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= 0022.0180.p
         (486 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309674|ref|YP_003773766.1| UDP-N-acetylmuramoyl-tripeptide...   887   0.0  
gi|300309673|ref|YP_003773765.1| UDP-N-acetylmuramoylalanyl-D-gl...    70   4e-13

>gi|300309674|ref|YP_003773766.1|
           UDP-N-acetylmuramoyl-tripeptide---D-alanyl-D-alanine
           ligase [Herbaspirillum seropedicae SmR1]
          Length = 486

 Score =  887 bits (2291), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 454/486 (93%), Positives = 472/486 (97%)

Query: 1   MMRFDFRQLLEWIRTAEEAASAHTVPGVVNAPAGVLELNDVVTDSRAVKPGNVFVALRGE 60
           MMRFDFRQ+LEW+RTAE AASAHTVPGVVNAPAG+L LNDVVTDSRAVKPGNVFVALRGE
Sbjct: 1   MMRFDFRQMLEWLRTAEAAASAHTVPGVVNAPAGLLALNDVVTDSRAVKPGNVFVALRGE 60

Query: 61  RFDAHDFLDAVVAQGAAAVVVDRVPPGLSVPAIVVPDIRAALGQIAHGWRVQRQIPVIGV 120
           RFDAHDFLDAV  QGAAAVVV+RVPPGL++PAIVVPD RAALGQIAHGWR+QRQIPVIGV
Sbjct: 61  RFDAHDFLDAVADQGAAAVVVERVPPGLALPAIVVPDTRAALGQIAHGWRMQRQIPVIGV 120

Query: 121 TGSNGKTTVKEMIAAILAAAFGEDGYLGTRGNFNNEIGVPLTLFRLRAQHQAAVIEMGMN 180
           TGSNGKTTVKEMIA ILAAAFGE+GYLGTRGNFNNEIGVPLTLFRLRAQHQAAVIEMGMN
Sbjct: 121 TGSNGKTTVKEMIATILAAAFGEEGYLGTRGNFNNEIGVPLTLFRLRAQHQAAVIEMGMN 180

Query: 181 HPGEIAVLSRIAAPTLGLVNNAQREHQEFMASVEAVARENGAVIRHLPADGVAVFPADDD 240
           HPGEIAVLSRIAAPTLGLVNNAQREHQEFMA+VEAVARENGAVIRHLPADGVAVFPADDD
Sbjct: 181 HPGEIAVLSRIAAPTLGLVNNAQREHQEFMATVEAVARENGAVIRHLPADGVAVFPADDD 240

Query: 241 FTALWREEAGARRVLTFGLNAQADVSASYQATAFGSTLQVTVKGLAVPPAQFKVELAAVG 300
           FT LWREEAGARRVL+FGL+AQADVSASYQATAFGSTLQV VKGLAVPPAQFKVELAAVG
Sbjct: 241 FTPLWREEAGARRVLSFGLSAQADVSASYQATAFGSTLQVAVKGLAVPPAQFKVELAAVG 300

Query: 301 EHNVRNALAAAACALGAGIPVDAVVRGLQSFAPVNGRLQRKQARSGALVIDDTYNANPDS 360
           EHNVRNALAAAACALGAGI ++AVVRGL+SFAPVNGRLQRK+ARSGALVIDDTYNANPDS
Sbjct: 301 EHNVRNALAAAACALGAGIAIEAVVRGLESFAPVNGRLQRKEARSGALVIDDTYNANPDS 360

Query: 361 VRAAIDVLASIAGPRVLVLGDMGEVGDQGPQFHAEIGAYARSRGIPLFFGLGELTKHAVT 420
           VRAAIDVLA+IAGPRVLVLGDMGEVGDQGPQFHAEIGAYARSRGIPLFFGLGELTKHAVT
Sbjct: 361 VRAAIDVLAAIAGPRVLVLGDMGEVGDQGPQFHAEIGAYARSRGIPLFFGLGELTKHAVT 420

Query: 421 SYGPALQNVAQAMHFDDIAALNAAVEQAAPQGATVLVKGSRFMKMERVVQHLVNVESLTQ 480
           +YG   Q VAQA+HFDDIAALNAAVEQAAPQGATVLVKGSRFMKMERVVQHLVNVES TQ
Sbjct: 421 AYGATPQGVAQALHFDDIAALNAAVEQAAPQGATVLVKGSRFMKMERVVQHLVNVESPTQ 480

Query: 481 HQQETH 486
           HQQETH
Sbjct: 481 HQQETH 486


>gi|300309673|ref|YP_003773765.1|
           UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-
           diaminopimelate ligase [Herbaspirillum seropedicae SmR1]
          Length = 508

 Score = 70.1 bits (170), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 106/396 (26%), Positives = 165/396 (41%), Gaps = 44/396 (11%)

Query: 41  VVTDSRAVKPGNVFVALRGERFDAHDFLDAVVAQGAAAVVVD----RVPPGLSVPAIVVP 96
           + +DSR V PG+VF A  G+  D   ++   V +GAAAVV +      P  + VP + V 
Sbjct: 24  LTSDSRRVAPGDVFFAYVGDA-DGRSYIADAVERGAAAVVYEAAGFTWPAQIDVPHLAVT 82

Query: 97  DIRAALGQIAHGWRVQ--RQIPVIGVTGSNGKTTVKEMIAAILAAAFGED--GYLGTRGN 152
           D+++  G+IA  W  Q  + +  + VTG+NGKT+    +   L+   G    G +GT G 
Sbjct: 83  DLKSHAGEIAASWYGQPDQGMLTVAVTGTNGKTSCAYWLGIALSRLAGASTAGVIGTLGV 142

Query: 153 FNNEIGVP-----------------LTLFRLRAQHQAAVIEMGMNHPGEIAVLSRIAAPT 195
            +   G P                  +LF+L AQ +   + +  +  G            
Sbjct: 143 GSFVNGKPQGFDVTGYTTPDAVLLQRSLFKL-AQGRVGALAIEASSIGLAQGRMNGMHVD 201

Query: 196 LGLVNNAQREHQEF---MASVEAVARENGAVIRHLPADGVAVFPADDDFTALWREEAGAR 252
           + L+ N  R+H +F   M + E   R+    +   P    AV   DDD           R
Sbjct: 202 VALLTNFTRDHLDFHGDMQTYEDAKRK----LFQWPGLKHAVVNLDDDMGQRLLPLLAER 257

Query: 253 RVLTFGLNAQADVSA-------SYQATAFGSTLQVTVKGLAVPPAQFKVELAAVGEHNVR 305
           +V   G  A AD          + +A+   S+   TV  +  P    +V+   VG  NV 
Sbjct: 258 KVPVIGY-AIADEQGGDPHGVPTLRASQLRSSHTGTVFHVDSPFGSGQVKTQLVGRFNVS 316

Query: 306 NALAAAACALGAGIPVDAVVRGLQSFAPVNGRLQRKQARSGALVIDDTYNANPDSVRAAI 365
           N L      L  G+  DAVV    + +P  GR+Q+       L++ D Y   PD++   +
Sbjct: 317 NVLGIMGVLLTQGVAWDAVVAAAAALSPAPGRMQQFGGPDVPLIVID-YAHTPDALDKTL 375

Query: 366 DVLASIAGPRVLVLGDM-GEVGDQGPQFHAEIGAYA 400
             L  +A  R   L  + G  GD+ P    ++G  A
Sbjct: 376 STLRQLATQRGGQLWCVFGCGGDRDPGKRPQMGQIA 411


  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    0.134    0.384 

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: 1,513,501
Number of extensions: 64066
Number of successful extensions: 276
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 273
Number of HSP's successfully gapped: 3
Length of query: 486
Length of database: 1,619,870
Length adjustment: 89
Effective length of query: 397
Effective length of database: 1,198,455
Effective search space: 475786635
Effective search space used: 475786635
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)