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= 044070
(903 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3EI4|A Chain A, Structure Of The Hsddb1-Hsddb2 Complex
pdb|3EI4|C Chain C, Structure Of The Hsddb1-Hsddb2 Complex
pdb|3EI4|E Chain E, Structure Of The Hsddb1-Hsddb2 Complex
Length = 1158
Score = 96.7 bits (239), Expect = 5e-20, Method: Compositional matrix adjust.
Identities = 68/235 (28%), Positives = 112/235 (47%), Gaps = 26/235 (11%)
Query: 446 MGDGMVLK------EENGRLVYTSPIQNIAPILDMSVVDYHDEKRDQMFACCGVAPEGSL 499
+GD ++K E+ +V N+ PI+DM VVD + + Q+ C G EGSL
Sbjct: 346 LGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSL 405
Query: 500 RIIRSGISLEKLLRTAPIYQGITGTWTVRMKVSDPYHSFLVLSFVEETRVLRVGLNFTDV 559
RIIR+GI + + + GI G W +R + + LVLSFV +TRVL + +
Sbjct: 406 RIIRNGIGIHE--HASIDLPGIKGLWPLRSDPNRETYDTLVLSFVGQTRVLMLNGEEVEE 463
Query: 560 TDSVGFRPDVCTLACGLVADGLLVQIHQNAVRLCMPTMVAHSGGIPLSYPVCTSWF-PEH 618
T+ +GF D T CG VA L+QI +VRL A + + W P+
Sbjct: 464 TELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVSQEPKA----------LVSEWKEPQA 513
Query: 619 VSISLGAVAHNMIIVSTSNPCFLFILGVRSLSVSHYEIYEMQHMRLQSELSCISI 673
+IS+ + + ++V+ + L + E+ ++ H ++ E++C+ I
Sbjct: 514 KNISVASCNSSQVVVAVGRALYY-------LQIHPQELRQISHTEMEHEVACLDI 561
Score = 33.1 bits (74), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 18/86 (20%), Positives = 40/86 (46%), Gaps = 3/86 (3%)
Query: 821 LPINLQLIATRR---IGITPVFLVPLSDSLDADMIALSDRPWLLQTARHSLAYTSISFQP 877
L I L++ R+ +G P L ++ A SDRP ++ ++ H L +++++ +
Sbjct: 634 LNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIYSSNHKLVFSNVNLKE 693
Query: 878 STHATPVCSVECPKGILFVAENSLNL 903
+ P+ S P + ++L +
Sbjct: 694 VNYMCPLNSDGYPDSLALANNSTLTI 719
>pdb|3I7H|A Chain A, Crystal Structure Of Ddb1 In Complex With The H-Box Motif
Of Hbx
pdb|3I7K|A Chain A, Crystal Structure Of Ddb1 In Complex With The H-Box Motif
Of Whx
pdb|3I7L|A Chain A, Crystal Structure Of Ddb1 In Complex With The H-Box Motif
Of Ddb2
pdb|3I7N|A Chain A, Crystal Structure Of Ddb1 In Complex With The H-Box Motif
Of Wdtc1
pdb|3I7O|A Chain A, Crystal Structure Of Ddb1 In Complex With The H-Box Motif
Of Iqwd1
pdb|3I7P|A Chain A, Crystal Structure Of Ddb1 In Complex With The H-Box Motif
Of Wdr40a
pdb|3I89|A Chain A, Crystal Structure Of Ddb1 In Complex With The H-Box Motif
Of Wdr22
pdb|3I8C|A Chain A, Crystal Structure Of Ddb1 In Complex With The H-Box Motif
Of Wdr21a
pdb|3I8E|A Chain A, Crystal Structure Of Ddb1 In Complex With The H-Box Motif
Of Wdr42a
pdb|3I8E|B Chain B, Crystal Structure Of Ddb1 In Complex With The H-Box Motif
Of Wdr42a
Length = 1143
Score = 96.7 bits (239), Expect = 6e-20, Method: Compositional matrix adjust.
Identities = 68/235 (28%), Positives = 112/235 (47%), Gaps = 26/235 (11%)
Query: 446 MGDGMVLK------EENGRLVYTSPIQNIAPILDMSVVDYHDEKRDQMFACCGVAPEGSL 499
+GD ++K E+ +V N+ PI+DM VVD + + Q+ C G EGSL
Sbjct: 331 LGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSL 390
Query: 500 RIIRSGISLEKLLRTAPIYQGITGTWTVRMKVSDPYHSFLVLSFVEETRVLRVGLNFTDV 559
RIIR+GI + + + GI G W +R + + LVLSFV +TRVL + +
Sbjct: 391 RIIRNGIGIHE--HASIDLPGIKGLWPLRSDPNRETYDTLVLSFVGQTRVLMLNGEEVEE 448
Query: 560 TDSVGFRPDVCTLACGLVADGLLVQIHQNAVRLCMPTMVAHSGGIPLSYPVCTSWF-PEH 618
T+ +GF D T CG VA L+QI +VRL A + + W P+
Sbjct: 449 TELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVSQEPKA----------LVSEWKEPQA 498
Query: 619 VSISLGAVAHNMIIVSTSNPCFLFILGVRSLSVSHYEIYEMQHMRLQSELSCISI 673
+IS+ + + ++V+ + L + E+ ++ H ++ E++C+ I
Sbjct: 499 KNISVASCNSSQVVVAVGRALYY-------LQIHPQELRQISHTEMEHEVACLDI 546
Score = 33.1 bits (74), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 18/86 (20%), Positives = 40/86 (46%), Gaps = 3/86 (3%)
Query: 821 LPINLQLIATRR---IGITPVFLVPLSDSLDADMIALSDRPWLLQTARHSLAYTSISFQP 877
L I L++ R+ +G P L ++ A SDRP ++ ++ H L +++++ +
Sbjct: 619 LNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIYSSNHKLVFSNVNLKE 678
Query: 878 STHATPVCSVECPKGILFVAENSLNL 903
+ P+ S P + ++L +
Sbjct: 679 VNYMCPLNSDGYPDSLALANNSTLTI 704
>pdb|2B5L|A Chain A, Crystal Structure Of Ddb1 In Complex With Simian Virus 5 V
Protein
pdb|2B5L|B Chain B, Crystal Structure Of Ddb1 In Complex With Simian Virus 5 V
Protein
pdb|2B5M|A Chain A, Crystal Structure Of Ddb1
pdb|2HYE|A Chain A, Crystal Structure Of The Ddb1-cul4a-rbx1-sv5v Complex
Length = 1140
Score = 96.3 bits (238), Expect = 6e-20, Method: Compositional matrix adjust.
Identities = 68/235 (28%), Positives = 112/235 (47%), Gaps = 26/235 (11%)
Query: 446 MGDGMVLK------EENGRLVYTSPIQNIAPILDMSVVDYHDEKRDQMFACCGVAPEGSL 499
+GD ++K E+ +V N+ PI+DM VVD + + Q+ C G EGSL
Sbjct: 328 LGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSL 387
Query: 500 RIIRSGISLEKLLRTAPIYQGITGTWTVRMKVSDPYHSFLVLSFVEETRVLRVGLNFTDV 559
RIIR+GI + + + GI G W +R + + LVLSFV +TRVL + +
Sbjct: 388 RIIRNGIGIHE--HASIDLPGIKGLWPLRSDPNRETYDTLVLSFVGQTRVLMLNGEEVEE 445
Query: 560 TDSVGFRPDVCTLACGLVADGLLVQIHQNAVRLCMPTMVAHSGGIPLSYPVCTSWF-PEH 618
T+ +GF D T CG VA L+QI +VRL A + + W P+
Sbjct: 446 TELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVSQEPKA----------LVSEWKEPQA 495
Query: 619 VSISLGAVAHNMIIVSTSNPCFLFILGVRSLSVSHYEIYEMQHMRLQSELSCISI 673
+IS+ + + ++V+ + L + E+ ++ H ++ E++C+ I
Sbjct: 496 KNISVASCNSSQVVVAVGRALYY-------LQIHPQELRQISHTEMEHEVACLDI 543
Score = 33.1 bits (74), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 18/86 (20%), Positives = 40/86 (46%), Gaps = 3/86 (3%)
Query: 821 LPINLQLIATRR---IGITPVFLVPLSDSLDADMIALSDRPWLLQTARHSLAYTSISFQP 877
L I L++ R+ +G P L ++ A SDRP ++ ++ H L +++++ +
Sbjct: 616 LNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIYSSNHKLVFSNVNLKE 675
Query: 878 STHATPVCSVECPKGILFVAENSLNL 903
+ P+ S P + ++L +
Sbjct: 676 VNYMCPLNSDGYPDSLALANNSTLTI 701
>pdb|3EI1|A Chain A, Structure Of Hsddb1-Drddb2 Bound To A 14 Bp 6-4
Photoproduct Containing Dna-Duplex
pdb|3EI2|A Chain A, Structure Of Hsddb1-Drddb2 Bound To A 16 Bp Abasic Site
Containing Dna-Duplex
pdb|3EI3|A Chain A, Structure Of The Hsddb1-Drddb2 Complex
Length = 1158
Score = 95.5 bits (236), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 68/235 (28%), Positives = 111/235 (47%), Gaps = 26/235 (11%)
Query: 446 MGDGMVLK------EENGRLVYTSPIQNIAPILDMSVVDYHDEKRDQMFACCGVAPEGSL 499
+GD ++K E+ +V N+ PI+DM VVD + + Q+ C G EGSL
Sbjct: 346 LGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSL 405
Query: 500 RIIRSGISLEKLLRTAPIYQGITGTWTVRMKVSDPYHSFLVLSFVEETRVLRVGLNFTDV 559
RIIR+GI + + + GI G W +R + LVLSFV +TRVL + +
Sbjct: 406 RIIRNGIGIHE--HASIDLPGIKGLWPLRSDPNRETDDTLVLSFVGQTRVLMLNGEEVEE 463
Query: 560 TDSVGFRPDVCTLACGLVADGLLVQIHQNAVRLCMPTMVAHSGGIPLSYPVCTSWF-PEH 618
T+ +GF D T CG VA L+QI +VRL A + + W P+
Sbjct: 464 TELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVSQEPKA----------LVSEWKEPQA 513
Query: 619 VSISLGAVAHNMIIVSTSNPCFLFILGVRSLSVSHYEIYEMQHMRLQSELSCISI 673
+IS+ + + ++V+ + L + E+ ++ H ++ E++C+ I
Sbjct: 514 KNISVASCNSSQVVVAVGRALYY-------LQIHPQELRQISHTEMEHEVACLDI 561
Score = 33.1 bits (74), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 18/86 (20%), Positives = 40/86 (46%), Gaps = 3/86 (3%)
Query: 821 LPINLQLIATRR---IGITPVFLVPLSDSLDADMIALSDRPWLLQTARHSLAYTSISFQP 877
L I L++ R+ +G P L ++ A SDRP ++ ++ H L +++++ +
Sbjct: 634 LNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIYSSNHKLVFSNVNLKE 693
Query: 878 STHATPVCSVECPKGILFVAENSLNL 903
+ P+ S P + ++L +
Sbjct: 694 VNYMCPLNSDGYPDSLALANNSTLTI 719
>pdb|4A0L|A Chain A, Structure Of Ddb1-Ddb2-Cul4b-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
pdb|4A0L|C Chain C, Structure Of Ddb1-Ddb2-Cul4b-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
Length = 1144
Score = 95.5 bits (236), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 68/235 (28%), Positives = 111/235 (47%), Gaps = 26/235 (11%)
Query: 446 MGDGMVLK------EENGRLVYTSPIQNIAPILDMSVVDYHDEKRDQMFACCGVAPEGSL 499
+GD ++K E+ +V N+ PI+DM VVD + + Q+ C G EGSL
Sbjct: 332 LGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSL 391
Query: 500 RIIRSGISLEKLLRTAPIYQGITGTWTVRMKVSDPYHSFLVLSFVEETRVLRVGLNFTDV 559
RIIR+GI + + + GI G W +R + LVLSFV +TRVL + +
Sbjct: 392 RIIRNGIGIHE--HASIDLPGIKGLWPLRSDPNRETDDTLVLSFVGQTRVLMLNGEEVEE 449
Query: 560 TDSVGFRPDVCTLACGLVADGLLVQIHQNAVRLCMPTMVAHSGGIPLSYPVCTSWF-PEH 618
T+ +GF D T CG VA L+QI +VRL A + + W P+
Sbjct: 450 TELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVSQEPKA----------LVSEWKEPQA 499
Query: 619 VSISLGAVAHNMIIVSTSNPCFLFILGVRSLSVSHYEIYEMQHMRLQSELSCISI 673
+IS+ + + ++V+ + L + E+ ++ H ++ E++C+ I
Sbjct: 500 KNISVASCNSSQVVVAVGRALYY-------LQIHPQELRQISHTEMEHEVACLDI 547
Score = 33.1 bits (74), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 18/86 (20%), Positives = 40/86 (46%), Gaps = 3/86 (3%)
Query: 821 LPINLQLIATRR---IGITPVFLVPLSDSLDADMIALSDRPWLLQTARHSLAYTSISFQP 877
L I L++ R+ +G P L ++ A SDRP ++ ++ H L +++++ +
Sbjct: 620 LNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIYSSNHKLVFSNVNLKE 679
Query: 878 STHATPVCSVECPKGILFVAENSLNL 903
+ P+ S P + ++L +
Sbjct: 680 VNYMCPLNSDGYPDSLALANNSTLTI 705
>pdb|4A11|A Chain A, Structure Of The Hsddb1-Hscsa Complex
pdb|4A0K|C Chain C, Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
Length = 1159
Score = 95.5 bits (236), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 68/235 (28%), Positives = 111/235 (47%), Gaps = 26/235 (11%)
Query: 446 MGDGMVLK------EENGRLVYTSPIQNIAPILDMSVVDYHDEKRDQMFACCGVAPEGSL 499
+GD ++K E+ +V N+ PI+DM VVD + + Q+ C G EGSL
Sbjct: 347 LGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSL 406
Query: 500 RIIRSGISLEKLLRTAPIYQGITGTWTVRMKVSDPYHSFLVLSFVEETRVLRVGLNFTDV 559
RIIR+GI + + + GI G W +R + LVLSFV +TRVL + +
Sbjct: 407 RIIRNGIGIHE--HASIDLPGIKGLWPLRSDPNRETDDTLVLSFVGQTRVLMLNGEEVEE 464
Query: 560 TDSVGFRPDVCTLACGLVADGLLVQIHQNAVRLCMPTMVAHSGGIPLSYPVCTSWF-PEH 618
T+ +GF D T CG VA L+QI +VRL A + + W P+
Sbjct: 465 TELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVSQEPKA----------LVSEWKEPQA 514
Query: 619 VSISLGAVAHNMIIVSTSNPCFLFILGVRSLSVSHYEIYEMQHMRLQSELSCISI 673
+IS+ + + ++V+ + L + E+ ++ H ++ E++C+ I
Sbjct: 515 KNISVASCNSSQVVVAVGRALYY-------LQIHPQELRQISHTEMEHEVACLDI 562
Score = 33.1 bits (74), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 18/86 (20%), Positives = 40/86 (46%), Gaps = 3/86 (3%)
Query: 821 LPINLQLIATRR---IGITPVFLVPLSDSLDADMIALSDRPWLLQTARHSLAYTSISFQP 877
L I L++ R+ +G P L ++ A SDRP ++ ++ H L +++++ +
Sbjct: 635 LNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIYSSNHKLVFSNVNLKE 694
Query: 878 STHATPVCSVECPKGILFVAENSLNL 903
+ P+ S P + ++L +
Sbjct: 695 VNYMCPLNSDGYPDSLALANNSTLTI 720
>pdb|4A08|A Chain A, Structure Of Hsddb1-Drddb2 Bound To A 13 Bp Cpd-Duplex (
Purine At D-1 Position) At 3.0 A Resolution (Cpd 1)
pdb|4A09|A Chain A, Structure Of Hsddb1-Drddb2 Bound To A 15 Bp Cpd-Duplex
(Purine At D-1 Position) At 3.1 A Resolution (Cpd 2)
Length = 1159
Score = 95.5 bits (236), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 68/235 (28%), Positives = 111/235 (47%), Gaps = 26/235 (11%)
Query: 446 MGDGMVLK------EENGRLVYTSPIQNIAPILDMSVVDYHDEKRDQMFACCGVAPEGSL 499
+GD ++K E+ +V N+ PI+DM VVD + + Q+ C G EGSL
Sbjct: 347 LGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSL 406
Query: 500 RIIRSGISLEKLLRTAPIYQGITGTWTVRMKVSDPYHSFLVLSFVEETRVLRVGLNFTDV 559
RIIR+GI + + + GI G W +R + LVLSFV +TRVL + +
Sbjct: 407 RIIRNGIGIHE--HASIDLPGIKGLWPLRSDPNRETDDTLVLSFVGQTRVLMLNGEEVEE 464
Query: 560 TDSVGFRPDVCTLACGLVADGLLVQIHQNAVRLCMPTMVAHSGGIPLSYPVCTSWF-PEH 618
T+ +GF D T CG VA L+QI +VRL A + + W P+
Sbjct: 465 TELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVSQEPKA----------LVSEWKEPQA 514
Query: 619 VSISLGAVAHNMIIVSTSNPCFLFILGVRSLSVSHYEIYEMQHMRLQSELSCISI 673
+IS+ + + ++V+ + L + E+ ++ H ++ E++C+ I
Sbjct: 515 KNISVASCNSSQVVVAVGRALYY-------LQIHPQELRQISHTEMEHEVACLDI 562
Score = 33.1 bits (74), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 18/86 (20%), Positives = 40/86 (46%), Gaps = 3/86 (3%)
Query: 821 LPINLQLIATRR---IGITPVFLVPLSDSLDADMIALSDRPWLLQTARHSLAYTSISFQP 877
L I L++ R+ +G P L ++ A SDRP ++ ++ H L +++++ +
Sbjct: 635 LNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIYSSNHKLVFSNVNLKE 694
Query: 878 STHATPVCSVECPKGILFVAENSLNL 903
+ P+ S P + ++L +
Sbjct: 695 VNYMCPLNSDGYPDSLALANNSTLTI 720
>pdb|4A0B|A Chain A, Structure Of Hsddb1-Drddb2 Bound To A 16 Bp Cpd-Duplex (
Pyrimidine At D-1 Position) At 3.8 A Resolution (Cpd 4)
pdb|4A0B|C Chain C, Structure Of Hsddb1-Drddb2 Bound To A 16 Bp Cpd-Duplex (
Pyrimidine At D-1 Position) At 3.8 A Resolution (Cpd 4)
Length = 1159
Score = 95.5 bits (236), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 68/235 (28%), Positives = 111/235 (47%), Gaps = 26/235 (11%)
Query: 446 MGDGMVLK------EENGRLVYTSPIQNIAPILDMSVVDYHDEKRDQMFACCGVAPEGSL 499
+GD ++K E+ +V N+ PI+DM VVD + + Q+ C G EGSL
Sbjct: 347 LGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSL 406
Query: 500 RIIRSGISLEKLLRTAPIYQGITGTWTVRMKVSDPYHSFLVLSFVEETRVLRVGLNFTDV 559
RIIR+GI + + + GI G W +R + LVLSFV +TRVL + +
Sbjct: 407 RIIRNGIGIHE--HASIDLPGIKGLWPLRSDPNRETDDTLVLSFVGQTRVLMLNGEEVEE 464
Query: 560 TDSVGFRPDVCTLACGLVADGLLVQIHQNAVRLCMPTMVAHSGGIPLSYPVCTSWF-PEH 618
T+ +GF D T CG VA L+QI +VRL A + + W P+
Sbjct: 465 TELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVSQEPKA----------LVSEWKEPQA 514
Query: 619 VSISLGAVAHNMIIVSTSNPCFLFILGVRSLSVSHYEIYEMQHMRLQSELSCISI 673
+IS+ + + ++V+ + L + E+ ++ H ++ E++C+ I
Sbjct: 515 KNISVASCNSSQVVVAVGRALYY-------LQIHPQELRQISHTEMEHEVACLDI 562
Score = 33.1 bits (74), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 18/86 (20%), Positives = 40/86 (46%), Gaps = 3/86 (3%)
Query: 821 LPINLQLIATRR---IGITPVFLVPLSDSLDADMIALSDRPWLLQTARHSLAYTSISFQP 877
L I L++ R+ +G P L ++ A SDRP ++ ++ H L +++++ +
Sbjct: 635 LNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIYSSNHKLVFSNVNLKE 694
Query: 878 STHATPVCSVECPKGILFVAENSLNL 903
+ P+ S P + ++L +
Sbjct: 695 VNYMCPLNSDGYPDSLALANNSTLTI 720
>pdb|4A0A|A Chain A, Structure Of Hsddb1-Drddb2 Bound To A 16 Bp Cpd-Duplex (
Pyrimidine At D-1 Position) At 3.6 A Resolution (Cpd 3)
Length = 1159
Score = 95.5 bits (236), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 68/235 (28%), Positives = 111/235 (47%), Gaps = 26/235 (11%)
Query: 446 MGDGMVLK------EENGRLVYTSPIQNIAPILDMSVVDYHDEKRDQMFACCGVAPEGSL 499
+GD ++K E+ +V N+ PI+DM VVD + + Q+ C G EGSL
Sbjct: 347 LGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSL 406
Query: 500 RIIRSGISLEKLLRTAPIYQGITGTWTVRMKVSDPYHSFLVLSFVEETRVLRVGLNFTDV 559
RIIR+GI + + + GI G W +R + LVLSFV +TRVL + +
Sbjct: 407 RIIRNGIGIHE--HASIDLPGIKGLWPLRSDPNRETDDTLVLSFVGQTRVLMLNGEEVEE 464
Query: 560 TDSVGFRPDVCTLACGLVADGLLVQIHQNAVRLCMPTMVAHSGGIPLSYPVCTSWF-PEH 618
T+ +GF D T CG VA L+QI +VRL A + + W P+
Sbjct: 465 TELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVSQEPKA----------LVSEWKEPQA 514
Query: 619 VSISLGAVAHNMIIVSTSNPCFLFILGVRSLSVSHYEIYEMQHMRLQSELSCISI 673
+IS+ + + ++V+ + L + E+ ++ H ++ E++C+ I
Sbjct: 515 KNISVASCNSSQVVVAVGRALYY-------LQIHPQELRQISHTEMEHEVACLDI 562
Score = 33.1 bits (74), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 18/86 (20%), Positives = 40/86 (46%), Gaps = 3/86 (3%)
Query: 821 LPINLQLIATRR---IGITPVFLVPLSDSLDADMIALSDRPWLLQTARHSLAYTSISFQP 877
L I L++ R+ +G P L ++ A SDRP ++ ++ H L +++++ +
Sbjct: 635 LNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIYSSNHKLVFSNVNLKE 694
Query: 878 STHATPVCSVECPKGILFVAENSLNL 903
+ P+ S P + ++L +
Sbjct: 695 VNYMCPLNSDGYPDSLALANNSTLTI 720
>pdb|3E0C|A Chain A, Crystal Structure Of Dna Damage-Binding Protein 1(Ddb1)
Length = 1140
Score = 95.5 bits (236), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 68/235 (28%), Positives = 111/235 (47%), Gaps = 26/235 (11%)
Query: 446 MGDGMVLK------EENGRLVYTSPIQNIAPILDMSVVDYHDEKRDQMFACCGVAPEGSL 499
+GD ++K E+ +V N+ PI+DM VVD + + Q+ C G EGSL
Sbjct: 328 LGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSL 387
Query: 500 RIIRSGISLEKLLRTAPIYQGITGTWTVRMKVSDPYHSFLVLSFVEETRVLRVGLNFTDV 559
RIIR+GI + + + GI G W +R + LVLSFV +TRVL + +
Sbjct: 388 RIIRNGIGIHE--HASIDLPGIKGLWPLRSDPNRETDDTLVLSFVGQTRVLMLNGEEVEE 445
Query: 560 TDSVGFRPDVCTLACGLVADGLLVQIHQNAVRLCMPTMVAHSGGIPLSYPVCTSWF-PEH 618
T+ +GF D T CG VA L+QI +VRL A + + W P+
Sbjct: 446 TELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVSQEPKA----------LVSEWKEPQA 495
Query: 619 VSISLGAVAHNMIIVSTSNPCFLFILGVRSLSVSHYEIYEMQHMRLQSELSCISI 673
+IS+ + + ++V+ + L + E+ ++ H ++ E++C+ I
Sbjct: 496 KNISVASCNSSQVVVAVGRALYY-------LQIHPQELRQISHTEMEHEVACLDI 543
Score = 32.7 bits (73), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 18/86 (20%), Positives = 40/86 (46%), Gaps = 3/86 (3%)
Query: 821 LPINLQLIATRR---IGITPVFLVPLSDSLDADMIALSDRPWLLQTARHSLAYTSISFQP 877
L I L++ R+ +G P L ++ A SDRP ++ ++ H L +++++ +
Sbjct: 616 LNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIYSSNHKLVFSNVNLKE 675
Query: 878 STHATPVCSVECPKGILFVAENSLNL 903
+ P+ S P + ++L +
Sbjct: 676 VNYMCPLNSDGYPDSLALANNSTLTI 701
>pdb|4E54|A Chain A, Damaged Dna Induced Uv-Damaged Dna-Binding Protein
(Uv-Ddb) Dimerization And Its Roles In Chromatinized Dna
Repair
pdb|4E5Z|A Chain A, Damaged Dna Induced Uv-Damaged Dna-Binding Protein
(Uv-Ddb) Dimerization And Its Roles In Chromatinized Dna
Repair
Length = 1150
Score = 95.5 bits (236), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 68/235 (28%), Positives = 111/235 (47%), Gaps = 26/235 (11%)
Query: 446 MGDGMVLK------EENGRLVYTSPIQNIAPILDMSVVDYHDEKRDQMFACCGVAPEGSL 499
+GD ++K E+ +V N+ PI+DM VVD + + Q+ C G EGSL
Sbjct: 338 LGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSL 397
Query: 500 RIIRSGISLEKLLRTAPIYQGITGTWTVRMKVSDPYHSFLVLSFVEETRVLRVGLNFTDV 559
RIIR+GI + + + GI G W +R + LVLSFV +TRVL + +
Sbjct: 398 RIIRNGIGIHE--HASIDLPGIKGLWPLRSDPNRETDDTLVLSFVGQTRVLMLNGEEVEE 455
Query: 560 TDSVGFRPDVCTLACGLVADGLLVQIHQNAVRLCMPTMVAHSGGIPLSYPVCTSWF-PEH 618
T+ +GF D T CG VA L+QI +VRL A + + W P+
Sbjct: 456 TELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVSQEPKA----------LVSEWKEPQA 505
Query: 619 VSISLGAVAHNMIIVSTSNPCFLFILGVRSLSVSHYEIYEMQHMRLQSELSCISI 673
+IS+ + + ++V+ + L + E+ ++ H ++ E++C+ I
Sbjct: 506 KNISVASCNSSQVVVAVGRALYY-------LQIHPQELRQISHTEMEHEVACLDI 553
Score = 32.7 bits (73), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 18/86 (20%), Positives = 40/86 (46%), Gaps = 3/86 (3%)
Query: 821 LPINLQLIATRR---IGITPVFLVPLSDSLDADMIALSDRPWLLQTARHSLAYTSISFQP 877
L I L++ R+ +G P L ++ A SDRP ++ ++ H L +++++ +
Sbjct: 626 LNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIYSSNHKLVFSNVNLKE 685
Query: 878 STHATPVCSVECPKGILFVAENSLNL 903
+ P+ S P + ++L +
Sbjct: 686 VNYMCPLNSDGYPDSLALANNSTLTI 711
>pdb|2B5N|A Chain A, Crystal Structure Of The Ddb1 Bpb Domain
pdb|2B5N|B Chain B, Crystal Structure Of The Ddb1 Bpb Domain
pdb|2B5N|C Chain C, Crystal Structure Of The Ddb1 Bpb Domain
pdb|2B5N|D Chain D, Crystal Structure Of The Ddb1 Bpb Domain
Length = 323
Score = 57.0 bits (136), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 42/155 (27%), Positives = 72/155 (46%), Gaps = 18/155 (11%)
Query: 520 GITGTWTVRMKVSDPYHSFLVLSFVEETRVLRVGLNFTDVTDSVGFRPDVCTLACGLVAD 579
GI G W +R + + LVLSFV +TRVL + + T+ +GF D T CG VA
Sbjct: 20 GIKGLWPLRSDPNRETYDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAH 79
Query: 580 GLLVQIHQNAVRLCMPTMVAHSGGIPLSYPVCTSWF-PEHVSISLGAVAHNMIIVSTSNP 638
L+QI +VRL A + + W P+ +IS+ + + ++V+
Sbjct: 80 QQLIQITSASVRLVSQEPKA----------LVSEWKEPQAKNISVASCNSSQVVVAVGRA 129
Query: 639 CFLFILGVRSLSVSHYEIYEMQHMRLQSELSCISI 673
+ L + E+ ++ H ++ E++C+ I
Sbjct: 130 LYY-------LQIHPQELRQISHTEMEHEVACLDI 157
Score = 32.0 bits (71), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 18/86 (20%), Positives = 40/86 (46%), Gaps = 3/86 (3%)
Query: 821 LPINLQLIATRR---IGITPVFLVPLSDSLDADMIALSDRPWLLQTARHSLAYTSISFQP 877
L I L++ R+ +G P L ++ A SDRP ++ ++ H L +++++ +
Sbjct: 230 LNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIYSSNHKLVFSNVNLKE 289
Query: 878 STHATPVCSVECPKGILFVAENSLNL 903
+ P+ S P + ++L +
Sbjct: 290 VNYMCPLNSDGYPDSLALANNSTLTI 315
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
0.322 0.137 0.418
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 25,008,703
Number of Sequences: 62578
Number of extensions: 997473
Number of successful extensions: 1655
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 1620
Number of HSP's gapped (non-prelim): 24
length of query: 903
length of database: 14,973,337
effective HSP length: 108
effective length of query: 795
effective length of database: 8,214,913
effective search space: 6530855835
effective search space used: 6530855835
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: 56 (26.2 bits)