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= 006790
(631 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4A15|A Chain A, Crystal Structure Of An Xpd Dna Complex
Length = 620
Score = 80.9 bits (198), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 134/625 (21%), Positives = 249/625 (39%), Gaps = 139/625 (22%)
Query: 28 LKRALDAKGHCLLEMPTGTGKTIALLSLITSYVLSKPENPVKLIYCTRTVHEMEKTLAEL 87
L+ +L LE PTG+GKTI L Y E +K++Y RT + E+ + EL
Sbjct: 15 LRSSLQKSYGVALESPTGSGKTIMALKSALQY---SSERKLKVLYLVRTNSQEEQVIKEL 71
Query: 88 KLLHNYQTRHLGPAAKILAIGLSSRKNLCVNSRV---LAAENRDSVDAACRKRTASWVRA 144
R L KI AI + R N+C+ R+ L N +S+ C + R
Sbjct: 72 --------RSLSSTMKIRAIPMQGRVNMCILYRMVDDLHEINAESLAKFCNMKK----RE 119
Query: 145 LAAENPNIETCEFFE-NYEKAASAAVLPPGVYTLQDLRAFGKQQGWCPYFLARHMVQFAN 203
+ A N C +F + L + T ++ +G++ CPY + + A+
Sbjct: 120 VMAGNE--AACPYFNFKIRSDETKRFLFDELPTAEEFYDYGERNNVCPYESMKAALPDAD 177
Query: 204 VVVYSYQYLLDPKVA-------GIISKEMQKESVVVFDEAHNIDNVCIEALSVSVRRQTL 256
+V+ Y Y L+ VA G+ ++ V++ DEAHN+ ++ S+ R ++
Sbjct: 178 IVIAPYAYFLNRSVAEKFLSHWGVSRNQI----VIILDEAHNLPDI---GRSIGSFRISV 230
Query: 257 EGATRNLSRINQEIERFKATDAGRLRAEYNRLVEGLALRGNLPIADAWLSNPALPSDILK 316
E +L+R ++E + + + + + + L+E + AL S + +
Sbjct: 231 E----SLNRADREAQAYGDPELSQ-KIHVSDLIE--------------MIRSALQSMVSE 271
Query: 317 EAVPGNIR-RAEHFLHVLRRLVQ-------------YLRGRLETENVEKEG--PVSFVAS 360
G++R R + F+ +R + + YL G EK G P S+ +S
Sbjct: 272 RCGKGDVRIRFQEFMEYMRIMNKRSEREIRSLLNYLYLFGEYVENEKEKVGKVPFSYCSS 331
Query: 361 ITAHAGIDQKTLRFCYERLHSLMLTLEITDTDEFLHIQTICDFATLVGTYTRGFSIIIEP 420
+ + + +D DE ++ I+ P
Sbjct: 332 VASR--------------------IIAFSDQDE------------------EKYAAILSP 353
Query: 421 FDERMPHIPDPVLQLSCHDASLAVKPVFDRFQSVVITSGTLSPIDLYPRLLNFHPVVSRS 480
D +Q +C D S ++ + + + SGTL P D Y + F +
Sbjct: 354 ED-------GGYMQAACLDPSGILEVL--KESKTIHMSGTLDPFDFYSDITGFEIPFKKI 404
Query: 481 FKMSLTRDCICPMVLTRGSDQLPVSTKFDMRSDPGVARNYGKLLVEMVSIVPDGIVCFFV 540
+ I P + VS+K+D + + R ++ +++ V + +F
Sbjct: 405 GE-------IFPPENRYIAYYDGVSSKYDTLDEKELDR-MATVIEDIILKVKKNTIVYFP 456
Query: 541 SYSYMDEIIATWNDSGILKEIMQHKLVFIETQDVVETTLALDNYRKACDCGRGAVFFSVA 600
SYS MD + + + + +++ + D E L +R+ D G F+V+
Sbjct: 457 SYSLMDRV----ENRVSFEHMKEYRGI-----DQKELYSMLKKFRR--DHG---TIFAVS 502
Query: 601 RGKVAEGIDFDRHYGRLVIMFGVPF 625
G+++EGI+F + ++I+ G+PF
Sbjct: 503 GGRLSEGINFPGNELEMIILAGLPF 527
>pdb|2VSF|A Chain A, Structure Of Xpd From Thermoplasma Acidophilum
Length = 602
Score = 79.7 bits (195), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 131/609 (21%), Positives = 243/609 (39%), Gaps = 131/609 (21%)
Query: 40 LEMPTGTGKTIALLSLITSYVLSKPENPVKLIYCTRTVHEMEKTLAELKLLHNYQTRHLG 99
LE PTG+GKTI L Y E +K++Y RT + E+ + EL R L
Sbjct: 9 LESPTGSGKTIMALKSALQY---SSERKLKVLYLVRTNSQEEQVIKEL--------RSLS 57
Query: 100 PAAKILAIGLSSRKNLCVNSRV---LAAENRDSVDAACRKRTASWVRALAAENPNIETCE 156
KI AI + R N+C+ R+ L N +S+ C + R + A N C
Sbjct: 58 STMKIRAIPMQGRVNMCILYRMVDDLHEINAESLAKFCNMKK----REVMAGNE--AACP 111
Query: 157 FFE-NYEKAASAAVLPPGVYTLQDLRAFGKQQGWCPYFLARHMVQFANVVVYSYQYLLDP 215
+F + L + T ++ +G++ CPY + + A++V+ Y Y L+
Sbjct: 112 YFNFKIRSDETKRFLFDELPTAEEFYDYGERNNVCPYESMKAALPDADIVIAPYAYFLNR 171
Query: 216 KVAGIISKEM---QKESVVVFDEAHNIDNVCIEALSVSVRRQTLEGATRNLSRINQEIER 272
VA + + V++ DEAHN+ ++ S+ R ++E +L+R ++E +
Sbjct: 172 SVAEKFLSHWGVSRNQIVIILDEAHNLPDI---GRSIGSFRISVE----SLNRADREAQA 224
Query: 273 FKATDAGRLRAEYNRLVEGLALRGNLPIADAWLSNPALPSDILKEAVPGNIR-RAEHFLH 331
+ + + + + L+E + AL S + + G++R R + F+
Sbjct: 225 YGDPELSQ-KIHVSDLIE--------------MIRSALQSMVSERCGKGDVRIRFQEFME 269
Query: 332 VLRRLVQ-------------YLRGRLETENVEKEG--PVSFVASITAHAGIDQKTLRFCY 376
+R + + YL G EK G P S+ +S+ +
Sbjct: 270 YMRIMNKRSEREIRSLLNYLYLFGEYVENEKEKVGKVPFSYCSSVASR------------ 317
Query: 377 ERLHSLMLTLEITDTDEFLHIQTICDFATLVGTYTRGFSIIIEPFDERMPHIPDPVLQLS 436
+ +D DE ++ I+ P D +Q +
Sbjct: 318 --------IIAFSDQDE------------------EKYAAILSPED-------GGYMQAA 344
Query: 437 CHDASLAVKPVFDRFQSVVITSGTLSPIDLYPRLLNFHPVVSRSFKMSLTRDCICPMVLT 496
C D S ++ + + + SGTL P D Y + F + + I P
Sbjct: 345 CLDPSGILEVL--KESKTIHMSGTLDPFDFYSDITGFEIPFKKIGE-------IFPPENR 395
Query: 497 RGSDQLPVSTKFDMRSDPGVARNYGKLLVEMVSIVPDGIVCFFVSYSYMDEIIATWNDSG 556
+ VS+K+D + + R ++ +++ V + +F SYS MD + +
Sbjct: 396 YIAYYDGVSSKYDTLDEKELDR-MATVIEDIILKVKKNTIVYFPSYSLMDRV----ENRV 450
Query: 557 ILKEIMQHKLVFIETQDVVETTLALDNYRKACDCGRGAVFFSVARGKVAEGIDFDRHYGR 616
+ + +++ + D E L +R+ D G F+V+ G+++EGI+F +
Sbjct: 451 SFEHMKEYRGI-----DQKELYSMLKKFRR--DHG---TIFAVSGGRLSEGINFPGNELE 500
Query: 617 LVIMFGVPF 625
++I+ G+PF
Sbjct: 501 MIILAGLPF 509
>pdb|3CRV|A Chain A, "xpd_helicase"
pdb|3CRW|1 Chain 1, "xpd_apo"
Length = 551
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 53/228 (23%), Positives = 102/228 (44%), Gaps = 36/228 (15%)
Query: 407 VGTYTRGFSII-IEPFDERMPHIPDPVLQLSCHDASLAVKPVFDRFQSVVITSGTLSPID 465
+G+ R FS++ I F +P L + + S + + D S+++ SGTL P +
Sbjct: 273 IGSILRFFSLLSIGSF---IPFSYSKRLVIKNPEISYYLNLLNDNELSIILMSGTLPPRE 329
Query: 466 LYPRLLN-----FHPVVSRSFKMSLTRDCICPMVLTRGSDQLPVSTKFDMRSDPGVARNY 520
++ + V R + ++ C + G D V++K+DMRSD + + Y
Sbjct: 330 YMEKVWGIKRNMLYLDVEREIQKRVSGSYECYI----GVD---VTSKYDMRSD-NMWKRY 381
Query: 521 GKLLVEMVSIVPDGIVCFFVSYSYMDEIIATWNDSGILKEIMQHKLVFIETQDVVETTLA 580
L+++ ++ F SY MD +++ I K ++E++D +
Sbjct: 382 ADYLLKIYFQAKANVLVVFPSYEIMDRVMS---------RISLPK--YVESEDS-----S 425
Query: 581 LDNYRKACDCGRGAVFFSVARGKVAEGIDF---DRHYGRLVIMFGVPF 625
+++ A + SV +GK+AEGI+ DR V++ G+P+
Sbjct: 426 VEDLYSAISANNKVLIGSVGKGKLAEGIELRNNDRSLISDVVIVGIPY 473
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 29/116 (25%), Positives = 58/116 (50%), Gaps = 9/116 (7%)
Query: 177 LQDLRAFGKQQGWCPYFLARHMVQFANVVVYSYQYLLDPKVAGIISKEMQKESVVVFDEA 236
++ L+ G Q +CPY+ + + A+V+ +Y Y + I ++ +E ++V DEA
Sbjct: 124 VKKLKKDGLQDKFCPYYSLLNSLYKADVIALTYPYFFIDRYREFIDIDL-REYMIVIDEA 182
Query: 237 HNIDNVC-IEALSVS-------VRRQTLEGATRNLSRINQEIERFKATDAGRLRAE 284
HN+D V +E S+S +++ E + R LS++ ++ D ++ E
Sbjct: 183 HNLDKVNELEERSLSEITIQMAIKQSKSEESRRILSKLLNQLREVVLPDEKYIKVE 238
>pdb|2VL7|A Chain A, Structure Of S. Tokodaii Xpd4
Length = 540
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 38/171 (22%), Positives = 77/171 (45%), Gaps = 32/171 (18%)
Query: 137 RTASWVRALAAENPNIETCEFFENYEKAASAAVLPPGVYTLQD------LRAFGKQQGWC 190
++AS + A E P+ C S L + T++D + F +C
Sbjct: 84 KSASCIYAQGDEEPDEINC----------SKCRLKDKIKTIEDKEPSKLIEEFKDAVDYC 133
Query: 191 PYFLARHMVQFANVVVYSYQYLLDPKVAGII--SKE---MQKESVVVFDEAHNIDNVCIE 245
PY+ R ++ +V+ +Y YL + + +K+ ++ ++V DEAHN+ +E
Sbjct: 134 PYYSLRANLKDKDVIAMTYPYLFQKPIRNSVFCNKDDCLKLEDYLIVIDEAHNL----LE 189
Query: 246 A---LSVSVRRQTLEGATRNLSRINQEIERFKATDAGRLRAEYNRLVEGLA 293
A + + R+ LE A + + + +ER DA +++ N L++ ++
Sbjct: 190 ADKWFTRKISRKMLERALKEI----EIVERLNRIDAKKVKDYINLLIDYMS 236
>pdb|2GK1|A Chain A, X-Ray Crystal Structure Of Ngt-Bound Hexa
pdb|2GK1|C Chain C, X-Ray Crystal Structure Of Ngt-Bound Hexa
pdb|2GK1|E Chain E, X-Ray Crystal Structure Of Ngt-Bound Hexa
pdb|2GK1|G Chain G, X-Ray Crystal Structure Of Ngt-Bound Hexa
pdb|2GJX|A Chain A, Crystallographic Structure Of Human Beta-Hexosaminidase A
pdb|2GJX|D Chain D, Crystallographic Structure Of Human Beta-Hexosaminidase A
pdb|2GJX|E Chain E, Crystallographic Structure Of Human Beta-Hexosaminidase A
pdb|2GJX|H Chain H, Crystallographic Structure Of Human Beta-Hexosaminidase A
Length = 507
Score = 30.0 bits (66), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 27/47 (57%), Gaps = 3/47 (6%)
Query: 393 EFLHIQTICDFATLVGTYTRGFSIIIEPFDERMPHIPDPVLQLSCHD 439
E +IQT+ D +V +Y +G+ + E FD ++ PD ++Q+ D
Sbjct: 330 ESFYIQTLLD---IVSSYGKGYVVWQEVFDNKVKIQPDTIIQVWRED 373
>pdb|1HKX|A Chain A, Crystal Structure Of CalciumCALMODULIN-Dependent Protein
Kinase
pdb|1HKX|B Chain B, Crystal Structure Of CalciumCALMODULIN-Dependent Protein
Kinase
pdb|1HKX|C Chain C, Crystal Structure Of CalciumCALMODULIN-Dependent Protein
Kinase
pdb|1HKX|D Chain D, Crystal Structure Of CalciumCALMODULIN-Dependent Protein
Kinase
pdb|1HKX|E Chain E, Crystal Structure Of CalciumCALMODULIN-Dependent Protein
Kinase
pdb|1HKX|F Chain F, Crystal Structure Of CalciumCALMODULIN-Dependent Protein
Kinase
pdb|1HKX|G Chain G, Crystal Structure Of CalciumCALMODULIN-Dependent Protein
Kinase
pdb|1HKX|H Chain H, Crystal Structure Of CalciumCALMODULIN-Dependent Protein
Kinase
pdb|1HKX|I Chain I, Crystal Structure Of CalciumCALMODULIN-Dependent Protein
Kinase
pdb|1HKX|J Chain J, Crystal Structure Of CalciumCALMODULIN-Dependent Protein
Kinase
pdb|1HKX|K Chain K, Crystal Structure Of CalciumCALMODULIN-Dependent Protein
Kinase
pdb|1HKX|L Chain L, Crystal Structure Of CalciumCALMODULIN-Dependent Protein
Kinase
pdb|1HKX|M Chain M, Crystal Structure Of CalciumCALMODULIN-Dependent Protein
Kinase
pdb|1HKX|N Chain N, Crystal Structure Of CalciumCALMODULIN-Dependent Protein
Kinase
Length = 147
Score = 29.3 bits (64), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 15/34 (44%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 581 LDNYRKACDCGRGAVFFSVARGKVAEGIDFDRHY 614
++Y K CD G A F A G + EG+DF R Y
Sbjct: 35 FESYTKMCDPGMTA-FEPEALGNLVEGLDFHRFY 67
>pdb|3SOA|A Chain A, Full-Length Human Camkii
Length = 444
Score = 29.3 bits (64), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 32/69 (46%), Gaps = 10/69 (14%)
Query: 555 SGILKEIMQHKLVFIETQDVVETTLAL---------DNYRKACDCGRGAVFFSVARGKVA 605
IL ++ + + Q++++ T L ++Y K CD G A F A G +
Sbjct: 301 GAILTVMLATRNFSVRKQEIIKVTEQLIEAISNGDFESYTKMCDPGMTA-FEPEALGNLV 359
Query: 606 EGIDFDRHY 614
EG+DF R Y
Sbjct: 360 EGLDFHRFY 368
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
0.323 0.138 0.409
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,814,032
Number of Sequences: 62578
Number of extensions: 710316
Number of successful extensions: 1581
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 19
Number of HSP's that attempted gapping in prelim test: 1568
Number of HSP's gapped (non-prelim): 27
length of query: 631
length of database: 14,973,337
effective HSP length: 105
effective length of query: 526
effective length of database: 8,402,647
effective search space: 4419792322
effective search space used: 4419792322
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (25.4 bits)