GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tyrP in Shewanella halifaxensis HAW-EB4

Align Tyrosine permease (characterized)
to candidate WP_012275403.1 SHAL_RS01375 tryptophan permease

Query= TCDB::P0AAD4
         (403 letters)



>NCBI__GCF_000019185.1:WP_012275403.1
          Length = 418

 Score =  265 bits (676), Expect = 2e-75
 Identities = 147/406 (36%), Positives = 225/406 (55%), Gaps = 13/406 (3%)

Query: 6   LGSVFIVAGTTIGAGMLAMPLAAAGVGFSVTLILLIGLWALMCYTALLLLEVYQHVPADT 65
           LG   I+AGT +GAGM ++P+  AG+ F  +L+++ G+W  M  + LLLLE   H     
Sbjct: 18  LGGAMIIAGTAVGAGMFSLPVVGAGMWFGYSLLMMAGVWFCMLVSGLLLLETNLHFKPGD 77

Query: 66  GLGTLAKRYLGRYGQWLTGFSMMFLMYALTAAYISGAGELLASSISDWTGISMSATAGVL 125
              TL +  LG + + + G S+ F++Y L  AYISG G ++  +++   GI +      L
Sbjct: 78  SFDTLTRTTLGNFWRIVNGLSIAFVLYILAYAYISGGGSIVNYNLAS-AGIELPQGIAGL 136

Query: 126 LFTFVAGGVVCVGTSLVDLFNRFLFSAKIIFLVVMLVLLLPHIHKVNLLT-------LPL 178
           +F      +V + T  VD     +    +I   + +  LL  +  V L +       LP 
Sbjct: 137 IFALGLAFIVFISTKAVDRITTIMLGGMLITFFLAVGNLLLDVESVKLFSPDGENKYLPY 196

Query: 179 QQGLALSAIPVIFTSFGFHGSVPSIVSYMDGNIRKLRWVFIIGSAIPLVAYIFWQVATLG 238
                L+A+P    SFG+HG+VPS+V Y   + R +    +IG+ I LV YI W VAT+G
Sbjct: 197 M----LAALPFGLVSFGYHGNVPSLVKYYGKDHRTIIKAIVIGTGIALVIYICWLVATMG 252

Query: 239 SIDSTTFMGLLANHAGLNGLLQALREMVASPHVELAVHLFADLALATSFLGVALGLFDYL 298
           +I  T F+G++     +  L+ AL  ++ S  +   + LFA+LA+A+SFLGV LGLFDYL
Sbjct: 253 NISRTDFIGIIEQGGNMGVLVNALSGVMTSDWLTTMLTLFANLAVASSFLGVTLGLFDYL 312

Query: 299 ADLFQRSNTVGGRLQTGAITFLPPLAFALFYPRGFVMALGYAGVALAVLALIIPSLLTWQ 358
           ADLF    +  GR +T A+TFLPP    L +P GF++A+G+A +A  + A I+P+++ ++
Sbjct: 313 ADLFGFDESRSGRFKTAAVTFLPPTVLGLLFPDGFLVAIGFAALAATIWAAIVPAMMAYK 372

Query: 359 SRKHNP-QAGYRVKGGRPALVVVFLCGIAVIGVQFLIAAGLLPEVG 403
            R   P  A Y+V GG   +V+V L G+       L  AG+LP  G
Sbjct: 373 VRVMYPDSASYKVPGGNAVIVIVILFGVITAACHLLAMAGMLPLYG 418


Lambda     K      H
   0.329    0.143    0.432 

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: 448
Number of extensions: 27
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: 403
Length of database: 418
Length adjustment: 31
Effective length of query: 372
Effective length of database: 387
Effective search space:   143964
Effective search space used:   143964
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 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