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= 004385
(757 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 = 91.7 bits (226), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 151/687 (21%), Positives = 276/687 (40%), Gaps = 150/687 (21%)
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 EGATRNLSRINQEIERFKATDAGRLRAEYNRLVEGLALRGNLPNAWLSNPALPSDILKEA 316
E +L+R ++E + + + + + + L+E + AL S + +
Sbjct: 231 E----SLNRADREAQAYGDPELSQ-KIHVSDLIE------------MIRSALQSMVSERC 273
Query: 317 VPGNIR-RAEHFLHVLRRLVQ-------------YLRGRLETENVEKEG--PVSFVASIT 360
G++R R + F+ +R + + YL G EK G P S+ +S+
Sbjct: 274 GKGDVRIRFQEFMEYMRIMNKRSEREIRSLLNYLYLFGEYVENEKEKVGKVPFSYCSSVA 333
Query: 361 AHAGIDQKTLRFCYERLHSLMLTLEITDTDEFLHIQTICDFATLVGTYTRGFSIIIEPFD 420
+ + +D DE ++ I+ P D
Sbjct: 334 SR--------------------IIAFSDQDE------------------EKYAAILSPED 355
Query: 421 ERMPHIPDPVLQLSCHDASLAVKPVFDRFQSVVITSGTLSPIDLYPRLLNFHPVVSRSFK 480
+Q +C D S + V +++ + SGTL P D Y + F + +
Sbjct: 356 -------GGYMQAACLDPS-GILEVLKESKTIHM-SGTLDPFDFYSDITGFEIPFKKIGE 406
Query: 481 MSLTRDCICPMVLTRGSDQLPVSTKFDMRSDPGVARNYGKLLVEMVSIVPDGIVCFFVSY 540
I P + VS+K+D + + R ++ +++ V + +F SY
Sbjct: 407 -------IFPPENRYIAYYDGVSSKYDTLDEKELDR-MATVIEDIILKVKKNTIVYFPSY 458
Query: 541 SYMDEIIATWNDSGILKEIMQHKLVFIETQDVVETTLALDNYRKACDCGRGAVFFSVARG 600
S MD + + + + +++ + D E L +R+ D G F+V+ G
Sbjct: 459 SLMDRV----ENRVSFEHMKEYRGI-----DQKELYSMLKKFRR--DHG---TIFAVSGG 504
Query: 601 KVAEGIDFDRHYGRLVIMFGVPFQY--TLSKILLARLEYLRDTFQIKEGDFLTFDALRQA 658
+++EGI+F + ++I+ G+PF +++ L D ++ K G + +
Sbjct: 505 RLSEGINFPGNELEMIILAGLPFPRPDAINRSLF-------DYYERKYGKGWEYSVVYPT 557
Query: 659 A----QCVGRVIRSKADYGMMIFADKR 681
A Q +GR+IRS D G + DKR
Sbjct: 558 AIKIRQEIGRLIRSAEDTGACVILDKR 584
>pdb|2VSF|A Chain A, Structure Of Xpd From Thermoplasma Acidophilum
Length = 602
Score = 89.7 bits (221), Expect = 5e-18, Method: Compositional matrix adjust.
Identities = 150/681 (22%), Positives = 274/681 (40%), Gaps = 150/681 (22%)
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 KVA-------GIISKEMQKESVVVFDEAHNIDNVCIEALSVSVRRQTLEGATRNLSRINQ 268
VA G+ ++ V++ DEAHN+ ++ S+ R ++E +L+R ++
Sbjct: 172 SVAEKFLSHWGVSRNQI----VIILDEAHNLPDI---GRSIGSFRISVE----SLNRADR 220
Query: 269 EIERFKATDAGRLRAEYNRLVEGLALRGNLPNAWLSNPALPSDILKEAVPGNIR-RAEHF 327
E + + + + + + L+E + AL S + + G++R R + F
Sbjct: 221 EAQAYGDPELSQ-KIHVSDLIE------------MIRSALQSMVSERCGKGDVRIRFQEF 267
Query: 328 LHVLRRLVQ-------------YLRGRLETENVEKEG--PVSFVASITAHAGIDQKTLRF 372
+ +R + + YL G EK G P S+ +S+ +
Sbjct: 268 MEYMRIMNKRSEREIRSLLNYLYLFGEYVENEKEKVGKVPFSYCSSVASR---------- 317
Query: 373 CYERLHSLMLTLEITDTDEFLHIQTICDFATLVGTYTRGFSIIIEPFDERMPHIPDPVLQ 432
+ +D DE ++ I+ P D +Q
Sbjct: 318 ----------IIAFSDQDE------------------EKYAAILSPED-------GGYMQ 342
Query: 433 LSCHDASLAVKPVFDRFQSVVITSGTLSPIDLYPRLLNFHPVVSRSFKMSLTRDCICPMV 492
+C D S + V +++ + SGTL P D Y + F + + I P
Sbjct: 343 AACLDPS-GILEVLKESKTIHM-SGTLDPFDFYSDITGFEIPFKKIGE-------IFPPE 393
Query: 493 LTRGSDQLPVSTKFDMRSDPGVARNYGKLLVEMVSIVPDGIVCFFVSYSYMDEIIATWND 552
+ VS+K+D + + R ++ +++ V + +F SYS MD + +
Sbjct: 394 NRYIAYYDGVSSKYDTLDEKELDR-MATVIEDIILKVKKNTIVYFPSYSLMDRV----EN 448
Query: 553 SGILKEIMQHKLVFIETQDVVETTLALDNYRKACDCGRGAVFFSVARGKVAEGIDFDRHY 612
+ + +++ + D E L +R+ D G F+V+ G+++EGI+F +
Sbjct: 449 RVSFEHMKEYRGI-----DQKELYSMLKKFRR--DHG---TIFAVSGGRLSEGINFPGNE 498
Query: 613 GRLVIMFGVPFQY--TLSKILLARLEYLRDTFQIKEGDFLTFDALRQAA----QCVGRVI 666
++I+ G+PF +++ L D ++ K G + + A Q +GR+I
Sbjct: 499 LEMIILAGLPFPRPDAINRSLF-------DYYERKYGKGWEYSVVYPTAIKIRQEIGRLI 551
Query: 667 RSKADYGMMIFADKRYSRHDK 687
RS D G + DKR + K
Sbjct: 552 RSAEDTGACVILDKRAGQFRK 572
>pdb|3CRV|A Chain A, "xpd_helicase"
pdb|3CRW|1 Chain 1, "xpd_apo"
Length = 551
Score = 51.6 bits (122), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 72/291 (24%), Positives = 128/291 (43%), Gaps = 44/291 (15%)
Query: 405 VGTYTRGFSII-IEPFDERMPHIPDPVLQLSCHDASLAVKPVFDRFQSVVITSGTLSPID 463
+G+ R FS++ I F +P L + + S + + D S+++ SGTL P +
Sbjct: 273 IGSILRFFSLLSIGSF---IPFSYSKRLVIKNPEISYYLNLLNDNELSIILMSGTLPPRE 329
Query: 464 LYPRLLN-----FHPVVSRSFKMSLTRDCICPMVLTRGSDQLPVSTKFDMRSDPGVARNY 518
++ + V R + ++ C + G D V++K+DMRSD + + Y
Sbjct: 330 YMEKVWGIKRNMLYLDVEREIQKRVSGSYECYI----GVD---VTSKYDMRSD-NMWKRY 381
Query: 519 GKLLVEMVSIVPDGIVCFFVSYSYMDEIIATWNDSGILKEIMQHKLVFIETQDVVETTLA 578
L+++ ++ F SY MD +++ I K ++E++D +
Sbjct: 382 ADYLLKIYFQAKANVLVVFPSYEIMDRVMS---------RISLPK--YVESEDS-----S 425
Query: 579 LDNYRKACDCGRGAVFFSVARGKVAEGIDF---DRHYGRLVIMFGVPF----QYTLSKIL 631
+++ A + SV +GK+AEGI+ DR V++ G+P+ Y KIL
Sbjct: 426 VEDLYSAISANNKVLIGSVGKGKLAEGIELRNNDRSLISDVVIVGIPYPPPDDYL--KIL 483
Query: 632 LARLEYLRDTFQIKEGDFLTFDALRQAAQCVGRVIRSKADYGMMIFADKRY 682
R+ L+ + +E F AL Q +GR IR D + DKR+
Sbjct: 484 AQRVS-LKMNRENEEFLF-KIPALVTIKQAIGRAIRDVNDKCNVWLLDKRF 532
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 = 0.003, 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
Score = 31.2 bits (69), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 23/92 (25%), Positives = 39/92 (42%), Gaps = 4/92 (4%)
Query: 597 VARGKVAEGIDFDRHYGRL--VIMFGVPFQYTLSKILLARLEYLRDTFQIKEGDFLTFDA 654
V R K +EG++F +++ G+P+ ++ R+E L K+ D + D
Sbjct: 435 VMRAKESEGVEFREKENLFESLVLAGLPYPNVSDDMVRKRIERL-SKLTGKDEDSIIHDL 493
Query: 655 LRQA-AQCVGRVIRSKADYGMMIFADKRYSRH 685
Q +GR R DY + D RY +
Sbjct: 494 TAIVIKQTIGRAFRDPNDYVKIYLCDSRYREY 525
>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 = 4.9, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 27/47 (57%), Gaps = 3/47 (6%)
Query: 391 EFLHIQTICDFATLVGTYTRGFSIIIEPFDERMPHIPDPVLQLSCHD 437
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 = 29.6 bits (65), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 15/34 (44%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 579 LDNYRKACDCGRGAVFFSVARGKVAEGIDFDRHY 612
++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 = 7.4, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 32/69 (46%), Gaps = 10/69 (14%)
Query: 553 SGILKEIMQHKLVFIETQDVVETTLAL---------DNYRKACDCGRGAVFFSVARGKVA 603
IL ++ + + Q++++ T L ++Y K CD G A F A G +
Sbjct: 301 GAILTVMLATRNFSVRKQEIIKVTEQLIEAISNGDFESYTKMCDPGMTA-FEPEALGNLV 359
Query: 604 EGIDFDRHY 612
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 0.407
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,291,112
Number of Sequences: 62578
Number of extensions: 854097
Number of successful extensions: 1923
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1908
Number of HSP's gapped (non-prelim): 14
length of query: 757
length of database: 14,973,337
effective HSP length: 106
effective length of query: 651
effective length of database: 8,340,069
effective search space: 5429384919
effective search space used: 5429384919
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: 55 (25.8 bits)