GapMind for catabolism of small carbon sources

 

Alignments for a candidate for D-LDH in Shewanella loihica PV-4

Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate 5208375 Shew_0887 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding (RefSeq)

Query= BRENDA::F8A9V0
         (325 letters)



>FitnessBrowser__PV4:5208375
          Length = 317

 Score =  144 bits (364), Expect = 2e-39
 Identities = 102/283 (36%), Positives = 146/283 (51%), Gaps = 27/283 (9%)

Query: 38  VEKAKGAQVVSLFVSDKADGPVLEALHSYG-VGLLALRSAGYDHIDIETAKRLGIKVVNV 96
           +++A+GAQV+ L      D   L AL     +G+LA    G + +D+  A+ LGIKV NV
Sbjct: 39  LDRAQGAQVL-LTNKTVLDADALRALPDLEYIGVLA---TGTNVVDLNAARELGIKVTNV 94

Query: 97  PAYSPHAIADHTLAIMLALIRRLHRAHDKVRLG------DFDLDGLMGFDLNGKVAGVIG 150
           P Y P A+A    A +L   +RL   H+ V  G      DF         L GK  G++G
Sbjct: 95  PGYGPDAVAQMVFAHILHHTQRLSDHHNAVVAGAWSQAPDFCFTLAPLQSLKGKTLGLVG 154

Query: 151 LGKIGRLVATRLKAFGCKVLGYDPYIQPEIVENV---DLDTLITQADIISIHCPLTRENF 207
            G IGR VA   KAF  +VL   P I+ ++ E V   + + L   ADIIS+HCPLT +  
Sbjct: 155 FGDIGRQVANIAKAFQMRVLVNTPSIKHDLPEGVSWCEREALFASADIISLHCPLTPDTE 214

Query: 208 HMFNEETFKRMKPGAILVNTARGGLIDTKALLEALKSGKLGGAALDVYEYERGLFFKNHQ 267
            + N E    MKP AIL+NTARGGL+D +AL  AL  G++  A +DV   E         
Sbjct: 215 KLINRERLSAMKPNAILINTARGGLVDEQALANALAQGEIAAAGVDVLSSE--------- 265

Query: 268 KEGIKDPYLAQLLGLANVVLTGHQAFLTREAVKNIEETTVENI 310
                +P    LL   ++ ++ H ++ T+EA + +    V+N+
Sbjct: 266 PPQADNP----LLSAPHISISPHNSWATKEARQQLLTIAVDNL 304


Lambda     K      H
   0.321    0.140    0.407 

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: 244
Number of extensions: 10
Number of successful extensions: 4
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: 325
Length of database: 317
Length adjustment: 28
Effective length of query: 297
Effective length of database: 289
Effective search space:    85833
Effective search space used:    85833
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 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