GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisN in Desulfobacter vibrioformis DSM 8776

Align Histidine biosynthesis bifunctional protein HisB; EC 3.1.3.15; EC 4.2.1.19 (characterized)
to candidate WP_035236717.1 Q366_RS04490 imidazoleglycerol-phosphate dehydratase HisB

Query= SwissProt::Q9S5G5
         (355 letters)



>NCBI__GCF_000745975.1:WP_035236717.1
          Length = 195

 Score =  159 bits (401), Expect = 7e-44
 Identities = 81/178 (45%), Positives = 114/178 (64%), Gaps = 2/178 (1%)

Query: 167 RYAHVVRNTKETQIDVQVWLDREGGSKINTGVGFFDHMLDQIATHGGFRMEINVKGDLYI 226
           R + V R TKET+ID+++ LD +G + + TG+ FFDHML     HG F + ++  GDL +
Sbjct: 3   RQSEVSRQTKETRIDIRLNLDGQGNADLCTGIPFFDHMLTAFTVHGFFDLRVSATGDLDV 62

Query: 227 DDHHTVEDTGLALGEALKIALGDKRGICRFGFV-LPMDECLARCALDISGRPHLEYKAEF 285
           D HHTVEDTGL LG+A++ AL +K GI RFG   +PMDE L+R  +D+S RP+L Y    
Sbjct: 63  DFHHTVEDTGLVLGQAIQQALSEKGGIQRFGDASVPMDESLSRVTIDLSNRPYLVYNIPE 122

Query: 286 TYQRVGDLSTEMIEHFFRSLSYTMGVTLHLKT-KGKNDHHRVESLFKAFGRTLRQAIR 342
             +  G     +   FF+++    G  LH+ T  G+N+HH +ES+FKAFGR+L  A R
Sbjct: 123 NLKSRGPFDAHLAREFFQAVCVKGGFNLHINTCYGENEHHVLESIFKAFGRSLHAATR 180


Lambda     K      H
   0.322    0.140    0.420 

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: 208
Number of extensions: 12
Number of successful extensions: 4
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: 355
Length of database: 195
Length adjustment: 25
Effective length of query: 330
Effective length of database: 170
Effective search space:    56100
Effective search space used:    56100
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 (21.9 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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