GapMind for Amino acid biosynthesis


Alignments for a candidate for hisC in Pseudomonas fluorescens FW300-N2E2

Align Histidinol-phosphate aminotransferase; EC; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate Pf6N2E2_5741 L-threonine 3-O-phosphate decarboxylase (EC

Query= curated2:Q1LT68
         (360 letters)

          Length = 330

 Score = 77.0 bits (188), Expect = 6e-19
 Identities = 47/130 (36%), Positives = 74/130 (56%), Gaps = 10/130 (7%)

           LD + ++ + +PNNPTG  + P    +LLD  HGR       LVVDEA++D  P  S+++

              H   L++LR+  K F LAG+R GF+LA   ++KLL + + P+ +S P   + +  L 

Query: 258 TKGIHQTKRR 267
               H  +R+
Sbjct: 237 DTDAHAYQRQ 246

Lambda     K      H
   0.323    0.138    0.428 

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: 248
Number of extensions: 15
Number of successful extensions: 3
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: 360
Length of database: 330
Length adjustment: 29
Effective length of query: 331
Effective length of database: 301
Effective search space:    99631
Effective search space used:    99631
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: 41 (22.0 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