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= 013559
(441 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4B4T|R Chain R, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 429
Score = 80.1 bits (196), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 55/189 (29%), Positives = 92/189 (48%), Gaps = 9/189 (4%)
Query: 233 LAARKFLEVGPDLGNSYN-----EVIAAQDVATYGGLCALASFDRAELKSKVIDNVNFRN 287
LA R F E L +S E+ + + +ATY + L + +R +LKSKVID+ +
Sbjct: 219 LAVRNFKEAAKLLVDSLATFTSIELTSYESIATYASVTGLFTLERTDLKSKVIDSPELLS 278
Query: 288 FLEL---VPEVRELINDFYSSRYASCLDYLGNLKANLLLDI-HLHDHVETLYDQIRNKAL 343
+ + + L Y+S YAS YL AN+L+ +L+ H + ++R K
Sbjct: 279 LISTTAALQSISSLTISLYASDYASYFPYLLETYANVLIPCKYLNRHADFFVREMRRKVY 338
Query: 344 IQYTHPFVSVDLHMMANAFKTSVAGIEKELEALITDNQIQARIDSHNKILYARHADQRNA 403
Q + ++ L MA+AF SVA ++ +L I + Q+ ID N I+ D +NA
Sbjct: 339 AQLLESYKTLSLKSMASAFGVSVAFLDNDLGKFIPNKQLNCVIDRVNGIVETNRPDNKNA 398
Query: 404 TFQRVLQTG 412
+ +++ G
Sbjct: 399 QYHLLVKQG 407
>pdb|4B4T|Q Chain Q, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 434
Score = 46.2 bits (108), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 52/240 (21%), Positives = 94/240 (39%), Gaps = 43/240 (17%)
Query: 213 TIAKLRCAAGLAHLEARKYKLAARKFLEVGPDLGNSYNEVIAAQDVATYGGLCALASFDR 272
T+A+L +G+ H E + YK A F E +Y L S+++
Sbjct: 214 TVAELDLMSGILHCEDKDYKTAFSYFFE----------------SFESYHNLTTHNSYEK 257
Query: 273 A--ELKSKVIDNVNFRNFLELVPEVRELIN-----DFYSSRYA-------------SCLD 312
A LK ++ + L L+ +V+ ++N + Y SR S LD
Sbjct: 258 ACQVLKYMLLSKI----MLNLIDDVKNILNAKYTKETYQSRGIDAMKAVAEAYNNRSLLD 313
Query: 313 Y---LGNLKANLLLDIHLHDHVETLYDQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGI 369
+ L + L+ D H LYD + L + PF V++ ++ +
Sbjct: 314 FNTALKQYEKELMGDELTRSHFNALYDTLLESNLCKIIEPFECVEISHISKIIGLDTQQV 373
Query: 370 EKELEALITDNQIQARIDSHNKILYARHADQRNATFQRVLQTGSEFDQDVRAMLLRANLL 429
E +L +I D +D N LY ++AT+ L+ + ++ V + +A++L
Sbjct: 374 EGKLSQMILDKIFYGVLDQGNGWLYVYETPNQDATYDSALELVGQLNKVVDQLFEKASVL 433
>pdb|3TXM|A Chain A, Crystal Structure Of Rpn6 From Drosophila Melanogaster,
Gd(3+) Complex
pdb|3TXN|A Chain A, Crystal Structure Of Rpn6 From Drosophila Melanogaster,
Native Data
Length = 394
Score = 45.4 bits (106), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 25/98 (25%), Positives = 47/98 (47%)
Query: 314 LGNLKANLLLDIHLHDHVETLYDQIRNKALIQYTHPFVSVDLHMMANAFKTSVAGIEKEL 373
L K L D+ + H+ TLYD + + L + P+ V + +A + + + +EK+L
Sbjct: 278 LKEYKKELAEDVIVQAHLGTLYDTMLEQNLCRIIEPYSRVQVAHVAESIQLPMPQVEKKL 337
Query: 374 EALITDNQIQARIDSHNKILYARHADQRNATFQRVLQT 411
+I D + +D +L + T++RVL+T
Sbjct: 338 SQMILDKKFSGILDQGEGVLIVFEETPVDKTYERVLET 375
>pdb|3IDE|A Chain A, Structure Of Ipnv Subviral Particle
pdb|3IDE|B Chain B, Structure Of Ipnv Subviral Particle
pdb|3IDE|C Chain C, Structure Of Ipnv Subviral Particle
pdb|3IDE|D Chain D, Structure Of Ipnv Subviral Particle
pdb|3IDE|E Chain E, Structure Of Ipnv Subviral Particle
Length = 442
Score = 29.6 bits (65), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 23/36 (63%), Gaps = 3/36 (8%)
Query: 198 YVSKAEQTPEALEPVTIAKLRCAAGLAHLEARKYKL 233
YV ++TP+ L+ + AK+RC A +A R+Y++
Sbjct: 174 YVRLEDETPQGLQSMNGAKMRCTAAIA---PRRYEI 206
>pdb|1VSY|4 Chain 4, Proteasome Activator Complex
pdb|1VSY|7 Chain 7, Proteasome Activator Complex
pdb|3L5Q|5 Chain 5, Proteasome Activator Complex
pdb|3L5Q|7 Chain 7, Proteasome Activator Complex
Length = 799
Score = 28.5 bits (62), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 30/155 (19%), Positives = 69/155 (44%), Gaps = 16/155 (10%)
Query: 270 FDRAELKSKVIDNVNF-------RNFLELVPEVRELINDFYS------SRYASCLDYLGN 316
FD+++ +S ++D +NF + ++P V ++ Y + C +
Sbjct: 121 FDKSK-ESLLVDTMNFLLSSLAPSTMMAVMPIVTSVVPYHYHIHSKIIDYFPFCYSIWSS 179
Query: 317 LKANLLLDIHLHDHVETLYDQIRNKAL-IQYTHPFVSVDLHMMANAFKTSVAGIEKELEA 375
+ AN+ +D H++D V ++ + NK L ++ V V+ + + L+
Sbjct: 180 VSANVAIDTHMYDFVGSISKDVHNKILSSEHEKDVVGVEFGEFGIFTDDQMTFMFNRLQG 239
Query: 376 -LITDNQIQARIDSHNKILYARHADQRNATFQRVL 409
L TD QI + + +YA + +++ F++++
Sbjct: 240 HLRTDGQIHSYSRTVKPFVYAINGSKKDRFFEKLV 274
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
0.320 0.133 0.380
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,262,974
Number of Sequences: 62578
Number of extensions: 475669
Number of successful extensions: 1273
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1266
Number of HSP's gapped (non-prelim): 7
length of query: 441
length of database: 14,973,337
effective HSP length: 102
effective length of query: 339
effective length of database: 8,590,381
effective search space: 2912139159
effective search space used: 2912139159
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)