GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisF in Pseudomonas fluorescens FW300-N2C3

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 AO356_09800 AO356_09800 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase

Query= curated2:Q0A5D3
         (265 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_09800
          Length = 245

 Score = 99.8 bits (247), Expect = 5e-26
 Identities = 76/247 (30%), Positives = 121/247 (48%), Gaps = 20/247 (8%)

Query: 7   IIPCLDVDGGRVVKGVKFVDIRDA----GDPVEIARRYDAMGADEITFLDITASHERRDT 62
           IIP +D+  G  V+ ++   + D+     DPV +A ++   G   +  +D+  + E +  
Sbjct: 3   IIPAIDLKDGACVR-LRQGRMEDSTVFSDDPVSMAAKWVEGGCRRLHLVDLNGAFEGQPV 61

Query: 63  MVQVVEKVASQV-FIPLTVGGGIREVADIRRMLNAGADKVGINTAAVARPEFVAEAAERF 121
             +VV  +A +   +P+ +GGGIR +  I   + AG   V I T AV  PEFVAEA   F
Sbjct: 62  NGEVVTAIAKRYPNLPIQIGGGIRSLETIEHYVKAGVSYVIIGTKAVKEPEFVAEACRAF 121

Query: 122 GSQCIVVAVDAKQVSRADEPARWEVFTHGGRKATGLDAVEWAGRMAELGAGEILLTSMDR 181
             + ++V +DAK            V T G  + + +  ++ A R    G   I+ T + +
Sbjct: 122 PGK-VIVGLDAKD---------GFVATDGWAEVSTVQVIDLAKRFEADGVSAIVYTDIAK 171

Query: 182 DGTQAGFDLALTRAVSDAVPVPVIASGGVGTLSD---LADGVLEGGADAVLAASIFHFGR 238
           DG   G ++  T A++ A  +PVIASGG+  L D   L D    G   A+   +I+  G 
Sbjct: 172 DGMMQGCNVPFTAALAAATKIPVIASGGIHNLGDIKALLDAKAPGIIGAITGRAIYE-GT 230

Query: 239 YTVAEAK 245
             VAEA+
Sbjct: 231 LDVAEAQ 237


Lambda     K      H
   0.320    0.136    0.388 

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: 166
Number of extensions: 11
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: 265
Length of database: 245
Length adjustment: 24
Effective length of query: 241
Effective length of database: 221
Effective search space:    53261
Effective search space used:    53261
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 (21.8 bits)
S2: 47 (22.7 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