GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisF in Pseudomonas simiae WCS417

Align Imidazole glycerol phosphate synthase subunit HisF; EC 4.3.2.10; IGP synthase cyclase subunit; IGP synthase subunit HisF; ImGP synthase subunit HisF; IGPS subunit HisF (uncharacterized)
to candidate GFF309 PS417_01575 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase

Query= curated2:Q8ZY16
         (253 letters)



>FitnessBrowser__WCS417:GFF309
          Length = 245

 Score =  100 bits (249), Expect = 3e-26
 Identities = 74/242 (30%), Positives = 117/242 (48%), Gaps = 10/242 (4%)

Query: 7   IIPCLDI-DGKAGVVVKGVNFQGIREVGDPVEMAVRYEEEGADEIAILDITAAPEGRATF 65
           IIP +D+ DG    + +G          DPV MA ++ E G   + ++D+  A EG+   
Sbjct: 3   IIPAIDLKDGACVRLRQGRMEDSTVFSDDPVSMAAKWVEGGCRRLHLVDLNGAFEGQPVN 62

Query: 66  IDSVKRVAEAV-SIPVLVGGGVRSLEDATTLFRAGADKVSVNTAAVRNPQLVALLAREFG 124
            + V  +A+   S+P+ +GGG+RSLE      +AG   V + T AV++P  VA   R F 
Sbjct: 63  GEVVTAIAKRYPSLPIQIGGGIRSLETIEHYVKAGVSYVIIGTKAVKDPAFVAEACRAFP 122

Query: 125 SQSTVVAIDAKWNGEYYEVYVKGGREATGLDAVKWAKEVEELGAGEILLTSIDRDGTGLG 184
            +  +V +DAK       V   G  E + +  +  AK+ E  G   I+ T I +DG   G
Sbjct: 123 GK-VIVGLDAKDG----FVATDGWAEISTVQVIDLAKQFEADGVSAIVYTDIAKDGMMQG 177

Query: 185 YDVELIRRVADSVRIPVIASGG---AGRVEHFYEAAAAGADAVLAASLFHFRVLSIAQVK 241
            +V     +A + +IPVIASGG    G ++   +A A G    +     +   L +A+ +
Sbjct: 178 CNVPFTAALAAATKIPVIASGGIHNLGDIKSLLDAKAPGIIGAITGRAIYEGTLDVAEAQ 237

Query: 242 RY 243
            Y
Sbjct: 238 AY 239


Lambda     K      H
   0.318    0.137    0.381 

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: 169
Number of extensions: 9
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: 253
Length of database: 245
Length adjustment: 24
Effective length of query: 229
Effective length of database: 221
Effective search space:    50609
Effective search space used:    50609
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: 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