GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisN in Thermophagus xiamenensis HS1

Align Histidinol-phosphatase [alternative form] (EC 3.1.3.15) (characterized)
to candidate WP_029626527.1 GQW_RS0105435 inositol monophosphatase

Query= reanno::Phaeo:GFF2154
         (250 letters)



>NCBI__GCF_000220155.1:WP_029626527.1
          Length = 267

 Score = 80.5 bits (197), Expect = 3e-20
 Identities = 65/215 (30%), Positives = 103/215 (47%), Gaps = 13/215 (6%)

Query: 29  DPVTIADRAAEQAMRSVLSELRPEDSILGEEFGETHGQSGR--TWVLDPIDGTRGFISGT 86
           D VT  D+A+EQ +   L  L PE   + EE  +T  + G+   W++DPIDGT  FI G 
Sbjct: 40  DFVTQIDKASEQKLVEALGNLLPEAGFIAEE--KTSDKVGKKFNWIIDPIDGTTNFIHGL 97

Query: 87  PTWGVLIALGDADGPFLGIVDQPYIGERFIGTPEG-ASLTGPLGHSALVTRATDSLSEAT 145
             + + IAL + D   LG+V +  + E F    +  A L G   H +      DSL    
Sbjct: 98  FPYAISIALQEDDQIVLGVVYEMGLDECFYSWKDAPAFLNGEEIHVSKTPTVADSL---- 153

Query: 146 LFTTFPEVGTEAERAAFQRVSAQVR----LTRYGMDCYAYALLAAGQCDLVIEAGLNAYD 201
           + T FP    +  +   + ++  ++    L R G      A +A G+ D   E  L A+D
Sbjct: 154 IATGFPYSNYQLIQNFMETLTFFMKNSHGLRRLGSAAVDLAYVACGRFDAFYEYNLKAWD 213

Query: 202 IQAPIAVIQAAGGVVTNWQGEPAHEGGQVLAAATA 236
           + A   ++Q AGG V++++G   +  G+ L +  A
Sbjct: 214 VAAGAFLVQQAGGKVSDFKGGNNYLFGRELVSGNA 248


Lambda     K      H
   0.317    0.134    0.392 

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: 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: 250
Length of database: 267
Length adjustment: 24
Effective length of query: 226
Effective length of database: 243
Effective search space:    54918
Effective search space used:    54918
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Jul 26 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