GapMind for Amino acid biosynthesis

 

Aligments for a candidate for cmutase in Herbaspirillum seropedicae SmR1

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 HSERO_RS19435 HSERO_RS19435 anthranilate synthase subunit I

Query= curated2:Q73XV3
         (450 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS19435 HSERO_RS19435
           anthranilate synthase subunit I
          Length = 498

 Score =  137 bits (344), Expect = 1e-36
 Identities = 90/259 (34%), Positives = 132/259 (50%), Gaps = 10/259 (3%)

Query: 187 YRDRVASAVAEIAAGRYHKVILSRCLQVPFAVDFP-STYRLARRHNTPVRSFLLRLGGIR 245
           Y   VA A   + AG   +V + + L+  + VD P   YR  R  N     +    G ++
Sbjct: 224 YLKAVARAKEYVMAGDLMQVQIGQRLKKSY-VDSPLMLYRALRSLNPSPYMYFYNFGDMQ 282

Query: 246 AVGYSPELVAAVRHDGV------VVTEPLAGTRAFGRGALHDRQARDDLESNSKEIVEHA 299
            VG SPE++  VR++ +      +   PLAGTR  G     D Q   +L ++ KEI EH 
Sbjct: 283 IVGASPEIL--VRNESIGEGQKKITIRPLAGTRPRGSTIERDEQLARELLADPKEIAEHV 340

Query: 300 ISVRSSLQEMAEIAEPGTAVVTDFMTVRERGSVQHLGSTVSGRLGTSNDRMDALEALFPA 359
           + +  +  ++  IA  G+  VTD M + +   VQH+ S V G L      +D L+A FPA
Sbjct: 341 MLIDLARNDIGRIATTGSVKVTDQMVIEKYSHVQHIVSNVEGILKPGMSNLDVLKATFPA 400

Query: 360 VTASGIPKAGGVEAILRLDEGPRGLYSGAVVMVSADGALDAALTLRAAYEHDGKTWLRAG 419
            T SG PK   +E I  L+   RG+Y GA   +S  G +D A+ +R     DG  +++A 
Sbjct: 401 GTLSGAPKVRAMEIIDELEPTKRGIYGGACGYLSFGGEMDVAIAIRTGVIKDGTLYVQAA 460

Query: 420 AGIIEESTPEREFEETCEK 438
           AGI+ +S PE E+EET  K
Sbjct: 461 AGIVADSVPEMEWEETENK 479


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: 398
Number of extensions: 17
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: 498
Length adjustment: 33
Effective length of query: 417
Effective length of database: 465
Effective search space:   193905
Effective search space used:   193905
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 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