GapMind for catabolism of small carbon sources

 

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

Align succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized)
to candidate AO353_11505 AO353_11505 succinate-semialdehyde dehydrogenase

Query= reanno::pseudo3_N2E3:AO353_11505
         (480 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_11505 AO353_11505
           succinate-semialdehyde dehydrogenase
          Length = 480

 Score =  942 bits (2436), Expect = 0.0
 Identities = 480/480 (100%), Positives = 480/480 (100%)

Query: 1   MQLKDTLLFRQQAFIDGAWVDADNGQTINVTNPATGEILGTVPKMGAAETRRAIEAADKA 60
           MQLKDTLLFRQQAFIDGAWVDADNGQTINVTNPATGEILGTVPKMGAAETRRAIEAADKA
Sbjct: 1   MQLKDTLLFRQQAFIDGAWVDADNGQTINVTNPATGEILGTVPKMGAAETRRAIEAADKA 60

Query: 61  LPAWRALTAKERANKLRRWFELIIENQDDLARLMTLEQGKPLAEAKGEIVYAASFIEWFA 120
           LPAWRALTAKERANKLRRWFELIIENQDDLARLMTLEQGKPLAEAKGEIVYAASFIEWFA
Sbjct: 61  LPAWRALTAKERANKLRRWFELIIENQDDLARLMTLEQGKPLAEAKGEIVYAASFIEWFA 120

Query: 121 EEAKRIYGDVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLK 180
           EEAKRIYGDVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLK
Sbjct: 121 EEAKRIYGDVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLK 180

Query: 181 PASQTPYSAFALAELAQRAGIPKGVLSVVTGSAGDIGSELTSNPIVRKLSFTGSTEIGRQ 240
           PASQTPYSAFALAELAQRAGIPKGVLSVVTGSAGDIGSELTSNPIVRKLSFTGSTEIGRQ
Sbjct: 181 PASQTPYSAFALAELAQRAGIPKGVLSVVTGSAGDIGSELTSNPIVRKLSFTGSTEIGRQ 240

Query: 241 LMAECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDS 300
           LMAECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDS
Sbjct: 241 LMAECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDS 300

Query: 301 VYDAFAEKLKVAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIADALSKGATLLAGGKV 360
           VYDAFAEKLKVAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIADALSKGATLLAGGKV
Sbjct: 301 VYDAFAEKLKVAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIADALSKGATLLAGGKV 360

Query: 361 MEGNFFEPTILTNVPKSAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARD 420
           MEGNFFEPTILTNVPKSAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARD
Sbjct: 361 MEGNFFEPTILTNVPKSAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARD 420

Query: 421 LGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLGI 480
           LGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLGI
Sbjct: 421 LGRVFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLGI 480


Lambda     K      H
   0.317    0.135    0.389 

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: 885
Number of extensions: 16
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: 480
Length of database: 480
Length adjustment: 34
Effective length of query: 446
Effective length of database: 446
Effective search space:   198916
Effective search space used:   198916
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 (21.7 bits)
S2: 51 (24.3 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 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