GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gcdG in Pseudomonas simiae WCS417

Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate GFF116 PS417_00585 CoA-transferase

Query= reanno::pseudo5_N2C3_1:AO356_10845
         (406 letters)



>lcl|FitnessBrowser__WCS417:GFF116 PS417_00585 CoA-transferase
          Length = 406

 Score =  741 bits (1913), Expect = 0.0
 Identities = 368/406 (90%), Positives = 385/406 (94%)

Query: 1   MGALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENT 60
           MGALSHLRVLDLSRVLAGPW+GQILADLGA+VIKVERPG+GDDTRAWGPPFLKDA GENT
Sbjct: 1   MGALSHLRVLDLSRVLAGPWSGQILADLGAEVIKVERPGSGDDTRAWGPPFLKDAYGENT 60

Query: 61  TEAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKA 120
           +EAAYYLSANRNKQSVTIDFTRPEGQ LVRELAAKSDILIENFKVGGLAAYGLDY+SLK 
Sbjct: 61  SEAAYYLSANRNKQSVTIDFTRPEGQALVRELAAKSDILIENFKVGGLAAYGLDYESLKE 120

Query: 121 INPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDI 180
           INP+LIYCSITGFGQTGPYA RAGYDFMIQGLGGLMSLTGRPEGD+GAGPVKVGVALTDI
Sbjct: 121 INPELIYCSITGFGQTGPYATRAGYDFMIQGLGGLMSLTGRPEGDDGAGPVKVGVALTDI 180

Query: 181 LTGLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHP 240
           LTGLYST AILAALAHRDH GGGQHIDMALLDVQVACLANQAMNYLTTG +PKRLGNAHP
Sbjct: 181 LTGLYSTVAILAALAHRDHDGGGQHIDMALLDVQVACLANQAMNYLTTGASPKRLGNAHP 240

Query: 241 NIVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLI 300
           NIVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRF+TNKVRVANRA LIPLI
Sbjct: 241 NIVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFSTNKVRVANRAELIPLI 300

Query: 301 RQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVAS 360
           RQATVFKTTAEWV+QLE+ GVPCGPINDLAQVFADPQV+ARGLAM LPH LAG VPQVAS
Sbjct: 301 RQATVFKTTAEWVSQLERVGVPCGPINDLAQVFADPQVKARGLAMALPHALAGMVPQVAS 360

Query: 361 PIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406
           PIRLS+TPVEYRNAPPLLGEHT +VLQ VLGL    V A + +GV+
Sbjct: 361 PIRLSKTPVEYRNAPPLLGEHTAQVLQDVLGLAGVNVAALKASGVI 406


Lambda     K      H
   0.319    0.137    0.408 

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: 713
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: 406
Length of database: 406
Length adjustment: 31
Effective length of query: 375
Effective length of database: 375
Effective search space:   140625
Effective search space used:   140625
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 (21.7 bits)
S2: 50 (23.9 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