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= 002940
         (863 letters)

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

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



>pdb|2E4M|A Chain A, Crystal Structure Of Hemagglutinin Subcomponent Complex
           (Ha- 33HA-17) From Clostridium Botulinum Serotype D
           Strain 4947
 pdb|2E4M|B Chain B, Crystal Structure Of Hemagglutinin Subcomponent Complex
           (Ha- 33HA-17) From Clostridium Botulinum Serotype D
           Strain 4947
          Length = 286

 Score = 33.9 bits (76), Expect = 0.42,   Method: Compositional matrix adjust.
 Identities = 14/33 (42%), Positives = 24/33 (72%), Gaps = 1/33 (3%)

Query: 720 LNDFIGKSVMLEPFDSPGMLVIQHETDDELVVT 752
           L D+I ++V+L  + +P  LV+Q+ TDD L+V+
Sbjct: 96  LQDYISRNVILRNYMNPN-LVLQYNTDDTLIVS 127


>pdb|2XIT|A Chain A, Crystal Structure Of Monomeric Mipz
 pdb|2XIT|B Chain B, Crystal Structure Of Monomeric Mipz
          Length = 294

 Score = 31.2 bits (69), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 30/133 (22%), Positives = 54/133 (40%), Gaps = 12/133 (9%)

Query: 542 RVTLTFSSKGSGLTTSLNLRIPTWTSSNGAKATLNGQDLPLPSPGNFLSVTKTWSSDDKL 601
           RV +  + KG    +++ + + T     GAK  +   DL   +   F    + W  + K+
Sbjct: 5   RVIVVGNEKGGAGKSTIAVHLVTALLYGGAKVAVIDLDLRQRTSARFFENRRAWLDNKKI 64

Query: 602 TIQLPLTLR---TEAIQDDRPEYASI--------QAILYGPYVLAGHSIGDWDITESATS 650
            +  PL L     +    +RPE   +        +A+    ++L     GD  IT  A  
Sbjct: 65  ELPEPLALNLSDNDVALAERPEEEQVAGFEAAFARAMAECDFILIDTPGGDSAITRMAHG 124

Query: 651 LSDW-ITPIPASY 662
            +D  +TP+  S+
Sbjct: 125 RADLVVTPMNDSF 137


>pdb|2QFZ|A Chain A, Crystal Structure Of Human Tbc1 Domain Family Member 22a
 pdb|2QFZ|B Chain B, Crystal Structure Of Human Tbc1 Domain Family Member 22a
          Length = 345

 Score = 30.8 bits (68), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 22/95 (23%), Positives = 45/95 (47%), Gaps = 7/95 (7%)

Query: 217 KEIGSGYLSAFPTEQFDRLEALIPVWAPYYTIHKILAGLLDQYTYADNAEALRMTTWMVE 276
           +E+ +  +S  P E    +EA       Y+ + K+L G+ D YT+A     ++M   M+E
Sbjct: 169 EEVDTVDVSGVPAEVLCNIEA-----DTYWCMSKLLDGIQDNYTFAQ--PGIQMKVKMLE 221

Query: 277 YFYNRVQNVIKKYSIERHWQTLNEEAGGMNDVLYK 311
              +R+   + ++  +   + L      MN++L +
Sbjct: 222 ELVSRIDEQVHRHLDQHEVRYLQFAFRWMNNLLMR 256


>pdb|2XJ4|A Chain A, Structure Of The Bacterial Cell Division Regulator Protein
           Mipz
          Length = 286

 Score = 30.8 bits (68), Expect = 3.3,   Method: Composition-based stats.
 Identities = 30/133 (22%), Positives = 54/133 (40%), Gaps = 12/133 (9%)

Query: 542 RVTLTFSSKGSGLTTSLNLRIPTWTSSNGAKATLNGQDLPLPSPGNFLSVTKTWSSDDKL 601
           RV +  + KG    +++ + + T     GAK  +   DL   +   F    + W  + K+
Sbjct: 5   RVIVVGNEKGGAGKSTIAVHLVTALLYGGAKVAVIDLDLRQRTSARFFENRRAWLDNKKI 64

Query: 602 TIQLPLTLR---TEAIQDDRPEYASI--------QAILYGPYVLAGHSIGDWDITESATS 650
            +  PL L     +    +RPE   +        +A+    ++L     GD  IT  A  
Sbjct: 65  ELPEPLALNLSDNDVALAERPEEEQVAGFEAAFARAMAECDFILIDTPGGDSAITRMAHG 124

Query: 651 LSDW-ITPIPASY 662
            +D  +TP+  S+
Sbjct: 125 RADLVVTPMNDSF 137


>pdb|3TX8|A Chain A, Crystal Structure Of A Succinyl-Diaminopimelate
           Desuccinylase (Arge) From Corynebacterium Glutamicum
           Atcc 13032 At 2.97 A Resolution
          Length = 369

 Score = 30.4 bits (67), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 21/61 (34%), Positives = 30/61 (49%), Gaps = 6/61 (9%)

Query: 157 TARLPAPGEPYGGWEEPSCE--LRGHFVGHYLSA-SALMWASTHNESLKEKMSAVVSALS 213
            A L   GEP GGW E  C+  LR     H + A SA  W     ++   K+S ++S ++
Sbjct: 157 AADLALLGEPTGGWIEAGCQGNLRIKVTAHGVRAHSARSWLG---DNAXHKLSPIISKVA 213

Query: 214 A 214
           A
Sbjct: 214 A 214


  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
   0.317    0.133    0.403 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 26,959,375
Number of Sequences: 62578
Number of extensions: 1153969
Number of successful extensions: 2631
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 2631
Number of HSP's gapped (non-prelim): 11
length of query: 863
length of database: 14,973,337
effective HSP length: 107
effective length of query: 756
effective length of database: 8,277,491
effective search space: 6257783196
effective search space used: 6257783196
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 bits)