GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aapJ in Sinorhizobium meliloti 1021

Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, periplasmic substrate-binding component (characterized)
to candidate SMc02118 SMc02118 general L-amino acid-binding periplasmic ABC transporter protein

Query= reanno::Smeli:SMc02118
         (341 letters)



>lcl|FitnessBrowser__Smeli:SMc02118 SMc02118 general L-amino
           acid-binding periplasmic ABC transporter protein
          Length = 341

 Score =  686 bits (1771), Expect = 0.0
 Identities = 341/341 (100%), Positives = 341/341 (100%)

Query: 1   MARRILTALVGAAVVGIGTHAASAATLDDVKAKGFVQCGVNTGLAGFAAPDASGNWSGFD 60
           MARRILTALVGAAVVGIGTHAASAATLDDVKAKGFVQCGVNTGLAGFAAPDASGNWSGFD
Sbjct: 1   MARRILTALVGAAVVGIGTHAASAATLDDVKAKGFVQCGVNTGLAGFAAPDASGNWSGFD 60

Query: 61  VDYCKAIAAAIFGDGSKVKYTPLSAKERFPALQSGEVDVLARNTTWSINRDTALGFNFRP 120
           VDYCKAIAAAIFGDGSKVKYTPLSAKERFPALQSGEVDVLARNTTWSINRDTALGFNFRP
Sbjct: 61  VDYCKAIAAAIFGDGSKVKYTPLSAKERFPALQSGEVDVLARNTTWSINRDTALGFNFRP 120

Query: 121 VNYYDGQGFMVRKELDVKSALELSGAAVCVQTGTTTELNLADYFKANNLQYNPVVFEKLE 180
           VNYYDGQGFMVRKELDVKSALELSGAAVCVQTGTTTELNLADYFKANNLQYNPVVFEKLE
Sbjct: 121 VNYYDGQGFMVRKELDVKSALELSGAAVCVQTGTTTELNLADYFKANNLQYNPVVFEKLE 180

Query: 181 EVNAAYDAGRCDVYTTDQSGLYSLRLTLSKPDDHIVLPEIISKEPLAPAVRQGDDQWFDI 240
           EVNAAYDAGRCDVYTTDQSGLYSLRLTLSKPDDHIVLPEIISKEPLAPAVRQGDDQWFDI
Sbjct: 181 EVNAAYDAGRCDVYTTDQSGLYSLRLTLSKPDDHIVLPEIISKEPLAPAVRQGDDQWFDI 240

Query: 241 VSWVHYALVQAEEFGVTQANLEEMKKSTNPDVQRFLGVEADSKIGTDLGLTNEWAVNIVK 300
           VSWVHYALVQAEEFGVTQANLEEMKKSTNPDVQRFLGVEADSKIGTDLGLTNEWAVNIVK
Sbjct: 241 VSWVHYALVQAEEFGVTQANLEEMKKSTNPDVQRFLGVEADSKIGTDLGLTNEWAVNIVK 300

Query: 301 AVGNYGEVFDRNIGAGSPLKIERGLNALWNKGGLQYAPPVR 341
           AVGNYGEVFDRNIGAGSPLKIERGLNALWNKGGLQYAPPVR
Sbjct: 301 AVGNYGEVFDRNIGAGSPLKIERGLNALWNKGGLQYAPPVR 341


Lambda     K      H
   0.317    0.134    0.399 

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: 575
Number of extensions: 11
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: 341
Length of database: 341
Length adjustment: 29
Effective length of query: 312
Effective length of database: 312
Effective search space:    97344
Effective search space used:    97344
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: 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