GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuD in Shewanella oneidensis MR-1

Align 3-isopropylmalate dehydratase small subunit 2; EC 4.2.1.33; Alpha-IPM isomerase 2; IPMI 2; Isopropylmalate isomerase 2 (uncharacterized)
to candidate 199538 SO0343 aconitate hydratase 1 (NCBI ptt file)

Query= curated2:Q8TW31
         (168 letters)



>FitnessBrowser__MR1:199538
          Length = 867

 Score = 44.7 bits (104), Expect = 4e-09
 Identities = 36/117 (30%), Positives = 55/117 (47%), Gaps = 15/117 (12%)

Query: 54  VIVAGKNFGCGSSREQAVMALQQAGVACVVARSFARIFYRNAINRGLPTVE--AEEDPTE 111
           +I+AG ++G GSSR+ A   ++ AGV  +VA  F RI   N +  G+  +E  A E+   
Sbjct: 739 IIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRAT 798

Query: 112 VVEDGNRV---------TVDLDELVLRAGSE--EVPL--REPPEFALQAWREGGLLE 155
              DG  V           DL  ++ R   E  EVP+  R      +  +  GG+L+
Sbjct: 799 YGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVLQ 855


Lambda     K      H
   0.318    0.138    0.419 

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: 334
Number of extensions: 20
Number of successful extensions: 1
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: 168
Length of database: 867
Length adjustment: 30
Effective length of query: 138
Effective length of database: 837
Effective search space:   115506
Effective search space used:   115506
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 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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