GapMind for catabolism of small carbon sources

 

Alignments for a candidate for D-LDH in Pseudomonas simiae WCS417

Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate GFF5281 PS417_27040 3-phosphoglycerate dehydrogenase

Query= BRENDA::A0A0M3KL04
         (335 letters)



>FitnessBrowser__WCS417:GFF5281
          Length = 409

 Score =  129 bits (324), Expect = 1e-34
 Identities = 91/252 (36%), Positives = 135/252 (53%), Gaps = 11/252 (4%)

Query: 79  GYDMIDLEQASERGLVVTNVPAYSPNSVAELALTQTMRLIRNLPLFDARGAEQDFRWAGL 138
           G + +DL  A ERG+ V N P  +  SVAEL L + + L+R +P  +A      +  +  
Sbjct: 85  GTNQVDLNAARERGIAVFNAPYSNTRSVAELVLAEAILLLRGIPEKNASCHRGGWIKSAA 144

Query: 139 MAREIRSLTVGIIGAGRIGGTVARLFKALGATVIANDIVERVELKDIVTYVSKEELLQAA 198
            + EIR   +GI+G G IG  ++ L + LG  V   D + ++ L +     S  ELL  +
Sbjct: 145 NSFEIRGKKLGIVGYGSIGTQLSVLAEGLGMQVFFYDTLTKLPLGNATQVASLTELLGMS 204

Query: 199 DVVTLHVPLMDSTTQLIDADALALMKNDAVLINASRGPVVDTDALIAALQNKQIAGAALD 258
           D+VTLHVP    T  +I    +  +K   +LINA+RG VV+ DAL  A+++K + GAA+D
Sbjct: 205 DIVTLHVPETAETQWMIGEKEIRAIKKGGILINAARGTVVELDALADAIKDKHLIGAAID 264

Query: 259 TLNGEEHFFNQDLCGKELPSEQLKVLRTLPNVLITPHIGFYTNKAVQNM-VEISLNDVLA 317
               EE   N D+   E P      LR L NV++TPHIG  T +A  N+ +E+S   ++ 
Sbjct: 265 VF-PEEPRSNDDIF--ESP------LRGLDNVILTPHIGGSTAEAQANIGLEVS-EKLVK 314

Query: 318 ILKTGTSEHQLN 329
               GTS   +N
Sbjct: 315 YSDNGTSVSSVN 326


Lambda     K      H
   0.317    0.133    0.364 

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: 285
Number of extensions: 16
Number of successful extensions: 3
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: 335
Length of database: 409
Length adjustment: 30
Effective length of query: 305
Effective length of database: 379
Effective search space:   115595
Effective search space used:   115595
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: 49 (23.5 bits)

This GapMind analysis is from Sep 17 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