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= psy2956
         (251 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>pdb|3KX2|B Chain B, Crystal Structure Of Prp43p In Complex With Adp
 pdb|3KX2|A Chain A, Crystal Structure Of Prp43p In Complex With Adp
          Length = 767

 Score =  241 bits (615), Expect = 3e-64,   Method: Compositional matrix adjust.
 Identities = 121/185 (65%), Positives = 147/185 (79%), Gaps = 4/185 (2%)

Query: 13  RQYFDNAPLMNVPGRTHPVEIFYTPEPERDYLEAAIRTVVQIHMCEEVEGDVLLFLTGQE 72
           ++YF++APL+ VPGRT+PVE++YTPE +RDYL++AIRTV+QIH  EE  GD+LLFLTG++
Sbjct: 256 QRYFNDAPLLAVPGRTYPVELYYTPEFQRDYLDSAIRTVLQIHATEEA-GDILLFLTGED 314

Query: 73  EIEEACKRIKKEIDNLGPE--AGELKCIPLYSTLPPNLQQRIFEAAPANKPNGGIGRKVV 130
           EIE+A ++I  E D L  E   G L   PLY +LPP+ QQRIFE AP +  NG  GRKVV
Sbjct: 315 EIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESH-NGRPGRKVV 373

Query: 131 VSTNIAETSLTIDGVVFVIDPGFAKQKVYNPRIRVESLLVSPISKASXXXXXXXXXXTRP 190
           +STNIAETSLTIDG+V+V+DPGF+KQKVYNPRIRVESLLVSPISKAS          TRP
Sbjct: 374 ISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRTRP 433

Query: 191 GKCFR 195
           GKCFR
Sbjct: 434 GKCFR 438



 Score =  105 bits (261), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 52/63 (82%), Positives = 58/63 (92%), Gaps = 4/63 (6%)

Query: 189 RPGKCFRYIVVVSTNIAETSLTIDGVVFVIDPGFAKQKVYNPRIRVESLLVSPISKASAQ 248
           RPG+     VV+STNIAETSLTIDG+V+V+DPGF+KQKVYNPRIRVESLLVSPISKASAQ
Sbjct: 367 RPGRK----VVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQ 422

Query: 249 QRA 251
           QRA
Sbjct: 423 QRA 425


>pdb|2XAU|A Chain A, Crystal Structure Of The Prp43p Deah-Box Rna Helicase In
           Complex With Adp
 pdb|2XAU|B Chain B, Crystal Structure Of The Prp43p Deah-Box Rna Helicase In
           Complex With Adp
          Length = 773

 Score =  241 bits (615), Expect = 3e-64,   Method: Compositional matrix adjust.
 Identities = 121/185 (65%), Positives = 147/185 (79%), Gaps = 4/185 (2%)

Query: 13  RQYFDNAPLMNVPGRTHPVEIFYTPEPERDYLEAAIRTVVQIHMCEEVEGDVLLFLTGQE 72
           ++YF++APL+ VPGRT+PVE++YTPE +RDYL++AIRTV+QIH  EE  GD+LLFLTG++
Sbjct: 256 QRYFNDAPLLAVPGRTYPVELYYTPEFQRDYLDSAIRTVLQIHATEEA-GDILLFLTGED 314

Query: 73  EIEEACKRIKKEIDNLGPE--AGELKCIPLYSTLPPNLQQRIFEAAPANKPNGGIGRKVV 130
           EIE+A ++I  E D L  E   G L   PLY +LPP+ QQRIFE AP +  NG  GRKVV
Sbjct: 315 EIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESH-NGRPGRKVV 373

Query: 131 VSTNIAETSLTIDGVVFVIDPGFAKQKVYNPRIRVESLLVSPISKASXXXXXXXXXXTRP 190
           +STNIAETSLTIDG+V+V+DPGF+KQKVYNPRIRVESLLVSPISKAS          TRP
Sbjct: 374 ISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRTRP 433

Query: 191 GKCFR 195
           GKCFR
Sbjct: 434 GKCFR 438



 Score =  105 bits (261), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 52/63 (82%), Positives = 58/63 (92%), Gaps = 4/63 (6%)

Query: 189 RPGKCFRYIVVVSTNIAETSLTIDGVVFVIDPGFAKQKVYNPRIRVESLLVSPISKASAQ 248
           RPG+     VV+STNIAETSLTIDG+V+V+DPGF+KQKVYNPRIRVESLLVSPISKASAQ
Sbjct: 367 RPGRK----VVISTNIAETSLTIDGIVYVVDPGFSKQKVYNPRIRVESLLVSPISKASAQ 422

Query: 249 QRA 251
           QRA
Sbjct: 423 QRA 425


  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
   0.319    0.137    0.392 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,806,892
Number of Sequences: 62578
Number of extensions: 258858
Number of successful extensions: 619
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 609
Number of HSP's gapped (non-prelim): 6
length of query: 251
length of database: 14,973,337
effective HSP length: 96
effective length of query: 155
effective length of database: 8,965,849
effective search space: 1389706595
effective search space used: 1389706595
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: 50 (23.9 bits)