GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdG in Pseudomonas fluorescens FW300-N1B4

Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate Pf1N1B4_1815 L-carnitine dehydratase/bile acid-inducible protein F

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1815
          Length = 406

 Score =  764 bits (1972), Expect = 0.0
 Identities = 380/406 (93%), Positives = 392/406 (96%)

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

Query: 61  TEAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKA 120
           +EAAYYLSANRNKQSVTIDFTRPEGQ+LVRELAAKSDILIENFKVGGLAAYGLDY+SLKA
Sbjct: 61  SEAAYYLSANRNKQSVTIDFTRPEGQQLVRELAAKSDILIENFKVGGLAAYGLDYESLKA 120

Query: 121 INPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDI 180
           INP+LIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDI
Sbjct: 121 INPKLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDI 180

Query: 181 LTGLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHP 240
           LTGLYST AILAALAHRD  GGGQHIDMALLDVQVACLANQAMNYLTTG APKRLGNAHP
Sbjct: 181 LTGLYSTVAILAALAHRDQGGGGQHIDMALLDVQVACLANQAMNYLTTGVAPKRLGNAHP 240

Query: 241 NIVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLI 300
           NIVPYQDFPTADGDFILTVGNDGQFRKFA+VAGQPQWADDPRFATNK+RVANRAVLIPLI
Sbjct: 241 NIVPYQDFPTADGDFILTVGNDGQFRKFAQVAGQPQWADDPRFATNKLRVANRAVLIPLI 300

Query: 301 RQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVAS 360
           RQATVFKTTAEWV QLEQAGVPCGPINDLAQ+FADPQVQARGLA+ELPH LAG VPQVAS
Sbjct: 301 RQATVFKTTAEWVAQLEQAGVPCGPINDLAQMFADPQVQARGLAIELPHALAGMVPQVAS 360

Query: 361 PIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406
           PIRLSETPVEYR+APPLLGEHTLEVLQRVLGLD   V  F+ +GVL
Sbjct: 361 PIRLSETPVEYRSAPPLLGEHTLEVLQRVLGLDAGVVAGFKASGVL 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: 731
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:

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