GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cmutase in Shewanella oneidensis MR-1

Align Salicylate synthase; Chorismate mutase; CM; Isochorismate synthase/isochorismate lyase; Mycobactin synthase protein; EC 5.4.99.5; EC 4.2.99.21; EC 5.4.4.2 (characterized)
to candidate 201372 SO2221 para-aminobenzoate synthase, component I (NCBI ptt file)

Query= SwissProt::P9WFX1
         (450 letters)



>FitnessBrowser__MR1:201372
          Length = 467

 Score =  118 bits (296), Expect = 4e-31
 Identities = 75/247 (30%), Positives = 123/247 (49%), Gaps = 1/247 (0%)

Query: 200 AGRYHKVILSRCVEVPFAIDFPLTYRLGRRHNTPVRSFLLQLGGIRALGYSPELVTAVRA 259
           +G  +++ L++  E  +  D    Y   R  N    S  ++L     L  SPE    +R 
Sbjct: 218 SGDCYQINLTQRFEAQYQGDEWSAYCKLRSANQAPFSAFMRLNDNTILSISPERFIQLRG 277

Query: 260 DGVVITEPLAGTRALGRGPAIDRLARDDLESNSKEIVEHAISVRSSLEEITDIAEPGSAA 319
           D +  T+P+ GT      PA+D+ A   L ++ K+  E+ + V     +I  +A PGS  
Sbjct: 278 DDIQ-TKPIKGTLPRHNDPALDKQAAQILANSPKDRAENVMIVDLLRNDIGKVAAPGSVQ 336

Query: 320 VIDFMTVRERGSVQHLGSTIRARLDPSSDRMAALEALFPAVTASGIPKAAGVEAIFRLDE 379
           V     V    +V HL ST+ A+LDP       L A FP  + +G PK   +E I  L+ 
Sbjct: 337 VPHLFAVESFPAVHHLVSTVTAKLDPQYQACDLLRAAFPGGSITGAPKIRAMEIIEELEP 396

Query: 380 CPRGLYSGAVVMLSADGGLDAALTLRAAYQVGGRTWLRAGAGIIEESEPEREFEETCEKL 439
             R LY G++  +S DG +D ++T+R      G+ +  AG GI+ +S+ + E++E+ +K+
Sbjct: 397 SRRSLYCGSIGYISQDGQMDTSITIRTIVAERGKLYCWAGGGIVADSDVDAEYQESFDKV 456

Query: 440 STLTPYL 446
           S + P L
Sbjct: 457 SRILPLL 463


Lambda     K      H
   0.319    0.135    0.386 

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: 348
Number of extensions: 11
Number of successful extensions: 1
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: 467
Length adjustment: 33
Effective length of query: 417
Effective length of database: 434
Effective search space:   180978
Effective search space used:   180978
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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