GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garR in Burkholderia phytofirmans PsJN

Align tartronate semialdehyde reductase 2 (characterized)
to candidate BPHYT_RS08825 BPHYT_RS08825 tartronate semialdehyde reductase

Query= ecocyc::G6278-MONOMER
         (292 letters)



>FitnessBrowser__BFirm:BPHYT_RS08825
          Length = 302

 Score =  370 bits (950), Expect = e-107
 Identities = 187/291 (64%), Positives = 230/291 (79%), Gaps = 1/291 (0%)

Query: 2   KLGFIGLGIMGTPMAINLARAGHQLHVTTIGPVADELLSLGAVSVETARQVTEASDIIFI 61
           K+GFIGLGIMG  MA NL + GH L V    PV ++L    +V V  +  V +A+DI+ I
Sbjct: 3   KIGFIGLGIMGAHMARNLIKGGHSLFVNGAYPVPEDLSKTTSV-VANSTAVAQAADIVII 61

Query: 62  MVPDTPQVEEVLFGENGCTKASLKGKTIVDMSSISPIETKRFARQVNELGGDYLDAPVSG 121
           MVPDTP V  VLF ++G      KGK ++DMSSISP++T+ FA+++N LG DYLDAPVSG
Sbjct: 62  MVPDTPDVANVLFADDGVAAGLSKGKLVIDMSSISPLDTQAFAKKINALGVDYLDAPVSG 121

Query: 122 GEIGAREGTLSIMVGGDEAVFERVKPLFELLGKNITLVGGNGDGQTCKVANQIIVALNIE 181
           GE+GARE +L+IMVGG E  F   KPLFEL+GKNI+L+G NG GQTCKVANQIIVALNIE
Sbjct: 122 GEVGAREASLTIMVGGPEKAFATAKPLFELMGKNISLIGENGAGQTCKVANQIIVALNIE 181

Query: 182 AVSEALLFASKAGADPVRVRQALMGGFASSRILEVHGERMIKRTFNPGFKIALHQKDLNL 241
           AV+EALLFA+++GADP RVR+ALMGGFASSRILEVHGERM KR F+PGF+I LHQKDLNL
Sbjct: 182 AVAEALLFAARSGADPERVRKALMGGFASSRILEVHGERMTKRKFDPGFRIELHQKDLNL 241

Query: 242 ALQSAKALALNLPNTATCQELFNTCAANGGSQLDHSALVQALELMANHKLA 292
           AL  A+ L + LP+TA+ Q+LF+ CAANGG   DHSA+V+ALE+MAN ++A
Sbjct: 242 ALDGARKLGIALPHTASAQQLFSVCAANGGKAWDHSAMVRALEIMANFEVA 292


Lambda     K      H
   0.318    0.135    0.376 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 328
Number of extensions: 8
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 292
Length of database: 302
Length adjustment: 26
Effective length of query: 266
Effective length of database: 276
Effective search space:    73416
Effective search space used:    73416
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 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate BPHYT_RS08825 BPHYT_RS08825 (tartronate semialdehyde reductase)
to HMM TIGR01505 (2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60))

Software error:

../bin/blast/fastacmd -i /tmp/list.13183.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.13183.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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