GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cmutase in Lentibacillus jeotgali Grbi

Align Bifunctional chorismate mutase/prephenate dehydratase; Chorismate mutase-prephenate dehydratase; P-protein; EC 5.4.99.5; EC 4.2.1.51 (characterized)
to candidate WP_010531115.1 ON01_RS11090 prephenate dehydratase

Query= SwissProt::P27603
         (365 letters)



>NCBI__GCF_000224785.1:WP_010531115.1
          Length = 286

 Score =  135 bits (339), Expect = 2e-36
 Identities = 92/282 (32%), Positives = 150/282 (53%), Gaps = 21/282 (7%)

Query: 95  LRVAYLGPEGTFSQAAALKHFG----HSVISKPMAAIDEVFREVVAGAVNFGVVPVENST 150
           +++ YLGP GTF++ A    F      S  + P   ID VF E     ++ GVVP+EN+ 
Sbjct: 2   VKIGYLGPRGTFTKLAVDTAFNGENKQSFTTVP-ECIDAVFHE----EIDIGVVPLENAI 56

Query: 151 EGAVNHTLDSFLEHDI--VICGEVELRIHHHLLV--GETTKTDRITRIYSHAQSLAQCRK 206
           EG V  T+D +L H +   +  E+ + I  +LLV  G T +   +  ++SH+ ++AQC +
Sbjct: 57  EGTVQITVD-YLVHQVRLPVVAEIVVPIQQNLLVKPGFTGEISEVLEVFSHSHAIAQCHQ 115

Query: 207 WLDAHYPNVERVAVSSNADAAKRVK-SEWNSAAIAGDMAAQLYGLSKLAEKIEDRPVNST 265
           +L  H P+ +    SS   AA+ V  S+ N AAI   +AA  YGL    E I D P N T
Sbjct: 116 FLHMHMPDAKLNFTSSTGKAAEVVSGSDRNIAAIGNRLAASEYGLDIFHENIHDYPNNHT 175

Query: 266 RFLIIGSQEV-----PPTGDDKTSIIVSMRNK-PGALHELLMPFHSNGIDLTRIETRPSR 319
           RF ++   +         G +KTS+++++ +   GAL+++L  F    ++L++IE+RP +
Sbjct: 176 RFAVLAKDKEIVNVKHEAGAEKTSLLITLPSDYAGALYQVLAAFAWRRMNLSKIESRPMK 235

Query: 320 SGKWTYVFFIDCMGHHQDPLIKNVLEKIGHEAVALKVLGSYP 361
           +G   Y F +D    + D L   V  ++      + +LG+YP
Sbjct: 236 TGLGNYFFIVDVNQPYDDVLFPGVKAELEALGCNVTILGTYP 277


Lambda     K      H
   0.319    0.133    0.390 

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: 213
Number of extensions: 11
Number of successful extensions: 5
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: 365
Length of database: 286
Length adjustment: 28
Effective length of query: 337
Effective length of database: 258
Effective search space:    86946
Effective search space used:    86946
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: 48 (23.1 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