GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisA in Salinicoccus carnicancri Crm

Align 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; EC 5.3.1.16; Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (uncharacterized)
to candidate WP_017550017.1 C792_RS0113620 imidazole glycerol phosphate synthase subunit HisF

Query= curated2:A3CTR9
         (239 letters)



>NCBI__GCF_000330705.1:WP_017550017.1
          Length = 254

 Score =  101 bits (251), Expect = 2e-26
 Identities = 69/227 (30%), Positives = 111/227 (48%), Gaps = 9/227 (3%)

Query: 3   IYPAVDILDGRCVQLVQGRPEAATVYGDPAAWAHRWLDEGADGLHVVNLDGAFGRARKNA 62
           I P +D+ DGR V+ V          GDP   A R+ +EGAD L  +++           
Sbjct: 6   IIPCLDVKDGRVVKGVNFI--GLRDIGDPVELAKRYNEEGADELVFLDISKTQEGHDLMI 63

Query: 63  DLIRAFTRETETFTELGGGIRSVEDAAGWLDAGVDRVIVSTQAVREPEMIRTLAEEFGGE 122
           D+IR   +E      +GGG+ SV D    L AG D+V +++ A+R+P +I+T A+ FG +
Sbjct: 64  DVIRDTAKELFIPLTIGGGVSSVGDIRQLLGAGADKVSINSAALRDPGLIKTAADVFGSQ 123

Query: 123 RVMAGIDARAGEVMIE------GWERPAG-SYLSWAERFESLGAGSLLYTNVDVEGLQQG 175
            +   ID +   V  +      G  +  G     W E+  +LGAG LL T++D +G++QG
Sbjct: 124 CICIAIDVKYDAVKADYFVFTHGGSKDTGIRAFEWIEQCAALGAGELLITSMDHDGVKQG 183

Query: 176 IAIEPVTELLARVKVPVVVSGGISSPGDVAALRDAGAAGAVLGSALY 222
                + +    V +P++ SGG   PG    L       A L ++++
Sbjct: 184 FNTVFLKQAKELVDIPIIASGGAGDPGHFIELFRETDVSAGLAASIF 230


Lambda     K      H
   0.317    0.135    0.397 

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: 123
Number of extensions: 7
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: 239
Length of database: 254
Length adjustment: 24
Effective length of query: 215
Effective length of database: 230
Effective search space:    49450
Effective search space used:    49450
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 (21.6 bits)
S2: 46 (22.3 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