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= 0002.0059.p
         (425 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309737|ref|YP_003773829.1| UDP-N-acetylmuramate:L-alanyl-g...   661   0.0  
gi|300309679|ref|YP_003773771.1| UDP-N-acetylmuramate-L-alanine ...    80   4e-16

>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 =  661 bits (1705), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 351/466 (75%), Positives = 377/466 (80%), Gaps = 47/466 (10%)

Query: 1   MHIHILGICGTFMGGLAVLAKEAGHKVTGCDANVYPPMSTQLEAQGIELIQGFDPGQVKL 60
           MHIHILGICGTFMGGLAVLAKEAGH VTGCDANVYPPMSTQLEAQGI L QGFD  QV+L
Sbjct: 1   MHIHILGICGTFMGGLAVLAKEAGHTVTGCDANVYPPMSTQLEAQGITLTQGFDAAQVEL 60

Query: 61  QPDLFVIGNVVSRGNPLMEEILNRGLPYVSGPEWMGNHILRDKWVLAVAGTHGKTTTSAM 120
           +PDLFVIGNVVSRGNPLMEEILNRGLPYVSGP+WMG +IL+DKWVLAVAGTHGKTTTSAM
Sbjct: 61  EPDLFVIGNVVSRGNPLMEEILNRGLPYVSGPQWMGENILQDKWVLAVAGTHGKTTTSAM 120

Query: 121 LAWILEDAGYAPGFLIGGVPMNFGISARLSGMKDGKKQDSIFFVIEADEYDTAFFDKRSK 180
           LAW+LE AGY PGFLIGGVPMNFG+SARL    DG+   + FFVIEADEYDTAFFDKRSK
Sbjct: 121 LAWVLEHAGYQPGFLIGGVPMNFGVSARLG--SDGQGGPAPFFVIEADEYDTAFFDKRSK 178

Query: 181 FVHYHARTAILNNLEYDHADIFPDLTAIETQFHHLVRTIPGIGRLVVNGREPALERVIAR 240
           FVHY  RTA+LNNLEYDHADIFPDL AIETQFHHLVRT+PGIGRL+VNGREPAL+RV+AR
Sbjct: 179 FVHYRTRTAVLNNLEYDHADIFPDLAAIETQFHHLVRTVPGIGRLIVNGREPALQRVLAR 238

Query: 241 GCWSEHENFGVNPGQSGWSLETRDDGSFDIGFNGVPQGTVNWSLTGEHNRMNALA----- 295
           GCWSE E+FGV  GQSGWSL T +DG FD+ F+G  QGTV W LTGEHNRMNALA     
Sbjct: 239 GCWSEREDFGVAQGQSGWSLLTHEDGRFDVFFDGQTQGTVEWQLTGEHNRMNALAAIAAA 298

Query: 296 ---------AIAAARAF---------------------------PIATTVAGLRKKVGKD 319
                    AIAA  AF                            IATTVAGLRKKV   
Sbjct: 299 RHVGVPVAQAIAALGAFQSVKRRMELRGSANGVAVYDDFAHHPTAIATTVAGLRKKV--- 355

Query: 320 GGGRIIAVLEPRSNTMKLGTMKDALPASLTDADLVFGYGAKGSGKEALGWDLAQALSPLG 379
           G  RI+AVLEPRSNTMKLGTMK ALP SL DADLVFG+GA  +G++ALGWDL +AL+PLG
Sbjct: 356 GAARILAVLEPRSNTMKLGTMKQALPGSLADADLVFGFGAH-TGRDALGWDLGEALAPLG 414

Query: 380 EKANAFDDLGALVQAIKQAARPGDHVLVMSNGGFGGVHQKLLDALA 425
            KA AFDDL ALVQA+K AARPGDHVLVMSNGGFGGVHQKLLDALA
Sbjct: 415 AKAAAFDDLAALVQAVKAAARPGDHVLVMSNGGFGGVHQKLLDALA 460


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

 Score = 79.7 bits (195), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 97/415 (23%), Positives = 163/415 (39%), Gaps = 75/415 (18%)

Query: 63  DLFVIGNVVSRGNPLMEEILNRGLPYVSGPEWMGNHILRDKWVLAVAGTHGKTTTSAMLA 122
           D  V    V   NP +     + +P V     +G  ++R K  +A+AGTHGKTTT++++A
Sbjct: 66  DAIVTSTAVKGDNPEVLAARKKHIPIVPRAVMLGE-LMRLKKGIAIAGTHGKTTTTSLVA 124

Query: 123 WILEDAGYAPGFLIGGVPMNFGISARLSGMKDGKKQDSIFFVIEADEYDTAFFDKRSKFV 182
            +L   G  P F+IGG   + G +A+L   +        F V EADE D +F +      
Sbjct: 125 SVLAQGGLDPTFVIGGRLTSAGANAKLGTGE--------FIVAEADESDASFLNLTPVI- 175

Query: 183 HYHARTAILNNLEYDHADIFP-DLTAIETQFHHLVRTIPGIGRLVVNGREPALERVIARG 241
                  ++ N++ DH + +  D   ++  F    + +P  G  V+   +P + R I   
Sbjct: 176 ------EVITNIDADHMETYNHDFARLKQAFVEFTQRLPFYGVAVLCLDDPHV-REIMPM 228

Query: 242 CWSEHENFGVNPGQSGWSLETRD-DG--SFDIGFNGVPQGTVNWSLTGEHNRMNALAAIA 298
                  +G +      +++ +  DG   F +  +G     V+ +  G HN  NA AAIA
Sbjct: 229 VSKPILTYGFHEDADVRAIDAKAVDGKMEFTVIQDGYAPMQVSLNQPGMHNVQNACAAIA 288

Query: 299 AARAFPI--------ATTVAGLRKKVGKDG------------------------------ 320
            AR   +         T   G+ ++  + G                              
Sbjct: 289 IARELDVDDAATQKALTEFNGVGRRFTRYGEVPLWDAEGKPAGHFTLVDDYGHHPVETAA 348

Query: 321 ----------GGRIIAVLEPRSNTMKLGTMKDALPASLTDADLVFGYGAKGSGKEAL--- 367
                     G R++   +P   T      +D +   L+  D++       +G+  +   
Sbjct: 349 TIAAARGAYPGRRLVLAFQPHRYTRTRDLFEDFVKV-LSSPDVLVLAEVYSAGEAPIVAA 407

Query: 368 -GWDLAQALSPLGEKANAF-DDLGALVQAIKQAARPGDHVLVMSNGGFGGVHQKL 420
            G  LA AL   G+    F DD+G + + I+   R GD V+ M  G    V  +L
Sbjct: 408 DGRSLAHALRAAGKVEPVFVDDIGDMPETIRNVVRDGDVVMTMGAGSISAVPGRL 462


  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
   0.320    0.138    0.422 

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: 1,436,057
Number of extensions: 62855
Number of successful extensions: 193
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 188
Number of HSP's successfully gapped: 2
Length of query: 425
Length of database: 1,619,870
Length adjustment: 88
Effective length of query: 337
Effective length of database: 1,203,190
Effective search space: 405475030
Effective search space used: 405475030
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: 132 (55.5 bits)