GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gcdG in Pseudomonas fluorescens GW456-L13

Align Succinate--hydroxymethylglutarate CoA-transferase; Dermal papilla-derived protein 13; SuccinylCoA:glutarate-CoA transferase; EC 2.8.3.13 (characterized)
to candidate PfGW456L13_3635 L-carnitine dehydratase/bile acid-inducible protein F

Query= SwissProt::Q9HAC7
         (445 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3635 L-carnitine
           dehydratase/bile acid-inducible protein F
          Length = 409

 Score =  315 bits (808), Expect = 1e-90
 Identities = 169/399 (42%), Positives = 247/399 (61%), Gaps = 5/399 (1%)

Query: 45  IKPLEGVKILDLTRVLAGPFATMNLGDLGAEVIKVERPGAGDDTRTWGPPFVGTESTYYL 104
           ++ ++GVKI+DL+R L+GPF TM L DLGA+VIK+E    GD +RTWGP F    STYYL
Sbjct: 1   MQAMQGVKIVDLSRALSGPFCTMVLADLGADVIKIEPGPTGDMSRTWGP-FDRGVSTYYL 59

Query: 105 SVNRNKKSIAVNIKDPKGVKIIKELAAVCDVFVENYVPGKLSAMGLGYEDIDEIAPHIIY 164
           S NRNK+ + ++++ P+G+  I++L    DV +EN+ PG L +MGLGYE +    P ++ 
Sbjct: 60  SCNRNKRGMCIDLRTPEGLTTIQQLIDDADVVIENFKPGTLESMGLGYEVLSARNPRLVL 119

Query: 165 CSITGYGQTGPISQRAGYDAVASAVSGLMHITGPENGDPVRPGVAMTDLATGLYAYGAIM 224
            SI  +G  GP+S   G+D +A   SGLM +TG  +GDP R G A+ DL +G++   A++
Sbjct: 120 GSINAFGADGPMSSWPGFDQIAQGYSGLMSLTGFVDGDPTRTGTAIGDLTSGMWLVTAVL 179

Query: 225 AGLIQKYKTGKGLFIDCNLLSSQVACLSHIAANYLIGQKEAKRWGTAHGSIVPYQAFKTK 284
           A L+++ +TG+G  +  +LL+S V  LS     YL      +R G AH  I PY  F+TK
Sbjct: 180 AALLERERTGRGQHVSTSLLASLVGLLSVHGQRYLSLGDVPRRTGNAHSVIAPYGVFQTK 239

Query: 285 DGYIVVGAGNNQQFATVCKILDLPELIDNSKYKTNHLRVHNRKELIKILSERFEEELTSK 344
           DG + +    +  +  +C +LDLPEL D+S++ TN  RV  R EL +IL  R +     +
Sbjct: 240 DGPLNLAPITSAMWGRLCILLDLPELPDDSRFATNEARVERRDELREILESRLKTRSKRE 299

Query: 345 WLYLFEGSGVPYGPINNMKNVFAEPQVLHNGLVMEMEHPTVGKI-SVPGPAVRYSKFKMS 403
           W  LF  +G+P GPIN +  VF +PQVLH+ L   + HPT+G +  V  P    +   +S
Sbjct: 300 WTSLFVDAGLPAGPINTLDEVFDDPQVLHSQLTETLTHPTLGALRQVVTPVFCANDSVVS 359

Query: 404 EARPPPLLGQHTTHILKEVLRYDDRAIGELLSAGVVDQH 442
             RPPPLLG+HT  +L+E   +D  +I  LL+A +V Q+
Sbjct: 360 --RPPPLLGEHTVEVLREA-GFDAASINALLAAKIVFQN 395


Lambda     K      H
   0.318    0.137    0.410 

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: 501
Number of extensions: 18
Number of successful extensions: 3
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: 445
Length of database: 409
Length adjustment: 32
Effective length of query: 413
Effective length of database: 377
Effective search space:   155701
Effective search space used:   155701
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 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