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= 0001.0307.p
         (700 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309676|ref|YP_003773768.1| UDP-N-acetylmuramoylalanine-D-g...  1030   0.0  

>gi|300309676|ref|YP_003773768.1|
           UDP-N-acetylmuramoylalanine-D-glutamate ligase
           [Herbaspirillum seropedicae SmR1]
          Length = 710

 Score = 1030 bits (2664), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 615/712 (86%), Positives = 641/712 (90%), Gaps = 16/712 (2%)

Query: 1   MNYSGKHVLVLGLGESGLAMARWLVYCGASVRVADTRSEAALAERLAALRADAPEAQAVL 60
           MNYSGKHVLVLGLGESGLAMARWLVYCGASVRVADTR EAALAERLAALRADAPEAQAVL
Sbjct: 1   MNYSGKHVLVLGLGESGLAMARWLVYCGASVRVADTRGEAALAERLAALRADAPEAQAVL 60

Query: 61  GQPLAAALLDGIDFVAVSPGLAPEGELAPLMPVIAERGLPLWGEIELFAQALLALREETL 120
           GQPL+ ALL+G+DFVAVSPGLAPEGELAPLMP IAER LPLWGEIELFAQAL+ALREETL
Sbjct: 61  GQPLSPALLEGVDFVAVSPGLAPEGELAPLMPAIAERSLPLWGEIELFAQALVALREETL 120

Query: 121 YQPKVLAITGTNGKTTVTRLTGLLCQRAGLSVQVAGNISPAALDVLREAVIKDQVFLAEL 180
           YQPKVLAITGTNGKTTVTRLTGLLCQRAGLSVQVAGNISPAALDVLREAVI+D+VFLAEL
Sbjct: 121 YQPKVLAITGTNGKTTVTRLTGLLCQRAGLSVQVAGNISPAALDVLREAVIRDKVFLAEL 180

Query: 181 AEQDALAAAQAQAEAEAQAAQQAVLDAQQAAEAEKHRRAAARIEEAAAIAVPVMAQQAAP 240
           AEQDALAAAQA AEAEAQAAQQAVLDAQQ AEAEKHRRAAARIEEAA+IAVPV+  Q+ P
Sbjct: 181 AEQDALAAAQAAAEAEAQAAQQAVLDAQQEAEAEKHRRAAARIEEAASIAVPVL--QSHP 238

Query: 241 SAPPEQPES------QLDLL-APTVDGQEPEDGQP-ATDAPADSAEAASEAQAEAG---- 288
            AP    ES      QLDLL A    G+  +D QP A D    +AEAAS+  A A     
Sbjct: 239 VAPASLSESEQETAAQLDLLDAADASGEHAQDHQPPAADVSPSAAEAASQVDASAADEPD 298

Query: 289 -SEAVAEAEVGNSANEDFVTSTVEATLQVASDVVPQADPDAPATTGEAMSLGDFMEVSRK 347
            SE VA  E    A +    +   ATL VASDVVPQA PDAPATTGEAM+LGDFMEVSRK
Sbjct: 299 TSERVATDEADAVAQD-ASAAAAAATLDVASDVVPQAQPDAPATTGEAMNLGDFMEVSRK 357

Query: 348 AEEEALVEVPPPPPPEPTYRGSMPQAWVLELSSFQLHTTHSLQAHAATVLNLTQDHLDWH 407
           AEE+ALVEVPPPPPPEPTYRGSMPQAWVLELSSFQLHTTHSLQA AATVLNLTQDHLDWH
Sbjct: 358 AEEDALVEVPPPPPPEPTYRGSMPQAWVLELSSFQLHTTHSLQADAATVLNLTQDHLDWH 417

Query: 408 GSMEHYAADKARIFGQDTVRVLNRDDALVMEMASTAAPLSTFGLDEPDTPNSFGLVNDNG 467
           GSMEHYAADKARIFGQ TVRVLNRDDALVM+MA+  + LSTFGLDEP  PNSFGLVNDNG
Sbjct: 418 GSMEHYAADKARIFGQHTVRVLNRDDALVMQMAAAGSALSTFGLDEPTAPNSFGLVNDNG 477

Query: 468 MLWLANAFVHEDDEVPEGKRRRKQKDMLPPPVTVKRLMPADALKIRGAHNAMNALAALAL 527
           MLWLANAFVHEDDEVPEGKRRRKQKDMLPPPVT+KRLMPADALKIRGAHNAMNALAALAL
Sbjct: 478 MLWLANAFVHEDDEVPEGKRRRKQKDMLPPPVTLKRLMPADALKIRGAHNAMNALAALAL 537

Query: 528 CRAIDLPMAPLLHGLREYTGEPHRVELVGVIQEVEYYDDSKGTNVGATVAALNGLGLGGR 587
           CRAIDLPMAPLLHGLR+YTGEPHRVELVGVIQEV+YYDDSKGTNVGATVAALNGLGLGGR
Sbjct: 538 CRAIDLPMAPLLHGLRDYTGEPHRVELVGVIQEVDYYDDSKGTNVGATVAALNGLGLGGR 597

Query: 588 PNRIVLIAGGDGKGQDFSPLDLPVQKYARAVLLIGRDAPAVRTALADSGVELIDCASLEQ 647
           PNRIVLIAGGDGKGQDFSPLDLPVQKYARAVLLIGRDAPA+R ALADSGVELIDCASLE 
Sbjct: 598 PNRIVLIAGGDGKGQDFSPLDLPVQKYARAVLLIGRDAPAIRAALADSGVELIDCASLEA 657

Query: 648 AVEQAGQIAKAGDIVLLSPACASLDMFRNYAHRAEVFVDAVHELALSRGEVL 699
           AVE+AG+IA AGDIVLLSPACASLDMFRNYAHRAEVFVDAV ELALSRGEVL
Sbjct: 658 AVEKAGEIATAGDIVLLSPACASLDMFRNYAHRAEVFVDAVRELALSRGEVL 709


  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
   0.315    0.130    0.367 

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: 1,724,263
Number of extensions: 62953
Number of successful extensions: 315
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 314
Number of HSP's successfully gapped: 1
Length of query: 700
Length of database: 1,619,870
Length adjustment: 92
Effective length of query: 608
Effective length of database: 1,184,250
Effective search space: 720024000
Effective search space used: 720024000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 bits)
S2: 134 (56.2 bits)