GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Limnohabitans curvus MWH-C5

Align NAD-dependent succinate semialdehyde dehydrogenase (EC 1.2.1.24) (characterized)
to candidate WP_108401587.1 B9Z44_RS02185 2-hydroxy-3-oxopropionate reductase

Query= metacyc::MONOMER-15565
         (287 letters)



>NCBI__GCF_003063475.1:WP_108401587.1
          Length = 292

 Score =  144 bits (364), Expect = 2e-39
 Identities = 92/283 (32%), Positives = 148/283 (52%), Gaps = 3/283 (1%)

Query: 3   EIGFLGIGIMGKAMAVNLLRHGFKVTVWNRTLSRCDELVQHGASVGETPAEVIKKCKYTI 62
           +IGF+G+GIMG  MA +LL  G ++ V  RT S+  E +   A V  T A+V +      
Sbjct: 2   KIGFIGLGIMGTPMAQHLLTAGHEMFV--RTRSKVPEALS-AAQVCATNADVARHADIIF 58

Query: 63  AMLSDPAAALSVVFDKHGALEHICAGKGYIDMSTVDADTSSQISQAITSKGGSFLEAPVS 122
            ML D     +V+F K G  E +  GK  +DMS++    +   +Q I + G  +L+APVS
Sbjct: 59  LMLPDTPDVDAVLFGKDGVAEGLSQGKIVVDMSSISPMDTKTFAQKINALGCEYLDAPVS 118

Query: 123 GSKKPAEDGQLVILAAGDKDLYDQVVPAFDVLGKKSFFLGKIGNGAKMKLVVNMIMGSMM 182
           G +  A+   L I+  G +  ++ V P F+++GK    +G  G+G   K+   +I+   +
Sbjct: 119 GGEVGAKAASLTIMVGGSETTFNTVKPLFELMGKNITLVGGNGDGQTTKVANQIIVALNI 178

Query: 183 NAFSEGIVLADKSGLDPHTLLDVLDLGAIANPMFKMKGPAMIKNSYPPAFPLKHQQKDMR 242
            A  E ++ A K+G DP  +   L  G  ++ + ++ G  MIK ++ P F +   QKD+ 
Sbjct: 179 AAVGEALLFASKAGADPAKVRAALMGGFASSRILEVHGERMIKRTFDPGFRIALHQKDLA 238

Query: 243 LALALGDENAVPMPVAAAANEAFKKARSLGLGDLDFSAVFETL 285
           LAL       V +P  A+A +  +   S G G LD SA+ ++L
Sbjct: 239 LALNGAKAIGVSLPQTASAAQLMQACASNGWGQLDHSALVKSL 281


Lambda     K      H
   0.318    0.135    0.384 

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: 180
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: 287
Length of database: 292
Length adjustment: 26
Effective length of query: 261
Effective length of database: 266
Effective search space:    69426
Effective search space used:    69426
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)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory