GapMind for Amino acid biosynthesis

 

Aligments for a candidate for hisA in Sphingomonas koreensis DSMZ 15582

Align 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; EC 5.3.1.16; Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (uncharacterized)
to candidate Ga0059261_1048 Ga0059261_1048 imidazoleglycerol phosphate synthase, cyclase subunit

Query= curated2:Q9HN14
         (242 letters)



>lcl|FitnessBrowser__Korea:Ga0059261_1048 Ga0059261_1048
           imidazoleglycerol phosphate synthase, cyclase subunit
          Length = 255

 Score =  134 bits (336), Expect = 2e-36
 Identities = 88/240 (36%), Positives = 135/240 (56%), Gaps = 9/240 (3%)

Query: 8   VLPAVDMQDGQVVQLVQGERGTERTYGDPVDAATDWVAAGAEALHLVDLDGAFEGARANA 67
           V+P +D+ +G+VV+ V       R  GDPV+ A  + AAGA+ L  +D+  + E      
Sbjct: 7   VIPCLDVANGRVVKGVNFVN--LRDAGDPVEQARAYDAAGADELCFLDITASHEARGTII 64

Query: 68  TAVEDILDATDVSVQVGGGIRSAEDATALLDRGVDRVILGTAAIETPDIVGEIAAAY-SD 126
             V    +   + + VGGG+RSAEDA ALL  G D+V + +AA+  P++V EIA  + S 
Sbjct: 65  DVVRRTAEVCFMPLTVGGGVRSAEDARALLLAGADKVAVNSAAVTRPEVVSEIAERFGSQ 124

Query: 127 GVLVSLDAK---DG--EVVVEGWTEGTGMDPVAAAQRYADLGAAGILFTDVDVEGKQEGV 181
            ++ S+DA+   DG  EV   G  + TG+D V  A   A LGA  +L T +D +G ++G 
Sbjct: 125 CIVASVDARRVADGRWEVFTHGGRKPTGIDAVEHALHLAKLGAGELLLTSMDRDGTRDGY 184

Query: 182 RTDPVRDLVDSVDIPVIASGGVATVDDVRALEAAGAAGAVVGTALYE-GNFTLADAQAAV 240
             D +R + D V +PV+ASGGV  +D + A    G A AV+  +++  G  ++  A AA+
Sbjct: 185 DLDLIRTIADRVRVPVVASGGVGNLDHLVAGIRDGHASAVLAASIFHFGEASIVGAHAAL 244


Lambda     K      H
   0.314    0.133    0.369 

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: 199
Number of extensions: 13
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: 242
Length of database: 255
Length adjustment: 24
Effective length of query: 218
Effective length of database: 231
Effective search space:    50358
Effective search space used:    50358
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 46 (22.3 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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