GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garR in Paraburkholderia bryophila 376MFSha3.1

Align tartronate semialdehyde reductase 2 (characterized)
to candidate H281DRAFT_00785 H281DRAFT_00785 2-hydroxy-3-oxopropionate reductase

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



>FitnessBrowser__Burk376:H281DRAFT_00785
          Length = 302

 Score =  377 bits (968), Expect = e-109
 Identities = 193/292 (66%), Positives = 233/292 (79%), Gaps = 3/292 (1%)

Query: 2   KLGFIGLGIMGTPMAINLARAGHQLHVTTIGPVADEL-LSLGAVSVETARQVTEASDIIF 60
           K+GFIGLGIMG  MA NL + GH L V    PV ++L  S   VS  TA  V +A+DI+ 
Sbjct: 3   KIGFIGLGIMGAHMARNLLKGGHTLFVNGAYPVPEDLGKSTNVVSDSTA--VAQAADIVI 60

Query: 61  IMVPDTPQVEEVLFGENGCTKASLKGKTIVDMSSISPIETKRFARQVNELGGDYLDAPVS 120
           IMVPDTP V  VLF ++G       GK ++DMSSISP++T+ FA+++N LG DYLDAPVS
Sbjct: 61  IMVPDTPDVANVLFADDGVAAGLTAGKLVIDMSSISPLDTQAFAKKINALGVDYLDAPVS 120

Query: 121 GGEIGAREGTLSIMVGGDEAVFERVKPLFELLGKNITLVGGNGDGQTCKVANQIIVALNI 180
           GGE+GARE TL+IMVGG E  F + KPLFEL+GKNI+L+G NG GQTCKVANQIIVALNI
Sbjct: 121 GGEVGAREATLTIMVGGPEKAFAQAKPLFELMGKNISLIGDNGAGQTCKVANQIIVALNI 180

Query: 181 EAVSEALLFASKAGADPVRVRQALMGGFASSRILEVHGERMIKRTFNPGFKIALHQKDLN 240
           EAV+EALLFAS++GADP RVR+ALMGGFASSRILEVHGERM KRTFNPGF+I LHQKDLN
Sbjct: 181 EAVAEALLFASRSGADPERVRKALMGGFASSRILEVHGERMTKRTFNPGFRIELHQKDLN 240

Query: 241 LALQSAKALALNLPNTATCQELFNTCAANGGSQLDHSALVQALELMANHKLA 292
           LAL  A+ L + LP+TA+ Q+LF+ CAANGG   DHSA+V+ALE+MAN+++A
Sbjct: 241 LALDGARKLGIALPHTASAQQLFSVCAANGGKAWDHSAMVRALEIMANYEVA 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: 322
Number of extensions: 6
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 H281DRAFT_00785 H281DRAFT_00785 (2-hydroxy-3-oxopropionate reductase)
to HMM TIGR01505 (2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60))

Software error:

../bin/blast/fastacmd -i /tmp/list.11111.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.11111.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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