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= 001003
(1192 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 50.4 bits (119), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 96/461 (20%), Positives = 172/461 (37%), Gaps = 116/461 (25%)
Query: 185 VDPQGRCGGVLVYGLQMIILKASQGGSGLVGDEDTFGSGGGFSARIESSHVINLRDLDMK 244
+DP+ R G+ +Y ++ + L F+ R+E HVI+++
Sbjct: 143 IDPECRMIGLRLYDGLFKVIPLDRDNKEL----------KAFNIRLEELHVIDVK----- 187
Query: 245 HVKDFIFVHGYIEPVMVILHERELTWAGRVSWKHHTCMISALSISTTLKQHPLIWSAMNL 304
F++G P + +++ GR H + P W N+
Sbjct: 188 ------FLYGCQAPTICFVYQDP---QGR-----HVKTYEVSLREKEFNKGP--WKQENV 231
Query: 305 PHDAYKLLAVPSPIGGVLVVGANTIHYHSQSASCALALNNYAVSLDSSQELPRSSFSV-- 362
+A ++AVPSP GG +++G +I YH+ A+A + + S V
Sbjct: 232 EAEASMVIAVPSPFGGAIIIGQESITYHNGDKYLAIA-----------PPIIKQSTIVCH 280
Query: 363 -ELDAAHATWLQNDVALLSTKTGDLVLLTV----VYDGRV-VQRLDLSKTNPSVLTSDIT 416
+D + +L D+ G L +L + DG V ++ L + + + +T
Sbjct: 281 NRVDPNGSRYLLGDME------GRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLT 334
Query: 417 TIGNSLFFLGSRLGDSLLVQFTCGS---GTSMLSSGLKEEFGDIEADAPSTKRLRRSSSD 473
+ N + F+GSRLGDS LV+ S G+ +++ G I D R+
Sbjct: 335 YLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPI-VDMCVVDLERQGQGQ 393
Query: 474 ALQDMVNGEELSLYGSASNNTESAQKTFSFAVRDSLVNIGPLKDFSYGLRINADASATGI 533
+ T S A ++ G L+ G+ I+ AS
Sbjct: 394 LV------------------------TCSGAFKE-----GSLRIIRNGIGIHEHAS---- 420
Query: 534 SKQSNYELVELPGCKGIWTVYHKSSRGHNADSSRMAAYDDEYHAYLIISLEARTMVLETA 593
++LPG KG+W + +R E L++S +T VL
Sbjct: 421 --------IDLPGIKGLWPLRSDPNR--------------ETDDTLVLSFVGQTRVLMLN 458
Query: 594 DLLTEVTESVDYFVQGRTIAAGNLFGRRRVIQVFERGARIL 634
E TE + + +T GN+ +++IQ+ R++
Sbjct: 459 GEEVEETELMGFVDDQQTFFCGNV-AHQQLIQITSASVRLV 498
>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 = 50.1 bits (118), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 95/461 (20%), Positives = 172/461 (37%), Gaps = 116/461 (25%)
Query: 185 VDPQGRCGGVLVYGLQMIILKASQGGSGLVGDEDTFGSGGGFSARIESSHVINLRDLDMK 244
+DP+ R G+ +Y ++ + L F+ R+E HVI+++
Sbjct: 124 IDPECRMIGLRLYDGLFKVIPLDRDNKEL----------KAFNIRLEELHVIDVK----- 168
Query: 245 HVKDFIFVHGYIEPVMVILHERELTWAGRVSWKHHTCMISALSISTTLKQHPLIWSAMNL 304
F++G P + +++ GR H + P W N+
Sbjct: 169 ------FLYGCQAPTICFVYQDP---QGR-----HVKTYEVSLREKEFNKGP--WKQENV 212
Query: 305 PHDAYKLLAVPSPIGGVLVVGANTIHYHSQSASCALALNNYAVSLDSSQELPRSSFSV-- 362
+A ++AVP P GG +++G +I YH+ A+A + + S V
Sbjct: 213 EAEASMVIAVPEPFGGAIIIGQESITYHNGDKYLAIA-----------PPIIKQSTIVCH 261
Query: 363 -ELDAAHATWLQNDVALLSTKTGDLVLLTV----VYDGRV-VQRLDLSKTNPSVLTSDIT 416
+D + +L D+ G L +L + DG V ++ L + + + +T
Sbjct: 262 NRVDPNGSRYLLGDME------GRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLT 315
Query: 417 TIGNSLFFLGSRLGDSLLVQFTCGS---GTSMLSSGLKEEFGDIEADAPSTKRLRRSSSD 473
+ N + F+GSRLGDS LV+ S G+ +++ G I D R+
Sbjct: 316 YLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPI-VDMCVVDLERQGQGQ 374
Query: 474 ALQDMVNGEELSLYGSASNNTESAQKTFSFAVRDSLVNIGPLKDFSYGLRINADASATGI 533
+ T S A ++ G L+ G+ I+ AS
Sbjct: 375 LV------------------------TCSGAFKE-----GSLRIIRNGIGIHEHAS---- 401
Query: 534 SKQSNYELVELPGCKGIWTVYHKSSRGHNADSSRMAAYDDEYHAYLIISLEARTMVLETA 593
++LPG KG+W + +R E + L++S +T VL
Sbjct: 402 --------IDLPGIKGLWPLRSDPNR--------------ETYDTLVLSFVGQTRVLMLN 439
Query: 594 DLLTEVTESVDYFVQGRTIAAGNLFGRRRVIQVFERGARIL 634
E TE + + +T GN+ +++IQ+ R++
Sbjct: 440 GEEVEETELMGFVDDQQTFFCGNV-AHQQLIQITSASVRLV 479
>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 = 50.1 bits (118), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 95/461 (20%), Positives = 172/461 (37%), Gaps = 116/461 (25%)
Query: 185 VDPQGRCGGVLVYGLQMIILKASQGGSGLVGDEDTFGSGGGFSARIESSHVINLRDLDMK 244
+DP+ R G+ +Y ++ + L F+ R+E HVI+++
Sbjct: 142 IDPECRMIGLRLYDGLFKVIPLDRDNKEL----------KAFNIRLEELHVIDVK----- 186
Query: 245 HVKDFIFVHGYIEPVMVILHERELTWAGRVSWKHHTCMISALSISTTLKQHPLIWSAMNL 304
F++G P + +++ GR H + P W N+
Sbjct: 187 ------FLYGCQAPTICFVYQDP---QGR-----HVKTYEVSLREKEFNKGP--WKQENV 230
Query: 305 PHDAYKLLAVPSPIGGVLVVGANTIHYHSQSASCALALNNYAVSLDSSQELPRSSFSV-- 362
+A ++AVP P GG +++G +I YH+ A+A + + S V
Sbjct: 231 EAEASMVIAVPEPFGGAIIIGQESITYHNGDKYLAIA-----------PPIIKQSTIVCH 279
Query: 363 -ELDAAHATWLQNDVALLSTKTGDLVLLTV----VYDGRV-VQRLDLSKTNPSVLTSDIT 416
+D + +L D+ G L +L + DG V ++ L + + + +T
Sbjct: 280 NRVDPNGSRYLLGDME------GRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLT 333
Query: 417 TIGNSLFFLGSRLGDSLLVQFTCGS---GTSMLSSGLKEEFGDIEADAPSTKRLRRSSSD 473
+ N + F+GSRLGDS LV+ S G+ +++ G I D R+
Sbjct: 334 YLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPI-VDMCVVDLERQGQGQ 392
Query: 474 ALQDMVNGEELSLYGSASNNTESAQKTFSFAVRDSLVNIGPLKDFSYGLRINADASATGI 533
+ T S A ++ G L+ G+ I+ AS
Sbjct: 393 LV------------------------TCSGAFKE-----GSLRIIRNGIGIHEHAS---- 419
Query: 534 SKQSNYELVELPGCKGIWTVYHKSSRGHNADSSRMAAYDDEYHAYLIISLEARTMVLETA 593
++LPG KG+W + +R E + L++S +T VL
Sbjct: 420 --------IDLPGIKGLWPLRSDPNR--------------ETYDTLVLSFVGQTRVLMLN 457
Query: 594 DLLTEVTESVDYFVQGRTIAAGNLFGRRRVIQVFERGARIL 634
E TE + + +T GN+ +++IQ+ R++
Sbjct: 458 GEEVEETELMGFVDDQQTFFCGNV-AHQQLIQITSASVRLV 497
>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 = 49.7 bits (117), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 95/461 (20%), Positives = 172/461 (37%), Gaps = 116/461 (25%)
Query: 185 VDPQGRCGGVLVYGLQMIILKASQGGSGLVGDEDTFGSGGGFSARIESSHVINLRDLDMK 244
+DP+ R G+ +Y ++ + L F+ R+E HVI+++
Sbjct: 127 IDPECRMIGLRLYDGLFKVIPLDRDNKEL----------KAFNIRLEELHVIDVK----- 171
Query: 245 HVKDFIFVHGYIEPVMVILHERELTWAGRVSWKHHTCMISALSISTTLKQHPLIWSAMNL 304
F++G P + +++ GR H + P W N+
Sbjct: 172 ------FLYGCQAPTICFVYQDP---QGR-----HVKTYEVSLREKEFNKGP--WKQENV 215
Query: 305 PHDAYKLLAVPSPIGGVLVVGANTIHYHSQSASCALALNNYAVSLDSSQELPRSSFSV-- 362
+A ++AVP P GG +++G +I YH+ A+A + + S V
Sbjct: 216 EAEASMVIAVPEPFGGAIIIGQESITYHNGDKYLAIA-----------PPIIKQSTIVCH 264
Query: 363 -ELDAAHATWLQNDVALLSTKTGDLVLLTV----VYDGRV-VQRLDLSKTNPSVLTSDIT 416
+D + +L D+ G L +L + DG V ++ L + + + +T
Sbjct: 265 NRVDPNGSRYLLGDME------GRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLT 318
Query: 417 TIGNSLFFLGSRLGDSLLVQFTCGS---GTSMLSSGLKEEFGDIEADAPSTKRLRRSSSD 473
+ N + F+GSRLGDS LV+ S G+ +++ G I D R+
Sbjct: 319 YLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPI-VDMCVVDLERQGQGQ 377
Query: 474 ALQDMVNGEELSLYGSASNNTESAQKTFSFAVRDSLVNIGPLKDFSYGLRINADASATGI 533
+ T S A ++ G L+ G+ I+ AS
Sbjct: 378 LV------------------------TCSGAFKE-----GSLRIIRNGIGIHEHAS---- 404
Query: 534 SKQSNYELVELPGCKGIWTVYHKSSRGHNADSSRMAAYDDEYHAYLIISLEARTMVLETA 593
++LPG KG+W + +R E + L++S +T VL
Sbjct: 405 --------IDLPGIKGLWPLRSDPNR--------------ETYDTLVLSFVGQTRVLMLN 442
Query: 594 DLLTEVTESVDYFVQGRTIAAGNLFGRRRVIQVFERGARIL 634
E TE + + +T GN+ +++IQ+ R++
Sbjct: 443 GEEVEETELMGFVDDQQTFFCGNV-AHQQLIQITSASVRLV 482
>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 = 49.3 bits (116), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 95/461 (20%), Positives = 172/461 (37%), Gaps = 116/461 (25%)
Query: 185 VDPQGRCGGVLVYGLQMIILKASQGGSGLVGDEDTFGSGGGFSARIESSHVINLRDLDMK 244
+DP+ R G+ +Y ++ + L F+ R+E HVI+++
Sbjct: 143 IDPECRMIGLRLYDGLFKVIPLDRDNKEL----------KAFNIRLEELHVIDVK----- 187
Query: 245 HVKDFIFVHGYIEPVMVILHERELTWAGRVSWKHHTCMISALSISTTLKQHPLIWSAMNL 304
F++G P + +++ GR H + + P W N+
Sbjct: 188 ------FLYGCQAPTICFVYQDP---QGR-----HVKTYAVSLREKEFNKGP--WKQENV 231
Query: 305 PHDAYKLLAVPSPIGGVLVVGANTIHYHSQSASCALALNNYAVSLDSSQELPRSSFSV-- 362
+A ++AVP P GG +++G +I YH+ A+A + + S V
Sbjct: 232 EAEASMVIAVPEPFGGAIIIGQESITYHNGDKYLAIA-----------PPIIKQSTIVCH 280
Query: 363 -ELDAAHATWLQNDVALLSTKTGDLVLLTV----VYDGRV-VQRLDLSKTNPSVLTSDIT 416
+D + +L D+ G L +L + DG V ++ L + + + +T
Sbjct: 281 NRVDPNGSRYLLGDME------GRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLT 334
Query: 417 TIGNSLFFLGSRLGDSLLVQFTCGS---GTSMLSSGLKEEFGDIEADAPSTKRLRRSSSD 473
+ N + F+GSRLGDS LV+ S G+ +++ G I D R+
Sbjct: 335 YLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPI-VDMCVVDLERQGQGQ 393
Query: 474 ALQDMVNGEELSLYGSASNNTESAQKTFSFAVRDSLVNIGPLKDFSYGLRINADASATGI 533
+ T S A ++ G L+ G+ I+ AS
Sbjct: 394 LV------------------------TCSGAFKE-----GSLRIIRNGIGIHEHAS---- 420
Query: 534 SKQSNYELVELPGCKGIWTVYHKSSRGHNADSSRMAAYDDEYHAYLIISLEARTMVLETA 593
++LPG KG+W + +R E L++S +T VL
Sbjct: 421 --------IDLPGIKGLWPLRSDPNR--------------ETDDTLVLSFVGQTRVLMLN 458
Query: 594 DLLTEVTESVDYFVQGRTIAAGNLFGRRRVIQVFERGARIL 634
E TE + + +T GN+ +++IQ+ R++
Sbjct: 459 GEEVEETELMGFVDDQQTFFCGNV-AHQQLIQITSASVRLV 498
>pdb|3E0C|A Chain A, Crystal Structure Of Dna Damage-Binding Protein 1(Ddb1)
Length = 1140
Score = 48.9 bits (115), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 95/461 (20%), Positives = 171/461 (37%), Gaps = 116/461 (25%)
Query: 185 VDPQGRCGGVLVYGLQMIILKASQGGSGLVGDEDTFGSGGGFSARIESSHVINLRDLDMK 244
+DP+ R G+ +Y ++ + L F+ R+E HVI+++
Sbjct: 124 IDPECRMIGLRLYDGLFKVIPLDRDNKEL----------KAFNIRLEELHVIDVK----- 168
Query: 245 HVKDFIFVHGYIEPVMVILHERELTWAGRVSWKHHTCMISALSISTTLKQHPLIWSAMNL 304
F++G P + +++ GR H + P W N+
Sbjct: 169 ------FLYGCQAPTICFVYQDP---QGR-----HVKTYEVSLREKEFNKGP--WKQENV 212
Query: 305 PHDAYKLLAVPSPIGGVLVVGANTIHYHSQSASCALALNNYAVSLDSSQELPRSSFSV-- 362
+A ++AVP P GG +++G +I YH+ A+A + + S V
Sbjct: 213 EAEASMVIAVPEPFGGAIIIGQESITYHNGDKYLAIA-----------PPIIKQSTIVCH 261
Query: 363 -ELDAAHATWLQNDVALLSTKTGDLVLLTV----VYDGRV-VQRLDLSKTNPSVLTSDIT 416
+D + +L D+ G L +L + DG V ++ L + + + +T
Sbjct: 262 NRVDPNGSRYLLGDME------GRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLT 315
Query: 417 TIGNSLFFLGSRLGDSLLVQFTCGS---GTSMLSSGLKEEFGDIEADAPSTKRLRRSSSD 473
+ N + F+GSRLGDS LV+ S G+ +++ G I D R+
Sbjct: 316 YLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPI-VDMCVVDLERQGQGQ 374
Query: 474 ALQDMVNGEELSLYGSASNNTESAQKTFSFAVRDSLVNIGPLKDFSYGLRINADASATGI 533
+ T S A ++ G L+ G+ I+ AS
Sbjct: 375 LV------------------------TCSGAFKE-----GSLRIIRNGIGIHEHAS---- 401
Query: 534 SKQSNYELVELPGCKGIWTVYHKSSRGHNADSSRMAAYDDEYHAYLIISLEARTMVLETA 593
++LPG KG+W + +R E L++S +T VL
Sbjct: 402 --------IDLPGIKGLWPLRSDPNR--------------ETDDTLVLSFVGQTRVLMLN 439
Query: 594 DLLTEVTESVDYFVQGRTIAAGNLFGRRRVIQVFERGARIL 634
E TE + + +T GN+ +++IQ+ R++
Sbjct: 440 GEEVEETELMGFVDDQQTFFCGNV-AHQQLIQITSASVRLV 479
>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 = 48.9 bits (115), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 95/461 (20%), Positives = 171/461 (37%), Gaps = 116/461 (25%)
Query: 185 VDPQGRCGGVLVYGLQMIILKASQGGSGLVGDEDTFGSGGGFSARIESSHVINLRDLDMK 244
+DP+ R G+ +Y ++ + L F+ R+E HVI+++
Sbjct: 134 IDPECRMIGLRLYDGLFKVIPLDRDNKEL----------KAFNIRLEELHVIDVK----- 178
Query: 245 HVKDFIFVHGYIEPVMVILHERELTWAGRVSWKHHTCMISALSISTTLKQHPLIWSAMNL 304
F++G P + +++ GR H + P W N+
Sbjct: 179 ------FLYGCQAPTICFVYQDP---QGR-----HVKTYEVSLREKEFNKGP--WKQENV 222
Query: 305 PHDAYKLLAVPSPIGGVLVVGANTIHYHSQSASCALALNNYAVSLDSSQELPRSSFSV-- 362
+A ++AVP P GG +++G +I YH+ A+A + + S V
Sbjct: 223 EAEASMVIAVPEPFGGAIIIGQESITYHNGDKYLAIA-----------PPIIKQSTIVCH 271
Query: 363 -ELDAAHATWLQNDVALLSTKTGDLVLLTV----VYDGRV-VQRLDLSKTNPSVLTSDIT 416
+D + +L D+ G L +L + DG V ++ L + + + +T
Sbjct: 272 NRVDPNGSRYLLGDME------GRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLT 325
Query: 417 TIGNSLFFLGSRLGDSLLVQFTCGS---GTSMLSSGLKEEFGDIEADAPSTKRLRRSSSD 473
+ N + F+GSRLGDS LV+ S G+ +++ G I D R+
Sbjct: 326 YLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPI-VDMCVVDLERQGQGQ 384
Query: 474 ALQDMVNGEELSLYGSASNNTESAQKTFSFAVRDSLVNIGPLKDFSYGLRINADASATGI 533
+ T S A ++ G L+ G+ I+ AS
Sbjct: 385 LV------------------------TCSGAFKE-----GSLRIIRNGIGIHEHAS---- 411
Query: 534 SKQSNYELVELPGCKGIWTVYHKSSRGHNADSSRMAAYDDEYHAYLIISLEARTMVLETA 593
++LPG KG+W + +R E L++S +T VL
Sbjct: 412 --------IDLPGIKGLWPLRSDPNR--------------ETDDTLVLSFVGQTRVLMLN 449
Query: 594 DLLTEVTESVDYFVQGRTIAAGNLFGRRRVIQVFERGARIL 634
E TE + + +T GN+ +++IQ+ R++
Sbjct: 450 GEEVEETELMGFVDDQQTFFCGNV-AHQQLIQITSASVRLV 489
>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 = 48.9 bits (115), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 95/461 (20%), Positives = 171/461 (37%), Gaps = 116/461 (25%)
Query: 185 VDPQGRCGGVLVYGLQMIILKASQGGSGLVGDEDTFGSGGGFSARIESSHVINLRDLDMK 244
+DP+ R G+ +Y ++ + L F+ R+E HVI+++
Sbjct: 143 IDPECRMIGLRLYDGLFKVIPLDRDNKEL----------KAFNIRLEELHVIDVK----- 187
Query: 245 HVKDFIFVHGYIEPVMVILHERELTWAGRVSWKHHTCMISALSISTTLKQHPLIWSAMNL 304
F++G P + +++ GR H + P W N+
Sbjct: 188 ------FLYGCQAPTICFVYQDP---QGR-----HVKTYEVSLREKEFNKGP--WKQENV 231
Query: 305 PHDAYKLLAVPSPIGGVLVVGANTIHYHSQSASCALALNNYAVSLDSSQELPRSSFSV-- 362
+A ++AVP P GG +++G +I YH+ A+A + + S V
Sbjct: 232 EAEASMVIAVPKPFGGAIIIGQESITYHNGDKYLAIA-----------PPIIKQSTIVCH 280
Query: 363 -ELDAAHATWLQNDVALLSTKTGDLVLLTV----VYDGRV-VQRLDLSKTNPSVLTSDIT 416
+D + +L D+ G L +L + DG V ++ L + + + +T
Sbjct: 281 NRVDPNGSRYLLGDME------GRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLT 334
Query: 417 TIGNSLFFLGSRLGDSLLVQFTCGS---GTSMLSSGLKEEFGDIEADAPSTKRLRRSSSD 473
+ N + F+GSRLGDS LV+ S G+ +++ G I D R+
Sbjct: 335 YLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPI-VDMCVVDLERQGQGQ 393
Query: 474 ALQDMVNGEELSLYGSASNNTESAQKTFSFAVRDSLVNIGPLKDFSYGLRINADASATGI 533
+ T S A ++ G L+ G+ I+ AS
Sbjct: 394 LV------------------------TCSGAFKE-----GSLRIIRNGIGIHEHAS---- 420
Query: 534 SKQSNYELVELPGCKGIWTVYHKSSRGHNADSSRMAAYDDEYHAYLIISLEARTMVLETA 593
++LPG KG+W + +R E L++S +T VL
Sbjct: 421 --------IDLPGIKGLWPLRSDPNR--------------ETDDTLVLSFVGQTRVLMLN 458
Query: 594 DLLTEVTESVDYFVQGRTIAAGNLFGRRRVIQVFERGARIL 634
E TE + + +T GN+ +++IQ+ R++
Sbjct: 459 GEEVEETELMGFVDDQQTFFCGNV-AHQQLIQITSASVRLV 498
>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 = 48.9 bits (115), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 95/461 (20%), Positives = 171/461 (37%), Gaps = 116/461 (25%)
Query: 185 VDPQGRCGGVLVYGLQMIILKASQGGSGLVGDEDTFGSGGGFSARIESSHVINLRDLDMK 244
+DP+ R G+ +Y ++ + L F+ R+E HVI+++
Sbjct: 143 IDPECRMIGLRLYDGLFKVIPLDRDNKEL----------KAFNIRLEELHVIDVK----- 187
Query: 245 HVKDFIFVHGYIEPVMVILHERELTWAGRVSWKHHTCMISALSISTTLKQHPLIWSAMNL 304
F++G P + +++ GR H + P W N+
Sbjct: 188 ------FLYGCQAPTICFVYQDP---QGR-----HVKTYEVSLREKEFNKGP--WKQENV 231
Query: 305 PHDAYKLLAVPSPIGGVLVVGANTIHYHSQSASCALALNNYAVSLDSSQELPRSSFSV-- 362
+A ++AVP P GG +++G +I YH+ A+A + + S V
Sbjct: 232 EAEASMVIAVPEPFGGAIIIGQESITYHNGDKYLAIA-----------PPIIKQSTIVCH 280
Query: 363 -ELDAAHATWLQNDVALLSTKTGDLVLLTV----VYDGRV-VQRLDLSKTNPSVLTSDIT 416
+D + +L D+ G L +L + DG V ++ L + + + +T
Sbjct: 281 NRVDPNGSRYLLGDME------GRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLT 334
Query: 417 TIGNSLFFLGSRLGDSLLVQFTCGS---GTSMLSSGLKEEFGDIEADAPSTKRLRRSSSD 473
+ N + F+GSRLGDS LV+ S G+ +++ G I D R+
Sbjct: 335 YLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPI-VDMCVVDLERQGQGQ 393
Query: 474 ALQDMVNGEELSLYGSASNNTESAQKTFSFAVRDSLVNIGPLKDFSYGLRINADASATGI 533
+ T S A ++ G L+ G+ I+ AS
Sbjct: 394 LV------------------------TCSGAFKE-----GSLRIIRNGIGIHEHAS---- 420
Query: 534 SKQSNYELVELPGCKGIWTVYHKSSRGHNADSSRMAAYDDEYHAYLIISLEARTMVLETA 593
++LPG KG+W + +R E L++S +T VL
Sbjct: 421 --------IDLPGIKGLWPLRSDPNR--------------ETDDTLVLSFVGQTRVLMLN 458
Query: 594 DLLTEVTESVDYFVQGRTIAAGNLFGRRRVIQVFERGARIL 634
E TE + + +T GN+ +++IQ+ R++
Sbjct: 459 GEEVEETELMGFVDDQQTFFCGNV-AHQQLIQITSASVRLV 498
>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 = 48.9 bits (115), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 95/461 (20%), Positives = 171/461 (37%), Gaps = 116/461 (25%)
Query: 185 VDPQGRCGGVLVYGLQMIILKASQGGSGLVGDEDTFGSGGGFSARIESSHVINLRDLDMK 244
+DP+ R G+ +Y ++ + L F+ R+E HVI+++
Sbjct: 142 IDPECRMIGLRLYDGLFKVIPLDRDNKEL----------KAFNIRLEELHVIDVK----- 186
Query: 245 HVKDFIFVHGYIEPVMVILHERELTWAGRVSWKHHTCMISALSISTTLKQHPLIWSAMNL 304
F++G P + +++ GR H + P W N+
Sbjct: 187 ------FLYGCQAPTICFVYQDP---QGR-----HVKTYEVSLREKEFNKGP--WKQENV 230
Query: 305 PHDAYKLLAVPSPIGGVLVVGANTIHYHSQSASCALALNNYAVSLDSSQELPRSSFSV-- 362
+A ++AVP P GG +++G +I YH+ A+A + + S V
Sbjct: 231 EAEASMVIAVPEPFGGAIIIGQESITYHNGDKYLAIA-----------PPIIKQSTIVCH 279
Query: 363 -ELDAAHATWLQNDVALLSTKTGDLVLLTV----VYDGRV-VQRLDLSKTNPSVLTSDIT 416
+D + +L D+ G L +L + DG V ++ L + + + +T
Sbjct: 280 NRVDPNGSRYLLGDME------GRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLT 333
Query: 417 TIGNSLFFLGSRLGDSLLVQFTCGS---GTSMLSSGLKEEFGDIEADAPSTKRLRRSSSD 473
+ N + F+GSRLGDS LV+ S G+ +++ G I D R+
Sbjct: 334 YLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPI-VDMCVVDLERQGQGQ 392
Query: 474 ALQDMVNGEELSLYGSASNNTESAQKTFSFAVRDSLVNIGPLKDFSYGLRINADASATGI 533
+ T S A ++ G L+ G+ I+ AS
Sbjct: 393 LV------------------------TCSGAFKE-----GSLRIIRNGIGIHEHAS---- 419
Query: 534 SKQSNYELVELPGCKGIWTVYHKSSRGHNADSSRMAAYDDEYHAYLIISLEARTMVLETA 593
++LPG KG+W + +R E L++S +T VL
Sbjct: 420 --------IDLPGIKGLWPLRSDPNR--------------ETDDTLVLSFVGQTRVLMLN 457
Query: 594 DLLTEVTESVDYFVQGRTIAAGNLFGRRRVIQVFERGARIL 634
E TE + + +T GN+ +++IQ+ R++
Sbjct: 458 GEEVEETELMGFVDDQQTFFCGNV-AHQQLIQITSASVRLV 497
>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 = 48.5 bits (114), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 95/461 (20%), Positives = 171/461 (37%), Gaps = 116/461 (25%)
Query: 185 VDPQGRCGGVLVYGLQMIILKASQGGSGLVGDEDTFGSGGGFSARIESSHVINLRDLDMK 244
+DP+ R G+ +Y ++ + L F+ R+E HVI+++
Sbjct: 128 IDPECRMIGLRLYDGLFKVIPLDRDNKEL----------KAFNIRLEELHVIDVK----- 172
Query: 245 HVKDFIFVHGYIEPVMVILHERELTWAGRVSWKHHTCMISALSISTTLKQHPLIWSAMNL 304
F++G P + +++ GR H + P W N+
Sbjct: 173 ------FLYGCQAPTICFVYQDP---QGR-----HVKTYEVSLREKEFNKGP--WKQENV 216
Query: 305 PHDAYKLLAVPSPIGGVLVVGANTIHYHSQSASCALALNNYAVSLDSSQELPRSSFSV-- 362
+A ++AVP P GG +++G +I YH+ A+A + + S V
Sbjct: 217 EAEASMVIAVPEPFGGAIIIGQESITYHNGDKYLAIA-----------PPIIKQSTIVCH 265
Query: 363 -ELDAAHATWLQNDVALLSTKTGDLVLLTV----VYDGRV-VQRLDLSKTNPSVLTSDIT 416
+D + +L D+ G L +L + DG V ++ L + + + +T
Sbjct: 266 NRVDPNGSRYLLGDME------GRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLT 319
Query: 417 TIGNSLFFLGSRLGDSLLVQFTCGS---GTSMLSSGLKEEFGDIEADAPSTKRLRRSSSD 473
+ N + F+GSRLGDS LV+ S G+ +++ G I D R+
Sbjct: 320 YLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPI-VDMCVVDLERQGQGQ 378
Query: 474 ALQDMVNGEELSLYGSASNNTESAQKTFSFAVRDSLVNIGPLKDFSYGLRINADASATGI 533
+ T S A ++ G L+ G+ I+ AS
Sbjct: 379 LV------------------------TCSGAFKE-----GSLRIIRNGIGIHEHAS---- 405
Query: 534 SKQSNYELVELPGCKGIWTVYHKSSRGHNADSSRMAAYDDEYHAYLIISLEARTMVLETA 593
++LPG KG+W + +R E L++S +T VL
Sbjct: 406 --------IDLPGIKGLWPLRSDPNR--------------ETDDTLVLSFVGQTRVLMLN 443
Query: 594 DLLTEVTESVDYFVQGRTIAAGNLFGRRRVIQVFERGARIL 634
E TE + + +T GN+ +++IQ+ R++
Sbjct: 444 GEEVEETELMGFVDDQQTFFCGNV-AHQQLIQITSASVRLV 483
>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 = 30.0 bits (66), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 22/93 (23%), Positives = 41/93 (44%), Gaps = 15/93 (16%)
Query: 542 VELPGCKGIWTVYHKSSRGHNADSSRMAAYDDEYHAYLIISLEARTMVLETADLLTEVTE 601
++LPG KG+W + +R E + L++S +T VL E TE
Sbjct: 16 IDLPGIKGLWPLRSDPNR--------------ETYDTLVLSFVGQTRVLMLNGEEVEETE 61
Query: 602 SVDYFVQGRTIAAGNLFGRRRVIQVFERGARIL 634
+ + +T GN+ +++IQ+ R++
Sbjct: 62 LMGFVDDQQTFFCGNV-AHQQLIQITSASVRLV 93
>pdb|1G8P|A Chain A, Crystal Structure Of Bchi Subunit Of Magnesium Chelatase
pdb|2X31|G Chain G, Modelling Of The Complex Between Subunits Bchi And Bchd Of
Magnesium Chelatase Based On Single-Particle Cryo-Em
Reconstruction At 7.5 Ang
pdb|2X31|H Chain H, Modelling Of The Complex Between Subunits Bchi And Bchd Of
Magnesium Chelatase Based On Single-Particle Cryo-Em
Reconstruction At 7.5 Ang
pdb|2X31|I Chain I, Modelling Of The Complex Between Subunits Bchi And Bchd Of
Magnesium Chelatase Based On Single-Particle Cryo-Em
Reconstruction At 7.5 Ang
pdb|2X31|J Chain J, Modelling Of The Complex Between Subunits Bchi And Bchd Of
Magnesium Chelatase Based On Single-Particle Cryo-Em
Reconstruction At 7.5 Ang
pdb|2X31|K Chain K, Modelling Of The Complex Between Subunits Bchi And Bchd Of
Magnesium Chelatase Based On Single-Particle Cryo-Em
Reconstruction At 7.5 Ang
pdb|2X31|L Chain L, Modelling Of The Complex Between Subunits Bchi And Bchd Of
Magnesium Chelatase Based On Single-Particle Cryo-Em
Reconstruction At 7.5 Ang
Length = 350
Score = 29.6 bits (65), Expect = 10.0, Method: Composition-based stats.
Identities = 32/98 (32%), Positives = 45/98 (45%), Gaps = 6/98 (6%)
Query: 308 AYKLLAVPSPIGGVLVVGANTIHYHSQSASCALALNNYAVSLDSSQELPRSSFSVELDAA 367
A L AV IGGVLV G + ++ AL +++ + P SS +VE+
Sbjct: 35 ALLLTAVDPGIGGVLVFGDRG----TGKSTAVRALAALLPEIEAVEGCPVSSPNVEMIPD 90
Query: 368 HATWLQNDVALLSTKTGDLVLLTVVYDGRVVQRLDLSK 405
AT L +V T DL L V + RVV LD+ +
Sbjct: 91 WATVLSTNVIRKPTPVVDLPL--GVSEDRVVGALDIER 126
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
0.319 0.135 0.399
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 33,377,030
Number of Sequences: 62578
Number of extensions: 1351934
Number of successful extensions: 2958
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 2915
Number of HSP's gapped (non-prelim): 46
length of query: 1192
length of database: 14,973,337
effective HSP length: 110
effective length of query: 1082
effective length of database: 8,089,757
effective search space: 8753117074
effective search space used: 8753117074
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 57 (26.6 bits)