GapMind for catabolism of small carbon sources

 

Aligments for a candidate for BPHYT_RS16930 in Pseudomonas fluorescens FW300-N2C3

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate AO356_20250 AO356_20250 L-arabinose transporter ATP-binding protein

Query= uniprot:A0A165ZSX8
         (514 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20250 AO356_20250
           L-arabinose transporter ATP-binding protein
          Length = 514

 Score =  980 bits (2533), Expect = 0.0
 Identities = 504/514 (98%), Positives = 505/514 (98%)

Query: 1   MQAQTATRQHNIGGSLRFNGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKI 60
           MQAQTATRQHNIGGSLRFNGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKI
Sbjct: 1   MQAQTATRQHNIGGSLRFNGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKI 60

Query: 61  LGGAYIPSSGDLQIGEQTMAFKGTADSIASGVAVIHQELHLVPEMTVAENLFLGHLPARF 120
           LGGAYIPSSGDLQIGEQTMAFKGTADSIASGVAVIHQELHLVPEMTVAENLFLGHLPARF
Sbjct: 61  LGGAYIPSSGDLQIGEQTMAFKGTADSIASGVAVIHQELHLVPEMTVAENLFLGHLPARF 120

Query: 121 GLVNRGVLRQQALTLLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTS 180
           GLVNRGVLRQQALTLLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTS
Sbjct: 121 GLVNRGVLRQQALTLLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTS 180

Query: 181 SLSAREIDRLMAIIGRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELT 240
           SLSAREIDRLMAII RLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELT
Sbjct: 181 SLSAREIDRLMAIIARLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELT 240

Query: 241 HDQLVTCMVGRDIQDIYDYRPRERGDVALQVKGLLGPGLHEPVSFQVHKGEILGLFGLVG 300
           HDQLVTCMVGRDIQDIYDYRPRERGDVALQVK LLGPGL EPVSFQVHKGEILGLFGLVG
Sbjct: 241 HDQLVTCMVGRDIQDIYDYRPRERGDVALQVKSLLGPGLREPVSFQVHKGEILGLFGLVG 300

Query: 301 AGRTELLRLLSGLERQREGSLVLHDKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVG 360
           AGRTEL RLLSGLERQ EGSLVLH KELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVG
Sbjct: 301 AGRTELFRLLSGLERQSEGSLVLHGKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVG 360

Query: 361 ENINISARPSHSTLGCLLRGDWERGNADKQIKSLKVKTPTAGQKIMYLSGGNQQKAILGR 420
           ENINISARP+HS LGCLLRGDWERGNADKQIKSLKVKTP A QKIMYLSGGNQQKAILGR
Sbjct: 361 ENINISARPAHSALGCLLRGDWERGNADKQIKSLKVKTPAASQKIMYLSGGNQQKAILGR 420

Query: 421 WLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVL 480
           WLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVL
Sbjct: 421 WLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVL 480

Query: 481 CEGAMRGELSRDQANESNLLQLALPRQRVADAAN 514
           CEGAMRGELSRDQANESNLLQLALPRQRVADAAN
Sbjct: 481 CEGAMRGELSRDQANESNLLQLALPRQRVADAAN 514


Lambda     K      H
   0.320    0.138    0.391 

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: 998
Number of extensions: 34
Number of successful extensions: 5
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: 514
Length of database: 514
Length adjustment: 35
Effective length of query: 479
Effective length of database: 479
Effective search space:   229441
Effective search space used:   229441
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: 52 (24.6 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 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