Alignments for a candidate for gadh1 in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for gadh1 in Burkholderia phytofirmans PsJN

Align gluconate 2-dehydrogenase (EC 1.1.1.215) (characterized)
to candidate BPHYT_RS30780 BPHYT_RS30780 GMC family oxidoreductase

Query= BRENDA::C0LE03
         (594 letters)



>FitnessBrowser__BFirm:BPHYT_RS30780
          Length = 594

 Score =  728 bits (1878), Expect = 0.0
 Identities = 355/597 (59%), Positives = 431/597 (72%), Gaps = 6/597 (1%)

Query: 1   MATVMK-KVDAVIVGFGWTGAIMAKELTEAGLNVLALERGPMQDTYPDGNYPQVIDELTY 59
           MA + K KVDAV+VG GW+G+IMA EL +AGL V+ LERG  +DTYPD  YP+V DELT+
Sbjct: 1   MANISKPKVDAVVVGMGWSGSIMAIELADAGLTVVGLERGENRDTYPDFAYPKVADELTH 60

Query: 60  SVRKKLFQDISKETVTIRHSVNDVALPNRQLGAFLPGNGVGGAGLHWSGVHFRVDPIELR 119
             R KL Q ++ ETVTIR    +VALP RQ GAFL G+GVGG+G+HW+G  +R    EL+
Sbjct: 61  VQRFKLMQSLAHETVTIRRQAQEVALPLRQYGAFLFGDGVGGSGVHWNGFTYRATEAELK 120

Query: 120 MRSHYEERYGKNFIPKDMTIQDFGVSYEELEPFFDYAEKVFGTSGQAWTVKGQLVGDGKG 179
           +RSHYE+RYGK FIP DMTIQD+ VS  ELEPF+D  E V GTSG+A  + GQ VG   G
Sbjct: 121 LRSHYEQRYGKGFIPDDMTIQDWPVSAAELEPFYDRFEYVAGTSGKAGNLNGQSVG---G 177

Query: 180 GNPYAPDRSDHFPLESQKNTYSAQLFQKAANEVGYKPYNLPSANTSGPYTNPYGAQMGPC 239
           GNP+   RS  + L      Y + LF +AA EVGY PY  P++  S  YTNPYG Q+GPC
Sbjct: 178 GNPFEAPRSRDYALPPLPTAYPSMLFDQAAREVGYHPYPTPASIASKAYTNPYGMQLGPC 237

Query: 240 NFCGFCSGYVCYMYSKASPNVNILPALKPLPNFELRPNSHVLRVNLDSSKTRATGVTYVD 299
           NFCG+C  + CYM+SKASP   ILPAL   PNFELR  S V++VNLDS+  RATGVTY+D
Sbjct: 238 NFCGYCELFGCYMFSKASPQSCILPALARKPNFELRDRSAVVKVNLDSTGKRATGVTYID 297

Query: 300 GQGREIEQPADLVILGAFQFHNVRLMLLSGIGKPYDPITGEGVVGKNFAYQNMATIKAYF 359
            QG  +EQPAD+V L A+Q HNVRL+LLSGIGKPYDP TGEG VGKN+AYQ  + I+ +F
Sbjct: 298 AQGHTVEQPADIVALCAYQMHNVRLLLLSGIGKPYDPATGEGTVGKNYAYQKNSKIQVFF 357

Query: 360 DKDVHTNNFIGAGGNGVAVDDFNADNFDHGPHGFVGGSPMWVNQAGSRPIAGTSNPPGTP 419
           DKDV  N FIG+G  GV  DDFNADNFDHGP  F+GG+  +    G RPIA    PPGTP
Sbjct: 358 DKDVAINPFIGSGAGGVVYDDFNADNFDHGPLNFIGGAITFATVTGGRPIAQALVPPGTP 417

Query: 420 AWGSAWKKATADYYTHQVSMDAHGAHQSYRGNYLDLDPVYRDAYGLPLLRMTFDWQENDI 479
            WGS WKKA  D+Y H  ++   G+  SYR NYLDLDP Y+DAYGLPLLRMTFDW++N+ 
Sbjct: 418 KWGSGWKKAVKDHYLHSFAISTQGSVMSYRDNYLDLDPTYKDAYGLPLLRMTFDWKDNEG 477

Query: 480 KMNRFMVEKMGKIAEAMNPK--AIALLGKKVGEHFNTASYQTTHLNGGAIMGTDPKTSAL 537
           +M +F+  K   +A AMNPK  ++A+   K G+HF+   YQ+TH  GGAI G  P  S +
Sbjct: 478 RMTQFVSHKAADVARAMNPKPQSVAINAGKPGDHFDVGPYQSTHTTGGAIAGDRPDNSVV 537

Query: 538 NRYLQSWDVHNVFVPGASAFPQGLGYNPTGLVAALTYWSARAIREQYLKNPGPLVQA 594
           N+YLQSWDV NVFV GA +FPQ LG NPTG + A+TY++A+ IRE YLKNPGPLVQA
Sbjct: 538 NKYLQSWDVPNVFVTGACSFPQNLGINPTGTIGAMTYYAAKTIRETYLKNPGPLVQA 594


Lambda     K      H
   0.317    0.136    0.422 

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: 1323
Number of extensions: 58
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: 594
Length of database: 594
Length adjustment: 37
Effective length of query: 557
Effective length of database: 557
Effective search space:   310249
Effective search space used:   310249
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: 53 (25.0 bits)

This GapMind analysis is from Sep 17 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