GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimD in Burkholderia phytofirmans PsJN

Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate BPHYT_RS32685 BPHYT_RS32685 acyl-CoA dehydrogenase

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



>FitnessBrowser__BFirm:BPHYT_RS32685
          Length = 387

 Score =  152 bits (383), Expect = 2e-41
 Identities = 100/317 (31%), Positives = 165/317 (52%), Gaps = 16/317 (5%)

Query: 45  EWYRILNKKGWAVTHWPKEYGGTGWSSVQHYIFNEELQAAPAPQPLAFGVSMVGPVIYTF 104
           E+   L K GW     P+++GG+G    +  +  EE+  A        G       +   
Sbjct: 40  EFVDALTKAGWLAALIPQDFGGSGLGLTEASVIMEEINRAGGNSGACHGQMYNMGTLLRH 99

Query: 105 GSEEQKKRFLPRIANVD-DWWCQGFSEPGSGSDLASLKTKAEKKGDKWIINGQKTWTTLA 163
           GSEEQK+++LP+IA  D      G +EP +G+D   +KT AE++GD+++INGQK W +  
Sbjct: 100 GSEEQKQKYLPKIACGDLRLQSMGVTEPSTGTDTTKIKTTAERRGDRYVINGQKVWISRV 159

Query: 164 QHADWIFCLCRTDPAA---KKQEGISFILVDMKT---KGITVRPIQTIDGGHEVNEVFFD 217
           QH+D +  L RT P A   KK EG+S  +VD++     G+TV+PI  +   HE NE+FFD
Sbjct: 160 QHSDLMILLARTTPLADVKKKSEGMSIFIVDLREAIGHGMTVQPILNM-VNHETNELFFD 218

Query: 218 DVEVPLENLVGQENKGWDYAKFLLGNERTGIAR--VGMSKERIRRIKQLAAQVESGGKPV 275
           ++E+P ENL+G+E +G+ Y    L  ERT IA   +G     + ++ + A +    G+P+
Sbjct: 219 NLEIPAENLIGEEGQGFKYILDGLNAERTLIAAECIGDGYWFVDKVTEYAKERVVFGRPI 278

Query: 276 IEDPKFRDKLAAVEIELKALELTQLRVVADEGKHGKGKPNPA-SSVLKIKGSEIQQATTE 334
            ++   +  +A   + ++A  L +         H   +P  A +++ K+  ++       
Sbjct: 279 GQNQGVQFPIARSFVNVEAASLMRFEAARRFDAH---QPCGAQANMAKLLAADASWEAAN 335

Query: 335 LLMEVIG--PFAAPYDV 349
             ++  G   FA  YDV
Sbjct: 336 ACLQFHGGFGFACEYDV 352


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: 347
Number of extensions: 19
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: 396
Length of database: 387
Length adjustment: 31
Effective length of query: 365
Effective length of database: 356
Effective search space:   129940
Effective search space used:   129940
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: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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