GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdG in Pseudomonas simiae WCS417

Align Succinate--hydroxymethylglutarate CoA-transferase; Dermal papilla-derived protein 13; SuccinylCoA:glutarate-CoA transferase; EC 2.8.3.13 (characterized)
to candidate GFF2916 PS417_14920 CoA-transferase

Query= SwissProt::Q9HAC7
         (445 letters)



>FitnessBrowser__WCS417:GFF2916
          Length = 397

 Score =  215 bits (548), Expect = 2e-60
 Identities = 133/401 (33%), Positives = 211/401 (52%), Gaps = 7/401 (1%)

Query: 42  MNNIKPLEGVKILDLTRVLAGPFATMNLGDLGAEVIKVERPGAGDDTRTWGPPFVGTEST 101
           M N +PL+G+ ++ L   +A PF T  L DLGA VIKVERPGAGD  R +     G  S 
Sbjct: 1   MTNPRPLDGITVVSLEHAIAAPFCTRQLADLGARVIKVERPGAGDFARGYDERVRGLAS- 59

Query: 102 YYLSVNRNKKSIAVNIKDPKGVKIIKELAAVCDVFVENYVPGKLSAMGLGYEDIDEIAPH 161
           +++  NR+K+S+ +++K  +   I+  L A  DV V+N  PG  + MGL +E + E  P 
Sbjct: 60  HFVWTNRSKESLTLDLKQEEAGTILDTLLADADVLVQNLAPGAAARMGLSFEALHERFPR 119

Query: 162 IIYCSITGYGQTGPISQRAGYDAVASAVSGLMHIT-GPENGDPVRPGVAMTDLATGLYAY 220
           +I C I+GYG+ GP  ++  YD +  +  G + +T GP      + G ++ D++ G+YAY
Sbjct: 120 LIVCDISGYGEGGPYEKKKAYDLLIQSEGGFLSVTGGPGEDQMAKAGCSIADISAGMYAY 179

Query: 221 GAIMAGLIQKYKTGKGLFIDCNLLSSQVACLSHIAANYLIGQKEAKRWGTAHGSIVPYQA 280
             I++ L+ + KTGKG  ID ++L S V  + +       G  +  R G AH +I PY  
Sbjct: 180 SGILSALLLRGKTGKGSRIDVSMLESLVEWMGYPMYYAFDGAPQPPRAGAAHSTIYPYGP 239

Query: 281 FKTKD-GYIVVGAGNNQQFATVC-KILDLPELIDNSKYKTNHLRVHNRKELIKILSERFE 338
           F T D G +++G  N +++A  C K+L  P L  + ++  N  R  NR+ L +I+ + F 
Sbjct: 240 FPTGDGGTVMLGLQNEREWAAFCDKVLLTPALATDERFSANFKRSANREVLRQIIVDSFA 299

Query: 339 EELTSKWLYLFEGSGVPYGPINNMKNVFAEPQVLHNGLVMEMEHPTVGKISVPGPAVRYS 398
           +      +   E + +    +N+M+ V+  PQ+        ++ P  G +    P  R +
Sbjct: 300 QLDAEAVIQRLESAQIASARVNDMQGVWDHPQLKARDSWRAVDSP-AGPLPALLPPARNA 358

Query: 399 KFKMSEARPPPLLGQHTTHILKEVLRYDDRAIGELLSAGVV 439
            F        P LGQH+  IL + L Y   AI  L + GV+
Sbjct: 359 AF-TPRMDGVPGLGQHSQGIL-DGLGYSTDAIDGLRARGVI 397


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: 444
Number of extensions: 22
Number of successful extensions: 4
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: 397
Length adjustment: 32
Effective length of query: 413
Effective length of database: 365
Effective search space:   150745
Effective search space used:   150745
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: 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