GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuD in Bacteroides thetaiotaomicron VPI-5482

Align 3-isopropylmalate dehydratase small subunit 1; EC 4.2.1.33; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1 (uncharacterized)
to candidate 351600 BT2072 aconitate hydratase (NCBI ptt file)

Query= curated2:Q9UZ06
         (164 letters)



>FitnessBrowser__Btheta:351600
          Length = 747

 Score = 49.7 bits (117), Expect = 1e-10
 Identities = 38/84 (45%), Positives = 49/84 (58%), Gaps = 8/84 (9%)

Query: 54  IIVAGENFGCGSSREHAPLAIKAAGVSCVIAKSFARIFYRNAINIG-LPILEAPQA-VDR 111
           I+VA EN+G GSSREHA +  +   V  ++AKSFARI   N    G L +  A +A  D+
Sbjct: 630 IVVAEENYGEGSSREHAAMEPRFLNVRVILAKSFARIHETNLKKQGMLALTFADKADYDK 689

Query: 112 IETGDELEV----DFSSGEIRNLT 131
           I+  D L V    DF+ G  RNLT
Sbjct: 690 IQEHDLLSVIGLPDFAPG--RNLT 711


Lambda     K      H
   0.320    0.139    0.415 

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: 302
Number of extensions: 16
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: 164
Length of database: 747
Length adjustment: 28
Effective length of query: 136
Effective length of database: 719
Effective search space:    97784
Effective search space used:    97784
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: 49 (23.5 bits)

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