GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutX in Pseudomonas simiae WCS417

Align ABC transporter for L-Histidine, periplasmic substrate-binding component (characterized)
to candidate GFF340 PS417_01730 histidine ABC transporter substrate-binding protein

Query= reanno::pseudo5_N2C3_1:AO356_09620
         (322 letters)



>FitnessBrowser__WCS417:GFF340
          Length = 321

 Score =  617 bits (1590), Expect = 0.0
 Identities = 302/322 (93%), Positives = 313/322 (97%), Gaps = 1/322 (0%)

Query: 1   MKSNKTLLTTLLSMGLLASAGATQAAGWCESGKPVKFAGLNWESGMLLTDVLQVVLEKGY 60
           MK +KTL+ TLLS G+LASAGA QAAGWCESGKPVKFAGLNWESGMLLTD+LQ VLEKGY
Sbjct: 1   MKMHKTLMATLLSAGVLASAGA-QAAGWCESGKPVKFAGLNWESGMLLTDILQTVLEKGY 59

Query: 61  DCKTDSLPGNSITMENALSSNDIQVFAEEWVGRSEVWNKAEKAGKVVGVGAPVVGAIEGW 120
           DCKTDSLPGNSITMENALSSNDIQVFAEEWVGRSEVWNKAEKAGKVVGVGAPVVGAIEGW
Sbjct: 60  DCKTDSLPGNSITMENALSSNDIQVFAEEWVGRSEVWNKAEKAGKVVGVGAPVVGAIEGW 119

Query: 121 YVPRYVVEGDAKRKLEAKAPGLKNIADLGQYAAVFKDPEEPSKGRFYNCPAGWTCELDNS 180
           YVPRYV+EGDAKRKLEAKAP LKNIADL +YA+VFKD EEPSKGRFYNCPAGWTCELDNS
Sbjct: 120 YVPRYVIEGDAKRKLEAKAPDLKNIADLAKYASVFKDQEEPSKGRFYNCPAGWTCELDNS 179

Query: 181 EMLKSYGLEKTYTNFRPGTGPALDAAVLSSYKRGEPILFYYWSPTPLMGQVDLVKLEEKP 240
           EMLKSYGLE TYTNFRPGTGPALDAAVLSSYKRGEPILFYYWSPTPLMGQVDLVKLEEKP
Sbjct: 180 EMLKSYGLESTYTNFRPGTGPALDAAVLSSYKRGEPILFYYWSPTPLMGQVDLVKLEEKP 239

Query: 241 GVDKSVSIKVGLSKTFHDEAPELVAVLEKVNLPIDILNQNLGRMAKERIESPKLAKIFLK 300
           GVDKSVSIKVGLSKTFH++APELVAVLEKVNLPID+LNQNLGRMAKERIESPKLAKIFLK
Sbjct: 240 GVDKSVSIKVGLSKTFHEQAPELVAVLEKVNLPIDLLNQNLGRMAKERIESPKLAKIFLK 299

Query: 301 EHPEVWHAWVSEDAAKKIDAAL 322
           EHPEVWHAWVS+DAAKKIDAAL
Sbjct: 300 EHPEVWHAWVSDDAAKKIDAAL 321


Lambda     K      H
   0.314    0.133    0.398 

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: 466
Number of extensions: 16
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: 322
Length of database: 321
Length adjustment: 28
Effective length of query: 294
Effective length of database: 293
Effective search space:    86142
Effective search space used:    86142
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (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