GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA6 in Marinobacter algicola DG893

Align L-2-keto-3-deoxyrhamnonate 4-dehydrogenase subunit (EC 1.1.1.401) (characterized)
to candidate WP_007154444.1 MDG893_RS13925 fumarylacetoacetate hydrolase family protein

Query= metacyc::MONOMER-16233
         (285 letters)



>NCBI__GCF_000170835.1:WP_007154444.1
          Length = 220

 Score =  124 bits (310), Expect = 2e-33
 Identities = 74/205 (36%), Positives = 112/205 (54%), Gaps = 6/205 (2%)

Query: 59  GVPVK-GIGKIVAIGLNYEDHAIESNLPIPTEPMMFMKALSSLNGPNDEVVLPKNSTHGD 117
           G PV   +GKIV IG NY +HA E N P+P EP++F+K  +S       +  P+N     
Sbjct: 11  GTPVHLPLGKIVCIGRNYAEHARELNNPVPDEPLLFIKPATSAVHITRPLDFPRNQGAVH 70

Query: 118 WEVELGVVIGETCRFVSEDEALSKVAGYVLVNDVSERFNQ---KQRGTQWSKGKGHDTFC 174
           +E EL V+IG      S  +A + + GY L  D++ R  Q   K++G  W + K  D  C
Sbjct: 71  FETELAVLIGRPLTNASASDAEAAILGYGLALDLTLRDVQSRLKEKGQPWERAKAFDGAC 130

Query: 175 PVGPWLVTPDEVGDPQDLDMHLNVNGTRMQTGNTKTMIFNVAQLISYVSEYITLYPGDLM 234
           P+ P++       D   L   L++N  R QTG+T+ M+  +  LI+++S   TL PGD++
Sbjct: 131 PLSPFVCIDRLRRD--HLTFTLDINRERQQTGDTRDMLNPIVPLIAHMSTQFTLMPGDVV 188

Query: 235 ITGTPPGVGEGKKPQAIYLKAGDVM 259
           +TGTP GVG  +  Q + L+  D +
Sbjct: 189 LTGTPKGVGPLESGQILSLELEDAL 213


Lambda     K      H
   0.316    0.137    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: 156
Number of extensions: 7
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: 285
Length of database: 220
Length adjustment: 24
Effective length of query: 261
Effective length of database: 196
Effective search space:    51156
Effective search space used:    51156
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: 42 (22.0 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 24 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