GapMind for catabolism of small carbon sources

 

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

Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate AO353_11105 AO353_11105 CoA-transferase

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



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_11105 AO353_11105
           CoA-transferase
          Length = 406

 Score =  765 bits (1976), Expect = 0.0
 Identities = 381/406 (93%), Positives = 395/406 (97%)

Query: 1   MGALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENT 60
           MGALSHLRVLDLSRVLAGPWAGQILADLGA+VIKVERPGNGDDTRAWGPPFLKDA GENT
Sbjct: 1   MGALSHLRVLDLSRVLAGPWAGQILADLGAEVIKVERPGNGDDTRAWGPPFLKDAYGENT 60

Query: 61  TEAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKA 120
           +EAAYYLSANRNKQSVTIDFT+ EGQRLVRELAA+SDILIENFKVGGLAAYGLDY++LKA
Sbjct: 61  SEAAYYLSANRNKQSVTIDFTQAEGQRLVRELAAQSDILIENFKVGGLAAYGLDYETLKA 120

Query: 121 INPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDI 180
           INP LIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDI
Sbjct: 121 INPDLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDI 180

Query: 181 LTGLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHP 240
           LTGLYST AILAALAHR+H GGGQHIDMALLDVQVACLANQAMNYLTTG APKRLGNAHP
Sbjct: 181 LTGLYSTVAILAALAHREHEGGGQHIDMALLDVQVACLANQAMNYLTTGIAPKRLGNAHP 240

Query: 241 NIVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLI 300
           NIVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNK+RVANRAVLIPLI
Sbjct: 241 NIVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKLRVANRAVLIPLI 300

Query: 301 RQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVAS 360
           RQATVFKTTAEWV QLEQAGVPCGPINDL+QVFADPQV+ARGLA+ELPH LAG VPQVAS
Sbjct: 301 RQATVFKTTAEWVAQLEQAGVPCGPINDLSQVFADPQVKARGLAIELPHALAGLVPQVAS 360

Query: 361 PIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406
           PIRLSETPVEYR+APPLLGEHTLEVLQRVLGL+ AAV AF+EAGVL
Sbjct: 361 PIRLSETPVEYRSAPPLLGEHTLEVLQRVLGLEAAAVAAFKEAGVL 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: 720
Number of extensions: 13
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 (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