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= 011878
(475 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 = 110 bits (276), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 122/510 (23%), Positives = 225/510 (44%), Gaps = 68/510 (13%)
Query: 4 TREALLLLLDVSPSMHSVLPDVE-------KLCSRLIQKKLIYGKNHEVGVILFGTEETE 56
+ A++L +DV +M + +P +E K+ + +Q+++ E+ ++LFGT+ T+
Sbjct: 6 NKAAVVLCMDVGFTMSNSIPGIESPFEQAKKVITMFVQRQVFAENKDEIALVLFGTDGTD 65
Query: 57 NELTKEVGG--YEHVKVLQDIKVVDGHLVQSLKHLPQ-GTCAGDFLDAIVVGVDMLI--- 110
N L+ GG Y+++ V + + + D L++ ++ Q G+ DFLDA++V +D++
Sbjct: 66 NPLS---GGDQYQNITVHRHLMLPDFDLLEDIESKIQPGSQQADFLDALIVSMDVIQHET 122
Query: 111 ------KKYGETYK------GKKHLCLITDAL--CPL-----------KDPDVGTKEDQV 145
K++ E + K L +I +L C + K+ G + D
Sbjct: 123 IGKKFEKRHIEIFTDLSSRFSKSQLDIIIHSLKKCDISLQFFLPFSLGKEDGSGDRGDGP 182
Query: 146 STIARQMVAFGLRMKNIVVRASLSGEPHMRVIIEN-DNLLNIFSKKSSAKTLFVDSTTSL 204
+ +F L+ + L + + +E D L I+S S + L V
Sbjct: 183 FRLGGHGPSFPLKGITEQQKEGLEIVKMVMISLEGEDGLDEIYSFSESLRKLCV-----F 237
Query: 205 RGARKTRDISPVTIFRGDLELSEKMKIKVWVYKKTGEEKFPTLKKYSDKAPSTDKFATHE 264
+ + P L + + I++ YK +E+ D +
Sbjct: 238 KKIERHSIHWPCR-----LTIGSNLSIRIAAYKSILQERVKKTWTVVD----AKTLKKED 288
Query: 265 VKVDYEYKSVEDPSKVVPPEQRIKGYRYGPQVVPISSAEWEAVKFKPE-KSVKLLGFTDA 323
++ + Y +D V E I+G+RYG +VP S + E +K+K E K +LGF +
Sbjct: 289 IQKETVYCLNDDDETEVLKEDIIQGFRYGSDIVPFSKVDEEQMKYKSEGKCFSVLGFCKS 348
Query: 324 SNILRHYYMKDVNL-FIAEPGNSRATVAVSALARAMKEMNKVAIVRCVWRQGQQSVVVGV 382
S + R ++M + L A + A VA+S+L A+ +++ VAIVR + + + + VGV
Sbjct: 349 SQVQRRFFMGNQVLKVFAARDDEAAAVALSSLIHALDDLDMVAIVRYAYDK-RANPQVGV 407
Query: 383 LTPNVSEKINIPDSFYFNVLPFAEDVREFQFPSFSKFPVSWQPNEQQQEAADNLVKMLDL 442
P++ + + LPF ED+R++ F S K + P E Q A D L+ + L
Sbjct: 408 AFPHIKHNY---ECLVYVQLPFMEDLRQYMFSSL-KNSKKYAPTEAQLNAVDALIDSMSL 463
Query: 443 APSGKG-----EILQPELTPNPALEVLNIC 467
A + ++ PNP + L C
Sbjct: 464 AKKDEKTDTLEDLFPTTKIPNPRFQRLFQC 493
>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 = 30.4 bits (67), Expect = 2.1, 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 = 5.5, 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-------WEA-VKFKPEKSVKLLG 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 = 28.9 bits (63), Expect = 5.9, 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-------WEA-VKFKPEKSVKLLG 319
+ + P+ S E W A KF ++++G
Sbjct: 280 KSFIKDYPVVSIEDPFDQDDWGAWQKFTASAGIQVVG 316
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 0.135 0.390
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,172,949
Number of Sequences: 62578
Number of extensions: 599222
Number of successful extensions: 1436
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1429
Number of HSP's gapped (non-prelim): 9
length of query: 475
length of database: 14,973,337
effective HSP length: 102
effective length of query: 373
effective length of database: 8,590,381
effective search space: 3204212113
effective search space used: 3204212113
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: 53 (25.0 bits)