Alignments for a candidate for D-LDH in Chromobacterium vaccinii MWU205

GapMind for catabolism of small carbon sources

Alignments for a candidate for D-LDH in Chromobacterium vaccinii MWU205

Align Respiratory FAD-dependent D-lactate dehydrogenase Dld; EC 1.1.2.4 (characterized, see rationale)
to candidate WP_046158449.1 VL52_RS18670 FAD-binding oxidoreductase

Query= uniprot:Q8EGS3
         (934 letters)



>NCBI__GCF_000971335.1:WP_046158449.1
          Length = 938

 Score =  733 bits (1893), Expect = 0.0
 Identities = 398/937 (42%), Positives = 564/937 (60%), Gaps = 29/937 (3%)

Query: 11  DLRTQLGDRPVTDDPVRRFAWSTDASYFRIVPEVVVHAETLEQVKLTLTVARKHNAPVTF 70
           DLR  + D+ +  DP+   A+ TDAS++R+ P++V   E+ ++V   L +AR H   VTF
Sbjct: 11  DLRRVMPDKRIYTDPLSTLAYGTDASFYRLRPQIVARVESEDEVAELLRLARLHRVAVTF 70

Query: 71  RAAGTSLSGQAIGEGILLILGHDGFRKIEVSSDAKQITLGAAVIGSDANAVLAPLNRKIG 130
           RAAGTSLSGQA+ + +L++LG DGF + EV     +I L   +IG+ ANA+LAP  RKIG
Sbjct: 71  RAAGTSLSGQAVSDSVLVLLG-DGFNRGEVLDGGARIRLAPGMIGAHANAMLAPYGRKIG 129

Query: 131 PDPATIASAKIGGIVANNASGMCCGTAQNSYQTIASAKLLFADGTELDTGCEKSKAEFAK 190
           PDPA+I +AKIGGI ANN+SGMCCGT  NSY T+ + +LL  DGT LDT    S A F +
Sbjct: 130 PDPASINTAKIGGIAANNSSGMCCGTRDNSYHTLQAIRLLLLDGTVLDTADPVSVAAFRE 189

Query: 191 THGKLLQDLSELSHLTRHNSALAERIRKKYSIKNTTGYGINSLIDFTDPFDIINHLMVGM 250
           +H  LL  L +LS     +  LAER+R+KY +KNTTGYGIN+L+DF DP ++++HLM+G 
Sbjct: 190 SHADLLDGLVQLSRQLAGDPQLAERVRRKYRLKNTTGYGINALLDFADPLEMLSHLMIGS 249

Query: 251 EGTLAFINEVTYHTVNEAKFKASAMAVFHNMEDAARAIPLINGE----SVSAAELLDWPS 306
           EGTL FI+E+T+HTV E   KASA+ +F ++E   RA+  ++       VSA EL+D  S
Sbjct: 250 EGTLGFISEITFHTVAEHPHKASALVLFDDLERCCRAVSALSAARDACGVSAVELIDSRS 309

Query: 307 IKAVTGKPGMPDWLSE-LPALSAILLIESRADDAQTLEHYTQDVTAKLAGFDFIRPMEFS 365
           I+AV GKPG+PD+L + +   S  LLIE RA D   L   +  +   LA +       FS
Sbjct: 310 IRAVQGKPGLPDFLYQPVGPGSTCLLIELRAGDEARLGEDSAAIERLLADYQPQVSSGFS 369

Query: 366 TNPAVYDKYWAMRKGLFPIVGGERPKGTSVIIEDVAFELEHLAAAAHDITELFHKHGYPE 425
            +    + YWA+RKGLFP VG  RP GT+V+IEDVAF +  LA     +T LF +HGY E
Sbjct: 370 RDARECETYWALRKGLFPAVGAARPVGTTVVIEDVAFPILQLADGVAKLTALFDRHGYDE 429

Query: 426 GCIYGHALAGNFHFIITPAFTTQADIDRFHAFMDDIADMVINKYNGSMKAEHGTGRAVAP 485
             ++GHAL GN HF+  P F + A++DR+ AFM D++D+V  +Y+GS+KAEHGTGR VAP
Sbjct: 430 ALLFGHALDGNLHFVFAPGFESPAEVDRYEAFMQDVSDLVAGEYDGSLKAEHGTGRNVAP 489

Query: 486 FVEKEWGQDAYTLMKNIKQVFDPQGILNPGVILNDDSNIHVKNIKPCPVVDDFVDKCIEC 545
           FV +EWG  A+ +M+ IK +FDP+G+LNPGVI+ D+  +H++N+KP P  DD VD+C EC
Sbjct: 490 FVRQEWGAAAWNIMRRIKALFDPEGLLNPGVIITDNDRLHLENLKPMPAADDLVDRCTEC 549

Query: 546 GFCEKTCPTSALNFSPRQRIATLREIERLEQSGDKA-AAAKMRADAKYDVIDTCAACQLC 604
           GFCE  CP+  L  SPRQRI   R I +LE+ G+ A   A +++  +Y  +DTCAA  +C
Sbjct: 550 GFCEPACPSHGLTLSPRQRIVAWRRIRQLEREGEGAMELAALKSGYRYRAVDTCAATGMC 609

Query: 605 TIACPVDNSMGQLVRKLRTPYISTTEQKVLDFQAKHFGAVNQVISTGFDVLGVIHKITGD 664
              CPV  + G L++KL  P   +    +  F A+H G +     TG   L + H +TG 
Sbjct: 610 ATRCPVGINTGLLMKKLHGP---SRRPALAGFAARHMGWMTAAARTG---LRLAH-LTGA 662

Query: 665 GITNALMKTGRLISKEVPYWNPDFPKGGKLPKPSPAKAGQ-ETVVYFPACGGRTFGPTPK 723
              N L +      K +P      P+      P P   G+ E VV F +C  R      +
Sbjct: 663 RRLNQLTRRQPGERKVIPLIPASLPRAA---APLPKLGGEGEPVVLFVSCVNRALA---E 716

Query: 724 DPDNRTLPEVVVTLLERAGYNVITPEKTRDLCCGQMWESKGDFKNADAKRQELIDVLSKM 783
                ++    + LL RAG+  I P     LCCGQ + S          +  L + L + 
Sbjct: 717 GEGGESVAAHTINLLRRAGFAPIYPPGHDGLCCGQPFASANAVDALAFSQASLNEALLRA 776

Query: 784 SNGGKIPVLVDALSCTYRTLTG------NPQVQITDLVEFMHDKLLDKLSINKKV-NVAL 836
           S  G+ PV +D   C  R          +P++Q+ D   F+ +K+L +LSI +++  +AL
Sbjct: 777 SGDGRHPVYLDNSPCAARVKQAQAEGLLDPRLQLFDAAGFLAEKVLPRLSIVRRLPQLAL 836

Query: 837 HLGCSARKMKLEPKMQAIANACSAQVLKPAGIECCGYAGEKGLYKPEINASALRNIKKLI 896
           H+ CSA  M     ++ +A +C  ++  P  I CCG+AG+KG   PE+NA +LR +K  +
Sbjct: 837 HIPCSATAMGAAGSLKQLAASCCDKLTVP-DIACCGFAGDKGFTVPELNAHSLRRLKPAL 895

Query: 897 PVEVKEGYYANRMCEVGLTQHSGISYRHLAYLLEECS 933
           P   + G   +R C++GLT+H GI Y  +  LL+ C+
Sbjct: 896 PDACRHGVSMSRTCQIGLTEHGGIPYASIEALLDFCT 932


Lambda     K      H
   0.319    0.135    0.402 

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: 2042
Number of extensions: 87
Number of successful extensions: 10
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: 934
Length of database: 938
Length adjustment: 43
Effective length of query: 891
Effective length of database: 895
Effective search space:   797445
Effective search space used:   797445
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 (21.7 bits)
S2: 57 (26.6 bits)

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources