GapMind for catabolism of small carbon sources

 

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

Align Branched-chain amino acid ABC transporter permease LivH; SubName: Full=Branched-chain amino acid transporter permease subunit LivH; SubName: Full=L-leucine ABC transporter membrane protein /L-isoleucine ABC transporter membrane protein /L-valine ABC transporter membrane protein (characterized, see rationale)
to candidate Pf6N2E2_2923 High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)

Query= uniprot:A0A0D9B2B6
         (307 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2923 High-affinity
           branched-chain amino acid transport system permease
           protein LivH (TC 3.A.1.4.1)
          Length = 307

 Score =  588 bits (1516), Expect = e-173
 Identities = 307/307 (100%), Positives = 307/307 (100%)

Query: 1   MPDIYHFFQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIAIAGL 60
           MPDIYHFFQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIAIAGL
Sbjct: 1   MPDIYHFFQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIAIAGL 60

Query: 61  AMMGLDSVPLLMTAAFIASIVVTSSYGYSIERIAYRPLRGSNRLIPLISAIGMSIFLQNT 120
           AMMGLDSVPLLMTAAFIASIVVTSSYGYSIERIAYRPLRGSNRLIPLISAIGMSIFLQNT
Sbjct: 61  AMMGLDSVPLLMTAAFIASIVVTSSYGYSIERIAYRPLRGSNRLIPLISAIGMSIFLQNT 120

Query: 121 VLLSQDSKDKSIPNLIPGNFAIGPGGAHEVLISYMQIVVFVVTLVAMLGLTLFISRSRLG 180
           VLLSQDSKDKSIPNLIPGNFAIGPGGAHEVLISYMQIVVFVVTLVAMLGLTLFISRSRLG
Sbjct: 121 VLLSQDSKDKSIPNLIPGNFAIGPGGAHEVLISYMQIVVFVVTLVAMLGLTLFISRSRLG 180

Query: 181 RACRACAEDIKMANLLGINTNNIIALTFVIGAALAAIAAVLLSMQYGVINPNAGFLVGLK 240
           RACRACAEDIKMANLLGINTNNIIALTFVIGAALAAIAAVLLSMQYGVINPNAGFLVGLK
Sbjct: 181 RACRACAEDIKMANLLGINTNNIIALTFVIGAALAAIAAVLLSMQYGVINPNAGFLVGLK 240

Query: 241 AFTAAVLGGIGSIPGAMLGGLVLGVAEAFGADIFGDQYKDVVAFGLLVLVLLFRPTGILG 300
           AFTAAVLGGIGSIPGAMLGGLVLGVAEAFGADIFGDQYKDVVAFGLLVLVLLFRPTGILG
Sbjct: 241 AFTAAVLGGIGSIPGAMLGGLVLGVAEAFGADIFGDQYKDVVAFGLLVLVLLFRPTGILG 300

Query: 301 RPEVEKV 307
           RPEVEKV
Sbjct: 301 RPEVEKV 307


Lambda     K      H
   0.327    0.144    0.411 

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: 507
Number of extensions: 7
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: 307
Length of database: 307
Length adjustment: 27
Effective length of query: 280
Effective length of database: 280
Effective search space:    78400
Effective search space used:    78400
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: 48 (23.1 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, 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