GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cycA in Pseudomonas fluorescens GW456-L13

Align L-alanine and D-alanine permease (characterized)
to candidate PfGW456L13_4790 D-serine/D-alanine/glycine transporter

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4790
          Length = 473

 Score =  905 bits (2340), Expect = 0.0
 Identities = 454/473 (95%), Positives = 458/473 (96%)

Query: 1   MPVGNHLPHGETAQGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYI 60
           MPVGNHLP GETAQGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYI
Sbjct: 1   MPVGNHLPQGETAQGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYI 60

Query: 61  IGGLAILVIMRALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITA 120
           IGGLAILVIMRALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITA
Sbjct: 61  IGGLAILVIMRALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITA 120

Query: 121 VAVYMGIWFPDVPRWIWALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVG 180
           VAVYMGIWFPDVPRWIWALAAL+SMGSINLIAVKAFGEFEFWFALIKIVTIIAMV+GG+G
Sbjct: 121 VAVYMGIWFPDVPRWIWALAALISMGSINLIAVKAFGEFEFWFALIKIVTIIAMVLGGIG 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
           VITAALSSCNGGIFSTGRMLYSLAQNGQAPAGFAKTS NGVPRRALLLSI ALLLGVLLN
Sbjct: 301 VITAALSSCNGGIFSTGRMLYSLAQNGQAPAGFAKTSNNGVPRRALLLSIGALLLGVLLN 360

Query: 361 YLVPEKVFVWVTSIATFGAIWTWVMILLAQLKFRKSLSASERAALKYRMWLYPVSSYLAL 420
           YLVPEKVFVWVT+IATFGAIWTWVMILLAQLKFRK LSASE A LKYRMWLYPVSSYLAL
Sbjct: 361 YLVPEKVFVWVTAIATFGAIWTWVMILLAQLKFRKGLSASEAAGLKYRMWLYPVSSYLAL 420

Query: 421 AFLVLVVGLMAYFPDTRVALYVGPAFLVLLTVLFYTFKLQPTGDVQRAVRSAS 473
           AFLVLVVGLMAYFPDTRVALYVGPAFLVLLTVLFY FKLQPT   Q A RS S
Sbjct: 421 AFLVLVVGLMAYFPDTRVALYVGPAFLVLLTVLFYVFKLQPTNVSQGAARSVS 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: 978
Number of extensions: 39
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 (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:

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. 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:

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:

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