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= 0001.0373.p
         (460 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...   835   0.0  
gi|300309679|ref|YP_003773771.1| UDP-N-acetylmuramate-L-alanine ...   110   2e-25

>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 =  835 bits (2157), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 421/460 (91%), Positives = 439/460 (95%)

Query: 1   MHIHILGICGTFMGGLAVLAKEAGHTVTGCDANVYPPMSTQLEAQGITLIQGFEPSQVDL 60
           MHIHILGICGTFMGGLAVLAKEAGHTVTGCDANVYPPMSTQLEAQGITL QGF+ +QV+L
Sbjct: 1   MHIHILGICGTFMGGLAVLAKEAGHTVTGCDANVYPPMSTQLEAQGITLTQGFDAAQVEL 60

Query: 61  KPDLFVIGNVVSRGNPLMEEILNRGLPYVSGPQWMGENILQDKWVLAVAGTHGKTTTSAM 120
           +PDLFVIGNVVSRGNPLMEEILNRGLPYVSGPQWMGENILQDKWVLAVAGTHGKTTTSAM
Sbjct: 61  EPDLFVIGNVVSRGNPLMEEILNRGLPYVSGPQWMGENILQDKWVLAVAGTHGKTTTSAM 120

Query: 121 LAWVLEQAGYQPGFLIGGVPMNFGISARLGSDGQGGPSPFFVIEADEYDTAFFDKRSKFV 180
           LAWVLE AGYQPGFLIGGVPMNFG+SARLGSDGQGGP+PFFVIEADEYDTAFFDKRSKFV
Sbjct: 121 LAWVLEHAGYQPGFLIGGVPMNFGVSARLGSDGQGGPAPFFVIEADEYDTAFFDKRSKFV 180

Query: 181 HYRTRTAILNNLEYDHADIFPDLAAIETQFHHLVRTVPGIGKLLVNAREAALQRVLARGC 240
           HYRTRTA+LNNLEYDHADIFPDLAAIETQFHHLVRTVPGIG+L+VN RE ALQRVLARGC
Sbjct: 181 HYRTRTAVLNNLEYDHADIFPDLAAIETQFHHLVRTVPGIGRLIVNGREPALQRVLARGC 240

Query: 241 WSGREDFGVAAGQPGWSLQTQEDGRFQVCFDGQLQGTVQWELTGEHNRMNAVAAIAAARH 300
           WS REDFGVA GQ GWSL T EDGRF V FDGQ QGTV+W+LTGEHNRMNA+AAIAAARH
Sbjct: 241 WSEREDFGVAQGQSGWSLLTHEDGRFDVFFDGQTQGTVEWQLTGEHNRMNALAAIAAARH 300

Query: 301 VGVPTAQAIEALGAFQSVKRRMELRGSANGVAVYDDFAHHPTAIATTVAGLRKKVGAARI 360
           VGVP AQAI ALGAFQSVKRRMELRGSANGVAVYDDFAHHPTAIATTVAGLRKKVGAARI
Sbjct: 301 VGVPVAQAIAALGAFQSVKRRMELRGSANGVAVYDDFAHHPTAIATTVAGLRKKVGAARI 360

Query: 361 LAVLEPRSNTMKLGTMKEALPGSLAEADMVFGYGAQSGRDALGWDLAEALAPLGQKAAAF 420
           LAVLEPRSNTMKLGTMK+ALPGSLA+AD+VFG+GA +GRDALGWDL EALAPLG KAAAF
Sbjct: 361 LAVLEPRSNTMKLGTMKQALPGSLADADLVFGFGAHTGRDALGWDLGEALAPLGAKAAAF 420

Query: 421 HDLDRLVQAVKAAAQPGDHVLVMSNGGFGGVHQKLLDALA 460
            DL  LVQAVKAAA+PGDHVLVMSNGGFGGVHQKLLDALA
Sbjct: 421 DDLAALVQAVKAAARPGDHVLVMSNGGFGGVHQKLLDALA 460


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

 Score =  110 bits (276), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 115/417 (27%), Positives = 176/417 (42%), Gaps = 44/417 (10%)

Query: 63  DLFVIGNVVSRGNPLMEEILNRGLPYVSGPQWMGENILQDKWVLAVAGTHGKTTTSAMLA 122
           D  V    V   NP +     + +P V     +GE +++ K  +A+AGTHGKTTT++++A
Sbjct: 66  DAIVTSTAVKGDNPEVLAARKKHIPIVPRAVMLGE-LMRLKKGIAIAGTHGKTTTTSLVA 124

Query: 123 WVLEQAGYQPGFLIGGVPMNFGISARLGSDGQGGPSPFFVIEADEYDTAFFDKRSKFVHY 182
            VL Q G  P F+IGG   + G +A+LG+        F V EADE D +F +        
Sbjct: 125 SVLAQGGLDPTFVIGGRLTSAGANAKLGT------GEFIVAEADESDASFLNLTPVI--- 175

Query: 183 RTRTAILNNLEYDHADIFP-DLAAIETQFHHLVRTVPGIGKLLVNAREAALQRVLARG-- 239
                ++ N++ DH + +  D A ++  F    + +P  G  ++   +  ++ ++     
Sbjct: 176 ----EVITNIDADHMETYNHDFARLKQAFVEFTQRLPFYGVAVLCLDDPHVREIMPMVSK 231

Query: 240 ---CWSGREDFGVAAGQPGWSLQTQEDGR--FQVCFDGQLQGTVQWELTGEHNRMNAVAA 294
               +   ED  V A           DG+  F V  DG     V     G HN  NA AA
Sbjct: 232 PILTYGFHEDADVRAID-----AKAVDGKMEFTVIQDGYAPMQVSLNQPGMHNVQNACAA 286

Query: 295 IAAARHVGVPTAQAIEALGAFQSVKRRMELRGS----------ANGVAVYDDFAHHPTAI 344
           IA AR + V  A   +AL  F  V RR    G           A    + DD+ HHP   
Sbjct: 287 IAIARELDVDDAATQKALTEFNGVGRRFTRYGEVPLWDAEGKPAGHFTLVDDYGHHPVET 346

Query: 345 ATTVAGLRKKVGAARILAVLEPRSNTMKLGTMKEALPGSLAEADM-----VFGYGAQSGR 399
           A T+A  R      R++   +P   T +   + E     L+  D+     V+  G     
Sbjct: 347 AATIAAARGAYPGRRLVLAFQPHRYT-RTRDLFEDFVKVLSSPDVLVLAEVYSAGEAPIV 405

Query: 400 DALGWDLAEALAPLGQKAAAF-HDLDRLVQAVKAAAQPGDHVLVMSNGGFGGVHQKL 455
            A G  LA AL   G+    F  D+  + + ++   + GD V+ M  G    V  +L
Sbjct: 406 AADGRSLAHALRAAGKVEPVFVDDIGDMPETIRNVVRDGDVVMTMGAGSISAVPGRL 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    0.136    0.412 

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: 1,551,426
Number of extensions: 68637
Number of successful extensions: 230
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 226
Number of HSP's successfully gapped: 3
Length of query: 460
Length of database: 1,619,870
Length adjustment: 88
Effective length of query: 372
Effective length of database: 1,203,190
Effective search space: 447586680
Effective search space used: 447586680
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)