GapMind for catabolism of small carbon sources

 

Aligments for a candidate for D-LDH in Shewanella amazonensis SB2B

Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate 6938846 Sama_2949 D-3-phosphoglycerate dehydrogenase (RefSeq)

Query= BRENDA::A0A0M3KL04
         (335 letters)



>lcl|FitnessBrowser__SB2B:6938846 Sama_2949 D-3-phosphoglycerate
           dehydrogenase (RefSeq)
          Length = 409

 Score =  131 bits (330), Expect = 3e-35
 Identities = 90/229 (39%), Positives = 125/229 (54%), Gaps = 9/229 (3%)

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

Query: 139 MAREIRSLTVGIIGAGRIGGTVARLFKALGATVIANDIVERVELKDIVTYVSKEELLQAA 198
            + E+R  T+G+IG G IG  +  L + LG  V   DI +++ L +     S EELL  A
Sbjct: 145 GSVEVRGKTLGVIGYGHIGTQLGILAETLGMRVKFFDIEDKLPLGNAQQVHSFEELLANA 204

Query: 199 DVVTLHVPLMDSTTQLIDADALALMKNDAVLINASRGPVVDTDALIAALQNKQIAGAALD 258
           DVV+LHVP    T  +I    LA MK  + LINASRG VVD DAL AAL+ + IAGAA+D
Sbjct: 205 DVVSLHVPETPQTKNMIGHTELATMKKGSFLINASRGTVVDIDALSAALKEEHIAGAAID 264

Query: 259 TLNGEEHFFNQDLCGKELPSEQLKVLRTLPNVLITPHIGFYTNKAVQNM 307
               E    N D+            LR L NV++TPH+G  T +A +N+
Sbjct: 265 VFPVEPK-SNDDVFQSP--------LRGLDNVILTPHVGGSTEEAQENI 304


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: 262
Number of extensions: 12
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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