Alignments for a candidate for xacD in Paraburkholderia phymatum STM815

GapMind for catabolism of small carbon sources

Alignments for a candidate for xacD in Paraburkholderia phymatum STM815

Align L-arabonate dehydratase; L-arabinonate dehydratase; EC 4.2.1.25 (characterized)
to candidate WP_012405897.1 BPHY_RS33425 dihydroxy-acid dehydratase

Query= SwissProt::Q1JUQ1
         (583 letters)



>NCBI__GCF_000020045.1:WP_012405897.1
          Length = 577

 Score =  999 bits (2583), Expect = 0.0
 Identities = 494/583 (84%), Positives = 531/583 (91%), Gaps = 6/583 (1%)

Query: 1   MSATKPRLRSTQWFGTNDKNGFMYRSWMKNQGIPDHEFDGRPIIGICNTWSELTPCNAHF 60
           MS  K +LRS QWFGT DKNGFMYRSWMKNQGIPDHEFDGRP+IGICNTWSELTPCNAHF
Sbjct: 1   MSDKKSKLRSAQWFGTADKNGFMYRSWMKNQGIPDHEFDGRPVIGICNTWSELTPCNAHF 60

Query: 61  RKLAEHVKRGISEAGGFPVEFPVFSNGESNLRPSAMLTRNLASMDVEEAIRGNPIDAVVL 120
           RK+AEHVKRGI EAGGFPVEFPVFSNGESNLRP+AMLTRNLA+MDVEEAIRGNPIDAVVL
Sbjct: 61  RKIAEHVKRGIYEAGGFPVEFPVFSNGESNLRPTAMLTRNLAAMDVEEAIRGNPIDAVVL 120

Query: 121 LAGCDKTTPALLMGAASCDVPAIVVSGGPMLNGKLEGKNIGSGTAVWQLHEALKAGEIDV 180
           L GCDKTTPALLMGAASCDVPAIVV+GGPMLNGKL+GK+IGSGTAVWQLHE+LKAGEID+
Sbjct: 121 LTGCDKTTPALLMGAASCDVPAIVVTGGPMLNGKLDGKDIGSGTAVWQLHESLKAGEIDL 180

Query: 181 HHFLSAEAGMSRSAGTCNTMGTASTMACMAEALGVALPHNAAIPAVDSRRYVLAHMSGIR 240
           H FLSAEAGMSRSAGTCNTMGTASTMACMAEALG +LPHNAAIPAVDSRRYVLAHMSG+R
Sbjct: 181 HKFLSAEAGMSRSAGTCNTMGTASTMACMAEALGTSLPHNAAIPAVDSRRYVLAHMSGMR 240

Query: 241 IVEMALEGLVLSKILTRAAFENAIRANAAIGGSTNAVIHLKAIAGRIGVPLELEDWMRIG 300
           IVEMA EGL LSKILTR AF NAIR NAAIGGSTNAVIHLKAIAGRIGV L+L+DW+RIG
Sbjct: 241 IVEMAHEGLTLSKILTREAFLNAIRVNAAIGGSTNAVIHLKAIAGRIGVKLDLDDWVRIG 300

Query: 301 RDTPTIVDLMPSGRFPMEEFYYAGGLPAVLRRLGEGGLLPNPDALTVNGKSLWDNVREAP 360
           R+TPTIVDLMPSGRF MEEFYYAGGLPAVLRRLGE  LLP+P A+T NGK+LW NV +AP
Sbjct: 301 RNTPTIVDLMPSGRFLMEEFYYAGGLPAVLRRLGEADLLPHPGAMTANGKALWHNVMDAP 360

Query: 361 NYDEEVIRPLDRPLIADGGIRILRGNLAPRGAVLKPSAASPELLKHRGRAVVFENLDHYK 420
            Y++EVIRPLD+PL+ DGGIR+LRGNLAPRGAVLKPSAA+P LLKHRGRAVVFEN +HYK
Sbjct: 361 IYNDEVIRPLDKPLVKDGGIRVLRGNLAPRGAVLKPSAATPALLKHRGRAVVFENFEHYK 420

Query: 421 ATINDEALDIDASSVMVLKNCGPRGYPGMAEVGNMGLPPKLLRQGVKDMVRISDARMSGT 480
             I DE LD+DA+SV+V+KNCGP+GYPGMAEVGNMGLPPKLLRQGVKDMVRISDARMSGT
Sbjct: 421 ERIVDETLDVDANSVLVMKNCGPKGYPGMAEVGNMGLPPKLLRQGVKDMVRISDARMSGT 480

Query: 481 AYGTVVLHVAPEAAAGGPLAAVRNGDWIELDCEAGTLHLDITDDELHRRLSDVDPTAAPG 540
           AYGTVVLHV PEAA GGPLAAV++GDWIELDC+AGTL +DI D+EL RRL    P   P 
Sbjct: 481 AYGTVVLHVTPEAADGGPLAAVQDGDWIELDCDAGTLRVDIGDEELARRLERHTPPEMP- 539

Query: 541 VAGQLGKGGYARLYIDHVLQADEGCDLDFLVGTRGAEVPSHSH 583
            AG    GGY RLYIDHVLQADEGCDLDFLVG RGA VP HSH
Sbjct: 540 -AG----GGYQRLYIDHVLQADEGCDLDFLVGCRGAGVPRHSH 577


Lambda     K      H
   0.319    0.136    0.412 

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: 1291
Number of extensions: 57
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: 583
Length of database: 577
Length adjustment: 36
Effective length of query: 547
Effective length of database: 541
Effective search space:   295927
Effective search space used:   295927
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 24 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