GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cmutase in Escherichia coli BW25113

Align Salicylate synthase; Chorismate mutase; CM; EC 5.4.99.5; Isochorismate synthase/isochorismate lyase; EC 4.2.99.21; EC 5.4.4.2; Mycobactin synthase protein (uncharacterized)
to candidate 15384 b1264 anthranilate synthase component I (NCBI)

Query= curated2:Q73XV3
         (450 letters)



>FitnessBrowser__Keio:15384
          Length = 520

 Score =  107 bits (266), Expect = 1e-27
 Identities = 80/250 (32%), Positives = 123/250 (49%), Gaps = 12/250 (4%)

Query: 198 IAAGRYHKVILSRCLQVPFAVDFPSTYRLARRHNTPVRSFLLRLGGIRAVGYSPELVAAV 257
           I AG   +V+ SR   +P      + Y L + + +P   F ++       G SPE  +++
Sbjct: 256 IRAGEIFQVVPSRRFSLPCPSPLAAYYVLKKSNPSPYM-FFMQDNDFTLFGASPE--SSL 312

Query: 258 RHDGV---VVTEPLAGTRAFGR---GAL-HDRQARDDLE--SNSKEIVEHAISVRSSLQE 308
           ++D     +   P+AGTR  GR   G+L  D  +R +LE  ++ KE+ EH + V  +  +
Sbjct: 313 KYDATSRQIEIYPIAGTRPRGRRADGSLDRDLDSRIELEMRTDHKELSEHLMLVDLARND 372

Query: 309 MAEIAEPGTAVVTDFMTVRERGSVQHLGSTVSGRLGTSNDRMDALEALFPAVTASGIPKA 368
           +A I  PG+  V D   V     V HL S V G L    D + A  A     T SG PK 
Sbjct: 373 LARICTPGSRYVADLTKVDRYSYVMHLVSRVVGELRHDLDALHAYRACMNMGTLSGAPKV 432

Query: 369 GGVEAILRLDEGPRGLYSGAVVMVSADGALDAALTLRAAYEHDGKTWLRAGAGIIEESTP 428
             ++ I   +   RG Y GAV   +A G LD  + +R+A   +G   ++AGAG++ +S P
Sbjct: 433 RAMQLIAEAEGRRRGSYGGAVGYFTAHGDLDTCIVIRSALVENGIATVQAGAGVVLDSVP 492

Query: 429 EREFEETCEK 438
           + E +ET  K
Sbjct: 493 QSEADETRNK 502


Lambda     K      H
   0.318    0.135    0.391 

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: 372
Number of extensions: 9
Number of successful extensions: 1
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: 520
Length adjustment: 34
Effective length of query: 416
Effective length of database: 486
Effective search space:   202176
Effective search space used:   202176
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 (21.7 bits)
S2: 52 (24.6 bits)

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

Links

Downloads

Related tools

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