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= 005544
(691 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1JEQ|B Chain B, Crystal Structure Of The Ku Heterodimer
pdb|1JEY|B Chain B, Crystal Structure Of The Ku Heterodimer Bound To Dna
Length = 565
Score = 120 bits (300), Expect = 3e-27, Method: Compositional matrix adjust.
Identities = 130/549 (23%), Positives = 243/549 (44%), Gaps = 70/549 (12%)
Query: 1 MART--REALLLLLDVSPSMHSVLPDVE-------KLCSRLIQKKLIYGKNHEVGVILFG 51
M R+ + A++L +DV +M + +P +E K+ + +Q+++ E+ ++LFG
Sbjct: 1 MVRSGNKAAVVLCMDVGFTMSNSIPGIESPFEQAKKVITMFVQRQVFAENKDEIALVLFG 60
Query: 52 TEETENELTKEVGG--YEHVKVLQDIKVVDGHLVQSLKHLPQ-GTCAGDFLDAIVVGVDM 108
T+ T+N L+ GG Y+++ V + + + D L++ ++ Q G+ DFLDA++V +D+
Sbjct: 61 TDGTDNPLS---GGDQYQNITVHRHLMLPDFDLLEDIESKIQPGSQQADFLDALIVSMDV 117
Query: 109 LI---------KKYGETYK------GKKHLCLITDAL--CPL-----------KDPDVGT 140
+ K++ E + K L +I +L C + K+ G
Sbjct: 118 IQHETIGKKFEKRHIEIFTDLSSRFSKSQLDIIIHSLKKCDISLQFFLPFSLGKEDGSGD 177
Query: 141 KEDQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIEN-DNLLNIFSKKSSAKTLFVD 199
+ D + +F L+ + L + + +E D L I+S S + L V
Sbjct: 178 RGDGPFRLGGHGPSFPLKGITEQQKEGLEIVKMVMISLEGEDGLDEIYSFSESLRKLCV- 236
Query: 200 STTSLRGARKTRDISPVTIFRGDLELSEKMKIKVWVYKKTGEEKFPTLKKYSDKAPSTDK 259
+ + P L + + I++ YK +E+ K +
Sbjct: 237 ----FKKIERHSIHWPCR-----LTIGSNLSIRIAAYKSILQERV----KKTWTVVDAKT 283
Query: 260 FATHEVKVDYEYKSVEDPSKVVPPEQRIKGYRYGPQVVPISSAEWEAVKFKPE-KSVKLL 318
+++ + Y +D V E I+G+RYG +VP S + E +K+K E K +L
Sbjct: 284 LKKEDIQKETVYCLNDDDETEVLKEDIIQGFRYGSDIVPFSKVDEEQMKYKSEGKCFSVL 343
Query: 319 GFTDASNILRHYYMKDVNL-FIAEPGNSRATVAVSALARAMKEMNKVAIVRCVWRQGQQS 377
GF +S + R ++M + L A + A VA+S+L A+ +++ VAIVR + + + +
Sbjct: 344 GFCKSSQVQRRFFMGNQVLKVFAARDDEAAAVALSSLIHALDDLDMVAIVRYAYDK-RAN 402
Query: 378 VVVGVLTPNVSEKINIPDSFYFNVLPFAEDVREFQFPSFSKFPVSWQPNEQQQEAADNLV 437
VGV P++ + + LPF ED+R++ F S K + P E Q A D L+
Sbjct: 403 PQVGVAFPHIKHNY---ECLVYVQLPFMEDLRQYMFSSL-KNSKKYAPTEAQLNAVDALI 458
Query: 438 KMLDLAPSGKG-----EILQPELTPNPALERFYHHLELKSEHQDAAPPPLDDSLKKITEP 492
+ LA + ++ PNP +R + L ++ H PP+ + + P
Sbjct: 459 DSMSLAKKDEKTDTLEDLFPTTKIPNPRFQRLFQCLLHRALHPREPLPPIQQHIWNMLNP 518
Query: 493 DPTLLAESQ 501
+ +SQ
Sbjct: 519 PAEVTTKSQ 527
>pdb|1RW2|A Chain A, Three-Dimensional Structure Of Ku80 Ctd
Length = 152
Score = 38.5 bits (88), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 25/128 (19%), Positives = 60/128 (46%), Gaps = 9/128 (7%)
Query: 559 TVDKIGDLTPIQDFEAMMSRRDCPDWVDKAIEDMKNKIFGLLE---NSNEGINYPKAVEL 615
+V +G + P ++F ++ ++ + E+ N++ +E ++NE + K+++
Sbjct: 27 SVTSVGSVNPAENFRVLVKQKKA------SFEEASNQLINHIEQFLDTNETPYFMKSIDC 80
Query: 616 LVALRKGCILEQEPKQFNDVLEKVCKICRKRNFSTFFDFXXXXXXXXXXXXEAVDSDITD 675
+ A R+ I E ++FN+ L+ + + + + F++ EA S +T
Sbjct: 81 IRAFREEAIKFSEEQRFNNFLKALQEKVEIKQLNHFWEIVVQDGITLITKEEASGSSVTA 140
Query: 676 DEAGSFIV 683
+EA F+
Sbjct: 141 EEAKKFLA 148
>pdb|1Q2Z|A Chain A, The 3d Solution Structure Of The C-Terminal Region Of Ku86
Length = 120
Score = 34.7 bits (78), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 24/123 (19%), Positives = 57/123 (46%), Gaps = 9/123 (7%)
Query: 564 GDLTPIQDFEAMMSRRDCPDWVDKAIEDMKNKIFGLLE---NSNEGINYPKAVELLVALR 620
G + P ++F ++ ++ + E+ N++ +E ++NE + K+++ + A R
Sbjct: 1 GPVNPAENFRVLVKQKKA------SFEEASNQLINHIEQFLDTNETPYFMKSIDCIRAFR 54
Query: 621 KGCILEQEPKQFNDVLEKVCKICRKRNFSTFFDFXXXXXXXXXXXXEAVDSDITDDEAGS 680
+ I E ++FN+ L+ + + + + F++ EA S +T +EA
Sbjct: 55 EEAIKFSEEQRFNNFLKALQEKVEIKQLNHFWEIVVQDGITLITKEEASGSSVTAEEAKK 114
Query: 681 FIV 683
F+
Sbjct: 115 FLA 117
>pdb|1N7R|A Chain A, Streptococcus Pneumoniae Hyaluronate Lyase
W291a/w292a/f343v Mutant Complex With Hexasaccharide
Hyaluronan
Length = 721
Score = 33.5 bits (75), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 37/71 (52%), Gaps = 2/71 (2%)
Query: 570 QDFEAMMSRRDCPDWVDKAIEDMKNKIFGLLENSNEGINYPKAVELLVALRKGCILEQEP 629
QD + + RD +W+ K + + + I G ++ I P+A+ ++L K ++E
Sbjct: 92 QDETVVRTVRDSMEWMHKHVYNSEKSIVG--NAADYEIGTPRAINNTLSLMKEYFSDEEI 149
Query: 630 KQFNDVLEKVC 640
K++ DV+EK
Sbjct: 150 KKYTDVIEKFV 160
>pdb|1N7Q|A Chain A, Streptococcus Pneumoniae Hyaluronate Lyase W291aW292A
DOUBLE MUTANT Complex With Hyaluronan Hexasacchride
Length = 721
Score = 33.5 bits (75), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 37/71 (52%), Gaps = 2/71 (2%)
Query: 570 QDFEAMMSRRDCPDWVDKAIEDMKNKIFGLLENSNEGINYPKAVELLVALRKGCILEQEP 629
QD + + RD +W+ K + + + I G ++ I P+A+ ++L K ++E
Sbjct: 92 QDETVVRTVRDSMEWMHKHVYNSEKSIVG--NAADYEIGTPRAINNTLSLMKEYFSDEEI 149
Query: 630 KQFNDVLEKVC 640
K++ DV+EK
Sbjct: 150 KKYTDVIEKFV 160
>pdb|1N7N|A Chain A, Streptococcus Pneumoniae Hyaluronate Lyase W292a Mutant
Length = 721
Score = 33.5 bits (75), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 2/71 (2%)
Query: 570 QDFEAMMSRRDCPDWVDKAIEDMKNKIFGLLENSNEGINYPKAVELLVALRKGCILEQEP 629
QD + + RD +W+ K + + + I G + G P+A+ ++L K ++E
Sbjct: 92 QDETVVRTVRDSMEWMHKHVYNSEKSIVGNWADYEIGT--PRAINNTLSLMKEYFSDEEI 149
Query: 630 KQFNDVLEKVC 640
K++ DV+EK
Sbjct: 150 KKYTDVIEKFV 160
>pdb|1N7P|A Chain A, Streptococcus Pneumoniae Hyaluronate Lyase W292aF343V
Double Mutant
Length = 721
Score = 33.5 bits (75), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 2/71 (2%)
Query: 570 QDFEAMMSRRDCPDWVDKAIEDMKNKIFGLLENSNEGINYPKAVELLVALRKGCILEQEP 629
QD + + RD +W+ K + + + I G + G P+A+ ++L K ++E
Sbjct: 92 QDETVVRTVRDSMEWMHKHVYNSEKSIVGNWADYEIGT--PRAINNTLSLMKEYFSDEEI 149
Query: 630 KQFNDVLEKVC 640
K++ DV+EK
Sbjct: 150 KKYTDVIEKFV 160
>pdb|1OJM|A Chain A, Specificity And Mechanism Of Streptococcus Pneumoniae
Hyaluronate Lyase: Complex With Unsulphated Chondroitin
Disaccharide
Length = 729
Score = 33.1 bits (74), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 2/71 (2%)
Query: 570 QDFEAMMSRRDCPDWVDKAIEDMKNKIFGLLENSNEGINYPKAVELLVALRKGCILEQEP 629
QD + + RD +W+ K + + + I G + G P+A+ ++L K ++E
Sbjct: 92 QDETVVRTVRDSMEWMHKHVYNSEKSIVGNWWDYEIGT--PRAINNTLSLMKEYFSDEEI 149
Query: 630 KQFNDVLEKVC 640
K++ DV+EK
Sbjct: 150 KKYTDVIEKFV 160
>pdb|1N7O|A Chain A, Streptococcus Pneumoniae Hyaluronate Lyase F343v Mutant
Length = 721
Score = 33.1 bits (74), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 2/71 (2%)
Query: 570 QDFEAMMSRRDCPDWVDKAIEDMKNKIFGLLENSNEGINYPKAVELLVALRKGCILEQEP 629
QD + + RD +W+ K + + + I G + G P+A+ ++L K ++E
Sbjct: 92 QDETVVRTVRDSMEWMHKHVYNSEKSIVGNWWDYEIGT--PRAINNTLSLMKEYFSDEEI 149
Query: 630 KQFNDVLEKVC 640
K++ DV+EK
Sbjct: 150 KKYTDVIEKFV 160
>pdb|1EGU|A Chain A, Crystal Structure Of Streptococcus Pneumoniae Hyaluronate
Lyase At 1.56 A Resolution
pdb|1F9G|A Chain A, Crystal Structure Of Streptococcus Pneumoniae Hyaluronate
Lyase Cocrystallized With Ascorbic Acid
pdb|1C82|A Chain A, Mechanism Of Hyaluronan Binding And Degradation: Structure
Of Streptococcus Pneumoniae Hyaluronate Lyase In Complex
With Hyaluronic Acid Disaccharide At 1.7 A Resolution
pdb|1OJP|A Chain A, Specificity And Mechanism Of Streptococcus Pneumoniae
Hyaluronate Lyase: Complex With 6-sulphated Chondroitin
Disaccharide
pdb|1W3Y|A Chain A, Crystal Structure Of S. Pneumoniae Hyaluronate Lyase In
Complex With Palmitoyl-Vitamin C
pdb|2BRP|A Chain A, Crystal Structure Of S.Pneumoniae Hyaluronate Lyase In
Complex With W249b
pdb|2BRV|X Chain X, Crystal Structure Of Streptococcus Pneumoniae Hyaluronate
Lyase From 70percent Saturated Malonate.
pdb|2BRW|A Chain A, Crystal Structure Of Streptococcus Pneumoniae Hyaluronate
Lyase From 30percent Pegmme.
pdb|2BRW|B Chain B, Crystal Structure Of Streptococcus Pneumoniae Hyaluronate
Lyase From 30percent Pegmme
Length = 731
Score = 33.1 bits (74), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 2/71 (2%)
Query: 570 QDFEAMMSRRDCPDWVDKAIEDMKNKIFGLLENSNEGINYPKAVELLVALRKGCILEQEP 629
QD + + RD +W+ K + + + I G + G P+A+ ++L K ++E
Sbjct: 94 QDETVVRTVRDSMEWMHKHVYNSEKSIVGNWWDYEIGT--PRAINNTLSLMKEYFSDEEI 151
Query: 630 KQFNDVLEKVC 640
K++ DV+EK
Sbjct: 152 KKYTDVIEKFV 162
>pdb|1LOH|A Chain A, Streptococcus Pneumoniae Hyaluronate Lyase In Complex With
Hexasaccharide Hyaluronan Substrate
pdb|1LXK|A Chain A, Streptococcus Pneumoniae Hyaluronate Lyase In Complex With
Tetrasaccharide Hyaluronan Substrate
Length = 721
Score = 33.1 bits (74), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 2/71 (2%)
Query: 570 QDFEAMMSRRDCPDWVDKAIEDMKNKIFGLLENSNEGINYPKAVELLVALRKGCILEQEP 629
QD + + RD +W+ K + + + I G + G P+A+ ++L K ++E
Sbjct: 92 QDETVVRTVRDSMEWMHKHVYNSEKSIVGNWWDYEIGT--PRAINNTLSLMKEYFSDEEI 149
Query: 630 KQFNDVLEKVC 640
K++ DV+EK
Sbjct: 150 KKYTDVIEKFV 160
>pdb|1OJN|A Chain A, Specificity And Mechanism Of Streptococcus Pneumoniae
Hyaluronate Lyase: Complex Of The Tyr408phe Mutant With
6-sulphated Chondroitin Disaccharide
Length = 731
Score = 33.1 bits (74), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 2/71 (2%)
Query: 570 QDFEAMMSRRDCPDWVDKAIEDMKNKIFGLLENSNEGINYPKAVELLVALRKGCILEQEP 629
QD + + RD +W+ K + + + I G + G P+A+ ++L K ++E
Sbjct: 94 QDETVVRTVRDSMEWMHKHVYNSEKSIVGNWWDYEIGT--PRAINNTLSLMKEYFSDEEI 151
Query: 630 KQFNDVLEKVC 640
K++ DV+EK
Sbjct: 152 KKYTDVIEKFV 162
>pdb|1OJO|A Chain A, Specificity And Mechanism Of Streptococcus Pneumoniae
Hyaluronate Lyase: Complex Of The Tyr408phe Mutant With
4-sulphated Chondroitin Disaccharide
Length = 731
Score = 33.1 bits (74), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 2/71 (2%)
Query: 570 QDFEAMMSRRDCPDWVDKAIEDMKNKIFGLLENSNEGINYPKAVELLVALRKGCILEQEP 629
QD + + RD +W+ K + + + I G + G P+A+ ++L K ++E
Sbjct: 94 QDETVVRTVRDSMEWMHKHVYNSEKSIVGNWWDYEIGT--PRAINNTLSLMKEYFSDEEI 151
Query: 630 KQFNDVLEKVC 640
K++ DV+EK
Sbjct: 152 KKYTDVIEKFV 162
>pdb|3VNY|A Chain A, Crystal Structure Of Beta-Glucuronidase From
Acidobacterium Capsulatum
pdb|3VNZ|A Chain A, Crystal Structure Of Beta-Glucuronidase From
Acidobacterium Capsulatum In Complex With D-Glucuronic
Acid
pdb|3VO0|A Chain A, Crystal Structure Of Beta-Glucuronidase From
Acidobacterium Capsulatum Covalent-Bonded With
2-Deoxy-2-Fluoro-D-Glucuronic Acid
Length = 488
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 26/44 (59%), Gaps = 2/44 (4%)
Query: 459 PALERFYHHLELKSEHQDAAPPPLDDSL--KKITEPDPTLLAES 500
P ++F H ++ S H A PP D S+ +++ +P+P LL E+
Sbjct: 226 PFADKFKHDVKFISSHYYAEGPPTDPSMTIERLMKPNPRLLGET 269
>pdb|4F1N|A Chain A, Crystal Structure Of Kluyveromyces Polysporus Argonaute
With A Guide Rna
pdb|4F1N|B Chain B, Crystal Structure Of Kluyveromyces Polysporus Argonaute
With A Guide Rna
Length = 1046
Score = 30.8 bits (68), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 45/173 (26%), Positives = 75/173 (43%), Gaps = 29/173 (16%)
Query: 161 NIVVRASLS--GEPHMRVIIENDNLLNIFSKKSSAKTLFVDSTTSLRGARKTRDISPV-- 216
N+V++ +L G H + IEN+ LL K+S+ L + S + + I+ +
Sbjct: 730 NVVMKMNLKLLGSNH-SLSIENNKLL--IDKESNLPILVLGSDVTHYPEKDQNSIASLVG 786
Query: 217 ------TIFRGDLELSEK------------MKIKVWVYKKTGEEKFPTLKKYSDKAPSTD 258
T F GD L + M ++ +Y+K K PT Y S D
Sbjct: 787 SYDDKFTQFPGDYMLQDGPGEEIITNVGSLMLNRLKIYQKHNNGKLPTKIMYFRDGVSVD 846
Query: 259 KFATHEVKVDYEYKSVEDPSKVVPPEQRIKGYRYGPQVVPISSAEWEAVKFKP 311
+F+ VK+ E KS+++ + P Q G +Y P V I++ + V+F P
Sbjct: 847 QFS-QVVKI--EVKSIKESVRKFGP-QLNGGNKYDPPVTCIATVKRNQVRFIP 895
>pdb|2PSN|A Chain A, Crystal Structure Of Enolase1
pdb|2PSN|B Chain B, Crystal Structure Of Enolase1
pdb|2PSN|C Chain C, Crystal Structure Of Enolase1
pdb|2PSN|D Chain D, Crystal Structure Of Enolase1
Length = 434
Score = 29.3 bits (64), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 28/97 (28%), Positives = 42/97 (43%), Gaps = 18/97 (18%)
Query: 241 EEKFPTLKKYSDKAPSTDKF------ATHEV----KVDYEYKSVEDPSKVVPPEQRIKGY 290
+E LK KA TDK A E K D ++KS +DPS+ + P+Q Y
Sbjct: 221 KEGLELLKTAIGKAGYTDKVVIGMDVAASEFFRSGKYDLDFKSPDDPSRYISPDQLADLY 280
Query: 291 RYGPQVVPISSAE-------WEAV-KFKPEKSVKLLG 319
+ + P+ S E W A KF ++++G
Sbjct: 281 KSFIKDYPVVSIEDPFDQDDWGAWQKFTASAGIQVVG 317
>pdb|3B97|A Chain A, Crystal Structure Of Human Enolase 1
pdb|3B97|B Chain B, Crystal Structure Of Human Enolase 1
pdb|3B97|C Chain C, Crystal Structure Of Human Enolase 1
pdb|3B97|D Chain D, Crystal Structure Of Human Enolase 1
Length = 433
Score = 29.3 bits (64), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 28/97 (28%), Positives = 42/97 (43%), Gaps = 18/97 (18%)
Query: 241 EEKFPTLKKYSDKAPSTDKF------ATHEV----KVDYEYKSVEDPSKVVPPEQRIKGY 290
+E LK KA TDK A E K D ++KS +DPS+ + P+Q Y
Sbjct: 220 KEGLELLKTAIGKAGYTDKVVIGMDVAASEFFRSGKYDLDFKSPDDPSRYISPDQLADLY 279
Query: 291 RYGPQVVPISSAE-------WEAV-KFKPEKSVKLLG 319
+ + P+ S E W A KF ++++G
Sbjct: 280 KSFIKDYPVVSIEDPFDQDDWGAWQKFTASAGIQVVG 316
>pdb|3PRH|A Chain A, Tryptophanyl-Trna Synthetase Val144pro Mutant From B.
Subtilis
pdb|3PRH|B Chain B, Tryptophanyl-Trna Synthetase Val144pro Mutant From B.
Subtilis
Length = 388
Score = 29.3 bits (64), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 37/71 (52%), Gaps = 8/71 (11%)
Query: 432 AADNLVKMLDLAPSGKGEILQPELTPNPALERF---YHHL----ELKSEHQDAAPPPLDD 484
AAD L+ DL P G+ + ELT N A ERF Y+ + E+K A L+D
Sbjct: 164 AADILLYGTDLVPPGEDQKQHLELTRNLA-ERFNKKYNDIFTIPEVKIPKVGARIMSLND 222
Query: 485 SLKKITEPDPT 495
LKK+++ DP
Sbjct: 223 PLKKMSKSDPN 233
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
0.316 0.134 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,394,338
Number of Sequences: 62578
Number of extensions: 866399
Number of successful extensions: 2023
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 19
Number of HSP's that attempted gapping in prelim test: 2010
Number of HSP's gapped (non-prelim): 28
length of query: 691
length of database: 14,973,337
effective HSP length: 106
effective length of query: 585
effective length of database: 8,340,069
effective search space: 4878940365
effective search space used: 4878940365
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)