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= 0020.0147.p
         (485 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...   962   0.0  
gi|300309673|ref|YP_003773765.1| UDP-N-acetylmuramoylalanyl-D-gl...    68   2e-12

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

 Score =  962 bits (2487), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 482/485 (99%), Positives = 482/485 (99%)

Query: 1   MRFDFRQMLEWLRTAEAAASAHTVPGVVNAPAGLLALNDVVTDSRAVKPGNVFVALRGER 60
           MRFDFRQMLEWLRTAEAAASAHTVPGVVNAPAGLLALNDVVTDSRAVKPGNVFVALRGER
Sbjct: 2   MRFDFRQMLEWLRTAEAAASAHTVPGVVNAPAGLLALNDVVTDSRAVKPGNVFVALRGER 61

Query: 61  FDAHDFLDAVAGQGAAAVVVERVPPGLALPAIVVPDTRAALGQIAHGWRMQRQIPVIGVT 120
           FDAHDFLDAVA QGAAAVVVERVPPGLALPAIVVPDTRAALGQIAHGWRMQRQIPVIGVT
Sbjct: 62  FDAHDFLDAVADQGAAAVVVERVPPGLALPAIVVPDTRAALGQIAHGWRMQRQIPVIGVT 121

Query: 121 GSNGKTTVKEMIAAILAAAFGEEGYLGTRGNFNNEIGVPLTLFRLRAQHQAAVIEMGMNH 180
           GSNGKTTVKEMIA ILAAAFGEEGYLGTRGNFNNEIGVPLTLFRLRAQHQAAVIEMGMNH
Sbjct: 122 GSNGKTTVKEMIATILAAAFGEEGYLGTRGNFNNEIGVPLTLFRLRAQHQAAVIEMGMNH 181

Query: 181 PGEIAVLSRIAAPTLGLVNNAQREHQEFMATVEAVARENGAVIRHLPADGVAVFPADDDF 240
           PGEIAVLSRIAAPTLGLVNNAQREHQEFMATVEAVARENGAVIRHLPADGVAVFPADDDF
Sbjct: 182 PGEIAVLSRIAAPTLGLVNNAQREHQEFMATVEAVARENGAVIRHLPADGVAVFPADDDF 241

Query: 241 TPLWREEAGARRVLSFGLSAQADVSASYQATAFGSTLQVTVKGLAVPPAQFKVELAAVGE 300
           TPLWREEAGARRVLSFGLSAQADVSASYQATAFGSTLQV VKGLAVPPAQFKVELAAVGE
Sbjct: 242 TPLWREEAGARRVLSFGLSAQADVSASYQATAFGSTLQVAVKGLAVPPAQFKVELAAVGE 301

Query: 301 HNVRNALAAAACALGAGIAIEAVVRGLESFAPVNGRLQRKEARSGALVIDDTYNANPDSV 360
           HNVRNALAAAACALGAGIAIEAVVRGLESFAPVNGRLQRKEARSGALVIDDTYNANPDSV
Sbjct: 302 HNVRNALAAAACALGAGIAIEAVVRGLESFAPVNGRLQRKEARSGALVIDDTYNANPDSV 361

Query: 361 RAAIDVLAAIAGPRVLVLGDMGEVGDQGPQFHAEIGAYARSRGIPLFFGLGELTKHAVTA 420
           RAAIDVLAAIAGPRVLVLGDMGEVGDQGPQFHAEIGAYARSRGIPLFFGLGELTKHAVTA
Sbjct: 362 RAAIDVLAAIAGPRVLVLGDMGEVGDQGPQFHAEIGAYARSRGIPLFFGLGELTKHAVTA 421

Query: 421 YGATPQGVAQALHFDDIAALNAAVEQAAPQGATVLVKGSRFMKMERVVQHLVNVESPTQH 480
           YGATPQGVAQALHFDDIAALNAAVEQAAPQGATVLVKGSRFMKMERVVQHLVNVESPTQH
Sbjct: 422 YGATPQGVAQALHFDDIAALNAAVEQAAPQGATVLVKGSRFMKMERVVQHLVNVESPTQH 481

Query: 481 QQETH 485
           QQETH
Sbjct: 482 QQETH 486


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

 Score = 67.8 bits (164), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 109/400 (27%), Positives = 167/400 (41%), Gaps = 52/400 (13%)

Query: 40  VVTDSRAVKPGNVFVALRGERFDAHDFLDAVAGQGAAAVVVE----RVPPGLALPAIVVP 95
           + +DSR V PG+VF A  G+  D   ++     +GAAAVV E      P  + +P + V 
Sbjct: 24  LTSDSRRVAPGDVFFAYVGDA-DGRSYIADAVERGAAAVVYEAAGFTWPAQIDVPHLAVT 82

Query: 96  DTRAALGQIAHGWRMQ--RQIPVIGVTGSNGKTTVKEMIAAILAAAFGEE--GYLGTRGN 151
           D ++  G+IA  W  Q  + +  + VTG+NGKT+    +   L+   G    G +GT G 
Sbjct: 83  DLKSHAGEIAASWYGQPDQGMLTVAVTGTNGKTSCAYWLGIALSRLAGASTAGVIGTLGV 142

Query: 152 FNNEIGVP-----------------LTLFRLRAQHQAAVIEMGMNHPGEIAVLSRIAAPT 194
            +   G P                  +LF+L AQ +   + +  +  G            
Sbjct: 143 GSFVNGKPQGFDVTGYTTPDAVLLQRSLFKL-AQGRVGALAIEASSIGLAQGRMNGMHVD 201

Query: 195 LGLVNNAQREHQEF---MATVEAVARENGAVIRHLPADGVAVFPADDD----FTPLWREE 247
           + L+ N  R+H +F   M T E   R+    +   P    AV   DDD      PL  E 
Sbjct: 202 VALLTNFTRDHLDFHGDMQTYEDAKRK----LFQWPGLKHAVVNLDDDMGQRLLPLLAE- 256

Query: 248 AGARRVLSFGLSAQADVSA-------SYQATAFGSTLQVTVKGLAVPPAQFKVELAAVGE 300
              R+V   G  A AD          + +A+   S+   TV  +  P    +V+   VG 
Sbjct: 257 ---RKVPVIGY-AIADEQGGDPHGVPTLRASQLRSSHTGTVFHVDSPFGSGQVKTQLVGR 312

Query: 301 HNVRNALAAAACALGAGIAIEAVVRGLESFAPVNGRLQRKEARSGALVIDDTYNANPDSV 360
            NV N L      L  G+A +AVV    + +P  GR+Q+       L++ D Y   PD++
Sbjct: 313 FNVSNVLGIMGVLLTQGVAWDAVVAAAAALSPAPGRMQQFGGPDVPLIVID-YAHTPDAL 371

Query: 361 RAAIDVLAAIAGPRVLVLGDM-GEVGDQGPQFHAEIGAYA 399
              +  L  +A  R   L  + G  GD+ P    ++G  A
Sbjct: 372 DKTLSTLRQLATQRGGQLWCVFGCGGDRDPGKRPQMGQIA 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
   0.319    0.133    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: 1,529,166
Number of extensions: 65411
Number of successful extensions: 264
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 262
Number of HSP's successfully gapped: 3
Length of query: 485
Length of database: 1,619,870
Length adjustment: 89
Effective length of query: 396
Effective length of database: 1,198,455
Effective search space: 474588180
Effective search space used: 474588180
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)