GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badK in Pseudomonas simiae WCS417

Align BadK (characterized)
to candidate GFF2094 PS417_10680 enoyl-CoA hydratase

Query= metacyc::MONOMER-943
         (258 letters)



>FitnessBrowser__WCS417:GFF2094
          Length = 263

 Score =  130 bits (327), Expect = 3e-35
 Identities = 94/265 (35%), Positives = 130/265 (49%), Gaps = 20/265 (7%)

Query: 4   NPILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRAFAA 63
           +P+LT+ Q  V  ITLNR    NAL+   +  L   L  F+ D  +  +V+ GN R+F A
Sbjct: 5   SPVLTQVQAGVAWITLNRGPQRNALDIPTLKHLHALLDTFNTDPAVRVVVLTGNGRSFCA 64

Query: 64  GADIASMAAWSYS---DVYGSNFITRNWET-IRQIRKPVLAAVAGLAYGGGCELALACDI 119
           GAD+A  AA       + YG         T +  + KP +AA+ G A G G +L L CD+
Sbjct: 65  GADLAEWAAAEARGALETYGWTDTAHALMTRLHTLDKPTIAAINGTAVGAGMDLTLCCDL 124

Query: 120 VIAGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSR 179
            +A +SA+F      +   P AG +  LPR IG  +A  +       +A+ A   GLV  
Sbjct: 125 RVAAQSARFKAGYTSMAYSPDAGASWHLPRLIGSEQAKRLLFLDELWSADRALAAGLVGE 184

Query: 180 VVDDDRLRDETVALATTIA-----AFSAPALM---ALKESLNRAFESTLAEGILFERREL 231
           VV DD L   T ALAT +A     AF+    +     + SL    ++ LA G+L  R   
Sbjct: 185 VVTDDHLHAHTNALATRLANGPTFAFAQTKTLIRDGAERSLPAQLQAELAAGLLCGR--- 241

Query: 232 HARFASADAREGIQAFLEKRAPCFS 256
                SAD  E ++A LEKR P FS
Sbjct: 242 -----SADGTEALRASLEKRLPIFS 261


Lambda     K      H
   0.321    0.135    0.389 

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: 126
Number of extensions: 6
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: 258
Length of database: 263
Length adjustment: 25
Effective length of query: 233
Effective length of database: 238
Effective search space:    55454
Effective search space used:    55454
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 47 (22.7 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