GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__psRCH2:GFF3583
          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.

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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