GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisH in Thermophagus xiamenensis HS1

Align Imidazole glycerol phosphate synthase subunit HisH; EC 4.3.2.10; IGP synthase glutaminase subunit; EC 3.5.1.2; IGP synthase subunit HisH; ImGP synthase subunit HisH; IGPS subunit HisH (uncharacterized)
to candidate WP_010526802.1 GQW_RS0104315 type 1 glutamine amidotransferase

Query= curated2:P58789
         (194 letters)



>NCBI__GCF_000220155.1:WP_010526802.1
          Length = 236

 Score = 45.8 bits (107), Expect = 6e-10
 Identities = 41/142 (28%), Positives = 62/142 (43%), Gaps = 22/142 (15%)

Query: 53  LAPIKDIIIEGINEGKPFLGICLGMQLLFEESEESPGKEGLGIFKGKVVKLKNVRTPHIG 112
           LA  K  I E I+ GK  LGICLG QL+                  KV K      P IG
Sbjct: 68  LAEEKKAIKEAIDRGKTVLGICLGSQLI------------AATLGAKVTKNPE---PEIG 112

Query: 113 WNQVWIKKECKLFEGLKNGSYFYFVHSYHA----VPQDPDIIATTTDYENAEFVSSVCFE 168
           W  V +  + K     KN    + +  +H     +P     +AT+   +N  FV     +
Sbjct: 113 WFDVTLTDQGKQNPLFKNIENTFKIFQWHGDTFEIPAGALHLATSPVCKNQAFVFG---D 169

Query: 169 NIFGVQFHPEKSSKNGLILLRN 190
            + G+QFH E ++++  ++LR+
Sbjct: 170 RVLGLQFHLEVTNESLNLMLRD 191


Lambda     K      H
   0.320    0.142    0.427 

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: 135
Number of extensions: 6
Number of successful extensions: 2
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: 194
Length of database: 236
Length adjustment: 22
Effective length of query: 172
Effective length of database: 214
Effective search space:    36808
Effective search space used:    36808
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: 45 (21.9 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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