GapMind for catabolism of small carbon sources

 

Aligments for a candidate for hutX in Pseudomonas fluorescens FW300-N2C3

Align HutX aka HISX, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate AO356_09620 AO356_09620 histidine ABC transporter substrate-binding protein

Query= TCDB::Q9KKE3
         (346 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_09620 AO356_09620
           histidine ABC transporter substrate-binding protein
          Length = 322

 Score =  342 bits (878), Expect = 6e-99
 Identities = 167/343 (48%), Positives = 232/343 (67%), Gaps = 24/343 (6%)

Query: 4   SISTMRLTFAAAGLMLAASASGANASYCGDGKTVTFAGIDWESGAFITEVMKTILSKGYD 63
           S  T+  T  + GL+ +A A+ A A +C  GK V FAG++WESG  +T+V++ +L KGYD
Sbjct: 3   SNKTLLTTLLSMGLLASAGATQA-AGWCESGKPVKFAGLNWESGMLLTDVLQVVLEKGYD 61

Query: 64  CQVDSIPGNSVTLEQATANNDVQIFAEEWLGRSDVWNKAVEEKKVIAVGKTFVGASEGWF 123
           C+ DS+PGNS+T+E A ++ND+Q+FAEEW+GRS+VWNKA +  KV+ VG   VGA EGW+
Sbjct: 62  CKTDSLPGNSITMENALSSNDIQVFAEEWVGRSEVWNKAEKAGKVVGVGAPVVGAIEGWY 121

Query: 124 VPDYVVHGDPARNIEAKAPDLKSVSQLTDPKIAEIFADPEEPSKGRFLNCPSGWTCEGVS 183
           VP YVV GD  R +EAKAP LK+++ L   + A +F DPEEPSKGRF NCP+GWTCE  +
Sbjct: 122 VPRYVVEGDAKRKLEAKAPGLKNIADL--GQYAAVFKDPEEPSKGRFYNCPAGWTCELDN 179

Query: 184 TAKLEAYKLGETYVNFRPGTGTALDAAITSAYLQGEPIFFYYWSPTAILGKFKLIQLEE- 242
           +  L++Y L +TY NFRPGTG ALDAA+ S+Y +GEPI FYYWSPT ++G+  L++LEE 
Sbjct: 180 SEMLKSYGLEKTYTNFRPGTGPALDAAVLSSYKRGEPILFYYWSPTPLMGQVDLVKLEEK 239

Query: 243 PAYNEACWKELSSANGKRDEGCAFPSVDVAYGVNSTFASEAPEIVEILEKATFPLDEVNA 302
           P  ++                    SV +  G++ TF  EAPE+V +LEK   P+D +N 
Sbjct: 240 PGVDK--------------------SVSIKVGLSKTFHDEAPELVAVLEKVNLPIDILNQ 279

Query: 303 SLAYMADNKVDATAAAAEFLKTKGDIWSKWVSDEARGKIEAGL 345
           +L  MA  ++++   A  FLK   ++W  WVS++A  KI+A L
Sbjct: 280 NLGRMAKERIESPKLAKIFLKEHPEVWHAWVSEDAAKKIDAAL 322


Lambda     K      H
   0.314    0.130    0.391 

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: 344
Number of extensions: 17
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: 346
Length of database: 322
Length adjustment: 28
Effective length of query: 318
Effective length of database: 294
Effective search space:    93492
Effective search space used:    93492
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 49 (23.5 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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