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= 001656
(1036 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 = 97.8 bits (242), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 160/689 (23%), Positives = 255/689 (37%), Gaps = 153/689 (22%)
Query: 31 SLQNKCNALLESPTGTGKTLCLLCATLAWRKSLGSFSTLXXXXXXXXXXXXXXXXXXXXX 90
SLQ LESPTG+GKT+ L + L +
Sbjct: 18 SLQKSYGVALESPTGSGKTIMALKSALQY-----------------------------SS 48
Query: 91 XXKLPTILYTSRTHSQLRQVIQELKT--SNYRPKMVILGSREQLCI-HREVSLLRGSAQN 147
KL +LY RT+SQ QVI+EL++ S + + + + R +CI +R V L
Sbjct: 49 ERKL-KVLYLVRTNSQEEQVIKELRSLSSTMKIRAIPMQGRVNMCILYRMVDDLHEINAE 107
Query: 148 NACRFLCKK------GTNRRCNHHSRVADYMKNNPHLGDEPIDIEDLVNIGRTFGPCPYF 201
+ +F K G C + + + L DE E+ + G CPY
Sbjct: 108 SLAKFCNMKKREVMAGNEAACPYFNFKIRSDETKRFLFDELPTAEEFYDYGERNNVCPYE 167
Query: 202 MTRELQKTVDIVFAPYNYLID----PWFRKGLGVEWKNSILIFDEAHNLEGICADAASFD 257
+ DIV APY Y ++ F GV ++I DEAHNL I SF
Sbjct: 168 SMKAALPDADIVIAPYAYFLNRSVAEKFLSHWGVSRNQIVIILDEAHNLPDIGRSIGSFR 227
Query: 258 LSSGLLTACISEAKNCIDISSTRRGQSSDETLNPDNFAILRALLLKLEKRIAEVPINSKE 317
+S L EA+ D +++ SD I AL + +R + + +
Sbjct: 228 ISVESLNRADREAQAYGDPELSQKIHVSDLIE-----MIRSALQSMVSERCGKGDVRIRF 282
Query: 318 LGFTKPGPYIYELLADLNITQETAYK-LIDIVEVAAELLQEDKLQNKK------STTACR 370
F E + +N E + L++ + + E ++ +K + K S+ A R
Sbjct: 283 QEFM-------EYMRIMNKRSEREIRSLLNYLYLFGEYVENEKEKVGKVPFSYCSSVASR 335
Query: 371 IESISNILKIIFRDKGTAHSAYYRVHVREADANAADVLKGKASRTLSWWCFNPGIAMQEF 430
I I F D+ + A +L + + C +P ++
Sbjct: 336 I--------IAFSDQD--------------EEKYAAILSPEDGGYMQAACLDPSGILE-- 371
Query: 431 SRLEVGSIILTSGTLSPMDSFAQELKLNFPLRV-------ENPHVITSKQIWAGIVPVGP 483
L+ I SGTL P D ++ P + EN ++ + G+
Sbjct: 372 -VLKESKTIHMSGTLDPFDFYSDITGFEIPFKKIGEIFPPENRYI----AYYDGV----- 421
Query: 484 SGYLLNSSYRNRDSIEYKQELGNTIVNIARIVPDGLLIFFPSYYLMDQCIACWKNTSHGN 543
+S Y D E + + I +I V +++FPSY LMD+
Sbjct: 422 -----SSKYDTLDEKELDR-MATVIEDIILKVKKNTIVYFPSYSLMDR------------ 463
Query: 544 LTTIWERIC-KHKKPVVEPRQSSLFPLAIEDYMAKLKDTSTSGAVFFAVCRGKVSEGLDF 602
+ R+ +H K Q L+ + LK FAV G++SEG++F
Sbjct: 464 ---VENRVSFEHMKEYRGIDQKELYSM--------LKKFRRDHGTIFAVSGGRLSEGINF 512
Query: 603 ADHAGRAVVITGMPFATMTDPKVRLKREYLDLQAQSQGGEYKETKLSFLSGEDW-YNQQA 661
+ +++ G+PF P + R D Y E K G+ W Y+
Sbjct: 513 PGNELEMIILAGLPFPR---PDA-INRSLFD---------YYERKY----GKGWEYSVVY 555
Query: 662 SRAVN--QAVGRVIRHRHDYGAIIFCDER 688
A+ Q +GR+IR D GA + D+R
Sbjct: 556 PTAIKIRQEIGRLIRSAEDTGACVILDKR 584
>pdb|2VSF|A Chain A, Structure Of Xpd From Thermoplasma Acidophilum
Length = 602
Score = 95.5 bits (236), Expect = 1e-19, 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 = 50.8 bits (120), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 43/176 (24%), Positives = 75/176 (42%), Gaps = 45/176 (25%)
Query: 519 LLIFFPSYYLMDQCIACWKNTSHGNLTTIWERICKHKKPVVEPRQSSLFPLAIEDYMAKL 578
+L+FFPSY +++ RI PV+E + + E+ + +
Sbjct: 387 VLVFFPSYEMLESV-----------------RIHLSGIPVIEENKKTRH----EEVLELM 425
Query: 579 KDTSTSGAVFFAVCRGKVSEGLDFADHAG--RAVVITGMPFATMTDPKVRLKREYLDLQA 636
K T + V R K SEG++F + ++V+ G+P+ ++D VR + E
Sbjct: 426 K---TGKYLVMLVMRAKESEGVEFREKENLFESLVLAGLPYPNVSDDMVRKRIE------ 476
Query: 637 QSQGGEYKETKLSFLSGED---WYNQQASRAVNQAVGRVIRHRHDYGAIIFCDERF 689
+LS L+G+D + + + Q +GR R +DY I CD R+
Sbjct: 477 ----------RLSKLTGKDEDSIIHDLTAIVIKQTIGRAFRDPNDYVKIYLCDSRY 522
Score = 34.3 bits (77), Expect = 0.34, 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 = 47.0 bits (110), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 46/234 (19%), Positives = 88/234 (37%), Gaps = 54/234 (23%)
Query: 19 DCQLVYMEKVIQSLQNKCNALLESPTGTGKTLCLLCATLAWRKSLGSFSTLXXXXXXXXX 78
D Q +KVI+ L+N L +PTG+GKTL L +L +
Sbjct: 6 DWQEKLKDKVIEGLRNNFLVALNAPTGSGKTLFSLLVSLEVK------------------ 47
Query: 79 XXXXXXXXXXXXXXKLPTILYTSRTHSQLRQVIQELKTSNYRPKMVI--LGSREQLCIHR 136
P +L+ RTH++ + ++L + + L + C++
Sbjct: 48 ----------------PKVLFVVRTHNEFYPIYRDLTKIREKRNITFSFLVGKPSSCLYA 91
Query: 137 EVSLLRGSAQNNACRFLCKKGTNRRCNHHSRVADYMKNNPHLGDEPID-IEDLVNIGRTF 195
E +++ C++ KG+ D P+ ++ L G
Sbjct: 92 EKG---AESEDIPCKYCELKGSIVEVKTD--------------DSPLSLVKKLKKDGLQD 134
Query: 196 GPCPYFMTRELQKTVDIVFAPYNYLIDPWFRKGLGVEWKNSILIFDEAHNLEGI 249
CPY+ D++ Y Y +R+ + ++ + +++ DEAHNL+ +
Sbjct: 135 KFCPYYSLLNSLYKADVIALTYPYFFIDRYREFIDIDLREYMIVIDEAHNLDKV 188
Score = 45.4 bits (106), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 69/281 (24%), Positives = 117/281 (41%), Gaps = 63/281 (22%)
Query: 437 SIILTSGTLSPMDSFAQE--LKLN-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|2OOD|A Chain A, Crystal Structure Of Guanine Deaminase From Bradyrhizobium
Japonicum
Length = 475
Score = 32.3 bits (72), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 32/69 (46%), Gaps = 5/69 (7%)
Query: 790 EIVPANRSSLSPYKGIWASELKNSSDLIQFEKKLLLSGRKSIQYRDHEFIDLTSNSSLHA 849
++ A R+ LSPY+G W+ L + L +K K + +F+ L N A
Sbjct: 363 DLAEAERNKLSPYRGFWSVTLGGAEGLYIDDKLGNFEPGK-----EADFVALDPNGGQLA 417
Query: 850 KPRKEELIA 858
+P + LIA
Sbjct: 418 QPWHQSLIA 426
>pdb|3H6Q|A Chain A, Macrocypin, A Beta-Trefoil Cysteine Protease Inhibitor
Length = 169
Score = 30.8 bits (68), Expect = 4.0, Method: Composition-based stats.
Identities = 23/67 (34%), Positives = 32/67 (47%), Gaps = 12/67 (17%)
Query: 695 KSQISLWIQPHIQCYSKFGDVVYTLTRFFREERICGSTNLKLIKTEVSGDVRELKPVDLL 754
+S+I WI Q GD +YT+T F + I G + ++TEV PV L
Sbjct: 47 QSKIRWWIARDPQA----GDDMYTITEFRIDNSIPGQWSRSPVETEV--------PVYLY 94
Query: 755 DKISLEE 761
D+I EE
Sbjct: 95 DRIKAEE 101
>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 = 29.6 bits (65), Expect = 8.1, 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
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
0.318 0.134 0.394
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 29,018,513
Number of Sequences: 62578
Number of extensions: 1159674
Number of successful extensions: 2674
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 2650
Number of HSP's gapped (non-prelim): 18
length of query: 1036
length of database: 14,973,337
effective HSP length: 109
effective length of query: 927
effective length of database: 8,152,335
effective search space: 7557214545
effective search space used: 7557214545
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 bits)