GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisH in Maridesulfovibrio zosterae DSM 11974

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_245577071.1 H589_RS0107915 aminodeoxychorismate/anthranilate synthase component II

Query= curated2:Q88UE1
         (208 letters)



>NCBI__GCF_000425265.1:WP_245577071.1
          Length = 189

 Score = 37.0 bits (84), Expect = 2e-07
 Identities = 33/121 (27%), Positives = 51/121 (42%), Gaps = 29/121 (23%)

Query: 66  QALARSGKPVLGICLGMQLLFESSSEYGEHAGL-GLLSGRVSALPTDLNVKVPQMGWNQN 124
           +A+ +SGKPVLG+CLGMQ++ E     G+ + L G   GR          K+   G   N
Sbjct: 72  EAVIKSGKPVLGVCLGMQIINEYCG--GKTSRLKGCFHGRTE--------KISFAGLQLN 121

Query: 125 ELRRPDSPFASIDAAYTYFVHSYYA--VCPATEIVATVQHGVQVPSIVQQQNVIGMQFHP 182
             R                 HS +   +    E+++    G+ +        ++G QFHP
Sbjct: 122 VAR----------------YHSLFCSEIGDGLEVISENNEGIPMAVSHGSLPLLGYQFHP 165

Query: 183 E 183
           E
Sbjct: 166 E 166


Lambda     K      H
   0.319    0.133    0.380 

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: 97
Number of extensions: 9
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 208
Length of database: 189
Length adjustment: 20
Effective length of query: 188
Effective length of database: 169
Effective search space:    31772
Effective search space used:    31772
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 25 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