GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisA in Kyrpidia tusciae DSM 2912

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_013076129.1 BTUS_RS10910 imidazole glycerol phosphate synthase subunit HisF

Query= curated2:Q18DL2
         (245 letters)



>NCBI__GCF_000092905.1:WP_013076129.1
          Length = 253

 Score =  114 bits (286), Expect = 1e-30
 Identities = 78/235 (33%), Positives = 124/235 (52%), Gaps = 14/235 (5%)

Query: 10  VIPAVDMQDGDVVQLVQGERGTETRYGDPVVAAKQWVEAGAKTLHLVDLDGAFEGDRMNA 69
           ++P  D+++G VV+ V      E   GDPV  A+ + E+GA  L L+D+  + EG    A
Sbjct: 6   IVPCFDVKNGRVVKNVSFLTN-ERDAGDPVELARYYDESGADELVLLDISASVEG---RA 61

Query: 70  TAVDAIIDA---VDIPVQLGGGIRTANDAASLLDRGVNRVILGTAAVENPDLVAELAESY 126
           T VD +      V IP+ +GGGI + +D   LL  G ++V + T AV++P LV E A+ Y
Sbjct: 62  TMVDVVARTAAEVFIPLTVGGGITSVDDIRVLLKAGADKVSINTGAVKHPQLVLEAAKRY 121

Query: 127 PGR-IIVSLDA------ADGEVVVSGWTESTGIDPAVAAARFADYGACGILFTDVDVEGK 179
             + I+V++D        D EV+++G    TG+     A +  + GA  IL T  D +G+
Sbjct: 122 GQQCIVVAIDGKYDGQKGDWEVLINGGRTRTGLSAVEWAKKMENLGAGEILLTSFDQDGR 181

Query: 180 LAGIQSSVTARVIDAVDIPVIASGGVASLDDIQTLHTTGAAATVVGTALYENKFT 234
             G   + T  + ++V+IPVIASGG    +    + T G A   +  +++  K T
Sbjct: 182 KDGYDLTFTRVISESVNIPVIASGGAGKKEHFYEVFTKGKADAALAASIFHFKET 236



 Score = 43.5 bits (101), Expect = 4e-09
 Identities = 33/113 (29%), Positives = 50/113 (44%), Gaps = 3/113 (2%)

Query: 129 RIIVSLDAADGEVV--VSGWT-ESTGIDPAVAAARFADYGACGILFTDVDVEGKLAGIQS 185
           RI+   D  +G VV  VS  T E    DP   A  + + GA  ++  D+    +      
Sbjct: 5   RIVPCFDVKNGRVVKNVSFLTNERDAGDPVELARYYDESGADELVLLDISASVEGRATMV 64

Query: 186 SVTARVIDAVDIPVIASGGVASLDDIQTLHTTGAAATVVGTALYENKFTLADA 238
            V AR    V IP+   GG+ S+DDI+ L   GA    + T   ++   + +A
Sbjct: 65  DVVARTAAEVFIPLTVGGGITSVDDIRVLLKAGADKVSINTGAVKHPQLVLEA 117


Lambda     K      H
   0.316    0.133    0.375 

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: 144
Number of extensions: 7
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 245
Length of database: 253
Length adjustment: 24
Effective length of query: 221
Effective length of database: 229
Effective search space:    50609
Effective search space used:    50609
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 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