GapMind for Amino acid biosynthesis

 

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

Align Imidazole glycerol phosphate synthase subunit HisF; IGP synthase cyclase subunit; IGP synthase subunit HisF; ImGP synthase subunit HisF; IGPS subunit HisF; EC 4.3.2.10 (characterized)
to candidate AO356_03380 AO356_03380 glycosyl amidation-associated protein WbuZ

Query= SwissProt::Q7SIB9
         (252 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_03380
          Length = 253

 Score =  167 bits (423), Expect = 2e-46
 Identities = 95/229 (41%), Positives = 141/229 (61%), Gaps = 4/229 (1%)

Query: 5   KRIVPCLDVHAGRVVKGVNFVNLRDAGDPVEAARAYDEAGADELVFLDISATHEERAILL 64
           KR++PCL +    +VK V F + +  GDPV A R ++E   DELV LDI A+   R    
Sbjct: 4   KRVIPCLLLKDRGLVKTVKFKSPKYVGDPVNAIRIFNEKEVDELVLLDIEASILGREPDY 63

Query: 65  DVVARVAERVFIPLTVGGGVRSLEDARKLLLSGADKVSVNSAAVRRPELIRELADHFGAQ 124
           +++A VA   F+P+  GGG+R+LE A+++   G +K+++N+AA+   EL+R++AD FG+Q
Sbjct: 64  ELLAEVAGECFMPICYGGGIRTLEHAQRVFALGVEKIALNTAALADVELLRKIADQFGSQ 123

Query: 125 AVVLAIDAR--WRGDFPEVHVAGGRVPTGLHAVEWAVKGVELGAGEILLTSMDRDGTKEG 182
           +VV +ID +    G +  V+   G   T +  VEWA +  + GAGEI L S+DRDGT +G
Sbjct: 124 SVVCSIDCKKSLLGRY-SVYSQSGTKDTKVSPVEWAKRVEDAGAGEIFLNSIDRDGTMQG 182

Query: 183 YDLRLTRMVAEAVGVPVIASGGAGRMEHFLEAFQ-AGAEAALAASVFHF 230
           +D+ L + V   V +PV+A GGAG +    E F+ AG  A  A S F F
Sbjct: 183 FDIPLIKSVVAGVHIPVVACGGAGSIADLNEPFEKAGVSAVAAGSFFVF 231


Lambda     K      H
   0.321    0.138    0.398 

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: 8
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: 252
Length of database: 253
Length adjustment: 24
Effective length of query: 228
Effective length of database: 229
Effective search space:    52212
Effective search space used:    52212
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 (21.9 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