GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuD in Phyllobacterium brassicacearum STM 196

Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate WP_106712703.1 CU102_RS19205 aconitate hydratase AcnA

Query= curated2:B4UAN1
         (191 letters)



>NCBI__GCF_003010955.1:WP_106712703.1
          Length = 895

 Score = 52.4 bits (124), Expect = 2e-11
 Identities = 40/118 (33%), Positives = 58/118 (49%), Gaps = 17/118 (14%)

Query: 70  ILVAGDNFGCGSSREHAPWALVDAGVRAVISTRIADIFRNNALKNGLVPVVLDAASHAKL 129
           ++ AG  +G GSSR+ A       GVRAVI+     I R+N +  G+VP VL+  +  + 
Sbjct: 769 VIFAGVEYGNGSSRDWAAKGTNLLGVRAVIAQSFERIHRSNLVGMGIVPFVLEEGTSWQS 828

Query: 130 LAAPGASVRVDVEA-----------QTVTLPDGSTARFPLDGFARYCLLNGVDELGFL 176
           L   G  V V +E             TVT  DGS+ + PL      C ++ +DEL +L
Sbjct: 829 LGLKGDEV-VSIEGLASIQPRQKTFATVTYADGSSKQVPL-----ICRIDTIDELEYL 880


Lambda     K      H
   0.321    0.138    0.411 

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: 404
Number of extensions: 21
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: 191
Length of database: 895
Length adjustment: 31
Effective length of query: 160
Effective length of database: 864
Effective search space:   138240
Effective search space used:   138240
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 (21.9 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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