GapMind for Amino acid biosynthesis

 

Aligments for a candidate for cmutase in Sphingomonas koreensis DSMZ 15582

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 Ga0059261_0256 Ga0059261_0256 anthranilate synthase component I, non-proteobacterial lineages

Query= curated2:Q73XV3
         (450 letters)



>lcl|FitnessBrowser__Korea:Ga0059261_0256 Ga0059261_0256
           anthranilate synthase component I, non-proteobacterial
           lineages
          Length = 508

 Score =  151 bits (381), Expect = 5e-41
 Identities = 113/334 (33%), Positives = 153/334 (45%), Gaps = 13/334 (3%)

Query: 124 RLAPGTALARVFWPNGRIVVTREAIQLFGTSTGRRDDVLGVLGDG-VPGLRDASAVDVVT 182
           RLA    L    WP      TR+       +  R D     L    +P      A+++  
Sbjct: 172 RLADSLFLVAPVWPGS----TRDPEARLADAAERIDATAARLATAPLPPKVAGDALEIAA 227

Query: 183 DPS----NYRDRVASAVAEIAAGRYHKVILSRCLQVPFAVDFPSTYRLARRHNTPVRSFL 238
            P+    +Y   VA A   I AG   +V+L++    PFA+     YR  RR N     + 
Sbjct: 228 RPTLADGDYAAMVARAKEYITAGDIFQVVLAQRFTAPFALPPIELYRALRRVNPSPFLYF 287

Query: 239 LRLGGIRAVGYSPELVAAVRHDGVVVTEPLAGTRAFGRGALHDRQARDDLESNSKEIVEH 298
           L L G    G SPE++  VR D V +  P+AGTR  G+ A  D   R  L ++ KE  EH
Sbjct: 288 LDLPGFALTGSSPEILVRVRDDEVTI-RPIAGTRPRGKTAAEDEANRTSLLADPKERAEH 346

Query: 299 AISVRSSLQEMAEIAEPGTAVVTDFMTVRERGSVQHLGSTVSGRLGTSNDRMDALEALFP 358
            + +     +   +A+ GT  VTD  TV     V H+ S V G+L    D +DAL A FP
Sbjct: 347 LMLLDLGRNDTGRVAQAGTVRVTDSYTVEFYSHVMHIVSNVVGKLRPDADALDALFAGFP 406

Query: 359 AVTASGIPKAGGVEAILRLDEGPRGLYSGAVVMVSADGALDAALTLRAAYEHDGKTWLRA 418
           A T SG PK    E I  L+   RG Y+G V   S DG++D+ + LR A   DG   + A
Sbjct: 407 AGTVSGAPKVRACEIIAELEREQRGPYAGGVGYFSPDGSMDSCIVLRTAIVKDGTMHVTA 466

Query: 419 GAGIIEEST---PEREFEETCEKLSTLAPYLIAR 449
           GAGI+ +S     +RE E     L   A   +AR
Sbjct: 467 GAGIVADSDAAYEQRECEAKAGALFAAAREAVAR 500


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: 468
Number of extensions: 15
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: 508
Length adjustment: 34
Effective length of query: 416
Effective length of database: 474
Effective search space:   197184
Effective search space used:   197184
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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