GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Pf6N2E2_5404 in Pseudomonas fluorescens FW300-N2E3

Align ABC transporter for D-Alanine, permease component 1 (characterized)
to candidate AO353_04605 AO353_04605 amino acid ABC transporter permease

Query= reanno::pseudo6_N2E2:Pf6N2E2_5404
         (365 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_04605 AO353_04605 amino acid
           ABC transporter permease
          Length = 365

 Score =  699 bits (1803), Expect = 0.0
 Identities = 340/365 (93%), Positives = 354/365 (96%)

Query: 1   MTTHTFKPDMPPPGSSIGVVAWMRANMFSSWINTLLTLFAFYLIYLIVPPLVQWAILDAN 60
           MTTH FKPDMPPPG+ IG++AWMR +MFSSWINTLLTLFAFYLIYL+VPP++ WAILDAN
Sbjct: 1   MTTHIFKPDMPPPGTRIGILAWMREHMFSSWINTLLTLFAFYLIYLVVPPILHWAILDAN 60

Query: 61  WVGTTRADCTKEGACWVFIQQRFGQFMYGYYPADLRWRVDLTVWLAVIGVAPLFISRFPR 120
           WVGTTRADCTKEGACWVFIQQRFGQFMYGYYP +LRWRVDLTVWLAVIGVAPLFISRFPR
Sbjct: 61  WVGTTRADCTKEGACWVFIQQRFGQFMYGYYPPELRWRVDLTVWLAVIGVAPLFISRFPR 120

Query: 121 KAIYGLSFLVLYPISAWCLLHGGVFGLDAVATSQWGGLMLTLVIATVGIVGALPLGIVLA 180
           KA+YGLSFLVLYPI A+ LLHG + GL  VATSQWGGLMLTLVIATVGIVGALPLGI+LA
Sbjct: 121 KAVYGLSFLVLYPIVAYILLHGDILGLTNVATSQWGGLMLTLVIATVGIVGALPLGIMLA 180

Query: 181 LGRRSNMPAIRVVCVTFIEFWRGVPLITVLFMSSVMLPLFLPEGMNFDKLLRALIGVILF 240
           LGRRSN+PAIRVVCVTFIEFWRGVPLITVLFMSSVMLPLFLPEGMNFDKLLRALIGVILF
Sbjct: 181 LGRRSNLPAIRVVCVTFIEFWRGVPLITVLFMSSVMLPLFLPEGMNFDKLLRALIGVILF 240

Query: 241 QSAYIAEVVRGGLQAIPKGQYEAAAAMGLGYWRSMGLVILPQALKLVIPGIVNTFIALFK 300
           QSAY+AEVVRGGLQAIPKGQYEAAAAMGLGYWRSMGLVILPQALKLVIPGIVNTFIALFK
Sbjct: 241 QSAYVAEVVRGGLQAIPKGQYEAAAAMGLGYWRSMGLVILPQALKLVIPGIVNTFIALFK 300

Query: 301 DTSLVIIIGLFDLLNSVKQAAADPKWLGMATEGYVFAALVFWIFCFGMSRYSMHLERKLD 360
           DTSLVIIIGLFDLLNSVKQAAADPKWLGMATEGYVFAALVFWIFCFGMSRYSMHLERKLD
Sbjct: 301 DTSLVIIIGLFDLLNSVKQAAADPKWLGMATEGYVFAALVFWIFCFGMSRYSMHLERKLD 360

Query: 361 TGHKR 365
           TGHKR
Sbjct: 361 TGHKR 365


Lambda     K      H
   0.330    0.144    0.469 

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: 792
Number of extensions: 30
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: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 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 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