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= 019648
         (337 letters)

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

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



>pdb|2IHM|A Chain A, Polymerase Mu In Ternary Complex With Gapped 11mer Dna
           Duplex And Bound Incoming Nucleotide
 pdb|2IHM|B Chain B, Polymerase Mu In Ternary Complex With Gapped 11mer Dna
           Duplex And Bound Incoming Nucleotide
          Length = 360

 Score = 35.4 bits (80), Expect = 0.041,   Method: Compositional matrix adjust.
 Identities = 36/160 (22%), Positives = 69/160 (43%), Gaps = 30/160 (18%)

Query: 108 EAESTVKKVSASMKEKISAATEEVKGTFRTGSTDTSAKHDDDVRDGFKASSGEEKQK--- 164
           +AE+  + + A++++ +  AT  + G FR G       HD D    F  +  EE Q+   
Sbjct: 158 DAEALQQLIEAAVRQTLPGATVTLTGGFRRGKLQ---GHDVD----FLITHPEEGQEVGL 210

Query: 165 -----QTVSSDTAETFYGKLKSSISSPKFTLAFQKLKEAKVVDLAKKGYDIVKDELSGSP 219
                  + S     ++   +S ++     L     + +  +D+ ++ + I+     G P
Sbjct: 211 LPKVMSCLQSQGLVLYHQYHRSHLADSAHNLR----QRSSTMDVFERSFCIL-----GLP 261

Query: 220 SKRKHL---EYTPSPSWTGEKSTRTDLVVTPSKKSMWSKL 256
             ++        P P+W   K+ R DLVVTPS +  ++ L
Sbjct: 262 QPQQAALAGALPPCPTW---KAVRVDLVVTPSSQFPFALL 298


>pdb|2ON7|A Chain A, Structure Of Nagst-1
 pdb|2ON7|B Chain B, Structure Of Nagst-1
 pdb|2ON7|C Chain C, Structure Of Nagst-1
 pdb|2ON7|D Chain D, Structure Of Nagst-1
          Length = 206

 Score = 31.6 bits (70), Expect = 0.62,   Method: Compositional matrix adjust.
 Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 2/70 (2%)

Query: 195 LKEAKVVDLAKKGYDIVKDELSGSPSKRKHLEYTPSPSWTGEKSTRTDLVVTPSKKSMWS 254
           ++E  V  L K+     +D+  G  +K   L+ +PS    G+  T  DL+V+    +M +
Sbjct: 112 MREGDVEQLKKEVLLPARDKFFGFITK--FLKKSPSGFLVGDSLTWVDLLVSEHNATMLT 169

Query: 255 KLKEKMQGYP 264
            + E ++GYP
Sbjct: 170 FVPEFLEGYP 179


>pdb|2QE7|G Chain G, Crystal Structure Of The F1-Atpase From The
           Thermoalkaliphilic Bacterium Bacillus Sp. Ta2.A1
          Length = 286

 Score = 29.6 bits (65), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 14/28 (50%), Positives = 22/28 (78%), Gaps = 1/28 (3%)

Query: 259 KMQGYPVFKRITGISE-PVVTKGQEIAE 285
           K +GYPV + +TGIS+ P +T+ Q+IA+
Sbjct: 127 KKRGYPVVEEVTGISDTPSLTEIQDIAQ 154


>pdb|3OI8|A Chain A, The Crystal Structure Of Functionally Unknown Conserved
           Protein Domain From Neisseria Meningitidis Mc58
 pdb|3OI8|B Chain B, The Crystal Structure Of Functionally Unknown Conserved
           Protein Domain From Neisseria Meningitidis Mc58
          Length = 156

 Score = 29.3 bits (64), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 20/64 (31%), Positives = 30/64 (46%), Gaps = 3/64 (4%)

Query: 198 AKVVDLAKKGYDIV---KDELSGSPSKRKHLEYTPSPSWTGEKSTRTDLVVTPSKKSMWS 254
           A V+D A   + ++   KDE+ G    +  L+Y  +P     KS     V  P  KS+ +
Sbjct: 64  AYVIDTAHSRFPVIGEDKDEVLGILHAKDLLKYXFNPEQFHLKSILRPAVFVPEGKSLTA 123

Query: 255 KLKE 258
            LKE
Sbjct: 124 LLKE 127


>pdb|1NT2|B Chain B, Crystal Structure Of FibrillarinNOP5P COMPLEX
          Length = 258

 Score = 27.7 bits (60), Expect = 8.5,   Method: Compositional matrix adjust.
 Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 2/78 (2%)

Query: 65  EFKHSVKELKKKAEEIKGVKE-ELKERTKQTTEQLYKQVDGVWMEAESTVKKVSASMKEK 123
           E   S+  L +K E+I+ VKE E+ E+ ++   +L +    V  E E  ++K++ +M E 
Sbjct: 86  EIDESINMLNEKLEDIRAVKESEITEKFEKKIRELRELRRDVEREIEEVMEKIAPNMTEL 145

Query: 124 ISAATEEVKGTFRTGSTD 141
           + A     K   R GS +
Sbjct: 146 VGAKV-AAKLLERAGSME 162


  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
   0.310    0.126    0.346 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,552,606
Number of Sequences: 62578
Number of extensions: 391387
Number of successful extensions: 1324
Number of sequences better than 100.0: 40
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 33
Number of HSP's that attempted gapping in prelim test: 1306
Number of HSP's gapped (non-prelim): 50
length of query: 337
length of database: 14,973,337
effective HSP length: 99
effective length of query: 238
effective length of database: 8,778,115
effective search space: 2089191370
effective search space used: 2089191370
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 52 (24.6 bits)