Aligments for a candidate for xacD in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Aligments for a candidate for xacD in Pseudomonas fluorescens GW456-L13

Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate PfGW456L13_3320 L-arabonate dehydratase (EC 4.2.1.25)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_3320
         (578 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3320
          Length = 578

 Score = 1166 bits (3016), Expect = 0.0
 Identities = 578/578 (100%), Positives = 578/578 (100%)

Query: 1   MSDKKPTLRSAQWFGTADKNGFMYRSWMKNQGIADHQFHGKPIIGICNTWSELTPCNAHF 60
           MSDKKPTLRSAQWFGTADKNGFMYRSWMKNQGIADHQFHGKPIIGICNTWSELTPCNAHF
Sbjct: 1   MSDKKPTLRSAQWFGTADKNGFMYRSWMKNQGIADHQFHGKPIIGICNTWSELTPCNAHF 60

Query: 61  RQIAEHVKRGVIEAGGFPVEFPVFSNGESNLRPTAMLTRNLASMDVEEAIRGNPIDGVVL 120
           RQIAEHVKRGVIEAGGFPVEFPVFSNGESNLRPTAMLTRNLASMDVEEAIRGNPIDGVVL
Sbjct: 61  RQIAEHVKRGVIEAGGFPVEFPVFSNGESNLRPTAMLTRNLASMDVEEAIRGNPIDGVVL 120

Query: 121 LTGCDKTTPALLMGAASCDVPAIVVTGGPMLNGKHKGKDIGSGTVVWQLSEQVKAGTISI 180
           LTGCDKTTPALLMGAASCDVPAIVVTGGPMLNGKHKGKDIGSGTVVWQLSEQVKAGTISI
Sbjct: 121 LTGCDKTTPALLMGAASCDVPAIVVTGGPMLNGKHKGKDIGSGTVVWQLSEQVKAGTISI 180

Query: 181 DDFLAAEGGMSRSAGTCNTMGTASTMACMAEALGTSLPHNAAIPAVDARRYVLAHMSGMR 240
           DDFLAAEGGMSRSAGTCNTMGTASTMACMAEALGTSLPHNAAIPAVDARRYVLAHMSGMR
Sbjct: 181 DDFLAAEGGMSRSAGTCNTMGTASTMACMAEALGTSLPHNAAIPAVDARRYVLAHMSGMR 240

Query: 241 AVEMVREDLKLSKILTKEAFENAIRVNAAIGGSTNAVIHLKAIAGRIGVELDLDDWTRIG 300
           AVEMVREDLKLSKILTKEAFENAIRVNAAIGGSTNAVIHLKAIAGRIGVELDLDDWTRIG
Sbjct: 241 AVEMVREDLKLSKILTKEAFENAIRVNAAIGGSTNAVIHLKAIAGRIGVELDLDDWTRIG 300

Query: 301 RGMPTIVDLQPSGRFLMEEFYYAGGLPAVLRRLGEANLIPNPNALTVNGKSIGENTRDAP 360
           RGMPTIVDLQPSGRFLMEEFYYAGGLPAVLRRLGEANLIPNPNALTVNGKSIGENTRDAP
Sbjct: 301 RGMPTIVDLQPSGRFLMEEFYYAGGLPAVLRRLGEANLIPNPNALTVNGKSIGENTRDAP 360

Query: 361 IYGEDEVIRTLDNPIRADGGICVLRGNLAPLGAVLKPSAATPELMQHRGRAVVFENFDMY 420
           IYGEDEVIRTLDNPIRADGGICVLRGNLAPLGAVLKPSAATPELMQHRGRAVVFENFDMY
Sbjct: 361 IYGEDEVIRTLDNPIRADGGICVLRGNLAPLGAVLKPSAATPELMQHRGRAVVFENFDMY 420

Query: 421 KARINDPELDVDANSILVMKNCGPKGYPGMAEVGNMGLPAKLLAQGVTDMVRISDARMSG 480
           KARINDPELDVDANSILVMKNCGPKGYPGMAEVGNMGLPAKLLAQGVTDMVRISDARMSG
Sbjct: 421 KARINDPELDVDANSILVMKNCGPKGYPGMAEVGNMGLPAKLLAQGVTDMVRISDARMSG 480

Query: 481 TAYGTVVLHVAPEAAAGGPLAAVKEGDWIELDCASGRLHLDIADTELAARMADLQPPQNL 540
           TAYGTVVLHVAPEAAAGGPLAAVKEGDWIELDCASGRLHLDIADTELAARMADLQPPQNL
Sbjct: 481 TAYGTVVLHVAPEAAAGGPLAAVKEGDWIELDCASGRLHLDIADTELAARMADLQPPQNL 540

Query: 541 IVGGYRQLYIDHVLQADQGCDFDFLVGCRGAEVPRHSH 578
           IVGGYRQLYIDHVLQADQGCDFDFLVGCRGAEVPRHSH
Sbjct: 541 IVGGYRQLYIDHVLQADQGCDFDFLVGCRGAEVPRHSH 578


Lambda     K      H
   0.319    0.136    0.410 

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: 1338
Number of extensions: 48
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: 578
Length of database: 578
Length adjustment: 36
Effective length of query: 542
Effective length of database: 542
Effective search space:   293764
Effective search space used:   293764
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 (21.8 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, or view the source code.

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