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= psy6893
(988 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4B4T|N Chain N, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 945
Score = 233 bits (594), Expect = 4e-61, Method: Compositional matrix adjust.
Identities = 157/444 (35%), Positives = 220/444 (49%), Gaps = 61/444 (13%)
Query: 477 LLHVAVSDVNDDVRREAVTALGFILFRTLFYVAPACTRSPWPGVISLLDDPMIELKEFS- 535
LL +A++ V + R ++ F + P C V+ L+D + L+ F
Sbjct: 189 LLTLAITTVTNSKFRSSILRKSFDFLMNM----PNCDYLTLNKVVVNLNDAGLALQLFKK 244
Query: 536 LKKLND------IVDDFWPENEKEKQLQARITKLS---------KILSGEVSIDLHLQFL 580
LK+ ND I D + ++ L+ +T+L+ ILSG + D + FL
Sbjct: 245 LKEENDEGLSAQIAFDLV-SSASQQLLEILVTELTAQGYDPALLNILSGLPTCDYYNTFL 303
Query: 581 IRSNKTDMLILKNTKESI--RVSICHTATIIANAFMHSGTTSDQFLRDNLEWLARATNWA 638
+ + D+ +L +K S+ + S+ HTA +AN FMH+GTT + F++ NL WL +A NWA
Sbjct: 304 LNNKNIDIGLLNKSKSSLDGKFSLFHTAVSVANGFMHAGTTDNSFIKANLPWLGKAQNWA 363
Query: 639 KLTATASLGVIHRGHETEALAHMQSYLPRETGPTSXXXXXXXXXXXXXIHANHGAVINDY 698
K TATASLGVIH+G+ E M YLP +S I+A G DY
Sbjct: 364 KFTATASLGVIHKGNLLEGKKVMAPYLPGSRA-SSRFIKGGSLYGLGLIYAGFGRDTTDY 422
Query: 699 LL-------GQVKDATNEMVRHXXXXXXXXXXXXXXRDDIYEQLKFNLYQDDAVTGEAAG 751
L G D +++ H ++YE LK LY D A +GEAA
Sbjct: 423 LKNIIVENSGTSGDEDVDVLLHGASLGIGLAAMGSANIEVYEALKEVLYNDSATSGEAAA 482
Query: 752 IAMGLVLLGSKSESAIQDMVAYAKETQHEKILRGLAVGISFIMYGQLENADDLVRDLCEE 811
+ MGL +LG+ AI DM Y++ETQH I RGLAVG++ I YG+ E ADDL+ +
Sbjct: 483 LGMGLCMLGTGKPEAIHDMFTYSQETQHGNITRGLAVGLALINYGRQELADDLITKMLAS 542
Query: 812 KDAILRRSGMYTIAMAYCGSGSNVATKRLLHDAILRRSGMYTIAMAYCGSGSNVATKRLL 871
+++LR G +TIA+AY G+G+N A KR LL
Sbjct: 543 DESLLRYGGAFTIALAYAGTGNNSAVKR------------------------------LL 572
Query: 872 HVAVSDVNDDVRREAVTALGFILF 895
HVAVSD NDDVRR AV ALGF+L
Sbjct: 573 HVAVSDSNDDVRRAAVIALGFVLL 596
Score = 213 bits (542), Expect = 4e-55, Method: Compositional matrix adjust.
Identities = 133/344 (38%), Positives = 174/344 (50%), Gaps = 73/344 (21%)
Query: 201 LSKILSGEVSIDLHLQFLIRSNKTDMLILKNTKESI--RVSICHTATIIANAFMHSGTTS 258
L ILSG + D + FL+ + D+ +L +K S+ + S+ HTA +AN FMH+GTT
Sbjct: 286 LLNILSGLPTCDYYNTFLLNNKNIDIGLLNKSKSSLDGKFSLFHTAVSVANGFMHAGTTD 345
Query: 259 DQFLRDNLEWLARATNWAKLTATASLGVIHRGHETEALAHMQSYLPRETGPTSXXXXXXX 318
+ F++ NL WL +A NWAK TATASLGVIH+G+ E M YLP +S
Sbjct: 346 NSFIKANLPWLGKAQNWAKFTATASLGVIHKGNLLEGKKVMAPYLPGSRA-SSRFIKGGS 404
Query: 319 XXXXXXIHANHGAVINDYL------------------------LG-----------QVKD 343
I+A G DYL LG +V +
Sbjct: 405 LYGLGLIYAGFGRDTTDYLKNIIVENSGTSGDEDVDVLLHGASLGIGLAAMGSANIEVYE 464
Query: 344 ATNE----DDAVTGEAAGIAMGLVLLGSKSESAIQDMVAYAKETQHEKILRGLAVGISFI 399
A E D A +GEAA + MGL +LG+ AI DM Y++ETQH I RGLAVG++ I
Sbjct: 465 ALKEVLYNDSATSGEAAALGMGLCMLGTGKPEAIHDMFTYSQETQHGNITRGLAVGLALI 524
Query: 400 MYGQLENADDLVRDLCEEKDAILRRSGMYTIAMAYCVSYLYFDLFSDLTYRIVKNRSGMY 459
YG+ E ADDL+ + +++LR G +T
Sbjct: 525 NYGRQELADDLITKMLASDESLLRYGGAFT------------------------------ 554
Query: 460 TIAMAYCGSGSNVATKRLLHVAVSDVNDDVRREAVTALGFILFR 503
IA+AY G+G+N A KRLLHVAVSD NDDVRR AV ALGF+L R
Sbjct: 555 -IALAYAGTGNNSAVKRLLHVAVSDSNDDVRRAAVIALGFVLLR 597
Score = 46.6 bits (109), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 29/105 (27%), Positives = 53/105 (50%), Gaps = 2/105 (1%)
Query: 43 LAMSSIQSRSFRAQILRTLVRLYHSLSVPDYVNMAQCWIYLDDPRSVANLLGKLVAGSAD 102
LA++++ + FR+ ILR ++ DY+ + + + L+D L KL +
Sbjct: 192 LAITTVTNSKFRSSILRKSFDFLMNMPNCDYLTLNKVVVNLNDAGLALQLFKKL--KEEN 249
Query: 103 DDLMAAQIGFDLYESATQAFLASVLQELKTCAPIPDATHVVVKVP 147
D+ ++AQI FDL SA+Q L ++ EL P +++ +P
Sbjct: 250 DEGLSAQIAFDLVSSASQQLLEILVTELTAQGYDPALLNILSGLP 294
>pdb|4ADY|A Chain A, Crystal Structure Of 26s Proteasome Subunit Rpn2
pdb|4ADY|B Chain B, Crystal Structure Of 26s Proteasome Subunit Rpn2
Length = 963
Score = 203 bits (516), Expect = 5e-52, Method: Compositional matrix adjust.
Identities = 154/444 (34%), Positives = 214/444 (48%), Gaps = 61/444 (13%)
Query: 477 LLHVAVSDVNDDVRREAVTALGFILFRTLFYVAPACTRSPWPGVISLLDDPMIELKEFS- 535
LL +A++ V + R ++ F P C V+ L+D + L+ F
Sbjct: 200 LLTLAITTVTNSKFRSSILRKSFDFLXN----XPNCDYLTLNKVVVNLNDAGLALQLFKK 255
Query: 536 LKKLND------IVDDFWPENEKEKQLQARITKLS---------KILSGEVSIDLHLQFL 580
LK+ ND I D + ++ L+ +T+L+ ILSG + D + FL
Sbjct: 256 LKEENDEGLSAQIAFDLV-SSASQQLLEILVTELTAQGYDPALLNILSGLPTCDYYNTFL 314
Query: 581 IRSNKTDMLILKNTKESI--RVSICHTATIIANAFMHSGTTSDQFLRDNLEWLARATNWA 638
+ + D+ +L +K S+ + S+ HTA +AN F H+GTT + F++ NL WL +A NWA
Sbjct: 315 LNNKNIDIGLLNKSKSSLDGKFSLFHTAVSVANGFXHAGTTDNSFIKANLPWLGKAQNWA 374
Query: 639 KLTATASLGVIHRGHETEALAHMQSYLPRETGPTSXXXXXXXXXXXXXIHANHGAVINDY 698
K TATASLGVIH+G+ E YLP +S I+A G DY
Sbjct: 375 KFTATASLGVIHKGNLLEGKKVXAPYLPGSRA-SSRFIKGGSLYGLGLIYAGFGRDTTDY 433
Query: 699 LL-------GQVKDATNEMVRHXXXXXXXXXXXXXXRDDIYEQLKFNLYQDDAVTGEAAG 751
L G D +++ H ++YE LK LY D A +GEAA
Sbjct: 434 LKNIIVENSGTSGDEDVDVLLHGASLGIGLAAXGSANIEVYEALKEVLYNDSATSGEAAA 493
Query: 752 IAMGLVLLGSKSESAIQDMVAYAKETQHEKILRGLAVGISFIMYGQLENADDLVRDLCEE 811
+ GL LG+ AI D Y++ETQH I RGLAVG++ I YG+ E ADDL+
Sbjct: 494 LGXGLCXLGTGKPEAIHDXFTYSQETQHGNITRGLAVGLALINYGRQELADDLITKXLAS 553
Query: 812 KDAILRRSGMYTIAMAYCGSGSNVATKRLLHDAILRRSGMYTIAMAYCGSGSNVATKRLL 871
+++LR G +TIA+AY G+G+N A KR LL
Sbjct: 554 DESLLRYGGAFTIALAYAGTGNNSAVKR------------------------------LL 583
Query: 872 HVAVSDVNDDVRREAVTALGFILF 895
HVAVSD NDDVRR AV ALGF+L
Sbjct: 584 HVAVSDSNDDVRRAAVIALGFVLL 607
Score = 186 bits (471), Expect = 8e-47, Method: Compositional matrix adjust.
Identities = 122/344 (35%), Positives = 163/344 (47%), Gaps = 73/344 (21%)
Query: 201 LSKILSGEVSIDLHLQFLIRSNKTDMLILKNTKESI--RVSICHTATIIANAFMHSGTTS 258
L ILSG + D + FL+ + D+ +L +K S+ + S+ HTA +AN F H+GTT
Sbjct: 297 LLNILSGLPTCDYYNTFLLNNKNIDIGLLNKSKSSLDGKFSLFHTAVSVANGFXHAGTTD 356
Query: 259 DQFLRDNLEWLARATNWAKLTATASLGVIHRGHETEALAHMQSYLPRETGPTSXXXXXXX 318
+ F++ NL WL +A NWAK TATASLGVIH+G+ E YLP +S
Sbjct: 357 NSFIKANLPWLGKAQNWAKFTATASLGVIHKGNLLEGKKVXAPYLPGSRA-SSRFIKGGS 415
Query: 319 XXXXXXIHANHGAVINDYLLGQVKDAT----NEDDAVTGEAAGIAMGLVLLGSKS----- 369
I+A G DYL + + + +ED V A + +GL GS +
Sbjct: 416 LYGLGLIYAGFGRDTTDYLKNIIVENSGTSGDEDVDVLLHGASLGIGLAAXGSANIEVYE 475
Query: 370 ------------------------------ESAIQDMVAYAKETQHEKILRGLAVGISFI 399
AI D Y++ETQH I RGLAVG++ I
Sbjct: 476 ALKEVLYNDSATSGEAAALGXGLCXLGTGKPEAIHDXFTYSQETQHGNITRGLAVGLALI 535
Query: 400 MYGQLENADDLVRDLCEEKDAILRRSGMYTIAMAYCVSYLYFDLFSDLTYRIVKNRSGMY 459
YG+ E ADDL+ +++LR G +T
Sbjct: 536 NYGRQELADDLITKXLASDESLLRYGGAFT------------------------------ 565
Query: 460 TIAMAYCGSGSNVATKRLLHVAVSDVNDDVRREAVTALGFILFR 503
IA+AY G+G+N A KRLLHVAVSD NDDVRR AV ALGF+L R
Sbjct: 566 -IALAYAGTGNNSAVKRLLHVAVSDSNDDVRRAAVIALGFVLLR 608
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 29/105 (27%), Positives = 52/105 (49%), Gaps = 2/105 (1%)
Query: 43 LAMSSIQSRSFRAQILRTLVRLYHSLSVPDYVNMAQCWIYLDDPRSVANLLGKLVAGSAD 102
LA++++ + FR+ ILR + DY+ + + + L+D L KL +
Sbjct: 203 LAITTVTNSKFRSSILRKSFDFLXNXPNCDYLTLNKVVVNLNDAGLALQLFKKL--KEEN 260
Query: 103 DDLMAAQIGFDLYESATQAFLASVLQELKTCAPIPDATHVVVKVP 147
D+ ++AQI FDL SA+Q L ++ EL P +++ +P
Sbjct: 261 DEGLSAQIAFDLVSSASQQLLEILVTELTAQGYDPALLNILSGLP 305
>pdb|3FID|A Chain A, Lpxr From Salmonella Typhimurium
pdb|3FID|B Chain B, Lpxr From Salmonella Typhimurium
Length = 296
Score = 30.8 bits (68), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 20/41 (48%), Gaps = 3/41 (7%)
Query: 261 FLRDNLEWLARATNWAKLTATASLGVIH---RGHETEALAH 298
FL LEW + ATNW + +GVI G E + AH
Sbjct: 82 FLHTGLEWNSLATNWLRYRLGTDIGVIGPDAGGQEVQNRAH 122
Score = 30.8 bits (68), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 20/41 (48%), Gaps = 3/41 (7%)
Query: 623 FLRDNLEWLARATNWAKLTATASLGVIH---RGHETEALAH 660
FL LEW + ATNW + +GVI G E + AH
Sbjct: 82 FLHTGLEWNSLATNWLRYRLGTDIGVIGPDAGGQEVQNRAH 122
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 0.385
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,922,282
Number of Sequences: 62578
Number of extensions: 787031
Number of successful extensions: 1961
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1934
Number of HSP's gapped (non-prelim): 18
length of query: 988
length of database: 14,973,337
effective HSP length: 108
effective length of query: 880
effective length of database: 8,214,913
effective search space: 7229123440
effective search space used: 7229123440
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: 56 (26.2 bits)