GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisF in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_1624 Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (EC 5.3.1.16)

Query= curated2:C4L176
         (255 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1624
          Length = 245

 Score =  107 bits (267), Expect = 2e-28
 Identities = 75/247 (30%), Positives = 128/247 (51%), Gaps = 15/247 (6%)

Query: 6   IIPCLDVKEGRVVKGIEFVQLRDI----GDPVEIAKYYDESGADELVFLDITASTERRQT 61
           IIP +D+K+G  V+ +   ++ D      DPV +A  + E G   L  +D+  + E +  
Sbjct: 3   IIPAIDLKDGACVR-LRQGRMEDSTVFSDDPVSMAAKWVEGGCRRLHLVDLNGAFEGQPV 61

Query: 62  MLDVVSAVARKV-FIPLTVGGGIRSLEDISSLLKAGADKVSLNTLAVESPSLIREAADRF 120
             +VV+A+A++   +P+ +GGGIRSLE I   +KAG   V + T AV+ P+ + EA   F
Sbjct: 62  NGEVVTAIAKRYPNLPIQIGGGIRSLETIEHYVKAGVSYVIIGTKAVKDPAFVAEACRAF 121

Query: 121 GSQCIVVAIDVKFKDGEYYVYTYGGKQKTDLLAVEWAKQVAALGAGELLVTSMNQDGKQS 180
             + ++V +D   KDG  +V T G  + + +  ++ AKQ  A G   ++ T + +DG   
Sbjct: 122 PGK-VIVGLDA--KDG--FVATDGWAEISTIQVIDLAKQFEADGVSAIVYTDIAKDGMMQ 176

Query: 181 GYDLSILEQLREVVDIPIIASGGAGNAEHVVEALEKVDAALLASI----LHDRKTTVEEV 236
           G ++S    L     IP+IASGG  N   +   L+     ++ +I    +++    V E 
Sbjct: 177 GCNVSYTAALAAATKIPVIASGGIHNLGDIKSLLDAKAPGIIGAITGRAIYEGTLDVAEA 236

Query: 237 KHVCKSH 243
           +  C S+
Sbjct: 237 QAFCDSY 243


Lambda     K      H
   0.318    0.135    0.373 

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: 157
Number of extensions: 10
Number of successful extensions: 5
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: 255
Length of database: 245
Length adjustment: 24
Effective length of query: 231
Effective length of database: 221
Effective search space:    51051
Effective search space used:    51051
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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