GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisA in Pseudomonas stutzeri RCH2

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 GFF156 Psest_0156 imidazoleglycerol phosphate synthase, cyclase subunit

Query= curated2:Q9HN14
         (242 letters)



>FitnessBrowser__psRCH2:GFF156
          Length = 256

 Score =  129 bits (324), Expect = 6e-35
 Identities = 81/242 (33%), Positives = 132/242 (54%), Gaps = 13/242 (5%)

Query: 8   VLPAVDMQDGQVVQLVQGERGTERTYGDPVDAATDWVAAGAEALHLVDLDGAFEGARANA 67
           ++P +D+ +G+VV+ VQ E    R  GDPV+ A  +   GA+ +  +D+  + +      
Sbjct: 7   IIPCLDVDNGRVVKGVQFEN--IRDAGDPVEIARRYDEQGADEITFLDITASVDNRDTTL 64

Query: 68  TAVEDILDATDVSVQVGGGIRSAEDATALLDRGVDRVILGTAAIETPDIVGEIAAAY-SD 126
             VE +     + + VGGG+RS +D   LL+ G D+V + TAA+  PD VGE A  + S 
Sbjct: 65  HTVERMASQVFIPLTVGGGVRSVQDIRNLLNAGADKVSINTAAVFNPDFVGEAADRFGSQ 124

Query: 127 GVLVSLDAKD---------GEVVVEGWTEGTGMDPVAAAQRYADLGAAGILFTDVDVEGK 177
            ++V++DAK           E+   G  + TG+D VA A++  DLGA  IL T +D +G 
Sbjct: 125 CIVVAIDAKKVSAPGEPGRWEIFTHGGRKPTGLDAVAWAKKMEDLGAGEILLTSMDQDGV 184

Query: 178 QEGVRTDPVRDLVDSVDIPVIASGGVATVDDVRALEAAGAAGAVVGTALYE-GNFTLADA 236
           + G      R + +++ IPVIASGGV  +  +      G A AV+  +++  G +T+ +A
Sbjct: 185 KSGYDLGVTRAISEALCIPVIASGGVGNLQHLADGILEGKADAVLAASIFHFGEYTIPEA 244

Query: 237 QA 238
           +A
Sbjct: 245 KA 246


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: 174
Number of extensions: 13
Number of successful extensions: 4
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: 256
Length adjustment: 24
Effective length of query: 218
Effective length of database: 232
Effective search space:    50576
Effective search space used:    50576
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:

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