GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisN in Geobacter metallireducens GS-15

Align Histidine biosynthesis bifunctional protein HisB; EC 3.1.3.15; EC 4.2.1.19 (characterized)
to candidate WP_004512358.1 GMET_RS01925 imidazoleglycerol-phosphate dehydratase HisB

Query= SwissProt::D2QPE6
         (382 letters)



>NCBI__GCF_000012925.1:WP_004512358.1
          Length = 195

 Score =  171 bits (432), Expect = 2e-47
 Identities = 89/195 (45%), Positives = 125/195 (64%), Gaps = 3/195 (1%)

Query: 190 ARTALVERNTKETQIRVELNLDGRGRADMHTGLGFFDHMLDQVAKHSGADLAIHVNGDLH 249
           +R A +ER TKETQI++ L +DG G A + T + F DHMLD  A+H   +L +   GD+ 
Sbjct: 2   SRKATIERVTKETQIKLSLEIDGAGEAKICTSVPFLDHMLDLFARHGLFNLQVDARGDID 61

Query: 250 IDEHHTIEDTALALGEAYRRALGDKRGISRYG-FLLPMDEALAQVGIDFSGRPWLVWDAE 308
           ID HHT+ED  + LG+A + ALGDK+GI RYG   +PMDE LA V +D SGRP+LV+   
Sbjct: 62  IDFHHTVEDIGIVLGQALKEALGDKKGIRRYGQASVPMDETLASVAVDISGRPYLVYHVA 121

Query: 309 FKREKIGDMPTEMFYHFFKSFSDTALCNLNIKV-EGDNEHHKIEAIFKAFAKAIKMAVRR 367
             + KIG+   E+   FF++  +    N+++ V  GDN HH +EA FKAFA+A+  A + 
Sbjct: 122 LPKVKIGEFDVELVREFFQAVVNNLGANIHVNVMYGDNVHHMVEACFKAFARAMDQATQV 181

Query: 368 DINELDNLPSTKGVL 382
           D   ++ + STKG L
Sbjct: 182 D-PRIEGVMSTKGKL 195


Lambda     K      H
   0.320    0.136    0.403 

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: 200
Number of extensions: 11
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: 382
Length of database: 195
Length adjustment: 25
Effective length of query: 357
Effective length of database: 170
Effective search space:    60690
Effective search space used:    60690
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: 47 (22.7 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