BLASTP 2.2.18 [Mar-02-2008]


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= 0002.0108.p
         (426 letters)

Database: BlastDatabases/689/689 
           4735 sequences; 1,619,870 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309816|ref|YP_003773908.1| 3-deoxy-d-manno-octulosonic-aci...   638   0.0  

>gi|300309816|ref|YP_003773908.1| 3-deoxy-d-manno-octulosonic-acid
           (KDO) transferase [Herbaspirillum seropedicae SmR1]
          Length = 428

 Score =  638 bits (1646), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 329/426 (77%), Positives = 360/426 (84%), Gaps = 3/426 (0%)

Query: 1   MRLLYSLVWWLVLPLVLLRLWRRGRKEPGYRAHVGERLGFYSQEARLSDPQARFIWVHAV 60
           MR LYS +WW  +PLVLLRLWRRGR+EPGYRAHV ERLGFY    RL DPQARFIWVHAV
Sbjct: 1   MRWLYSALWWFAMPLVLLRLWRRGRQEPGYRAHVAERLGFYP---RLPDPQARFIWVHAV 57

Query: 61  SVGETRAAEPLIDALLQQYPQHSILLTCMTATGRETGTQVYGKHGARVVQSFLPYDTGWM 120
           SVGETRAAEPL+DALL +YP   ILLTCMTATGR TG QV+GKHGARVVQSFLPYDTGWM
Sbjct: 58  SVGETRAAEPLVDALLSRYPDCKILLTCMTATGRATGAQVFGKHGARVVQSFLPYDTGWM 117

Query: 121 CARFLRHFRPVLCVLMETEVWPNLIRQCRRHQVPVMLANARLSERSLRRGQRFAALLRPA 180
           C+RFLRHFRP+ C+LMETEVWPNLIRQCRRH VPVMLANARLSERSLRRGQRFA+LLRPA
Sbjct: 118 CSRFLRHFRPLACILMETEVWPNLIRQCRRHDVPVMLANARLSERSLRRGQRFASLLRPA 177

Query: 181 AEAIDVVAAQSPADAERLRAFGARHVEVTGSLKFDVQPPAEMVERGLAWKRAIGERKILL 240
           AEAIDVV AQS  DA RL AFGARHVEVTGSLKFDVQPP ++VERG  WKRA+GERK+LL
Sbjct: 178 AEAIDVVGAQSDGDARRLLAFGARHVEVTGSLKFDVQPPMQVVERGREWKRALGERKVLL 237

Query: 241 CASTREGEEALILDALARLGKTGWLTVIVPRHPQRFAEVAGMIQAQGLRLRRRDALGQGG 300
           CASTREGEE LILDALA+LG+  WLTVIVPRHPQRF EVA +I+A+GLRLRRR  L Q  
Sbjct: 238 CASTREGEEVLILDALAKLGRPDWLTVIVPRHPQRFDEVAALIRARGLRLRRRSELAQDF 297

Query: 301 DWDQVDVVLGDSMGEMFAYYALCDVAFIGGSLLPLGGQNLIEALALGKPVLVGEHTFNFL 360
             + VDVVLGDSMGEMFAYYAL DV+FIGGSLLPLGGQNLIEALALGKPVL+GEHTFNFL
Sbjct: 298 AVEDVDVVLGDSMGEMFAYYALSDVSFIGGSLLPLGGQNLIEALALGKPVLIGEHTFNFL 357

Query: 361 SITDQAIEAGAACRISSTEQLWDMTSALFADPDRIAAMTHAAHGFAGAHQGASHKTTELL 420
            IT++A+  GAA R+    +L    S L A+PDRI  M  AA  FA  HQGA+ ++  LL
Sbjct: 358 RITEEAVADGAAVRVGDAVELLRQWSILIAEPDRIDEMAQAALSFAQRHQGATDRSLVLL 417

Query: 421 APLLAR 426
           APLL R
Sbjct: 418 APLLER 423


  Database: BlastDatabases/689/689
    Posted date:  Apr 10, 2011 12:15 AM
  Number of letters in database: 1,619,870
  Number of sequences in database:  4735
  
Lambda     K      H
   0.325    0.137    0.426 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 4735
Number of Hits to DB: 1,264,256
Number of extensions: 53663
Number of successful extensions: 260
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 259
Number of HSP's successfully gapped: 1
Length of query: 426
Length of database: 1,619,870
Length adjustment: 88
Effective length of query: 338
Effective length of database: 1,203,190
Effective search space: 406678220
Effective search space used: 406678220
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 132 (55.5 bits)