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= 0035.0027.p
         (331 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309679|ref|YP_003773771.1| UDP-N-acetylmuramate-L-alanine ...   599   e-172
gi|300309737|ref|YP_003773829.1| UDP-N-acetylmuramate:L-alanyl-g...   102   6e-23

>gi|300309679|ref|YP_003773771.1| UDP-N-acetylmuramate-L-alanine
           ligase [Herbaspirillum seropedicae SmR1]
          Length = 475

 Score =  599 bits (1544), Expect = e-172,   Method: Compositional matrix adjust.
 Identities = 304/318 (95%), Positives = 311/318 (97%)

Query: 1   MKHRVKNIHFVGIGGSGMSGIAEVLLNLGYGVSGSDLGSNAATQRLAQLGARILYGHAAE 60
           MKHRVKNIHFVGIGGSGMSGIAEVLLNLGYGVSGSDLGSNAATQRLAQLGA I YGHAA 
Sbjct: 1   MKHRVKNIHFVGIGGSGMSGIAEVLLNLGYGVSGSDLGSNAATQRLAQLGACIRYGHAAG 60

Query: 61  NIENADAIVTSTAVKGDNPEVVAARKKHIPIVPRAVMLGELMRLKAGIAIAGTHGKTTTT 120
           NIE ADAIVTSTAVKGDNPEV+AARKKHIPIVPRAVMLGELMRLK GIAIAGTHGKTTTT
Sbjct: 61  NIEGADAIVTSTAVKGDNPEVLAARKKHIPIVPRAVMLGELMRLKKGIAIAGTHGKTTTT 120

Query: 121 SLVASVLAQGGLDPTFVIGGRLTSAGANAKLGSGDFIVAEADESDASFLNLTPVIEVITN 180
           SLVASVLAQGGLDPTFVIGGRLTSAGANAKLG+G+FIVAEADESDASFLNLTPVIEVITN
Sbjct: 121 SLVASVLAQGGLDPTFVIGGRLTSAGANAKLGTGEFIVAEADESDASFLNLTPVIEVITN 180

Query: 181 IDADHMETYNHDFAKLKQAFVEFTQRLPFYGVAVLCLDDPHVREIMPMISKPILTYGFHE 240
           IDADHMETYNHDFA+LKQAFVEFTQRLPFYGVAVLCLDDPHVREIMPM+SKPILTYGFHE
Sbjct: 181 IDADHMETYNHDFARLKQAFVEFTQRLPFYGVAVLCLDDPHVREIMPMVSKPILTYGFHE 240

Query: 241 DADIRAIDAKAVDGKMEFTVIQDGYAPMQVSLNQPGMHNVQNACAAVAIARELDVADADT 300
           DAD+RAIDAKAVDGKMEFTVIQDGYAPMQVSLNQPGMHNVQNACAA+AIARELDV DA T
Sbjct: 241 DADVRAIDAKAVDGKMEFTVIQDGYAPMQVSLNQPGMHNVQNACAAIAIARELDVDDAAT 300

Query: 301 QKALTEFNGVGRRFTRYG 318
           QKALTEFNGVGRRFTRYG
Sbjct: 301 QKALTEFNGVGRRFTRYG 318


>gi|300309737|ref|YP_003773829.1|
           UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-
           diaminopimelate ligase transmembrane protein
           [Herbaspirillum seropedicae SmR1]
          Length = 460

 Score =  102 bits (253), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 103/336 (30%), Positives = 154/336 (45%), Gaps = 35/336 (10%)

Query: 7   NIHFVGIGGSGMSGIAEVLLNLGYGVSGSD--LGSNAATQRLAQLGARILYGHAAENIE- 63
           +IH +GI G+ M G+A +    G+ V+G D  +    +TQ  AQ G  +  G  A  +E 
Sbjct: 2   HIHILGICGTFMGGLAVLAKEAGHTVTGCDANVYPPMSTQLEAQ-GITLTQGFDAAQVEL 60

Query: 64  NADAIVTSTAVKGDNPEVVAARKKHIPIVPRAVMLGE-LMRLKAGIAIAGTHGKTTTTSL 122
             D  V    V   NP +     + +P V     +GE +++ K  +A+AGTHGKTTT+++
Sbjct: 61  EPDLFVIGNVVSRGNPLMEEILNRGLPYVSGPQWMGENILQDKWVLAVAGTHGKTTTSAM 120

Query: 123 VASVLAQGGLDPTFVIGGRLTSAGANAKLGS------GDFIVAEADESDASFLNLTPVI- 175
           +A VL   G  P F+IGG   + G +A+LGS        F V EADE D +F +      
Sbjct: 121 LAWVLEHAGYQPGFLIGGVPMNFGVSARLGSDGQGGPAPFFVIEADEYDTAFFDKRSKFV 180

Query: 176 ------EVITNIDADHMETYNHDFAKLKQAFVEFTQRLPFYGVAVLCLDDPHVREIMPMI 229
                  V+ N++ DH + +  D A ++  F    + +P  G+  L ++    RE  P +
Sbjct: 181 HYRTRTAVLNNLEYDHADIFP-DLAAIETQFHHLVRTVP--GIGRLIVNG---RE--PAL 232

Query: 230 SKPILTYGFHEDADIRAIDAKA-------VDGKMEFTVIQDGYAPMQVSLNQPGMHNVQN 282
            + +    + E  D      ++        DG+  F V  DG     V     G HN  N
Sbjct: 233 QRVLARGCWSEREDFGVAQGQSGWSLLTHEDGR--FDVFFDGQTQGTVEWQLTGEHNRMN 290

Query: 283 ACAAVAIARELDVADADTQKALTEFNGVGRRFTRYG 318
           A AA+A AR + V  A    AL  F  V RR    G
Sbjct: 291 ALAAIAAARHVGVPVAQAIAALGAFQSVKRRMELRG 326


  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
   0.319    0.134    0.383 

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: 1,010,306
Number of extensions: 42119
Number of successful extensions: 176
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 174
Number of HSP's successfully gapped: 2
Length of query: 331
Length of database: 1,619,870
Length adjustment: 86
Effective length of query: 245
Effective length of database: 1,212,660
Effective search space: 297101700
Effective search space used: 297101700
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 131 (55.1 bits)