GapMind for Amino acid biosynthesis

 

Aligments for a candidate for cmutase in Pseudomonas stutzeri RCH2

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 GFF3583 Psest_3650 anthranilate synthase component I, non-proteobacterial lineages

Query= curated2:Q73XV3
         (450 letters)



>lcl|FitnessBrowser__psRCH2:GFF3583 Psest_3650 anthranilate synthase
           component I, non-proteobacterial lineages
          Length = 494

 Score =  149 bits (377), Expect = 2e-40
 Identities = 88/253 (34%), Positives = 132/253 (52%), Gaps = 1/253 (0%)

Query: 186 NYRDRVASAVAEIAAGRYHKVILSRCLQVPFAVDFPSTYRLARRHNTPVRSFLLRLGGIR 245
           +Y   V      I AG   +V++S+ + +PF       YR  R  N     +    G   
Sbjct: 225 DYEQAVNRIKDYILAGDCMQVVISQRMSIPFKAAPIDLYRALRCFNPTPYMYFFNFGDFH 284

Query: 246 AVGYSPELVAAVRHDGVVVTEPLAGTRAFGRGALHDRQARDDLESNSKEIVEHAISVRSS 305
            VG SPE++  V  +G+V   P+AGTR  G     D     DL S++KE+ EH + +   
Sbjct: 285 VVGSSPEVLVRVE-EGLVTVRPIAGTRPRGASEEADLALEQDLLSDAKELAEHLMLIDLG 343

Query: 306 LQEMAEIAEPGTAVVTDFMTVRERGSVQHLGSTVSGRLGTSNDRMDALEALFPAVTASGI 365
             ++  +AE GT  +T+ M +    +V H+ S V+G+L      MDAL A+ PA T SG 
Sbjct: 344 RNDVGRVAETGTVRLTEKMVIERYSNVMHIVSNVTGQLKAPLTAMDALRAILPAGTLSGA 403

Query: 366 PKAGGVEAILRLDEGPRGLYSGAVVMVSADGALDAALTLRAAYEHDGKTWLRAGAGIIEE 425
           PK   +E I  L+   RG+Y GAV  ++ +G +D A+ +R A   DG+  ++AGAGI+ +
Sbjct: 404 PKIRAMEIIDELEPVKRGVYGGAVGYLAWNGNMDTAIAIRTAVIKDGELHVQAGAGIVAD 463

Query: 426 STPEREFEETCEK 438
           S P  E+EET  K
Sbjct: 464 SQPALEWEETLNK 476


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: 424
Number of extensions: 21
Number of successful extensions: 2
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: 494
Length adjustment: 33
Effective length of query: 417
Effective length of database: 461
Effective search space:   192237
Effective search space used:   192237
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: 51 (24.3 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 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