GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aatJ in Pseudomonas putida KT2440

Align PP1071, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate PP_1071 PP_1071 glutamate / aspartate ABC transporter - periplasmic binding protein

Query= TCDB::Q88NY2
         (306 letters)



>lcl|FitnessBrowser__Putida:PP_1071 PP_1071 glutamate / aspartate
           ABC transporter - periplasmic binding protein
          Length = 306

 Score =  601 bits (1550), Expect = e-177
 Identities = 306/306 (100%), Positives = 306/306 (100%)

Query: 1   MMRIVRQLLGAAIAAAVIASPAMAEELTGTLKKIKESGTITLGHRDSSIPFSYLAGKPEP 60
           MMRIVRQLLGAAIAAAVIASPAMAEELTGTLKKIKESGTITLGHRDSSIPFSYLAGKPEP
Sbjct: 1   MMRIVRQLLGAAIAAAVIASPAMAEELTGTLKKIKESGTITLGHRDSSIPFSYLAGKPEP 60

Query: 61  VGYSHDIQLAVVDALKKQLGTDIKVRYNLVTSQTRIPLVQNGTVDLECGSTTNNVERQQQ 120
           VGYSHDIQLAVVDALKKQLGTDIKVRYNLVTSQTRIPLVQNGTVDLECGSTTNNVERQQQ
Sbjct: 61  VGYSHDIQLAVVDALKKQLGTDIKVRYNLVTSQTRIPLVQNGTVDLECGSTTNNVERQQQ 120

Query: 121 VGFSVGIFEVGTRLLTKVKDGQPAYKDFPDLAGKNVVTTAGTTSERILKAMNADKQMKMN 180
           VGFSVGIFEVGTRLLTKVKDGQPAYKDFPDLAGKNVVTTAGTTSERILKAMNADKQMKMN
Sbjct: 121 VGFSVGIFEVGTRLLTKVKDGQPAYKDFPDLAGKNVVTTAGTTSERILKAMNADKQMKMN 180

Query: 181 VISAKDHGEAFNMLESGRAVAFMMDDALLAGEMAKARKPADWVITGTPQSYEIYGCMVRK 240
           VISAKDHGEAFNMLESGRAVAFMMDDALLAGEMAKARKPADWVITGTPQSYEIYGCMVRK
Sbjct: 181 VISAKDHGEAFNMLESGRAVAFMMDDALLAGEMAKARKPADWVITGTPQSYEIYGCMVRK 240

Query: 241 DDAAFKKAVDDAIVAYFKSGEVNKSYEKWFMQPIPPKGLNLNFQMSEELKKLIAEPTDKA 300
           DDAAFKKAVDDAIVAYFKSGEVNKSYEKWFMQPIPPKGLNLNFQMSEELKKLIAEPTDKA
Sbjct: 241 DDAAFKKAVDDAIVAYFKSGEVNKSYEKWFMQPIPPKGLNLNFQMSEELKKLIAEPTDKA 300

Query: 301 ADEKKS 306
           ADEKKS
Sbjct: 301 ADEKKS 306


Lambda     K      H
   0.315    0.131    0.366 

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: 453
Number of extensions: 5
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: 306
Length of database: 306
Length adjustment: 27
Effective length of query: 279
Effective length of database: 279
Effective search space:    77841
Effective search space used:    77841
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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 (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