GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisB in Leptospirillum ferrooxidans C2-3

Align Imidazoleglycerol-phosphate dehydratase; Short=IGPD; EC 4.2.1.19 (characterized, see rationale)
to candidate WP_014450185.1 LFE_RS10415 imidazoleglycerol-phosphate dehydratase HisB

Query= uniprot:Q9HU41
         (197 letters)



>NCBI__GCF_000284315.1:WP_014450185.1
          Length = 204

 Score =  211 bits (537), Expect = 7e-60
 Identities = 106/197 (53%), Positives = 135/197 (68%), Gaps = 2/197 (1%)

Query: 2   AERKASVARDTLETQIKVSIDLDGTGKARFDTGVPFLDHMMDQIARHGLIDLDIECKGDL 61
           A R  SV R T ETQI  S++LDGTG++R DTG+PFLDHM+DQIARHG +D+++  KGDL
Sbjct: 9   ANRTFSVERKTRETQIVASLNLDGTGRSRVDTGIPFLDHMIDQIARHGHMDIELSVKGDL 68

Query: 62  HIDDHHTVEDIGITLGQAFAKAIGDKKGIRRYGHAYVPLDEALSRVVIDFSGRPGLQMHV 121
            +D HHTVED G+  G+   + +GD+ GI R+GH + PLDE+L+ VVID SGRP L   +
Sbjct: 69  EVDFHHTVEDAGLVFGELVDRCLGDRVGIARFGHFFAPLDESLAHVVIDLSGRPYLVWDL 128

Query: 122 PFTRAS-VGGFDVDLFMEFFQGFVNHAQVTLHIDNLRGHNTHHQIETVFKAFGRALRMAI 180
           PF R   VG  D DL M+FFQ     ++ T+H   L G N HH+IE +FKAF R L MA 
Sbjct: 129 PFERGERVGNMDPDLIMDFFQAVAVASRSTIHGRILYGRNLHHKIEAIFKAFARCLMMAA 188

Query: 181 ELDERMAGQMPSTKGCL 197
           E+D R    +PSTKG L
Sbjct: 189 EIDPRQK-SVPSTKGIL 204


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: 166
Number of extensions: 9
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: 197
Length of database: 204
Length adjustment: 21
Effective length of query: 176
Effective length of database: 183
Effective search space:    32208
Effective search space used:    32208
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 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