GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimC in Cupriavidus basilensis 4G11

Align pimeloyl-CoA dehydrogenase small subunit (EC 1.3.1.62) (characterized)
to candidate RR42_RS36650 RR42_RS36650 acyl-CoA dehydrogenase

Query= metacyc::MONOMER-20677
         (380 letters)



>FitnessBrowser__Cup4G11:RR42_RS36650
          Length = 375

 Score =  311 bits (796), Expect = 2e-89
 Identities = 165/372 (44%), Positives = 223/372 (59%), Gaps = 4/372 (1%)

Query: 1   MDFDLSEEQRLLKESVEGLLKGSYDFDSRKKYAKEKGGWSRAVWGKFAEQGLLGLPFSEE 60
           MDF+ SEEQ++L +S+   +   Y FD R+K A+  G  +RA W + AE G+LGL    E
Sbjct: 1   MDFNYSEEQQMLADSLRRFIDTEYTFDKRRKSARGGGSLNRATWAQLAEMGVLGLTVPGE 60

Query: 61  DGGFGAGAVETMIVMEALGHSLVLEPYLPTVVIGGGFLRRAGSAAQKAAHLPGIIDGSKT 120
            GGFG  A   ++V   LG  LVLEP  PT V+    L   GS AQK   LP I  G + 
Sbjct: 61  YGGFGESAASQLVVQRELGRGLVLEPVTPTAVMATAVLSAYGSDAQKNDWLPAIAAGERV 120

Query: 121 FAFAQLEKNSRWDLGDVSTTAKKSGDGWVIDGEKFVVLNGEAADTLIVTARTKGGQRDRT 180
              A LE  +R+       +A++ GDG+V++G K +  +GEAAD  ++TAR  G      
Sbjct: 121 VTLAYLEPTTRYRPETARASAERKGDGYVLNGNKSLAWHGEAADAFLLTARVCGSNE--- 177

Query: 181 GVGVFLVPADAKGITRKGYPTQDGLHAADITFTGVQVGADAAIGDPENALELIEAVVDDA 240
            + +FLVP +A G+T  GYPT D L AAD+    V V A A IG+  + L  +   +D  
Sbjct: 178 -LALFLVPGNAAGLTVHGYPTMDSLRAADLALQNVIVDASAMIGNAADGLPALLHGIDHG 236

Query: 241 RTALCAEAVGLMDESLTTTVEYIKTRKQFGVPIGSFQVLQHRAADMFVATEQARSMAMFA 300
             ALCAEA G M++ +  T EY++TR+QFG P+  FQ LQHR ADM V  E A SMA  A
Sbjct: 237 IAALCAEAAGAMEKLIEITAEYLRTRQQFGKPLAVFQALQHRMADMLVQKELALSMAYVA 296

Query: 301 TMAAEFDDAKERAGAIAAAKVQIGKSGKFVGQQSIQLHGGIGMTMEAKIGHYFKRLTMIE 360
             A +  D  +R   ++AAKV + K+G+ VGQQ++QLHGG+GMT E ++G YFKRLTMI+
Sbjct: 297 AQALDETDPAQRRRMLSAAKVTVAKAGRLVGQQAVQLHGGMGMTDELEVGDYFKRLTMID 356

Query: 361 QTFGDTDHHLAR 372
              GD+D H+ R
Sbjct: 357 PLLGDSDFHVQR 368


Lambda     K      H
   0.318    0.135    0.388 

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: 366
Number of extensions: 14
Number of successful extensions: 2
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: 380
Length of database: 375
Length adjustment: 30
Effective length of query: 350
Effective length of database: 345
Effective search space:   120750
Effective search space used:   120750
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