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= 019080
         (346 letters)

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

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



>pdb|3A21|A Chain A, Crystal Structure Of Streptomyces Avermitilis Beta-L-
           Arabinopyranosidase
 pdb|3A21|B Chain B, Crystal Structure Of Streptomyces Avermitilis Beta-L-
           Arabinopyranosidase
 pdb|3A22|A Chain A, Crystal Structure Of Beta-L-Arabinopyranosidase Complexed
           With L- Arabinose
 pdb|3A22|B Chain B, Crystal Structure Of Beta-L-Arabinopyranosidase Complexed
           With L- Arabinose
 pdb|3A23|A Chain A, Crystal Structure Of Beta-l-arabinopyranosidase Complexed
           With D- Galactose
 pdb|3A23|B Chain B, Crystal Structure Of Beta-l-arabinopyranosidase Complexed
           With D- Galactose
          Length = 614

 Score = 32.3 bits (72), Expect = 0.45,   Method: Compositional matrix adjust.
 Identities = 25/54 (46%), Positives = 30/54 (55%), Gaps = 10/54 (18%)

Query: 55  SANVLEEALNGT-----VTVRPLPI--GTSVSGKVEKQCAHFFGVTI-NDQQAE 100
           SAN L  AL+G      +TVRPLP   G  V+GK   +CA  +  TI N  QAE
Sbjct: 463 SANTL--ALSGGPATEGITVRPLPGTNGALVTGKQSGRCADIYNNTITNGTQAE 514


>pdb|2O8B|B Chain B, Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G T MISPAIR
 pdb|2O8C|B Chain B, Human Mutsalpha (msh2/msh6) Bound To Adp And An
            O6-methyl-guanine T Mispair
 pdb|2O8D|B Chain B, Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G DU MISPAIR
 pdb|2O8E|B Chain B, Human Mutsalpha (Msh2MSH6) BOUND TO A G T MISPAIR, WITH ADP
            BOUND TO Msh2 Only
 pdb|2O8F|B Chain B, Human Mutsalpha (Msh2MSH6) BOUND TO DNA WITH A SINGLE BASE T
            INSERT
          Length = 1022

 Score = 30.4 bits (67), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 20/66 (30%), Positives = 41/66 (62%), Gaps = 5/66 (7%)

Query: 211  IEALCAKSYEDNSQKLKDIEAQILRK-RKELREFEIEYRKALARFQE---ATNRYSQEKQ 266
            I+  C KSY  N+ +L ++  ++++K  ++ REFE +  ++L  F+E   A+ R + + +
Sbjct: 952  IKGACPKSYGFNAARLANLPEEVIQKGHRKAREFE-KMNQSLRLFREVCLASERSTVDAE 1010

Query: 267  SVDELL 272
            +V +LL
Sbjct: 1011 AVHKLL 1016


>pdb|1QVR|A Chain A, Crystal Structure Analysis Of Clpb
 pdb|1QVR|B Chain B, Crystal Structure Analysis Of Clpb
 pdb|1QVR|C Chain C, Crystal Structure Analysis Of Clpb
          Length = 854

 Score = 29.6 bits (65), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 19/68 (27%), Positives = 39/68 (57%), Gaps = 3/68 (4%)

Query: 212 EALCAKSYEDNSQKLKDIEAQILRKRKELREFEIEY---RKALARFQEATNRYSQEKQSV 268
           EAL  +   D+ ++LK IEA+I +  +E+ +   E+   R+ L + +EA +R  + ++ +
Sbjct: 418 EALKKEKDPDSQERLKAIEAEIAKLTEEIAKLRAEWEREREILRKLREAQHRLDEVRREI 477

Query: 269 DELLKQRD 276
           +   +Q D
Sbjct: 478 ELAERQYD 485


>pdb|4HSE|A Chain A, Crystal Structure Of Clpb Nbd1 In Complex With Guanidinium
           Chloride And Adp
          Length = 397

 Score = 28.5 bits (62), Expect = 5.9,   Method: Compositional matrix adjust.
 Identities = 19/68 (27%), Positives = 39/68 (57%), Gaps = 3/68 (4%)

Query: 212 EALCAKSYEDNSQKLKDIEAQILRKRKELREFEIEY---RKALARFQEATNRYSQEKQSV 268
           EAL  +   D+ ++LK IEA+I +  +E+ +   E+   R+ L + +EA +R  + ++ +
Sbjct: 281 EALKKEKDPDSQERLKAIEAEIAKLTEEIAKLRAEWEREREILRKLREAQHRLDEVRREI 340

Query: 269 DELLKQRD 276
           +   +Q D
Sbjct: 341 ELAERQYD 348


  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    0.131    0.364 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,254,478
Number of Sequences: 62578
Number of extensions: 298241
Number of successful extensions: 796
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 789
Number of HSP's gapped (non-prelim): 12
length of query: 346
length of database: 14,973,337
effective HSP length: 100
effective length of query: 246
effective length of database: 8,715,537
effective search space: 2144022102
effective search space used: 2144022102
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: 52 (24.6 bits)