Alignments for a candidate for dddA in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for dddA in Burkholderia phytofirmans PsJN

Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate BPHYT_RS20800 BPHYT_RS20800 alanine-phosphoribitol ligase

Query= metacyc::MONOMER-15202
         (579 letters)



>FitnessBrowser__BFirm:BPHYT_RS20800
          Length = 557

 Score =  347 bits (890), Expect = e-100
 Identities = 225/549 (40%), Positives = 294/549 (53%), Gaps = 32/549 (5%)

Query: 36  FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRF 95
           +DY++VG G AGC LA RL+ D  NRVLL+EAG  D   +IH+PVG+      P T W +
Sbjct: 2   YDYVIVGGGAAGCALAARLTEDAGNRVLLLEAGPADTDPYIHMPVGFFKMTGGPLT-WGY 60

Query: 96  RTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRW-DNCLP 154
           RT        R + + +G+ LGG  SIN M+Y RGQ  DYDGW E  G   W + D  LP
Sbjct: 61  RTTAAEHTQRRQIPFAQGRVLGGGGSINAMVYTRGQPADYDGW-ERDGCTGWGFRDGVLP 119

Query: 155 DFMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRTRD 214
              R ED+ RL           ++HG GG   +       ++   F  A  EAG+P   D
Sbjct: 120 YLRRMEDNERLCN---------EYHGVGGPLGVSDLISVNELTKAFVLAGQEAGMPYNSD 170

Query: 215 FNRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSEPR 274
           FN    EGV  ++V QRSG R +A+  +LR    R NLTV     V ++    G     R
Sbjct: 171 FNGAQQEGVGVYQVTQRSGKRCSAAVGYLRDARSRPNLTVRTDCLVSRIVIEKG-----R 225

Query: 275 CCGVTVERAGKKV-VTTARCE--VVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLP 331
             GV     G++  VT AR E  V+++AGAIGSP+LL LSGIG    L    +  V  L 
Sbjct: 226 AVGVEFAPRGERANVTIARAEREVIVTAGAIGSPKLLMLSGIGRAEDLERVGVKPVHALN 285

Query: 332 GVGENLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKIGLEYILKRSGPMSMAPSQLCIFT 391
           GVG+NLQDH  I  +Y++ G  +L+  A   +     GLEY L   GP++   ++   F 
Sbjct: 286 GVGQNLQDHFDIDIVYELNGPYSLDKYAKKHM-MLLAGLEYKLFNKGPVTSNIAEGGAFW 344

Query: 392 RSSKEYEHPNLEYHVQPLSLEAFGQPLHDFPAITASVCNLN-----PTSRGTVRIKSGNP 446
            S      P+L++H  P +    G P    P  + S C LN     P SRG+V + S +P
Sbjct: 345 YSDSSVPTPDLQFHFLPGAGVEAGVP----PVPSGSGCTLNSYFLRPRSRGSVTLHSADP 400

Query: 447 RQAPAISPNYLSTEEDRQVAADSLRVTRHIASQPAFAKYDPEEFKPGVQYQSDEDLARLA 506
             AP I P Y+    D +VA D +R +R I SQ A  KY   E  PG   ++  +    A
Sbjct: 401 ADAPLIDPAYIRDPYDLKVAVDGIRQSREIMSQHALRKYIRSEHFPGGLVRTQAEYETYA 460

Query: 507 GDIGTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLM 566
              G T +HPVGT KMG D+  M+VVD  LRVRG+ GLRV D+S+MP I S NTN+PTLM
Sbjct: 461 QQYGRTGYHPVGTCKMGVDE--MSVVDPQLRVRGIEGLRVADSSVMPRIVSSNTNAPTLM 518

Query: 567 IAEKAAGWI 575
           IAEKAA  I
Sbjct: 519 IAEKAADLI 527


Lambda     K      H
   0.318    0.135    0.418 

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: 863
Number of extensions: 57
Number of successful extensions: 7
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: 579
Length of database: 557
Length adjustment: 36
Effective length of query: 543
Effective length of database: 521
Effective search space:   282903
Effective search space used:   282903
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.

Downloads

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