GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisN in Trichodesmium erythraeum IMS101

Align Histidine biosynthesis bifunctional protein HisB; EC 3.1.3.15; EC 4.2.1.19 (characterized)
to candidate WP_011611646.1 TERY_RS09605 imidazoleglycerol-phosphate dehydratase

Query= SwissProt::D2QPE6
         (382 letters)



>NCBI__GCF_000014265.1:WP_011611646.1
          Length = 213

 Score =  184 bits (467), Expect = 2e-51
 Identities = 92/199 (46%), Positives = 132/199 (66%), Gaps = 2/199 (1%)

Query: 186 LRLPARTALVERNTKETQIRVELNLDGRGRADMHTGLGFFDHMLDQVAKHSGADLAIHVN 245
           L LP R A V+R T ET + V LNLDG G    +TG+ F DHML Q++ H   DL +   
Sbjct: 15  LNLPVRRASVKRKTGETDVTVNLNLDGVGNCQANTGIPFLDHMLHQISSHGLIDLDVQAV 74

Query: 246 GDLHIDEHHTIEDTALALGEAYRRALGDKRGISRYG-FLLPMDEALAQVGIDFSGRPWLV 304
           GD+ ID+HHT ED  + LG+A ++ALGD++GI R+G FL P+DEAL +V +DFSGRP L 
Sbjct: 75  GDIEIDDHHTNEDVGITLGQALKQALGDRKGIVRFGHFLAPLDEALVEVALDFSGRPHLS 134

Query: 305 WDAEFKREKIGDMPTEMFYHFFKSFSDTALCNLNIK-VEGDNEHHKIEAIFKAFAKAIKM 363
           +  E   +++G+  T++   FF + ++ +L  L+I+ + G N HH IEA FKAFA++++M
Sbjct: 135 YGLEMPTQRVGNYDTQLVREFFVALANNSLMTLHIRQLGGINSHHIIEAGFKAFARSLRM 194

Query: 364 AVRRDINELDNLPSTKGVL 382
           A   D   +  +PS+KGVL
Sbjct: 195 ATEIDPRRVGEIPSSKGVL 213


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: 216
Number of extensions: 12
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: 213
Length adjustment: 26
Effective length of query: 356
Effective length of database: 187
Effective search space:    66572
Effective search space used:    66572
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