GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garR in Pseudomonas fluorescens FW300-N2C3

Align tartronate semialdehyde reductase 2 (characterized)
to candidate AO356_19610 AO356_19610 2-hydroxy-3-oxopropionate reductase

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_19610
          Length = 296

 Score =  373 bits (958), Expect = e-108
 Identities = 189/291 (64%), Positives = 230/291 (79%), Gaps = 1/291 (0%)

Query: 2   KLGFIGLGIMGTPMAINLARAGHQLHVTTIGPVAD-ELLSLGAVSVETARQVTEASDIIF 60
           K+GFIG GIMG PMA+NL +AGH L ++     A  +LL+ GAV++   ++V + ++ I 
Sbjct: 3   KIGFIGTGIMGHPMALNLQKAGHSLFLSQHHDAAPADLLAGGAVALANPKEVAQEAEFII 62

Query: 61  IMVPDTPQVEEVLFGENGCTKASLKGKTIVDMSSISPIETKRFARQVNELGGDYLDAPVS 120
           +MVPDTPQVE+VL   +G       GK ++DMSSISP  TK FA ++NE G  YLDAPVS
Sbjct: 63  VMVPDTPQVEDVLLRADGIAAGVGAGKVVIDMSSISPTATKAFAAKINEKGAQYLDAPVS 122

Query: 121 GGEIGAREGTLSIMVGGDEAVFERVKPLFELLGKNITLVGGNGDGQTCKVANQIIVALNI 180
           GGE+GA+  TLSIMVGGD A FER  PLF+ +GKNITLVGGNGDGQT KVANQIIVALNI
Sbjct: 123 GGEVGAKAATLSIMVGGDSAAFERALPLFQAMGKNITLVGGNGDGQTAKVANQIIVALNI 182

Query: 181 EAVSEALLFASKAGADPVRVRQALMGGFASSRILEVHGERMIKRTFNPGFKIALHQKDLN 240
           +AV+EALLFA+K GADP +VR+ALMGGFASS+ILEVHGERMIK TF+PGF+I+LHQKDLN
Sbjct: 183 QAVAEALLFAAKNGADPAKVREALMGGFASSKILEVHGERMIKGTFDPGFRISLHQKDLN 242

Query: 241 LALQSAKALALNLPNTATCQELFNTCAANGGSQLDHSALVQALELMANHKL 291
           LALQ AK L +NLPNTA  Q++F+TCAA GGS  DHSAL++ LE MAN  +
Sbjct: 243 LALQGAKELNINLPNTANAQQVFSTCAAIGGSHWDHSALIKGLEHMANFSI 293


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: 326
Number of extensions: 5
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: 296
Length adjustment: 26
Effective length of query: 266
Effective length of database: 270
Effective search space:    71820
Effective search space used:    71820
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 AO356_19610 AO356_19610 (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.7299.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.7299.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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