GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisN in Nocardiopsis lucentensis DSM 44048

Align Histidine biosynthesis bifunctional protein HisB; EC 3.1.3.15; EC 4.2.1.19 (characterized)
to candidate WP_017600198.1 D471_RS0119675 imidazoleglycerol-phosphate dehydratase HisB

Query= SwissProt::D2QPE6
         (382 letters)



>NCBI__GCF_000341125.1:WP_017600198.1
          Length = 197

 Score =  187 bits (474), Expect = 3e-52
 Identities = 106/197 (53%), Positives = 132/197 (67%), Gaps = 5/197 (2%)

Query: 190 ARTALVERNTKETQIRVELNLDGRGRADMHTGLGFFDHMLDQVAKHSGADLAIHVNGDLH 249
           +RT  VER TKET++ VE++LDG G AD+ TG+GFFDHMLDQ+AKH   DL +   GDLH
Sbjct: 2   SRTGRVERTTKETKVLVEIDLDGTGVADVSTGVGFFDHMLDQLAKHGLFDLTVRTEGDLH 61

Query: 250 IDEHHTIEDTALALGEAYRRALGDKRGISRYG-FLLPMDEALAQVGIDFSGRPWLVW-DA 307
           ID HHT+EDTALALG A+R ALGDKRGI R+    +P+DEALA+V +D SGRP+LV  + 
Sbjct: 62  IDSHHTMEDTALALGAAFREALGDKRGIRRFADTKVPLDEALAEVTVDVSGRPYLVHSEP 121

Query: 308 EFKREKIG-DMPTEMFYHFFKSFSDTALCNLNIKVE-GDNEHHKIEAIFKAFAKAIKMAV 365
           E     IG D  T M  H  +SF   A   L++ V  G N HH +E  FKA A+A++ A 
Sbjct: 122 EGMAPIIGRDYDTTMTRHILESFVAQARVALHVHVPYGRNAHHIVECQFKALARALRAAT 181

Query: 366 RRDINELDNLPSTKGVL 382
             D    D +PSTKG L
Sbjct: 182 ENDPRVTD-IPSTKGAL 197


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: 220
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: 197
Length adjustment: 25
Effective length of query: 357
Effective length of database: 172
Effective search space:    61404
Effective search space used:    61404
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 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