Alignments for a candidate for xacD in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for xacD in Herbaspirillum seropedicae SmR1

Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate HSERO_RS05205 HSERO_RS05205 dihydroxy-acid dehydratase

Query= reanno::HerbieS:HSERO_RS05205
         (585 letters)



>FitnessBrowser__HerbieS:HSERO_RS05205
          Length = 585

 Score = 1180 bits (3052), Expect = 0.0
 Identities = 585/585 (100%), Positives = 585/585 (100%)

Query: 1   MSSDKKDKSRTLRSAGWFGTADKNGFMYRSWMKNQGIPDHEFQGKPVIGICNTWSELTPC 60
           MSSDKKDKSRTLRSAGWFGTADKNGFMYRSWMKNQGIPDHEFQGKPVIGICNTWSELTPC
Sbjct: 1   MSSDKKDKSRTLRSAGWFGTADKNGFMYRSWMKNQGIPDHEFQGKPVIGICNTWSELTPC 60

Query: 61  NAHFRKIAEHVRRGIIEAGGFPVEFPVFSNGESNLRPTAMLTRNLASMDVEESIRGNPID 120
           NAHFRKIAEHVRRGIIEAGGFPVEFPVFSNGESNLRPTAMLTRNLASMDVEESIRGNPID
Sbjct: 61  NAHFRKIAEHVRRGIIEAGGFPVEFPVFSNGESNLRPTAMLTRNLASMDVEESIRGNPID 120

Query: 121 AVVLLTGCDKTTPALLMGAASCDVPAIVVTGGPMLNGKHQGRDIGSGTVVWQLSEQVKAG 180
           AVVLLTGCDKTTPALLMGAASCDVPAIVVTGGPMLNGKHQGRDIGSGTVVWQLSEQVKAG
Sbjct: 121 AVVLLTGCDKTTPALLMGAASCDVPAIVVTGGPMLNGKHQGRDIGSGTVVWQLSEQVKAG 180

Query: 181 EITIHDFMAAEAGMSRSAGTCNTMGTASTMACMAESLGVSLPHNAAIPAVDARRYVLAHL 240
           EITIHDFMAAEAGMSRSAGTCNTMGTASTMACMAESLGVSLPHNAAIPAVDARRYVLAHL
Sbjct: 181 EITIHDFMAAEAGMSRSAGTCNTMGTASTMACMAESLGVSLPHNAAIPAVDARRYVLAHL 240

Query: 241 SGMRIVDMVWEGLTLSKILTRKAFENAIRTNAAIGGSTNAVIHLKAIAGRIGVDLELEDW 300
           SGMRIVDMVWEGLTLSKILTRKAFENAIRTNAAIGGSTNAVIHLKAIAGRIGVDLELEDW
Sbjct: 241 SGMRIVDMVWEGLTLSKILTRKAFENAIRTNAAIGGSTNAVIHLKAIAGRIGVDLELEDW 300

Query: 301 TRIGRGTPTIVDLQPSGRYLMEEFYYAGGLPAVLRRLGEADLLPHKDALTVNGQTMWDNV 360
           TRIGRGTPTIVDLQPSGRYLMEEFYYAGGLPAVLRRLGEADLLPHKDALTVNGQTMWDNV
Sbjct: 301 TRIGRGTPTIVDLQPSGRYLMEEFYYAGGLPAVLRRLGEADLLPHKDALTVNGQTMWDNV 360

Query: 361 KDAPIYNDEVVRPLAKPLIEDGGICILRGNLAPRGAVLKPSAATPELMKHRGRAVVFEDF 420
           KDAPIYNDEVVRPLAKPLIEDGGICILRGNLAPRGAVLKPSAATPELMKHRGRAVVFEDF
Sbjct: 361 KDAPIYNDEVVRPLAKPLIEDGGICILRGNLAPRGAVLKPSAATPELMKHRGRAVVFEDF 420

Query: 421 NHYKERINDPDLDVDASCVLVMKNVGPKGYPGMAEVGNMGLPPKVLATGVKDMVRISDAR 480
           NHYKERINDPDLDVDASCVLVMKNVGPKGYPGMAEVGNMGLPPKVLATGVKDMVRISDAR
Sbjct: 421 NHYKERINDPDLDVDASCVLVMKNVGPKGYPGMAEVGNMGLPPKVLATGVKDMVRISDAR 480

Query: 481 MSGTAYGTVILHVAPEAAAGGPLGIVQDGDFIELDAYAGKLQLDISEEEMKRRLEARAKV 540
           MSGTAYGTVILHVAPEAAAGGPLGIVQDGDFIELDAYAGKLQLDISEEEMKRRLEARAKV
Sbjct: 481 MSGTAYGTVILHVAPEAAAGGPLGIVQDGDFIELDAYAGKLQLDISEEEMKRRLEARAKV 540

Query: 541 LAERKPEMVGGYQSLYVDRVLQADEGCDFDFLVGCRGAAVPKHSH 585
           LAERKPEMVGGYQSLYVDRVLQADEGCDFDFLVGCRGAAVPKHSH
Sbjct: 541 LAERKPEMVGGYQSLYVDRVLQADEGCDFDFLVGCRGAAVPKHSH 585


Lambda     K      H
   0.319    0.136    0.409 

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: 1395
Number of extensions: 51
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: 585
Length of database: 585
Length adjustment: 37
Effective length of query: 548
Effective length of database: 548
Effective search space:   300304
Effective search space used:   300304
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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