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_RS23025 BPHYT_RS23025 GMC family oxidoreductase

Query= BRENDA::C0LE03
         (594 letters)



>FitnessBrowser__BFirm:BPHYT_RS23025
          Length = 592

 Score =  925 bits (2391), Expect = 0.0
 Identities = 437/585 (74%), Positives = 496/585 (84%), Gaps = 3/585 (0%)

Query: 8   VDAVIVGFGWTGAIMAKELTEAGLNVLALERGPMQDTYPDGNYPQVIDELTYSVRKKLFQ 67
           VDAVIVGFGWTGAI+AKELTEAGL V+ALERG  +DTYPDG YP  IDELTY+VRKKLF 
Sbjct: 9   VDAVIVGFGWTGAILAKELTEAGLKVVALERGEYRDTYPDGAYPNTIDELTYNVRKKLFL 68

Query: 68  DISKETVTIRHSVNDVALPNRQLGAFLPGNGVGGAGLHWSGVHFRVDPIELRMRSHYEER 127
           D+SK TV+IRH+ ND ALP RQL AFLPG GVGGAGLHWSGVHFR+ P ELR++SHYEER
Sbjct: 69  DLSKTTVSIRHAPNDTALPYRQLAAFLPGEGVGGAGLHWSGVHFRITPEELRLKSHYEER 128

Query: 128 YGKNFIPKDMTIQDFGVSYEELEPFFDYAEKVFGTSGQAWTVKGQLVGDGKGGNPYAPDR 187
           YGK FIP+ MTIQD+GVSY+ELEP FD+AEKVFGTSGQA+ V G++VGDG   N Y   R
Sbjct: 129 YGKRFIPEGMTIQDYGVSYDELEPHFDFAEKVFGTSGQAYKVNGKVVGDG---NIYEAPR 185

Query: 188 SDHFPLESQKNTYSAQLFQKAANEVGYKPYNLPSANTSGPYTNPYGAQMGPCNFCGFCSG 247
           SD+FPL +Q NTYSA+ F KAA E+G  PY LPSANTSGPYTNPYG QMGPCNFCGFCSG
Sbjct: 186 SDNFPLAAQLNTYSAERFGKAARELGLNPYRLPSANTSGPYTNPYGVQMGPCNFCGFCSG 245

Query: 248 YVCYMYSKASPNVNILPALKPLPNFELRPNSHVLRVNLDSSKTRATGVTYVDGQGREIEQ 307
           Y CYMYSKASPN+NILPALK  PNFELR   HVLRV LD +K RA GVTYVD  G E+ Q
Sbjct: 246 YACYMYSKASPNLNILPALKQSPNFELRSRCHVLRVELDDTKKRAKGVTYVDPAGNEVFQ 305

Query: 308 PADLVILGAFQFHNVRLMLLSGIGKPYDPITGEGVVGKNFAYQNMATIKAYFDKDVHTNN 367
           PADLVI+ AFQ+HNV L+LLSGIGKPYDPI+GEGVVG+NFAYQN++TI A+FDKD  TN 
Sbjct: 306 PADLVIVAAFQYHNVHLLLLSGIGKPYDPISGEGVVGRNFAYQNLSTITAFFDKDTFTNP 365

Query: 368 FIGAGGNGVAVDDFNADNFDHGPHGFVGGSPMWVNQAGSRPIAGTSNPPGTPAWGSAWKK 427
           FIGAGGNGVAVDDFNADNFDHGP GFVGGSP+WVNQAG++PI+G + P GTP WG+ WKK
Sbjct: 366 FIGAGGNGVAVDDFNADNFDHGPLGFVGGSPLWVNQAGAKPISGIATPAGTPNWGADWKK 425

Query: 428 ATADYYTHQVSMDAHGAHQSYRGNYLDLDPVYRDAYGLPLLRMTFDWQENDIKMNRFMVE 487
           +  D+Y H +SMDAHG++ SYR  +LDLDP YRD+YG PLLRMTFDW++NDIKM R++  
Sbjct: 426 SVKDHYAHTISMDAHGSNMSYRDVFLDLDPTYRDSYGQPLLRMTFDWKDNDIKMARYVTG 485

Query: 488 KMGKIAEAMNPKAIALLGKKVGEHFNTASYQTTHLNGGAIMGTDPKTSALNRYLQSWDVH 547
           +M KIA+ M PK+I +  ++ G HF++  YQTTHL GGA+MGTDPKTS LNRYLQSWDVH
Sbjct: 486 QMQKIAQQMGPKSINVYTREFGAHFDSRRYQTTHLVGGAVMGTDPKTSVLNRYLQSWDVH 545

Query: 548 NVFVPGASAFPQGLGYNPTGLVAALTYWSARAIREQYLKNPGPLV 592
           NVFV GASAFPQG+GYNPTGLVAAL YWSARAIR QYLKNPGPLV
Sbjct: 546 NVFVMGASAFPQGIGYNPTGLVAALAYWSARAIRTQYLKNPGPLV 590


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: 1475
Number of extensions: 70
Number of successful extensions: 2
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: 592
Length adjustment: 37
Effective length of query: 557
Effective length of database: 555
Effective search space:   309135
Effective search space used:   309135
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