GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisF in Pseudomonas fluorescens FW300-N2E2

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 Pf6N2E2_3839 Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (EC 5.3.1.16)

Query= curated2:Q7UKJ9
         (262 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3839
          Length = 245

 Score =  102 bits (253), Expect = 1e-26
 Identities = 69/222 (31%), Positives = 116/222 (52%), Gaps = 16/222 (7%)

Query: 9   CLDVHGGRVVKGTNFVNLRDAGDPVEVARRYEAEGADELVFLDITASHEERAILLDVVRR 68
           C+ +  GR+   T F     + DPV +A ++   G   L  +D+  + E + +  +VV  
Sbjct: 14  CVRLRQGRMEDSTVF-----SDDPVSMAAKWVEGGCRRLHLVDLNGAFEGQPVNGEVVTA 68

Query: 69  TAEQV-FMPLTVGGGVRTVEDVRALLSAGCDKVSINSSAVTNPDFIRQAADRFGRQCIVV 127
            A++   +P+ +GGG+R++E +   + AG   V I + AV  P+F+ +A   F  + ++V
Sbjct: 69  IAKRYPNLPIQIGGGIRSLETIEHYVKAGVSYVIIGTKAVKEPEFVAEACRAFPGK-VIV 127

Query: 128 NIDPKRVQKDGEEFWEVHINGGRKPTGLQAVQWAKRVEELGAGEIVLTSMDADGTCDGYD 187
            +D K    DG     V  +G  + + +Q +  AKR E  G   IV T +  DG   G +
Sbjct: 128 GLDAK----DGF----VATDGWAEVSTVQVIDLAKRFEADGVSAIVYTDIAKDGMMQGCN 179

Query: 188 IPITRAVSEAVRIPVVASGGAGNPDHLVEAIRDGKADAVLAA 229
           +P T A++ A RIPV+ASGG  N    ++A+ D KA  ++ A
Sbjct: 180 VPFTAALAAATRIPVIASGGIHNLGD-IKALLDAKAPGIIGA 220


Lambda     K      H
   0.320    0.137    0.404 

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: 186
Number of extensions: 7
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: 262
Length of database: 245
Length adjustment: 24
Effective length of query: 238
Effective length of database: 221
Effective search space:    52598
Effective search space used:    52598
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: 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