GapMind for Amino acid biosynthesis

 

Aligments for a candidate for cmutase in Caulobacter crescentus NA1000

Align Salicylate synthase; Chorismate mutase; CM; Isochorismate synthase/isochorismate lyase; Mycobactin synthase protein; EC 5.4.99.5; EC 4.2.99.21; EC 5.4.4.2 (characterized)
to candidate CCNA_03048 CCNA_03048 para-aminobenzoate synthetase component I

Query= SwissProt::P9WFX1
         (450 letters)



>lcl|FitnessBrowser__Caulo:CCNA_03048 CCNA_03048 para-aminobenzoate
           synthetase component I
          Length = 524

 Score =  112 bits (280), Expect = 3e-29
 Identities = 83/270 (30%), Positives = 126/270 (46%), Gaps = 9/270 (3%)

Query: 180 VSDDPSGFRRRVAVAVDEIAAGRYHKVILSRCVEVPFAID---FPLTYRLGRRHNTPVRS 236
           V+ DP+ +   VA  V  I  G   +  ++R      A     F L  RL  +   P  +
Sbjct: 251 VASDPATYETAVAQVVARIVGGEIFQANIARAWTGRLAAGVDPFDLFVRLRAQSPAPFSA 310

Query: 237 FLLQLGGIRALGYSPELVTAVRADGVVITEPLAGTRALGRGPAIDRLARDDLESNSKEIV 296
           +  +L G   +  SPE    + A G + T+P+ GTR  GR P  DR    +L ++ K+  
Sbjct: 311 YW-RLPGRALVSNSPERFLKLDAAGAIQTQPIKGTRPRGRDPVEDRALAAELLASDKDRA 369

Query: 297 EHAISVRSSLEEITDIAEPGSAAVIDFMTVRERGSVQHLGSTIRARLDPSSDRMAALEAL 356
           E+ + V     ++  ++  GS    +   V    +V HL ST+ ARL P       L A 
Sbjct: 370 ENLMIVDLMRNDLARVSPAGSVRAPELFKVESFANVHHLVSTVTARLAPGRGVADLLRAS 429

Query: 357 FPAVTASGIPKAAGVEAIFRLDECPRGLYSGAVVMLSADGGLDAALTLRAAYQV----GG 412
           FP  + +G PK   ++ I  L E PRG Y G++     DG  D+++ +R    V    G 
Sbjct: 430 FPPGSITGAPKVQAMKVIAEL-EPPRGPYCGSLFWAGVDGAFDSSVLIRTVGLVQDGAGW 488

Query: 413 RTWLRAGAGIIEESEPEREFEETCEKLSTL 442
           R   RAGAGI+ +S+P  E  ET  K++ L
Sbjct: 489 RLEARAGAGIVADSDPRGERLETEAKIAAL 518


Lambda     K      H
   0.319    0.135    0.386 

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: 554
Number of extensions: 33
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: 450
Length of database: 524
Length adjustment: 34
Effective length of query: 416
Effective length of database: 490
Effective search space:   203840
Effective search space used:   203840
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: 52 (24.6 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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