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= 042609
         (540 letters)

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

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



>pdb|3SPA|A Chain A, Crystal Structure Of Human Mitochondrial Rna Polymerase
          Length = 1134

 Score = 34.7 bits (78), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 26/84 (30%), Positives = 42/84 (50%), Gaps = 4/84 (4%)

Query: 446 YHTLIRGYCKLEEFDCALKLLNEMKDVGVQPNVDEYNKLIQSLCLKALDWRTAEKLLEDM 505
           Y+ ++ G+ +   F   + +L  +KD G+ P++  Y   +Q +  +  D  T E+ LE M
Sbjct: 168 YNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQM 227

Query: 506 RLKGLHLNGITRALIRAVKELEED 529
             +GL L     AL  AV   EED
Sbjct: 228 SQEGLKLQ----ALFTAVLLSEED 247


>pdb|4G24|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
           A. Thaliana With Mn
 pdb|4G26|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
           A. Thaliana With Ca
          Length = 501

 Score = 29.3 bits (64), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 28/140 (20%), Positives = 52/140 (37%), Gaps = 14/140 (10%)

Query: 363 KMISEGPPPGNAVFNSVISAYSKAGDMTPAMEMLKLMRSRGLKPDVYTYTGLM------- 415
           K I + P    A+    +   SK GD+  A+ +    R  G++   Y Y  L+       
Sbjct: 19  KAIQQSP---EALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAE 75

Query: 416 ---SGYANGGQMEEACEILNEAKKNHSRLSPVTYHTLIRGYCKLEEFDCALKLLNEMKDV 472
                  N G +    +I  +   +    +  T+    R     ++ + A  ++ +MK  
Sbjct: 76  AATESSPNPG-LSRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAF 134

Query: 473 GVQPNVDEYNKLIQSLCLKA 492
           G+QP +  Y   +   C K 
Sbjct: 135 GIQPRLRSYGPALFGFCRKG 154


>pdb|3MKR|B Chain B, Crystal Structure Of Yeast AlphaEPSILON-Cop Subcomplex Of
           The Copi Vesicular Coat
          Length = 320

 Score = 28.5 bits (62), Expect = 9.1,   Method: Compositional matrix adjust.
 Identities = 21/73 (28%), Positives = 33/73 (45%), Gaps = 6/73 (8%)

Query: 423 QMEEACEILNEAKKNHSRLSPVTYHTLIRG----YCKLEEFDCALKLLNEMKDVGVQPNV 478
           Q +  CE+   A   HS L PV    ++R     + KL+ F  A      + ++G +P V
Sbjct: 176 QQKRICEM--AAYFTHSNLQPVHMILVLRTALNLFFKLKNFRTAAAFARRLLELGPKPEV 233

Query: 479 DEYNKLIQSLCLK 491
            +  + I S C K
Sbjct: 234 AQQTRKILSACEK 246


  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    0.132    0.381 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,436,298
Number of Sequences: 62578
Number of extensions: 618605
Number of successful extensions: 1370
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1366
Number of HSP's gapped (non-prelim): 9
length of query: 540
length of database: 14,973,337
effective HSP length: 104
effective length of query: 436
effective length of database: 8,465,225
effective search space: 3690838100
effective search space used: 3690838100
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: 54 (25.4 bits)