GapMind for catabolism of small carbon sources

 

Alignments for a candidate for maiA in Klebsiella michiganensis M5al

Align Maleylacetoacetate isomerase (EC 5.2.1.2) (characterized)
to candidate BWI76_RS25335 BWI76_RS25335 stringent starvation protein A

Query= reanno::psRCH2:GFF3446
         (219 letters)



>FitnessBrowser__Koxy:BWI76_RS25335
          Length = 212

 Score = 55.5 bits (132), Expect = 8e-13
 Identities = 41/113 (36%), Positives = 57/113 (50%), Gaps = 8/113 (7%)

Query: 5   LTLYGYWRSSAAYRVRIALNLKGLAYRQVPVHLVKDGGQQRAADYRALNPQQLVPLLVDE 64
           +TL+       +++VRI L  KG+++     H+ KD   Q   D   LNP Q VP LVD 
Sbjct: 11  MTLFSGPTDIYSHQVRIVLAEKGVSFEIE--HVEKDNPPQDLID---LNPNQSVPTLVDR 65

Query: 65  GNGGARISQSLAILEYLDEVFPVPALLPADPVERAQVRSLAMHIACEIHPLNN 117
                 + +S  I+EYLDE FP P L+P  PV R + R     I  + + L N
Sbjct: 66  E---LTLWESRIIMEYLDERFPHPPLMPVYPVARGESRLYMQRIEKDWYSLMN 115


Lambda     K      H
   0.321    0.137    0.412 

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: 103
Number of extensions: 7
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: 219
Length of database: 212
Length adjustment: 22
Effective length of query: 197
Effective length of database: 190
Effective search space:    37430
Effective search space used:    37430
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 (21.8 bits)
S2: 45 (21.9 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