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= 048778
         (902 letters)

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

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



>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 = 38.1 bits (87), Expect = 0.021,   Method: Compositional matrix adjust.
 Identities = 33/128 (25%), Positives = 55/128 (42%), Gaps = 11/128 (8%)

Query: 282 GRLDEAFSLKDEMCEKGWQPSTRTYTVLIKALCDISLT----------DKALSLFDEMVV 331
           G + EA  L DE    G Q S   Y VL+  +C ++             +   +F +M+V
Sbjct: 40  GDVLEALRLYDEARRNGVQLSQYHYNVLL-YVCSLAEAATESSPNPGLSRGFDIFKQMIV 98

Query: 332 KRCKPNAHTYTVLIDRLCREGKIDEANGMCGKMLQDGHFPGVVTYNVLINGYCKQGRIIA 391
            +  PN  T+T        +   + A  M  +M   G  P + +Y   + G+C++G    
Sbjct: 99  DKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADK 158

Query: 392 AFELLALM 399
           A+E+ A M
Sbjct: 159 AYEVDAHM 166


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

 Score = 32.0 bits (71), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 21/88 (23%), Positives = 41/88 (46%), Gaps = 3/88 (3%)

Query: 621 YTVIINGLCQRGRFKEAEMLLFKMFDLGVSPNHITYSILVRAHASTGRLDHAFKIVSFMV 680
           Y  ++ G  ++G FKE   +LF + D G++P+ ++Y+  ++     GR D     +   +
Sbjct: 168 YNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQC---MGRQDQDAGTIERCL 224

Query: 681 ANGCQLNSNVYSALLAGLVSSNKASGVL 708
               Q    + +   A L+S    + VL
Sbjct: 225 EQMSQEGLKLQALFTAVLLSEEDRATVL 252


>pdb|1C9M|A Chain A, Bacillus Lentus Subtilsin (Ser 87) N76dS103AV104I
          Length = 269

 Score = 31.2 bits (69), Expect = 2.8,   Method: Composition-based stats.
 Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 5/79 (6%)

Query: 647 LGVSPNHITYSILVRAHASTGRLDHAFKIVSFMVANGCQ-----LNSNVYSALLAGLVSS 701
           LGV+P+   Y++ V   + +G +    + + +   NG       L S   SA L   V+S
Sbjct: 80  LGVAPSAELYAVKVLGASGSGAISSIAQGLEWAGNNGMHVANLSLGSPSPSATLEQAVNS 139

Query: 702 NKASGVLSISTSCHSDAGS 720
             + GVL ++ S +S AGS
Sbjct: 140 ATSRGVLVVAASGNSGAGS 158


>pdb|2GHA|A Chain A, Thermotoga Maritima Maltotriose Binding Protein Bound With
           Maltotriose
 pdb|2GHA|B Chain B, Thermotoga Maritima Maltotriose Binding Protein Bound With
           Maltotriose
 pdb|2GHB|A Chain A, Thermotoga Maritima Maltotriose Binding Protein, Ligand
           Free Form
 pdb|2GHB|B Chain B, Thermotoga Maritima Maltotriose Binding Protein, Ligand
           Free Form
 pdb|2GHB|C Chain C, Thermotoga Maritima Maltotriose Binding Protein, Ligand
           Free Form
          Length = 382

 Score = 30.8 bits (68), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 21/58 (36%), Positives = 29/58 (50%), Gaps = 8/58 (13%)

Query: 426 KAVHLLKRVVDGGLFPDEITYNILVDGFCREGQLDI------ALKIFNSMSI-FGLVP 476
           K V LLKR+VD G+      Y I+ D   REGQ  +      A+K +    I +G+ P
Sbjct: 191 KGVKLLKRLVDEGILDPSDNYQIM-DSMFREGQAAMIINGPWAIKAYKDAGIDYGVAP 247


>pdb|4G23|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
           A. Thaliana With Mn
 pdb|4G25|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
           A. Thaliana, Semet Substituted Form With Sr
          Length = 501

 Score = 30.4 bits (67), Expect = 5.1,   Method: Compositional matrix adjust.
 Identities = 29/126 (23%), Positives = 51/126 (40%), Gaps = 11/126 (8%)

Query: 282 GRLDEAFSLKDEMCEKGWQPSTRTYTVLIKALCDISLT----------DKALSLFDEMVV 331
           G + EA  L DE    G Q S   Y VL+  +C ++             +   +F + +V
Sbjct: 40  GDVLEALRLYDEARRNGVQLSQYHYNVLL-YVCSLAEAATESSPNPGLSRGFDIFKQXIV 98

Query: 332 KRCKPNAHTYTVLIDRLCREGKIDEANGMCGKMLQDGHFPGVVTYNVLINGYCKQGRIIA 391
            +  PN  T+T        +   + A     +    G  P + +Y   + G+C++G    
Sbjct: 99  DKVVPNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFCRKGDADK 158

Query: 392 AFELLA 397
           A+E+ A
Sbjct: 159 AYEVDA 164


  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
   0.324    0.140    0.421 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 25,815,552
Number of Sequences: 62578
Number of extensions: 1059729
Number of successful extensions: 2510
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 2495
Number of HSP's gapped (non-prelim): 26
length of query: 902
length of database: 14,973,337
effective HSP length: 108
effective length of query: 794
effective length of database: 8,214,913
effective search space: 6522640922
effective search space used: 6522640922
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 56 (26.2 bits)