GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Klebsiella michiganensis M5al

Align Acetolactate synthase isozyme 1 small subunit; EC 2.2.1.6; Acetohydroxy-acid synthase I small subunit; AHAS-I; ALS-I (uncharacterized)
to candidate BWI76_RS27810 BWI76_RS27810 acetolactate synthase isozyme 1 small subunit

Query= curated2:P0ADG0
         (96 letters)



>FitnessBrowser__Koxy:BWI76_RS27810
          Length = 96

 Score =  170 bits (431), Expect = 3e-48
 Identities = 82/96 (85%), Positives = 90/96 (93%)

Query: 1  MQNTTHDNVILELTVRNHPGVMTHVCGLFARRAFNVEGILCLPIQDSDKSHIWLLVNDDQ 60
          MQ  TH+NVIL+LTVRNHPGVMTHVCGLFARRAFNVEGILCLPIQDS++S IWLLVNDDQ
Sbjct: 1  MQQATHENVILQLTVRNHPGVMTHVCGLFARRAFNVEGILCLPIQDSNQSRIWLLVNDDQ 60

Query: 61 RLEQMISQIDKLEDVVKVQRNQSDPTMFNKIAVFFQ 96
          RL QMISQI+KLEDV KV RNQSDP+MF+KIAVFF+
Sbjct: 61 RLGQMISQIEKLEDVEKVVRNQSDPSMFSKIAVFFE 96


Lambda     K      H
   0.324    0.137    0.410 

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: 88
Number of extensions: 4
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: 96
Length of database: 96
Length adjustment: 10
Effective length of query: 86
Effective length of database: 86
Effective search space:     7396
Effective search space used:     7396
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (21.1 bits)
S2: 39 (19.6 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