GapMind for catabolism of small carbon sources

 

Aligments for a candidate for cycA in Pseudomonas fluorescens FW300-N2E2

Align L-alanine and D-alanine permease (characterized)
to candidate Pf6N2E2_5459 D-serine/D-alanine/glycine transporter

Query= reanno::pseudo5_N2C3_1:AO356_17670
         (473 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5459
           D-serine/D-alanine/glycine transporter
          Length = 473

 Score =  916 bits (2368), Expect = 0.0
 Identities = 461/473 (97%), Positives = 463/473 (97%)

Query: 1   MPVGNHLPHGETAQGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYI 60
           M VGNHLPHGETAQGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYI
Sbjct: 1   MAVGNHLPHGETAQGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYI 60

Query: 61  IGGLAILVIMRALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITA 120
           IGGLAILVIMRALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITA
Sbjct: 61  IGGLAILVIMRALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITA 120

Query: 121 VAVYMGIWFPDVPRWIWALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVG 180
           VAVYMGIWFPDVPRWIWALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVG
Sbjct: 121 VAVYMGIWFPDVPRWIWALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVG 180

Query: 181 IIAFGFGNDGVALGISNLWAHGGFMPNGVSGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQ 240
           IIAFGFGNDGVALGISNLW HGGFMPNGV GVLMSLQMVMFAYLGVEMIGLTAGEAKNPQ
Sbjct: 181 IIAFGFGNDGVALGISNLWTHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQ 240

Query: 241 KTIPNAIGSVFWRILLFYVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFV 300
           KTIPNAIGSVFWRILLFYVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFV
Sbjct: 241 KTIPNAIGSVFWRILLFYVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFV 300

Query: 301 VITAALSSCNGGIFSTGRMLYSLAQNGQAPAGFAKTSTNGVPRRALLLSIAALLLGVLLN 360
           VITAALSSCNGGIFSTGRMLYSLAQNGQAPAGFA TS NGVPRRALLLSIAALLLGVLLN
Sbjct: 301 VITAALSSCNGGIFSTGRMLYSLAQNGQAPAGFATTSANGVPRRALLLSIAALLLGVLLN 360

Query: 361 YLVPEKVFVWVTSIATFGAIWTWVMILLAQLKFRKSLSASERAALKYRMWLYPVSSYLAL 420
           YLVPEKVFVWVTSIATFGAIWTWVMILLAQLKFRKSLSASERAALKYRMWLYPVSSYLAL
Sbjct: 361 YLVPEKVFVWVTSIATFGAIWTWVMILLAQLKFRKSLSASERAALKYRMWLYPVSSYLAL 420

Query: 421 AFLVLVVGLMAYFPDTRVALYVGPAFLVLLTVLFYTFKLQPTGDVQRAVRSAS 473
           AFLVLVVGLMAYFPDTRVALYVGPAFLVLLTVLFY FKLQPTG+   +VRS S
Sbjct: 421 AFLVLVVGLMAYFPDTRVALYVGPAFLVLLTVLFYVFKLQPTGETHGSVRSVS 473


Lambda     K      H
   0.328    0.142    0.444 

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: 986
Number of extensions: 35
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: 473
Length of database: 473
Length adjustment: 33
Effective length of query: 440
Effective length of database: 440
Effective search space:   193600
Effective search space used:   193600
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.3 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

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:

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. Gaps may be due to:

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 preprint 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