GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3635
          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:

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