GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuD in Acidithiobacillus ferrooxidans ATCC 23270

Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate WP_012536129.1 AFE_RS01995 aconitate hydratase

Query= curated2:O27440
         (162 letters)



>NCBI__GCF_000021485.1:WP_012536129.1
          Length = 645

 Score = 75.9 bits (185), Expect = 1e-18
 Identities = 54/168 (32%), Positives = 88/168 (52%), Gaps = 17/168 (10%)

Query: 7   KFPDDVDTDIIIPGRYLVM---RDPEKLREHVMEGLDPEFPSKVKP--GDFIVAGKNFGC 61
           +  DD+ TD I+P    V+    +   + E V   +D  FP++ K   G FIVAG N+G 
Sbjct: 473 RLEDDITTDHIMPAGAKVLPLRSNLPAISEFVFHMVDETFPARAKAAGGGFIVAGHNYGQ 532

Query: 62  GSSREHAPLALKGAGIAAVIAESFARIFYRNAINVGIPLLEAPGITE--KLNEGDEIEVD 119
           GSSREHA LA +  G+ AV+ +SFARI   N +N GI  L      +  K+  GD + ++
Sbjct: 533 GSSREHAALAPRYLGVRAVLVKSFARIHLANLVNFGILPLTFVDAADYAKVQAGDRLSLE 592

Query: 120 -----LDRGVIIRGD-DEFPFKKLPDFM----VEILEKGGLIPYLKKK 157
                L++ + +R +   F    +P       +E++ KGG + + +++
Sbjct: 593 LGGLALNKALTLRDETGGFEISVMPQLASARDLELILKGGALSWAREQ 640


Lambda     K      H
   0.320    0.146    0.436 

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: 284
Number of extensions: 14
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: 162
Length of database: 645
Length adjustment: 27
Effective length of query: 135
Effective length of database: 618
Effective search space:    83430
Effective search space used:    83430
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 (21.7 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Apr 10 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