Alignments for a candidate for xad in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for xad in Paraburkholderia bryophila 376MFSha3.1

Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate H281DRAFT_05919 H281DRAFT_05919 dihydroxy-acid dehydratase

Query= reanno::pseudo5_N2C3_1:AO356_28760
         (594 letters)



>FitnessBrowser__Burk376:H281DRAFT_05919
          Length = 594

 Score = 1003 bits (2592), Expect = 0.0
 Identities = 483/594 (81%), Positives = 542/594 (91%)

Query: 1   MSDTPERRLRSEQWFNDPAHADMTALYVERYMNYGMTREELQSGRPIIGIAQTGSDLTPC 60
           M+    RRLRS++WF+DPA+ADMTALYVER+MNYG+TREELQSGRPIIGIAQTGSDL PC
Sbjct: 1   MTQLNARRLRSQEWFDDPANADMTALYVERFMNYGLTREELQSGRPIIGIAQTGSDLAPC 60

Query: 61  NRHHLELAQRVKAGIRDAGGIPMEFPVHPIAEQSRRPTAALDRNLAYLGLVEILHGYPLD 120
           NRHH+ELA R KAGIRDAGGIPMEFPVHP+AEQSRRPTAALDRNLAYLGLVEILHG+PLD
Sbjct: 61  NRHHIELATRTKAGIRDAGGIPMEFPVHPLAEQSRRPTAALDRNLAYLGLVEILHGFPLD 120

Query: 121 GVVLTTGCDKTTPACLMAAATTDLPAIVLSGGPMLDGHHKGELIGSGTVLWHARNLMAAG 180
           GVVLTTGCDKTTPACLMAAAT D+PAIVLSGGPMLDG H+G+ +GSGTV+WHARNL+AAG
Sbjct: 121 GVVLTTGCDKTTPACLMAAATVDMPAIVLSGGPMLDGWHQGKRVGSGTVIWHARNLLAAG 180

Query: 181 EIDYEGFMEMTTAASPSVGHCNTMGTALSMNALAEALGMSLPGCASIPAPYRERGQMAYA 240
           EIDYEGFME+TTA+SPS+GHCNTMGTALSMN+LAEALGMSLPGCASIPA YRERGQMAYA
Sbjct: 181 EIDYEGFMELTTASSPSIGHCNTMGTALSMNSLAEALGMSLPGCASIPAAYRERGQMAYA 240

Query: 241 TGKRICELVLQDIRPSQIMTRQAFENAIAVASALGASSNCPPHLIAIARHMGVELSLDDW 300
           TGKRI +LV  D+RPS+IMT+ AFENAI VASALGASSNCPPHLIAIARHMGVELSL+DW
Sbjct: 241 TGKRIVDLVRDDVRPSKIMTKAAFENAIVVASALGASSNCPPHLIAIARHMGVELSLNDW 300

Query: 301 QRIGEDVPLLVNCMPAGKYLGEGFHRAGGVPSVMHELQKAGRLHEDCATVSGRTIGEIVS 360
           QR+GE VPL+VNCMPAG+YLGE FHRAGGVP+V+ EL +AG +H DC TVSG+ IG I  
Sbjct: 301 QRVGEKVPLIVNCMPAGEYLGESFHRAGGVPAVLRELDRAGLVHRDCLTVSGQVIGAIAD 360

Query: 361 SSLTSNADVIHPFDTPLKHRAGFIVLSGNFFDSAIMKMSVVGEAFRKTYLSEPGAENSFE 420
           ++   + DVI   D PLKH AGFIVLSGNFFDSAIMKMSVVG+AFR TYLSEPGAENSFE
Sbjct: 361 NAAQPDRDVIKTTDEPLKHGAGFIVLSGNFFDSAIMKMSVVGDAFRNTYLSEPGAENSFE 420

Query: 421 ARAIVFEGPEDYHARIDDPALDIDERCILVIRGVGTVGYPGSAEVVNMAPPAALIKQGID 480
            RAIVF+GPEDYH+RI+DP+L+ID+ CILVIRG GTVGYPGSAEVVNMAPPA L++QGI 
Sbjct: 421 TRAIVFDGPEDYHSRINDPSLNIDQHCILVIRGAGTVGYPGSAEVVNMAPPAELVRQGIT 480

Query: 481 SLPCLGDGRQSGTSASPSILNMSPEAAVGGGLALLQTNDRLKVDLNTRTVNLLIDDEEMA 540
           SLP +GDGRQSGTSASPSILNMSPEAA+GGGLALLQT DR++VDLNTRTVN+L+D++E+A
Sbjct: 481 SLPTMGDGRQSGTSASPSILNMSPEAAIGGGLALLQTGDRIRVDLNTRTVNVLVDEDELA 540

Query: 541 RRRLEWTPNIPPSQTPWQELYRQLVGQLSTGGCLEPATLHLRVIARSGEPRHSH 594
           RRR   + +IPP+QTPWQELYRQ VGQLSTGGCLEPATL+L+VIA  G PRHSH
Sbjct: 541 RRRETVSFDIPPAQTPWQELYRQTVGQLSTGGCLEPATLYLKVIAERGNPRHSH 594


Lambda     K      H
   0.319    0.135    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: 1216
Number of extensions: 38
Number of successful extensions: 1
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 ( 7.4 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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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