GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natH in Phaeobacter inhibens BS107

Align NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate GFF2619 PGA1_c26600 amino acid ABC transporter, permease protein

Query= TCDB::Q8YPM7
         (381 letters)



>FitnessBrowser__Phaeo:GFF2619
          Length = 273

 Score =  129 bits (323), Expect = 1e-34
 Identities = 86/251 (34%), Positives = 136/251 (54%), Gaps = 18/251 (7%)

Query: 144 PWLSLIWLLSFPIILWLIGGGFGLRPVSSNLWNGLLLTLLMAAISIVLSFPIGVLLALGR 203
           PW     LL    ++W +        + S L  G+ LT+ +  IS  L+  +G+ LAL  
Sbjct: 19  PWWLAAVLLIGGTLIWRVASDDLYLSILSTLMRGVQLTIFVTLISFFLASLLGLGLALAA 78

Query: 204 TSNLPVVRWFSILYIEIVRGVPLIGIL-FLAQVMLPL------FFAADVRLDRVL----- 251
            S   V+R  +  YIE+VRG+P+I +L ++A V+ P       +    + LD +      
Sbjct: 79  GSRWLVIRQGARFYIEVVRGIPIIVLLLYVAFVLAPALVELRNWLGDHIGLDPIRTRNFP 138

Query: 252 ---RAIAGLVLFSAAYMAENVRGGLQAVSRGQVEAAKALGLNTFFVVLLIVLPQALRAVI 308
              RAI  L++  +A+++E  R GLQ+V  GQ+EAAK+LGL+ +     IV PQA+R ++
Sbjct: 139 LLWRAIIALMIAYSAFISEVFRAGLQSVDEGQIEAAKSLGLSRWHRFRFIVFPQAIRTIL 198

Query: 309 PALVGQFIGLFKDTSLLSLVGLVELTGIARSILAQPQFIGRYAEVYLFIGLIYWLFCYSM 368
           P L   F+ L KD+SL+S++G+ ++T + + + A   F  RY E Y  + LIY      +
Sbjct: 199 PPLGNDFVALVKDSSLVSVLGVADVTQLGK-LTAVGNF--RYFETYNVVALIYLTLTIGL 255

Query: 369 SLASRRLERQL 379
           SL  RR E+ L
Sbjct: 256 SLLLRRFEKHL 266


Lambda     K      H
   0.332    0.145    0.452 

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: 323
Number of extensions: 19
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: 381
Length of database: 273
Length adjustment: 28
Effective length of query: 353
Effective length of database: 245
Effective search space:    86485
Effective search space used:    86485
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 48 (23.1 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