GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__Korea:Ga0059261_0256
          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 (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