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= 004379
(758 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 = 98.2 bits (243), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 162/705 (22%), Positives = 262/705 (37%), Gaps = 153/705 (21%)
Query: 15 FEAYDCQLVYMEKVIQSLQNKCNALLESPTGTGKTLCLLCATLAWRKSLGSFSTLXXXXX 74
+E Q+ ++ + SLQ LESPTG+GKT+ L + L +
Sbjct: 2 YENRQYQVEAIDFLRSSLQKSYGVALESPTGSGKTIMALKSALQY--------------- 46
Query: 75 XXXXXXXXXXXXXXXXXXKLPTILYTSRTHSQLRQVIQELKT--SNYRPKMVILGSREQL 132
KL +LY RT+SQ QVI+EL++ S + + + + R +
Sbjct: 47 --------------SSERKL-KVLYLVRTNSQEEQVIKELRSLSSTMKIRAIPMQGRVNM 91
Query: 133 CI-HREVSLLRGSAQNNACRFLCKK------GTNRRCNHHSRVADYMKNNPHLGDEPIDI 185
CI +R V L + +F K G C + + + L DE
Sbjct: 92 CILYRMVDDLHEINAESLAKFCNMKKREVMAGNEAACPYFNFKIRSDETKRFLFDELPTA 151
Query: 186 EDLVNIGRTFGPCPYFMTRELQKTVDIVFAPYNYLID----PWFRKGLGVEWKNSILIFD 241
E+ + G CPY + DIV APY Y ++ F GV ++I D
Sbjct: 152 EEFYDYGERNNVCPYESMKAALPDADIVIAPYAYFLNRSVAEKFLSHWGVSRNQIVIILD 211
Query: 242 EAHNLEGICADAASFDLSSGLLTACISEAKNCIDISSTRRGQSSDETLNPDNFAILRALL 301
EAHNL I SF +S L EA+ D +++ SD I AL
Sbjct: 212 EAHNLPDIGRSIGSFRISVESLNRADREAQAYGDPELSQKIHVSDLIE-----MIRSALQ 266
Query: 302 LKLEKRIAEVPINSKELGFTKPGPYIYELLADLNITQETAYK-LIDIVEVAAELLQEDKL 360
+ +R + + + F E + +N E + L++ + + E ++ +K
Sbjct: 267 SMVSERCGKGDVRIRFQEFM-------EYMRIMNKRSEREIRSLLNYLYLFGEYVENEKE 319
Query: 361 QNKK------STTACRIESISNILKIIFRDKGTAHSAYYRVHVREADANAADVLKGKASR 414
+ K S+ A RI I F D+ + A +L +
Sbjct: 320 KVGKVPFSYCSSVASRI--------IAFSDQD--------------EEKYAAILSPEDGG 357
Query: 415 TLSWWCFNPGIAMQEFSRLEVGSIILTSGTLSPMDSFAQELKLNFPLRV-------ENPH 467
+ C +P ++ L+ I SGTL P D ++ P + EN +
Sbjct: 358 YMQAACLDPSGILE---VLKESKTIHMSGTLDPFDFYSDITGFEIPFKKIGEIFPPENRY 414
Query: 468 VITSKQIWAGIVPVGPSGYLLNSSYRNRDSIEYKQELGNTIVNIARIVPDGLLIFFPSYY 527
+ + G+ +S Y D E + + I +I V +++FPSY
Sbjct: 415 I----AYYDGV----------SSKYDTLDEKELDR-MATVIEDIILKVKKNTIVYFPSYS 459
Query: 528 LMDQCIACWKNTSHGNLTTIWERIC-KHKKPVVEPRQSSLFPLAIEDYMAKLKDTSTSGA 586
LMD+ + R+ +H K Q L+ + LK
Sbjct: 460 LMDR---------------VENRVSFEHMKEYRGIDQKELYSM--------LKKFRRDHG 496
Query: 587 VFFAVCRGKVSEGLDFADHAGRAVVITGMPFATMTDPKVRLKREYLDLQAQSQGGEYKET 646
FAV G++SEG++F + +++ G+PF P + R D Y E
Sbjct: 497 TIFAVSGGRLSEGINFPGNELEMIILAGLPFPR---PDA-INRSLFD---------YYER 543
Query: 647 KLSFLSGEDW-YNQQASRAVN--QAVGRVIRHRHDYGAIIFCDER 688
K G+ W Y+ A+ Q +GR+IR D GA + D+R
Sbjct: 544 KY----GKGWEYSVVYPTAIKIRQEIGRLIRSAEDTGACVILDKR 584
>pdb|2VSF|A Chain A, Structure Of Xpd From Thermoplasma Acidophilum
Length = 602
Score = 95.9 bits (237), Expect = 7e-20, Method: Compositional matrix adjust.
Identities = 158/688 (22%), Positives = 254/688 (36%), Gaps = 153/688 (22%)
Query: 32 LQNKCNALLESPTGTGKTLCLLCATLAWRKSLGSFSTLXXXXXXXXXXXXXXXXXXXXXX 91
+Q LESPTG+GKT+ L + L +
Sbjct: 1 MQKSYGVALESPTGSGKTIMALKSALQY-----------------------------SSE 31
Query: 92 XKLPTILYTSRTHSQLRQVIQELKT--SNYRPKMVILGSREQLCI-HREVSLLRGSAQNN 148
KL +LY RT+SQ QVI+EL++ S + + + + R +CI +R V L +
Sbjct: 32 RKL-KVLYLVRTNSQEEQVIKELRSLSSTMKIRAIPMQGRVNMCILYRMVDDLHEINAES 90
Query: 149 ACRFLCKK------GTNRRCNHHSRVADYMKNNPHLGDEPIDIEDLVNIGRTFGPCPYFM 202
+F K G C + + + L DE E+ + G CPY
Sbjct: 91 LAKFCNMKKREVMAGNEAACPYFNFKIRSDETKRFLFDELPTAEEFYDYGERNNVCPYES 150
Query: 203 TRELQKTVDIVFAPYNYLID----PWFRKGLGVEWKNSILIFDEAHNLEGICADAASFDL 258
+ DIV APY Y ++ F GV ++I DEAHNL I SF +
Sbjct: 151 MKAALPDADIVIAPYAYFLNRSVAEKFLSHWGVSRNQIVIILDEAHNLPDIGRSIGSFRI 210
Query: 259 SSGLLTACISEAKNCIDISSTRRGQSSDETLNPDNFAILRALLLKLEKRIAEVPINSKEL 318
S L EA+ D +++ SD I AL + +R + + +
Sbjct: 211 SVESLNRADREAQAYGDPELSQKIHVSDLIE-----MIRSALQSMVSERCGKGDVRIRFQ 265
Query: 319 GFTKPGPYIYELLADLNITQETAYK-LIDIVEVAAELLQEDKLQNKK------STTACRI 371
F E + +N E + L++ + + E ++ +K + K S+ A RI
Sbjct: 266 EFM-------EYMRIMNKRSEREIRSLLNYLYLFGEYVENEKEKVGKVPFSYCSSVASRI 318
Query: 372 ESISNILKIIFRDKGTAHSAYYRVHVREADANAADVLKGKASRTLSWWCFNPGIAMQEFS 431
I F D+ + A +L + + C +P ++
Sbjct: 319 --------IAFSDQD--------------EEKYAAILSPEDGGYMQAACLDPSGILE--- 353
Query: 432 RLEVGSIILTSGTLSPMDSFAQELKLNFPLRV-------ENPHVITSKQIWAGIVPVGPS 484
L+ I SGTL P D ++ P + EN ++ + G+
Sbjct: 354 VLKESKTIHMSGTLDPFDFYSDITGFEIPFKKIGEIFPPENRYI----AYYDGV------ 403
Query: 485 GYLLNSSYRNRDSIEYKQELGNTIVNIARIVPDGLLIFFPSYYLMDQCIACWKNTSHGNL 544
+S Y D E + + I +I V +++FPSY LMD+
Sbjct: 404 ----SSKYDTLDEKELDR-MATVIEDIILKVKKNTIVYFPSYSLMDR------------- 445
Query: 545 TTIWERIC-KHKKPVVEPRQSSLFPLAIEDYMAKLKDTSTSGAVFFAVCRGKVSEGLDFA 603
+ R+ +H K Q L+ + LK FAV G++SEG++F
Sbjct: 446 --VENRVSFEHMKEYRGIDQKELYSM--------LKKFRRDHGTIFAVSGGRLSEGINFP 495
Query: 604 DHAGRAVVITGMPFATMTDPKVRLKREYLDLQAQSQGGEYKETKLSFLSGEDW-YNQQAS 662
+ +++ G+PF P + R D Y E K G+ W Y+
Sbjct: 496 GNELEMIILAGLPFPR---PDA-INRSLFD---------YYERKY----GKGWEYSVVYP 538
Query: 663 RAVN--QAVGRVIRHRHDYGAIIFCDER 688
A+ Q +GR+IR D GA + D+R
Sbjct: 539 TAIKIRQEIGRLIRSAEDTGACVILDKR 566
>pdb|2VL7|A Chain A, Structure Of S. Tokodaii Xpd4
Length = 540
Score = 51.6 bits (122), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 43/177 (24%), Positives = 75/177 (42%), Gaps = 45/177 (25%)
Query: 518 GLLIFFPSYYLMDQCIACWKNTSHGNLTTIWERICKHKKPVVEPRQSSLFPLAIEDYMAK 577
+L+FFPSY +++ RI PV+E + + E+ +
Sbjct: 386 SVLVFFPSYEMLESV-----------------RIHLSGIPVIEENKKTRH----EEVLEL 424
Query: 578 LKDTSTSGAVFFAVCRGKVSEGLDFADHAG--RAVVITGMPFATMTDPKVRLKREYLDLQ 635
+K T + V R K SEG++F + ++V+ G+P+ ++D VR + E
Sbjct: 425 MK---TGKYLVMLVMRAKESEGVEFREKENLFESLVLAGLPYPNVSDDMVRKRIE----- 476
Query: 636 AQSQGGEYKETKLSFLSGED---WYNQQASRAVNQAVGRVIRHRHDYGAIIFCDERF 689
+LS L+G+D + + + Q +GR R +DY I CD R+
Sbjct: 477 -----------RLSKLTGKDEDSIIHDLTAIVIKQTIGRAFRDPNDYVKIYLCDSRY 522
Score = 34.7 bits (78), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 36/157 (22%), Positives = 58/157 (36%), Gaps = 30/157 (19%)
Query: 97 ILYTSRTHSQLRQVIQELKTSNYRPKMVILGSREQLCIHREVSLLRGSAQNNACRFLCKK 156
+L +RTHSQL + + K +LG + I + S + C K
Sbjct: 54 VLIFTRTHSQLDSIYKNAK---------LLGLKTGFLIGKSASCIYAQGDEEPDEINCSK 104
Query: 157 GTNRRCNHHSRVADYMKNNP-HLGDEPIDIEDLVNIGRTFGPCPYFMTRELQKTVDIVFA 215
C ++ P L +E D D CPY+ R K D++
Sbjct: 105 -----CRLKDKIKTIEDKEPSKLIEEFKDAVDY---------CPYYSLRANLKDKDVIAM 150
Query: 216 PYNYLIDPWFRKGL------GVEWKNSILIFDEAHNL 246
Y YL R + ++ ++ +++ DEAHNL
Sbjct: 151 TYPYLFQKPIRNSVFCNKDDCLKLEDYLIVIDEAHNL 187
>pdb|3CRV|A Chain A, "xpd_helicase"
pdb|3CRW|1 Chain 1, "xpd_apo"
Length = 551
Score = 48.1 bits (113), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 68/306 (22%), Positives = 120/306 (39%), Gaps = 72/306 (23%)
Query: 19 DCQLVYMEKVIQSLQNKCNALLESPTGTGKTLCLLCATLAWRKSLGSFSTLXXXXXXXXX 78
D Q +KVI+ L+N L +PTG+GKTL L +L +
Sbjct: 6 DWQEKLKDKVIEGLRNNFLVALNAPTGSGKTLFSLLVSLEVK------------------ 47
Query: 79 XXXXXXXXXXXXXXKLPTILYTSRTHSQLRQVIQELKTSNYRPKMVI----LGSREQLCI 134
P +L+ RTH++ + ++L + R K I L + C+
Sbjct: 48 ----------------PKVLFVVRTHNEFYPIYRDL--TKIREKRNITFSFLVGKPSSCL 89
Query: 135 HREVSLLRGSAQNNACRFLCKKGTNRRCNHHSRVADYMKNNPHLGDEPID-IEDLVNIGR 193
+ E +++ C++ KG+ D P+ ++ L G
Sbjct: 90 YAEKG---AESEDIPCKYCELKGSIVEVKTD--------------DSPLSLVKKLKKDGL 132
Query: 194 TFGPCPYFMTRELQKTVDIVFAPYNYLIDPWFRKGLGVEWKNSILIFDEAHNLEGICADA 253
CPY+ D++ Y Y +R+ + ++ + +++ DEAHNL+ + +
Sbjct: 133 QDKFCPYYSLLNSLYKADVIALTYPYFFIDRYREFIDIDLREYMIVIDEAHNLDKV-NEL 191
Query: 254 ASFDLSSGLLTACISEAKNCIDISSTRRGQSSDETLNPDNFAILRALLLKLEK--RIAEV 311
LS + I ++K+ +RR S + LN LR ++L EK ++ V
Sbjct: 192 EERSLSEITIQMAIKQSKS----EESRRILS--KLLNQ-----LREVVLPDEKYIKVENV 240
Query: 312 PINSKE 317
P SKE
Sbjct: 241 PKLSKE 246
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 69/281 (24%), Positives = 117/281 (41%), Gaps = 63/281 (22%)
Query: 437 SIILTSGTLSPMDSFAQ--ELKLN-FPLRVE---NPHVITSKQIWAGIVPVGPSGYLLNS 490
SIIL SGTL P + + +K N L VE V S + + G+ + S
Sbjct: 317 SIILMSGTLPPREYMEKVWGIKRNMLYLDVEREIQKRVSGSYECYIGVD--------VTS 368
Query: 491 SYRNRDSIEYKQELGNTIVNIARIVPDGLLIFFPSYYLMDQCIACWKNTSHGNLTTIWER 550
Y R +K+ + ++ I +L+ FPSY +MD+ ++ R
Sbjct: 369 KYDMRSDNMWKR-YADYLLKIYFQAKANVLVVFPSYEIMDRVMS---------------R 412
Query: 551 ICKHKKPVVEPRQSSLFPLAIEDYMAKLKDTSTSGAVFFAVCRGKVSEGLDFADHAGRA- 609
I K VE SS +ED + + ++ + + +V +GK++EG++ ++
Sbjct: 413 ISLPK--YVESEDSS-----VEDLYSAI--SANNKVLIGSVGKGKLAEGIELRNNDRSLI 463
Query: 610 --VVITGMPFATMTDPKVRLKREYLDLQAQSQGGEYKETKLSFLSGEDWYNQQASRAVNQ 667
VVI G+P+ D YL + AQ + FL + A + Q
Sbjct: 464 SDVVIVGIPYPPPDD--------YLKILAQRVSLKMNRENEEFL-----FKIPALVTIKQ 510
Query: 668 AVGRVIRHRHDYGAIIFCDERFAHPSRKSQISLWIQPHIQC 708
A+GR IR +D + D+RF SL+ + +++C
Sbjct: 511 AIGRAIRDVNDKCNVWLLDKRFE--------SLYWKKNLKC 543
>pdb|2BUJ|A Chain A, Crystal Structure Of The Human Serine-Threonine Kinase 16
In Complex With Staurosporine
pdb|2BUJ|B Chain B, Crystal Structure Of The Human Serine-Threonine Kinase 16
In Complex With Staurosporine
Length = 317
Score = 30.4 bits (67), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 36/127 (28%), Positives = 50/127 (39%), Gaps = 16/127 (12%)
Query: 120 RPKMVILGSREQLCIHREVSLLRGSAQNNACRFLCKKGTNRRCNHHSRVADYMKNNPH-L 178
+P ++ LGS Q CIH E S + Q+ A +RC R + H +
Sbjct: 172 QPVLMDLGSMNQACIHVEGSRQALTLQDWAA---------QRCTISYRAPELFSVQSHCV 222
Query: 179 GDEPIDIEDL--VNIGRTFGPCPYFMTRELQKTVDIVFAPYNYLIDPWFRKGLGVEWK-- 234
DE D+ L V FG PY M QK + A N L P + W+
Sbjct: 223 IDERTDVWSLGCVLYAMMFGEGPYDMV--FQKGDSVALAVQNQLSIPQSPRHSSALWQLL 280
Query: 235 NSILIFD 241
NS++ D
Sbjct: 281 NSMMTVD 287
>pdb|4EQB|A Chain A, 1.5 Angstrom Crystal Structure Of SpermidinePUTRESCINE ABC
Transporter Substrate-Binding Protein From Streptococcus
Pneumoniae Strain Canada Mdr_19a In Complex With Calcium
And Hepes.
pdb|4EQB|B Chain B, 1.5 Angstrom Crystal Structure Of SpermidinePUTRESCINE ABC
Transporter Substrate-Binding Protein From Streptococcus
Pneumoniae Strain Canada Mdr_19a In Complex With Calcium
And Hepes
Length = 330
Score = 30.0 bits (66), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 33/111 (29%), Positives = 54/111 (48%), Gaps = 27/111 (24%)
Query: 169 ADYMKNNPHLGDE----PID---IEDLVNIG-----RTFGPCPYFMTRELQKTVDIVF-- 214
++YM N + DE P+D IE + NIG ++F P F T+ IV+
Sbjct: 64 SEYMIN--KMKDEDLLVPLDYSKIEGIENIGPEFLNQSFDPGNKFSIPYFWGTLGIVYNE 121
Query: 215 -----APYNYLIDPWFRKGLGVEWKNSILIFDEAHNLEGICADAASFDLSS 260
AP ++ D W +E+KNSI++FD A + G+ ++ + L+S
Sbjct: 122 TMVDEAPEHW-DDLW-----KLEYKNSIMLFDGAREVLGLGLNSLGYSLNS 166
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 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,477,009
Number of Sequences: 62578
Number of extensions: 858623
Number of successful extensions: 1953
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1930
Number of HSP's gapped (non-prelim): 14
length of query: 758
length of database: 14,973,337
effective HSP length: 106
effective length of query: 652
effective length of database: 8,340,069
effective search space: 5437724988
effective search space used: 5437724988
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: 55 (25.8 bits)