GapMind for Amino acid biosynthesis

 

Aligments for a candidate for hisB in Desulfovibrio vulgaris Miyazaki F

Align Imidazoleglycerol-phosphate dehydratase; Short=IGPD; EC 4.2.1.19 (characterized, see rationale)
to candidate 8502416 DvMF_3122 Imidazoleglycerol-phosphate dehydratase (RefSeq)

Query= uniprot:Q9HU41
         (197 letters)



>lcl|FitnessBrowser__Miya:8502416 DvMF_3122
           Imidazoleglycerol-phosphate dehydratase (RefSeq)
          Length = 196

 Score =  155 bits (392), Expect = 4e-43
 Identities = 85/198 (42%), Positives = 117/198 (59%), Gaps = 4/198 (2%)

Query: 1   MAERKASVARDTLETQIKVSIDLDGTGKARFDTGVPFLDHMMDQIARHGLIDLDIECKGD 60
           M++R A+V R+T ET I++ + +DG G     TG    DH++   A     DL + C GD
Sbjct: 1   MSQRSAAVFRETKETSIRLDLVVDGQGLVNVHTGFGMADHVITLAAFWAGFDLTLSCTGD 60

Query: 61  LHIDDHHTVEDIGITLGQAFAKAIGDKKGIRRYGHAYVPLDEALSRVVIDFSGRPGLQMH 120
           L ID HHTVED+G+ LGQA A+A+G++ GI R G A VP+DEAL+ V ID SGRP L+  
Sbjct: 61  LEIDAHHTVEDVGLCLGQALAEALGERSGIARVGFARVPMDEALADVCIDISGRPWLEWR 120

Query: 121 -VPFTRASVGGFDVDLFMEFFQGFVNHAQVTLHIDNLRGHNTHHQIETVFKAFGRALRMA 179
                   + G + DL+ EF + F + A++ LH+  L G N HH +E+  K  G ALR A
Sbjct: 121 GDDLLPPVIAGQERDLWREFLKAFASAARMNLHVSFLYGRNGHHLLESAAKGLGLALRQA 180

Query: 180 IELDERMAGQMPSTKGCL 197
           +  D      + STKG L
Sbjct: 181 VRRDRE---TLLSTKGSL 195


Lambda     K      H
   0.325    0.141    0.421 

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: 141
Number of extensions: 12
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: 197
Length of database: 196
Length adjustment: 20
Effective length of query: 177
Effective length of database: 176
Effective search space:    31152
Effective search space used:    31152
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 45 (21.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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