GapMind for catabolism of small carbon sources

 

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

Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate AO356_00010 AO356_00010 ABC transporter ATP-binding protein

Query= reanno::pseudo5_N2C3_1:AO356_00010
         (365 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_00010 AO356_00010 ABC
           transporter ATP-binding protein
          Length = 365

 Score =  708 bits (1828), Expect = 0.0
 Identities = 365/365 (100%), Positives = 365/365 (100%)

Query: 1   MATLKIENLKKGFEGLSIIKGIDLEVKDKEFVVFVGPSGCGKSTLLRLIAGLEDVTSGTI 60
           MATLKIENLKKGFEGLSIIKGIDLEVKDKEFVVFVGPSGCGKSTLLRLIAGLEDVTSGTI
Sbjct: 1   MATLKIENLKKGFEGLSIIKGIDLEVKDKEFVVFVGPSGCGKSTLLRLIAGLEDVTSGTI 60

Query: 61  ELDGRDITEVTPAKRDLAMVFQTYALYPHMTVRKNLSFALDLAGEKKPDVERKVAEAARI 120
           ELDGRDITEVTPAKRDLAMVFQTYALYPHMTVRKNLSFALDLAGEKKPDVERKVAEAARI
Sbjct: 61  ELDGRDITEVTPAKRDLAMVFQTYALYPHMTVRKNLSFALDLAGEKKPDVERKVAEAARI 120

Query: 121 LELGSLLDRKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQTRLELSRLH 180
           LELGSLLDRKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQTRLELSRLH
Sbjct: 121 LELGSLLDRKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQTRLELSRLH 180

Query: 181 KELQATMIYVTHDQVEAMTLATKVVVLNAGRIEQIGSPLELYHHPANLFVAGFLGTPKMG 240
           KELQATMIYVTHDQVEAMTLATKVVVLNAGRIEQIGSPLELYHHPANLFVAGFLGTPKMG
Sbjct: 181 KELQATMIYVTHDQVEAMTLATKVVVLNAGRIEQIGSPLELYHHPANLFVAGFLGTPKMG 240

Query: 241 FLQATVHAVHASGVEVRFASGTTLLIPRDSSALSVGQSVTIGIRPEHLTLGAEGQVLVTT 300
           FLQATVHAVHASGVEVRFASGTTLLIPRDSSALSVGQSVTIGIRPEHLTLGAEGQVLVTT
Sbjct: 241 FLQATVHAVHASGVEVRFASGTTLLIPRDSSALSVGQSVTIGIRPEHLTLGAEGQVLVTT 300

Query: 301 DVTERLGSDTFCHVNVDSGESLTVRVQGDCEVPYAARRYLTLDVAHCHLFDESGLSVSPA 360
           DVTERLGSDTFCHVNVDSGESLTVRVQGDCEVPYAARRYLTLDVAHCHLFDESGLSVSPA
Sbjct: 301 DVTERLGSDTFCHVNVDSGESLTVRVQGDCEVPYAARRYLTLDVAHCHLFDESGLSVSPA 360

Query: 361 ASRAA 365
           ASRAA
Sbjct: 361 ASRAA 365


Lambda     K      H
   0.319    0.136    0.381 

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: 593
Number of extensions: 13
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: 365
Length of database: 365
Length adjustment: 30
Effective length of query: 335
Effective length of database: 335
Effective search space:   112225
Effective search space used:   112225
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: 49 (23.5 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 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