GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tyrP in Shewanella amazonensis SB2B

Align Tyrosine permease (characterized)
to candidate 6938836 Sama_2939 tyrosine-specific transport protein, putative (RefSeq)

Query= TCDB::P0AAD4
         (403 letters)



>FitnessBrowser__SB2B:6938836
          Length = 395

 Score =  308 bits (788), Expect = 2e-88
 Identities = 171/401 (42%), Positives = 244/401 (60%), Gaps = 13/401 (3%)

Query: 1   MKNRTLGSVFIVAGTTIGAGMLAMPLAAAGVGFSVTLILLIGLWALMCYTALLLLEVYQH 60
           M  +TLGS+ IVAGT IGAGMLA+PLA A +G    L+LL+ +WA+  YT+LL+LE+   
Sbjct: 1   MNLKTLGSIAIVAGTAIGAGMLALPLATAALGVIPALLLLLVVWAISAYTSLLMLEINLR 60

Query: 61  VPADTGLGTLAKRYLGRYGQWLTGFSMMFLMYALTAAYISGAGELLASSISDWTGISMSA 120
                 +  +  + LG+ GQ + G S + L+YALTAAY++G   LL   +     I++  
Sbjct: 61  SGVGDNVHAITGKTLGKKGQLIQGASFLSLLYALTAAYLTGGSSLLVHRMESVFSINLDG 120

Query: 121 TAGVLLFTFVAGGVVCVGTSLVDLFNRFLFSAKIIFLVVMLVLLLPHIHKVNLLTLPLQQ 180
              VLLFT V G V  +G S VD  +R LFS  ++ LV+++  LLP I    +     ++
Sbjct: 121 QLAVLLFTLVLGSVAALGVSWVDKLSRLLFSLMVVLLVLVVGFLLPEIRPSVIAADAFEK 180

Query: 181 GLA---LSAIPVIFTSFGFHGSVPSIVSYMDGNIRKLRWVFIIGSAIPLVAYIFWQVATL 237
             A   ++AIPV+FTSFGFH  + ++V Y+DG+   LR V +IGS IPLV YI W + TL
Sbjct: 181 VSANAWMAAIPVVFTSFGFHVCIATLVRYLDGDAVNLRKVLLIGSTIPLVCYILWLLVTL 240

Query: 238 GSI---DSTTFMGLLANHAGLNGLLQALREMVASPHVELAVHLFADLALATSFLGVALGL 294
           G++   +  TF G L        L+ AL+E+ A P V  ++ +FADLAL TSFLGV + L
Sbjct: 241 GTVGGDEIATFNGALPK------LISALQELAAHPVVGQSIAVFADLALVTSFLGVTMSL 294

Query: 295 FDYLADLFQRSNTVGGRLQTGAITFLPPLAFALFYPRGFVMALGYAGVALAVLALIIPSL 354
           FD+LA++ +    +GGRLQT  ITFLPPL  ALF P GFV  LG+A + L  + + +P  
Sbjct: 295 FDFLAEMTRSKGGIGGRLQTWIITFLPPLLCALFVPEGFVAVLGFAAIPLVFMIIFLPIA 354

Query: 355 LTWQSRKHNPQAGYRVKGGRPALVVVFLCGIAVIGVQFLIA 395
           +    R    + GY+V GG+ AL ++ + G+A+I  Q  +A
Sbjct: 355 MALNQRAQY-RDGYQVSGGKLALSLIGVAGVAIIAAQLWVA 394


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: 485
Number of extensions: 21
Number of successful extensions: 4
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: 395
Length adjustment: 31
Effective length of query: 372
Effective length of database: 364
Effective search space:   135408
Effective search space used:   135408
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 17 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