GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimD in Acidovorax sp. GW101-3H11

Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate Ac3H11_2717 Acyl-CoA dehydrogenase, long-chain specific, mitochondrial precursor (EC 1.3.99.13)

Query= metacyc::MONOMER-20676
         (396 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2717
          Length = 329

 Score =  169 bits (427), Expect = 1e-46
 Identities = 119/345 (34%), Positives = 176/345 (51%), Gaps = 29/345 (8%)

Query: 61  PKEYGGTGWSSVQHYIFNEELQAAPAPQPLAFGVS-MVGPVIYTFGSEEQKKRFLPRIAN 119
           P +YGG   S    Y+  EEL AA AP    +      GP+I  +G+E Q++++LP I  
Sbjct: 4   PHQYGGHDASPWARYVVIEELLAAGAPVSAHWIADRQSGPLILRYGTEAQRQKYLPGICK 63

Query: 120 VDDWWCQGFSEPGSGSDLASLKTKA---EKKGD-KWIINGQKTWTTLAQHADWIFCLCRT 175
            + ++C G SEP SGSDLAS++++A   E  GD  W ++GQK WTT A HA ++  L RT
Sbjct: 64  GEVYFCIGMSEPNSGSDLASIRSRAVRDEAAGDGSWRLSGQKVWTTNAHHAQYMIALVRT 123

Query: 176 DPA----AKKQEGISFILVDMKTKGITVRPIQTIDGGHEVNEVFFDDVEVPLENLVGQEN 231
             A    A + EG+S  ++D+K  G+TVRPI+ + GG   NEV+ DDV +  + L+G E 
Sbjct: 124 GAATGEKAARHEGMSQFIIDLKAAGVTVRPIRDLAGGEHFNEVYLDDVRLDADALIGTEG 183

Query: 232 KGWDYAKFLLGNERTGIARVGMSKERIRRIKQLAAQVESGGKPVIEDPKFRDKLAAVEIE 291
           +GW+     L  ER+G  R   S   +  +         G +P         +L+A  + 
Sbjct: 184 QGWEQVTAELAFERSGPERFLSSMALLHTLIDAV-----GAQPDALQAHAVGRLSARLVV 238

Query: 292 LKALELTQLRVVADEGKHGKGKPNPASSVLKIKGSEIQQATTELLMEVIGPFAAPYDVHG 351
           L+ + L     +A       G P  A+S LK  G+  +Q   EL  +V+    A   V G
Sbjct: 239 LRQMSLAVTAELA-----AGGNPAWAASCLKDLGAAFEQEIPELAQQVLDVAPA---VGG 290

Query: 352 DDDSNETMDWTAQIAPGYFNNRKVSIYGGSNEIQRNIICKAVLGL 396
             D  + +    Q+AP +      S+ GG+ EI R II +  LGL
Sbjct: 291 GSDHAQVLAALMQMAPSF------SLRGGTREILRGIIARG-LGL 328


Lambda     K      H
   0.317    0.135    0.411 

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: 296
Number of extensions: 12
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: 396
Length of database: 329
Length adjustment: 29
Effective length of query: 367
Effective length of database: 300
Effective search space:   110100
Effective search space used:   110100
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 (21.6 bits)
S2: 49 (23.5 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