GapMind for Amino acid biosynthesis


Alignments for a candidate for leuD in Herbaspirillum seropedicae SmR1

Align 3-isopropylmalate dehydratase small subunit 2; EC; Alpha-IPM isomerase 2; IPMI 2; Isopropylmalate isomerase 2 (uncharacterized)
to candidate HSERO_RS14940 HSERO_RS14940 aconitate hydratase

Query= curated2:Q9V1I9
         (163 letters)

          Length = 903

 Score = 50.4 bits (119), Expect = 8e-11
 Identities = 38/125 (30%), Positives = 60/125 (48%), Gaps = 21/125 (16%)

           +V GG+ +G GSSR+ AA   +  GV  +IA+SF RI   N V +G+ PL     D ++ 

                 +   +    GE+           RKNG+T + + L        ++  + GGIL 

Query: 153 FIRRR 157
           F+ R+
Sbjct: 895 FVLRQ 899

Lambda     K      H
   0.321    0.142    0.425 

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: 325
Number of extensions: 17
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: 163
Length of database: 903
Length adjustment: 30
Effective length of query: 133
Effective length of database: 873
Effective search space:   116109
Effective search space used:   116109
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 Apr 09 2024. The underlying query database was built on Apr 09 2024.



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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