster (6-4) Photolyase Bound To Double
Stranded Dna Containing A T(6-4)c Photolesion
pdb|3CVV|A Chain A, Drosophila Melanogaster (6-4) Photolyase Bound To Ds Dna
With A T-T (6-4) Photolesion And F0 Cofactor
pdb|2WQ6|A Chain A, Structure Of The 6-4 Photolyase Of D. Melanogaster In
Complex With The Non-Natural N4-Methyl T(Dewar)c Lesion
pdb|2WQ7|A Chain A, Structure Of The 6-4 Photolyase Of D. Melanogaster In
Complex With The Non-Natural N4-Methyl T(6-4)c Lesion
Length = 543
Score = 367 bits (941), Expect = e-102, Method: Compositional matrix adjust.
Identities = 178/282 (63%), Positives = 215/282 (76%), Gaps = 16/282 (5%)
Query: 1 MTYQKLVSVLESLPKPKPADDAPTSLPRECQGILHPDEHLV----------PTMKEMGLD 50
+TYQK + ++E L PK +P + + + P + V PTMK++
Sbjct: 180 ITYQKFLGIVEQLKVPKV-----LGVPEKLKNMPTPPKDEVEQKDSAAYDCPTMKQLVKR 234
Query: 51 ESSIPLCKFPGGETEALKRLEKSLANKEWVRKFEKPNTAPNSLEPSTTVLSPYLKFGCLS 110
+ KFPGGETEAL+R+E+SL ++ WV +FEKPNTAPNSLEPSTTVLSPYLKFGCLS
Sbjct: 235 PEELGPNKFPGGETEALRRMEESLKDEIWVARFEKPNTAPNSLEPSTTVLSPYLKFGCLS 294
Query: 111 VRLFYHELKKILATGP-HAKPPVSLLGQIYWREFYYVVGSDTPNFDKMKGNKICCQVDWD 169
RLF +LK+I+ P H++PPVSL+GQ+ WREFYY V + PNFD+M GN C Q+ W
Sbjct: 295 ARLFNQKLKEIIKRQPKHSQPPVSLIGQLMWREFYYTVAAAEPNFDRMLGNVYCMQIPWQ 354
Query: 170 TNEKYLEAWSHGKTGYPFIDAIMRQLRLEGWIHHLARHAVACFLTRGDLYLSWEEGQSVF 229
+ +LEAW+HG+TGYPFIDAIMRQLR EGWIHHLARHAVACFLTRGDL++SWEEGQ VF
Sbjct: 355 EHPDHLEAWTHGRTGYPFIDAIMRQLRQEGWIHHLARHAVACFLTRGDLWISWEEGQRVF 414
Query: 230 EELLLDADWAMNAGNWMWLSASAFFHQFFRVYSPVAFGKKTD 271
E+LLLD DWA+NAGNWMWLSASAFFHQ+FRVYSPVAFGKKTD
Sbjct: 415 EQLLLDQDWALNAGNWMWLSASAFFHQYFRVYSPVAFGKKTD 456
>pdb|3CVW|A Chain A, Drosophila Melanogaster (6-4) Photolyase H365n Mutant
Bound To Ds Dna With A T-T (6-4) Photolesion And
Cofactor F0
Length = 543
Score = 364 bits (935), Expect = e-101, Method: Compositional matrix adjust.
Identities = 177/282 (62%), Positives = 215/282 (76%), Gaps = 16/282 (5%)
Query: 1 MTYQKLVSVLESLPKPKPADDAPTSLPRECQGILHPDEHLV----------PTMKEMGLD 50
+TYQK + ++E L PK +P + + + P + V PTMK++
Sbjct: 180 ITYQKFLGIVEQLKVPKV-----LGVPEKLKNMPTPPKDEVEQKDSAAYDCPTMKQLVKR 234
Query: 51 ESSIPLCKFPGGETEALKRLEKSLANKEWVRKFEKPNTAPNSLEPSTTVLSPYLKFGCLS 110
+ KFPGGETEAL+R+E+SL ++ WV +FEKPNTAPNSLEPSTTVLSPYLKFGCLS
Sbjct: 235 PEELGPNKFPGGETEALRRMEESLKDEIWVARFEKPNTAPNSLEPSTTVLSPYLKFGCLS 294
Query: 111 VRLFYHELKKILATGP-HAKPPVSLLGQIYWREFYYVVGSDTPNFDKMKGNKICCQVDWD 169
RLF +LK+I+ P H++PPVSL+GQ+ WREFYY V + PNFD+M GN C Q+ W
Sbjct: 295 ARLFNQKLKEIIKRQPKHSQPPVSLIGQLMWREFYYTVAAAEPNFDRMLGNVYCMQIPWQ 354
Query: 170 TNEKYLEAWSHGKTGYPFIDAIMRQLRLEGWIHHLARHAVACFLTRGDLYLSWEEGQSVF 229
+ +LEAW+HG+TGYPFIDAIMRQLR EGWIH+LARHAVACFLTRGDL++SWEEGQ VF
Sbjct: 355 EHPDHLEAWTHGRTGYPFIDAIMRQLRQEGWIHNLARHAVACFLTRGDLWISWEEGQRVF 414
Query: 230 EELLLDADWAMNAGNWMWLSASAFFHQFFRVYSPVAFGKKTD 271
E+LLLD DWA+NAGNWMWLSASAFFHQ+FRVYSPVAFGKKTD
Sbjct: 415 EQLLLDQDWALNAGNWMWLSASAFFHQYFRVYSPVAFGKKTD 456
>pdb|3CVX|A Chain A, Drosophila Melanogaster (6-4) Photolyase H369m Mutant
Bound To Ds Dna With A T-T (6-4) Photolesion
Length = 543
Score = 363 bits (933), Expect = e-101, Method: Compositional matrix adjust.
Identities = 177/282 (62%), Positives = 214/282 (75%), Gaps = 16/282 (5%)
Query: 1 MTYQKLVSVLESLPKPKPADDAPTSLPRECQGILHPDEHLV----------PTMKEMGLD 50
+TYQK + ++E L PK +P + + + P + V PTMK++
Sbjct: 180 ITYQKFLGIVEQLKVPKV-----LGVPEKLKNMPTPPKDEVEQKDSAAYDCPTMKQLVKR 234
Query: 51 ESSIPLCKFPGGETEALKRLEKSLANKEWVRKFEKPNTAPNSLEPSTTVLSPYLKFGCLS 110
+ KFPGGETEAL+R+E+SL ++ WV +FEKPNTAPNSLEPSTTVLSPYLKFGCLS
Sbjct: 235 PEELGPNKFPGGETEALRRMEESLKDEIWVARFEKPNTAPNSLEPSTTVLSPYLKFGCLS 294
Query: 111 VRLFYHELKKILATGP-HAKPPVSLLGQIYWREFYYVVGSDTPNFDKMKGNKICCQVDWD 169
RLF +LK+I+ P H++PPVSL+GQ+ WREFYY V + PNFD+M GN C Q+ W
Sbjct: 295 ARLFNQKLKEIIKRQPKHSQPPVSLIGQLMWREFYYTVAAAEPNFDRMLGNVYCMQIPWQ 354
Query: 170 TNEKYLEAWSHGKTGYPFIDAIMRQLRLEGWIHHLARHAVACFLTRGDLYLSWEEGQSVF 229
+ +LEAW+HG+TGYPFIDAIMRQLR EGWIHHLAR AVACFLTRGDL++SWEEGQ VF
Sbjct: 355 EHPDHLEAWTHGRTGYPFIDAIMRQLRQEGWIHHLARMAVACFLTRGDLWISWEEGQRVF 414
Query: 230 EELLLDADWAMNAGNWMWLSASAFFHQFFRVYSPVAFGKKTD 271
E+LLLD DWA+NAGNWMWLSASAFFHQ+FRVYSPVAFGKKTD
Sbjct: 415 EQLLLDQDWALNAGNWMWLSASAFFHQYFRVYSPVAFGKKTD 456
>pdb|3FY4|A Chain A, (6-4) Photolyase Crystal Structure
pdb|3FY4|B Chain B, (6-4) Photolyase Crystal Structure
pdb|3FY4|C Chain C, (6-4) Photolyase Crystal Structure
Length = 537
Score = 298 bits (762), Expect = 4e-81, Method: Compositional matrix adjust.
Identities = 141/234 (60%), Positives = 176/234 (75%), Gaps = 3/234 (1%)
Query: 41 VPTMKEMGL-DESSIPLCKFPGGETEALKRLEKSLANKEWVRKFEKPNTAPNS-LEPSTT 98
VP+++E+G D+ F GGE+EALKRL KS+++K WV FEKP P++ L+P+TT
Sbjct: 199 VPSLEELGYKDDEQADWTPFRGGESEALKRLTKSISDKAWVANFEKPKGDPSAFLKPATT 258
Query: 99 VLSPYLKFGCLSVRLFYHELKKILA-TGPHAKPPVSLLGQIYWREFYYVVGSDTPNFDKM 157
V+SPYLKFGCLS R FY L+ I H PPVSLLGQ+ WREF+Y TPNFDKM
Sbjct: 259 VMSPYLKFGCLSSRYFYQCLQNIYKDVKKHTSPPVSLLGQLLWREFFYTTAFGTPNFDKM 318
Query: 158 KGNKICCQVDWDTNEKYLEAWSHGKTGYPFIDAIMRQLRLEGWIHHLARHAVACFLTRGD 217
KGN+IC Q+ W+ + L AW GKTGYP+IDAIM QL GW+HHLARH VACFLTRGD
Sbjct: 319 KGNRICKQIPWNEDHAMLAAWRDGKTGYPWIDAIMVQLLKWGWMHHLARHCVACFLTRGD 378
Query: 218 LYLSWEEGQSVFEELLLDADWAMNAGNWMWLSASAFFHQFFRVYSPVAFGKKTD 271
L++ WE+G+ VFE LL+D+DWA+N GNWMWLS S+FF+QF R+YSP++FGKK D
Sbjct: 379 LFIHWEQGRDVFERLLIDSDWAINNGNWMWLSCSSFFYQFNRIYSPISFGKKYD 432
>pdb|4GU5|A Chain A, Structure Of Full-Length Drosophila Cryptochrome
pdb|4GU5|B Chain B, Structure Of Full-Length Drosophila Cryptochrome
Length = 539
Score = 183 bits (464), Expect = 1e-46, Method: Compositional matrix adjust.
Identities = 99/224 (44%), Positives = 135/224 (60%), Gaps = 13/224 (5%)
Query: 61 GGETEALKRLEKSLANKE--WVRKFEKPNTAPNSLEPSTTVLSPYLKFGCLSVRLFY--- 115
GGET+AL L++ L ++ + R F PN A ++ S +S +L+FGCLSVR FY
Sbjct: 225 GGETQALLLLDERLKVEQHAFERGFYLPNQALPNIHDSPKSMSAHLRFGCLSVRRFYWSV 284
Query: 116 HELKKIL-----ATGPHAKPPVSLLGQIYWREFYYVVGSDTPNFDKMKGNKICCQVDW-D 169
H+L K + G + GQ+ WRE++Y + + PN+D+M+GN IC + W
Sbjct: 285 HDLFKNVQLRACVRGVQMTGGAHITGQLIWREYFYTMSVNNPNYDRMEGNDICLSIPWAK 344
Query: 170 TNEKYLEAWSHGKTGYPFIDAIMRQLRLEGWIHHLARHAVACFLTRGDLYLSWEEGQSVF 229
NE L++W G+TG+P ID MRQL EGW+HH R+ VA FLTRG L+ SWE G F
Sbjct: 345 PNENLLQSWRLGQTGFPLIDGAMRQLLAEGWLHHTLRNTVATFLTRGGLWQSWEHGLQHF 404
Query: 230 EELLLDADWAMNAGNWMWLSASAFFHQFFR--VYSPVAFGKKTD 271
+ LLDADW++ AGNWMW+S+SAF V PVA K+ D
Sbjct: 405 LKYLLDADWSVCAGNWMWVSSSAFERLLDSSLVTCPVALAKRLD 448
>pdb|1OWL|A Chain A, Structure Of Apophotolyase From Anacystis Nidulans
pdb|1OWM|A Chain A, Data1:dna Photolyase RECEIVED X-Rays Dose 1.2 Exp15
PhotonsMM2
pdb|1OWN|A Chain A, Data3:dna Photolyase RECEIVED X-Rays Dose 4.8 Exp15
PhotonsMM2
pdb|1OWO|A Chain A, Data4:photoreduced Dna Photolyase RECEIVED X-Rays Dose
1.2 Exp15 PhotonsMM2
pdb|1OWP|A Chain A, Data6:photoreduced Dna Pholyase RECEIVED X-Rays Dose 4.8
Exp15 PhotonsMM2
pdb|1QNF|A Chain A, Structure Of Photolyase
Length = 484
Score = 124 bits (312), Expect = 5e-29, Method: Compositional matrix adjust.
Identities = 86/273 (31%), Positives = 130/273 (47%), Gaps = 25/273 (9%)
Query: 11 ESLPKPKPADDAPTSL----PRECQGILHPDEHLVPTMKEMGLD-ESSIPLCKFPGGETE 65
++ PKP P PT L P + I +PT+K++G D + P+ GET
Sbjct: 157 QAQPKPTPVA-TPTELVDLSPEQLTAIAPLLLSELPTLKQLGFDWDGGFPVEP---GETA 212
Query: 66 ALKRLE----KSLANKEWVRKFEKPNTAPNSLEPSTTVLSPYLKFGCLSVR--LFYHELK 119
A+ RL+ +++A+ + R F E T+ LSP LKFG + +R
Sbjct: 213 AIARLQEFCDRAIADYDPQRNFPA--------EAGTSGLSPALKFGAIGIRQAWQAASAA 264
Query: 120 KILATGPHAKPPVSLLGQ-IYWREFYYVVGSDTPNFDKMKGNKICCQVDWDTNEKYLEAW 178
L+ A+ + + Q + WREFY P+ + Q W+ E AW
Sbjct: 265 HALSRSDEARNSIRVWQQELAWREFYQHALYHFPSLADGPYRSLWQQFPWENREALFTAW 324
Query: 179 SHGKTGYPFIDAIMRQLRLEGWIHHLARHAVACFLTRGDLYLSWEEGQSVFEELLLDADW 238
+ +TGYP +DA MRQL GW+H+ R VA FLT+ DL + W G+ F + L+D D
Sbjct: 325 TQAQTGYPIVDAAMRQLTETGWMHNRCRMIVASFLTK-DLIIDWRRGEQFFMQHLVDGDL 383
Query: 239 AMNAGNWMWLSASAFFHQFFRVYSPVAFGKKTD 271
A N G W W ++S + R+++P + KK D
Sbjct: 384 AANNGGWQWSASSGMDPKPLRIFNPASQAKKFD 416
>pdb|1TEZ|A Chain A, Complex Between Dna And The Dna Photolyase From Anacystis
Nidulans
pdb|1TEZ|B Chain B, Complex Between Dna And The Dna Photolyase From Anacystis
Nidulans
pdb|1TEZ|C Chain C, Complex Between Dna And The Dna Photolyase From Anacystis
Nidulans
pdb|1TEZ|D Chain D, Complex Between Dna And The Dna Photolyase From Anacystis
Nidulans
Length = 474
Score = 124 bits (312), Expect = 5e-29, Method: Compositional matrix adjust.
Identities = 86/273 (31%), Positives = 130/273 (47%), Gaps = 25/273 (9%)
Query: 11 ESLPKPKPADDAPTSL----PRECQGILHPDEHLVPTMKEMGLD-ESSIPLCKFPGGETE 65
++ PKP P PT L P + I +PT+K++G D + P+ GET
Sbjct: 156 QAQPKPTPVA-TPTELVDLSPEQLTAIAPLLLSELPTLKQLGFDWDGGFPVEP---GETA 211
Query: 66 ALKRLE----KSLANKEWVRKFEKPNTAPNSLEPSTTVLSPYLKFGCLSVR--LFYHELK 119
A+ RL+ +++A+ + R F E T+ LSP LKFG + +R
Sbjct: 212 AIARLQEFCDRAIADYDPQRNFPA--------EAGTSGLSPALKFGAIGIRQAWQAASAA 263
Query: 120 KILATGPHAKPPVSLLGQ-IYWREFYYVVGSDTPNFDKMKGNKICCQVDWDTNEKYLEAW 178
L+ A+ + + Q + WREFY P+ + Q W+ E AW
Sbjct: 264 HALSRSDEARNSIRVWQQELAWREFYQHALYHFPSLADGPYRSLWQQFPWENREALFTAW 323
Query: 179 SHGKTGYPFIDAIMRQLRLEGWIHHLARHAVACFLTRGDLYLSWEEGQSVFEELLLDADW 238
+ +TGYP +DA MRQL GW+H+ R VA FLT+ DL + W G+ F + L+D D
Sbjct: 324 TQAQTGYPIVDAAMRQLTETGWMHNRCRMIVASFLTK-DLIIDWRRGEQFFMQHLVDGDL 382
Query: 239 AMNAGNWMWLSASAFFHQFFRVYSPVAFGKKTD 271
A N G W W ++S + R+++P + KK D
Sbjct: 383 AANNGGWQWSASSGMDPKPLRIFNPASQAKKFD 415
>pdb|1DNP|A Chain A, Structure Of Deoxyribodipyrimidine Photolyase
pdb|1DNP|B Chain B, Structure Of Deoxyribodipyrimidine Photolyase
Length = 471
Score = 110 bits (276), Expect = 9e-25, Method: Compositional matrix adjust.
Identities = 76/225 (33%), Positives = 112/225 (49%), Gaps = 13/225 (5%)
Query: 52 SSIPLCKFPGGETEALKRLEKSLANKEWVRKFEKPNTAPNSLEPSTTVLSPYLKFGCLSV 111
S FP E A+ +L + N ++E+ P ++E T+ LS L G LS
Sbjct: 193 QSFDTAHFPVEEKAAIAQLRQFCQNG--AGEYEQQRDFP-AVE-GTSRLSASLATGGLSP 248
Query: 112 RLFYHELKKILATGPHA---KPPVSLLGQIYWREFYYVVGSDTPNFDKMKGNKI-CCQVD 167
R H ++LA P A L ++ WREFY + + P+ K + +V
Sbjct: 249 RQCLH---RLLAEQPQALDGGAGSVWLNELIWREFYRHLITYHPSLCKHRPFIAWTDRVQ 305
Query: 168 WDTNEKYLEAWSHGKTGYPFIDAIMRQLRLEGWIHHLARHAVACFLTRGDLYLSWEEGQS 227
W +N +L+AW GKTGYP +DA MRQL GW+H+ R A FL + DL + W EG+
Sbjct: 306 WQSNPAHLQAWQEGKTGYPIVDAAMRQLNSTGWMHNRLRMITASFLVK-DLLIDWREGER 364
Query: 228 VFEELLLDADWAMNAGNWMWLSASAF-FHQFFRVYSPVAFGKKTD 271
F L+D D A N G W W +++ +FR+++P G+K D
Sbjct: 365 YFMSQLIDGDLAANNGGWQWAASTGTDAAPYFRIFNPTTQGEKFD 409
>pdb|2E0I|A Chain A, Crystal Structure Of Archaeal Photolyase From Sulfolobus
Tokodaii With Two Fad Molecules: Implication Of A Novel
Light-Harvesting Cofactor
pdb|2E0I|B Chain B, Crystal Structure Of Archaeal Photolyase From Sulfolobus
Tokodaii With Two Fad Molecules: Implication Of A Novel
Light-Harvesting Cofactor
pdb|2E0I|C Chain C, Crystal Structure Of Archaeal Photolyase From Sulfolobus
Tokodaii With Two Fad Molecules: Implication Of A Novel
Light-Harvesting Cofactor
pdb|2E0I|D Chain D, Crystal Structure Of Archaeal Photolyase From Sulfolobus
Tokodaii With Two Fad Molecules: Implication Of A Novel
Light-Harvesting Cofactor
Length = 440
Score = 108 bits (271), Expect = 3e-24, Method: Compositional matrix adjust.
Identities = 70/216 (32%), Positives = 110/216 (50%), Gaps = 25/216 (11%)
Query: 59 FPGGETEALKRLEKSLANKEWVRKFEKPNTAPNSLEPSTTVLSPYLKFGCLSVRLFYHEL 118
F GG E L L +++ R+ + P E + LSP+LKFG +S+R Y+
Sbjct: 185 FRGGRREGLYLLHRNVD----FRRRDYP------AENNNYRLSPHLKFGTISMREAYYT- 233
Query: 119 KKILATGPHAKPPVSLLGQIYWREFYYVVGSDTPNFDKMKGNKICCQVDWDTNEKYLEAW 178
K + ++YWR+F+ ++ P+ + + W+ NE Y EAW
Sbjct: 234 ---------QKGKEEFVRELYWRDFFTLLAYYNPHVFGHCYRREYDNISWENNESYFEAW 284
Query: 179 SHGKTGYPFIDAIMRQLRLEGWIHHLARHAVACFLTRGDLYLSWEEGQSVFEELLLDADW 238
G+TGYP IDA MR L G+I+ R VA FL + L++ W G+ F L+D D
Sbjct: 285 KEGRTGYPIIDAGMRMLNSTGYINGRVRMLVAFFLVKV-LFVDWRWGERYFATKLVDYDP 343
Query: 239 AMNAGNWMWLSASAFFHQFFRVYSPVAFGKKTDKFE 274
A+N GNW W++++ + FRV++P K+ +KF+
Sbjct: 344 AINNGNWQWIASTGVDYM-FRVFNP---WKQQEKFD 375
>pdb|2J4D|A Chain A, Cryptochrome 3 From Arabidopsis Thaliana
pdb|2J4D|B Chain B, Cryptochrome 3 From Arabidopsis Thaliana
Length = 525
Score = 105 bits (262), Expect = 3e-23, Method: Compositional matrix adjust.
Identities = 64/209 (30%), Positives = 105/209 (50%), Gaps = 5/209 (2%)
Query: 41 VPTMKEMGLDESSIPL-CKFPGGETEALKRLEKSLANKEWVRKFEKPNTAPNSLEPS-TT 98
VPT++++G++ + +F GGE+ + R+ + K+ ++ +++ T L P +T
Sbjct: 229 VPTLEKLGVEPQEVTRGMRFVGGESAGVGRVFEYFWKKDLLKVYKE--TRNGMLGPDYST 286
Query: 99 VLSPYLKFGCLSVRLFYHELKKILATGPHAKPPVSLLGQIYWREFYYVVGSDTPNFDKMK 158
SP+L FGC+S R Y E+++ +L ++ WR+++ + N
Sbjct: 287 KFSPWLAFGCISPRFIYEEVQRYEKERVANNSTYWVLFELIWRDYFRFLSIKCGNSLFHL 346
Query: 159 GNKICCQVDWDTNEKYLEAWSHGKTGYPFIDAIMRQLRLEGWIHHLARHAVACFLTRGDL 218
G Q W ++K E+W KTGYP IDA M++L G++ + R V FL R D+
Sbjct: 347 GGPRNVQGKWSQDQKLFESWRDAKTGYPLIDANMKELSTTGFMSNRGRQIVCSFLVR-DM 405
Query: 219 YLSWEEGQSVFEELLLDADWAMNAGNWMW 247
L W G FE LLD D N GNW +
Sbjct: 406 GLDWRMGAEWFETCLLDYDPCSNYGNWTY 434
>pdb|2IJG|X Chain X, Crystal Structure Of Cryptochrome 3 From Arabidopsis
Thaliana
pdb|2VTB|A Chain A, Structure Of Cryptochrome 3 - Dna Complex
pdb|2VTB|C Chain C, Structure Of Cryptochrome 3 - Dna Complex
pdb|2VTB|D Chain D, Structure Of Cryptochrome 3 - Dna Complex
pdb|2VTB|E Chain E, Structure Of Cryptochrome 3 - Dna Complex
pdb|2VTB|F Chain F, Structure Of Cryptochrome 3 - Dna Complex
Length = 526
Score = 105 bits (262), Expect = 3e-23, Method: Compositional matrix adjust.
Identities = 64/209 (30%), Positives = 105/209 (50%), Gaps = 5/209 (2%)
Query: 41 VPTMKEMGLDESSIPL-CKFPGGETEALKRLEKSLANKEWVRKFEKPNTAPNSLEPS-TT 98
VPT++++G++ + +F GGE+ + R+ + K+ ++ +++ T L P +T
Sbjct: 230 VPTLEKLGVEPQEVTRGMRFVGGESAGVGRVFEYFWKKDLLKVYKE--TRNGMLGPDYST 287
Query: 99 VLSPYLKFGCLSVRLFYHELKKILATGPHAKPPVSLLGQIYWREFYYVVGSDTPNFDKMK 158
SP+L FGC+S R Y E+++ +L ++ WR+++ + N
Sbjct: 288 KFSPWLAFGCISPRFIYEEVQRYEKERVANNSTYWVLFELIWRDYFRFLSIKCGNSLFHL 347
Query: 159 GNKICCQVDWDTNEKYLEAWSHGKTGYPFIDAIMRQLRLEGWIHHLARHAVACFLTRGDL 218
G Q W ++K E+W KTGYP IDA M++L G++ + R V FL R D+
Sbjct: 348 GGPRNVQGKWSQDQKLFESWRDAKTGYPLIDANMKELSTTGFMSNRGRQIVCSFLVR-DM 406
Query: 219 YLSWEEGQSVFEELLLDADWAMNAGNWMW 247
L W G FE LLD D N GNW +
Sbjct: 407 GLDWRMGAEWFETCLLDYDPCSNYGNWTY 435
>pdb|2VTB|B Chain B, Structure Of Cryptochrome 3 - Dna Complex
Length = 525
Score = 103 bits (257), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 63/209 (30%), Positives = 104/209 (49%), Gaps = 5/209 (2%)
Query: 41 VPTMKEMGLDESSIPL-CKFPGGETEALKRLEKSLANKEWVRKFEKPNTAPNSLEPS-TT 98
VPT++++G++ + +F GGE+ + R+ + K+ ++ +++ T L P +T
Sbjct: 230 VPTLEKLGVEPQEVTRGMRFVGGESAGVGRVFEYFWKKDLLKVYKE--TRNGMLGPDYST 287
Query: 99 VLSPYLKFGCLSVRLFYHELKKILATGPHAKPPVSLLGQIYWREFYYVVGSDTPNFDKMK 158
SP+L FGC+S R Y E+++ +L ++ WR+++ + N
Sbjct: 288 KFSPWLAFGCISPRFIYEEVQRYEKERVANNSTYWVLFELIWRDYFRFLSIKCGNSLFHL 347
Query: 159 GNKICCQVDWDTNEKYLEAWSHGKTGYPFIDAIMRQLRLEGWIHHLARHAVACFLTRGDL 218
G W ++K E+W KTGYP IDA M++L G++ + R V FL R D+
Sbjct: 348 GGPRNVNGKWSQDQKLFESWRDAKTGYPLIDANMKELSTTGFMSNRGRQIVCSFLVR-DM 406
Query: 219 YLSWEEGQSVFEELLLDADWAMNAGNWMW 247
L W G FE LLD D N GNW +
Sbjct: 407 GLDWRMGAEWFETCLLDYDPCSNYGNWTY 435
>pdb|1NP7|A Chain A, Crystal Structure Analysis Of Synechocystis Sp. Pcc6803
Cryptochrome
pdb|1NP7|B Chain B, Crystal Structure Analysis Of Synechocystis Sp. Pcc6803
Cryptochrome
Length = 489
Score = 102 bits (253), Expect = 3e-22, Method: Compositional matrix adjust.
Identities = 63/217 (29%), Positives = 103/217 (47%), Gaps = 4/217 (1%)
Query: 46 EMGLDESSIPLCKFPGGETEALKRLEKSLANKEWVRKFEKPNTAPNSLEPSTTVLSPYLK 105
++ D S+ F GGET L RL+ + + ++ +++ + S+ SP+L
Sbjct: 201 QINFDHRSV--LAFQGGETAGLARLQDYFWHGDRLKDYKETRNGMVGADYSSK-FSPWLA 257
Query: 106 FGCLSVRLFYHELKKILATGPHAKPPVSLLGQIYWREFYYVVGSDTPNFDKMKGNKICCQ 165
GCLS R Y E+K+ L+ ++ WR+F+ V N +G +
Sbjct: 258 LGCLSPRFIYQEVKRYEQERVSNDSTHWLIFELLWRDFFRFVAQKYGNKLFNRGGLLNKN 317
Query: 166 VDWDTNEKYLEAWSHGKTGYPFIDAIMRQLRLEGWIHHLARHAVACFLTRGDLYLSWEEG 225
W ++ E W G+TGYP +DA MR+L L G++ + R VA FL + +L + W G
Sbjct: 318 FPWQEDQVRFELWRSGQTGYPLVDANMRELNLTGFMSNRGRQNVASFLCK-NLGIDWRWG 376
Query: 226 QSVFEELLLDADWAMNAGNWMWLSASAFFHQFFRVYS 262
FE L+D D N GNW + + + FR ++
Sbjct: 377 AEWFESCLIDYDVCSNWGNWNYTAGIGNDARDFRYFN 413
>pdb|1IQR|A Chain A, Crystal Structure Of Dna Photolyase From Thermus
Thermophilus
pdb|1IQU|A Chain A, Crystal Structure Of Photolyase-Thymine Complex
pdb|2J07|A Chain A, Thermus Dna Photolyase With 8-Hdf Antenna Chromophore
pdb|2J08|A Chain A, Thermus Dna Photolyase With 8-Iod-Riboflavin Antenna
Chromophore
pdb|2J09|A Chain A, Thermus Dna Photolyase With Fmn Antenna Chromophore
Length = 420
Score = 87.0 bits (214), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 55/175 (31%), Positives = 81/175 (46%), Gaps = 7/175 (4%)
Query: 98 TVLSPYLKFGCLSVRLFYHELKKILATGPHAKPPVSLLGQIYWREFYYVVGSDTPNFDKM 157
+ LSPY G LS RL E ++ G + ++ WR+F Y + P +
Sbjct: 210 SRLSPYFALGVLSPRLAAWEAERRGGEGAR-----KWVAELLWRDFSYHLLYHFPWMAER 264
Query: 158 KGNKICCQVDWDTNEKYLEAWSHGKTGYPFIDAIMRQLRLEGWIHHLARHAVACFLTRGD 217
+ W +E +AW GKTG P +DA MR+L G++ + AR A F +
Sbjct: 265 PLDPRFQAFPWQEDEALFQAWYEGKTGVPLVDAAMRELHATGFLSNRARMNAAQFAVK-H 323
Query: 218 LYLSWEEGQSVFEELLLDADWAMNAGNWMWLSASAF-FHQFFRVYSPVAFGKKTD 271
L L W+ + F LLLD D A+N W W +FRV++PV G++ D
Sbjct: 324 LLLPWKRCEEAFRHLLLDGDRAVNLQGWQWAGGLGVDAAPYFRVFNPVLQGERHD 378
>pdb|1U3C|A Chain A, Crystal Structure Of The Phr Domain Of Cryptochrome 1 From
Arabidopsis Thaliana
pdb|1U3D|A Chain A, Crystal Structure Of The Phr Domain Of Cryptochrome 1 From
Arabidopsis Thaliana With Amppnp Bound
Length = 509
Score = 73.2 bits (178), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 58/183 (31%), Positives = 89/183 (48%), Gaps = 8/183 (4%)
Query: 96 STTVLSPYLKFGCLSVRLFYH--ELKKIL---ATGPHAKPPVSL-LGQIYWREFYYVVGS 149
+T+ LSP+L FG +SVR +H +K++ + V+L L I RE+ +
Sbjct: 246 TTSFLSPHLHFGEVSVRKVFHLVRIKQVAWANEGNEAGEESVNLFLKSIGLREYSRYISF 305
Query: 150 DTPNFDKMKGNKICCQVDWDTNEKYLEAWSHGKTGYPFIDAIMRQLRLEGWIHHLARHAV 209
+ P + W +E Y +AW G+TGYP +DA MR+L GW+H R V
Sbjct: 306 NHPYSHERPLLGHLKFFPWAVDENYFKAWRQGRTGYPLVDAGMRELWATGWLHDRIRVVV 365
Query: 210 ACFLTRGDLYLSWEEGQSVFEELLLDADWAMNAGNWMWLSAS-AFFHQFFRVYSPVAFGK 268
+ F + L L W G F + LLDAD +A W +++ + +F R+ +P G
Sbjct: 366 SSFFVK-VLQLPWRWGMKYFWDTLLDADLESDALGWQYITGTLPDSREFDRIDNPQFEGY 424
Query: 269 KTD 271
K D
Sbjct: 425 KFD 427
>pdb|3QR1|A Chain A, Crystal Structure Of L. Pealei Plc21
pdb|3QR1|D Chain D, Crystal Structure Of L. Pealei Plc21
Length = 813
Score = 33.5 bits (75), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 14/25 (56%), Positives = 17/25 (68%)
Query: 213 LTRGDLYLSWEEGQSVFEELLLDAD 237
L +GD +L WEEG S F E+LL D
Sbjct: 22 LIKGDKFLKWEEGSSSFTEILLRVD 46
>pdb|3QR0|A Chain A, Crystal Structure Of S. Officinalis Plc21
Length = 816
Score = 32.0 bits (71), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 14/25 (56%), Positives = 17/25 (68%)
Query: 213 LTRGDLYLSWEEGQSVFEELLLDAD 237
L +GD +L WEEG S F E+LL D
Sbjct: 22 LIKGDKFLKWEEGSSGFIEILLRVD 46
>pdb|4E1J|A Chain A, Crystal Structure Of Glycerol Kinase In Complex With
Glycerol From Sinorhizobium Meliloti 1021
pdb|4E1J|B Chain B, Crystal Structure Of Glycerol Kinase In Complex With
Glycerol From Sinorhizobium Meliloti 1021
pdb|4E1J|C Chain C, Crystal Structure Of Glycerol Kinase In Complex With
Glycerol From Sinorhizobium Meliloti 1021
pdb|4E1J|D Chain D, Crystal Structure Of Glycerol Kinase In Complex With
Glycerol From Sinorhizobium Meliloti 1021
Length = 520
Score = 29.3 bits (64), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 11/44 (25%), Positives = 22/44 (50%)
Query: 168 WDTNEKYLEAWSHGKTGYPFIDAIMRQLRLEGWIHHLARHAVAC 211
W E + ++W+ + P D R+++L+GW + R +A
Sbjct: 477 WPNQEAFAKSWARDRRFEPHXDEATRKVKLKGWRSAVKRTLIAA 520
>pdb|2XRY|A Chain A, X-Ray Structure Of Archaeal Class Ii Cpd Photolyase From
Methanosarcina Mazei
pdb|2XRZ|A Chain A, X-Ray Structure Of Archaeal Class Ii Cpd Photolyase From
Methanosarcina Mazei In Complex With Intact Cpd-Lesion
pdb|2XRZ|B Chain B, X-Ray Structure Of Archaeal Class Ii Cpd Photolyase From
Methanosarcina Mazei In Complex With Intact Cpd-Lesion
Length = 482
Score = 28.9 bits (63), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 44/158 (27%), Positives = 69/158 (43%), Gaps = 19/158 (12%)
Query: 59 FPGGETEALKRLEKSLANKEWVRKFEKPNTAPNSLEPSTTVLSPYLKFGCLSVRLFYHEL 118
F GE A K +E +A++ + + N L + LSPYL FG +S + E+
Sbjct: 248 FEPGEKAAKKVMESFIADRLDSYGALRNDPTKNML----SNLSPYLHFGQISSQRVVLEV 303
Query: 119 KKILATGPHAKPPVSLLGQI-YWREF-----YYVVGSDT----PNFDKMKGNKICCQVDW 168
+K + P +K + L +I W+E YY G D P++ K N + D
Sbjct: 304 EKA-ESNPGSKK--AFLDEILIWKEISDNFCYYNPGYDGFESFPSWAKESLN--AHRNDV 358
Query: 169 DTNEKYLEAWSHGKTGYPFIDAIMRQLRLEGWIHHLAR 206
++ LE + GKT P +A +L G +H R
Sbjct: 359 RSHIYTLEEFEAGKTHDPLWNASQMELLSTGKMHGYTR 396
>pdb|3IG4|A Chain A, Structure Of A Putative Aminopeptidase P From Bacillus
Anthracis
pdb|3IG4|B Chain B, Structure Of A Putative Aminopeptidase P From Bacillus
Anthracis
pdb|3IG4|C Chain C, Structure Of A Putative Aminopeptidase P From Bacillus
Anthracis
pdb|3IG4|D Chain D, Structure Of A Putative Aminopeptidase P From Bacillus
Anthracis
pdb|3IG4|E Chain E, Structure Of A Putative Aminopeptidase P From Bacillus
Anthracis
pdb|3IG4|F Chain F, Structure Of A Putative Aminopeptidase P From Bacillus
Anthracis
Length = 427
Score = 28.5 bits (62), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 8/74 (10%)
Query: 81 RKFEKPNTAPNSLEPSTTVLSPYLKFGCLSVRLFYHELKKILATGPHAKPPVS---LLGQ 137
R+ + N N+L+ +T ++ P LKF L+ KK+LA G A + L +
Sbjct: 281 RQKQIYNIVLNALKETTEIIKPGLKFAALN-----EHAKKVLAEGCKAVGLIQEDEELSK 335
Query: 138 IYWREFYYVVGSDT 151
Y+ + +G DT
Sbjct: 336 YYYHGVSHFLGLDT 349
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
0.321 0.136 0.446
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,072,483
Number of Sequences: 62578
Number of extensions: 492871
Number of successful extensions: 915
Number of sequences better than 100.0: 30
Number of HSP's better than 100.0 without gapping: 18
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 850
Number of HSP's gapped (non-prelim): 44
length of query: 315
length of database: 14,973,337
effective HSP length: 99
effective length of query: 216
effective length of database: 8,778,115
effective search space: 1896072840
effective search space used: 1896072840
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)