GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutX in Pseudomonas fluorescens FW300-N1B4

Align ABC transporter for L-Histidine, periplasmic substrate-binding component (characterized)
to candidate Pf1N1B4_562 Histidine transporter, periplasmic histidine-binding protein

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_562
          Length = 337

 Score =  327 bits (839), Expect = 2e-94
 Identities = 165/342 (48%), Positives = 232/342 (67%), Gaps = 25/342 (7%)

Query: 1   MKSNKTLL-TTLLSMGLLASAGATQAAGWCESGKPVKFAGLNWESGMLLTDVLQVVLEKG 59
           M+S KTLL ++LL++ L+A  G   AA   E   P+ F  + WESG L+T++L++++EKG
Sbjct: 1   MRSIKTLLGSSLLALSLVA--GHVPAA---EKTTPIHFGDITWESGSLITEILRLIVEKG 55

Query: 60  YDCKTDSLPGNSITMENALSSNDIQVFAEEWVGRSEVWNKAEKAGKVVGVGAPVVGAIEG 119
           Y   TD+LPG+++++E AL+ NDIQV  EEW GRS  W KA   GKV G+G  V GA EG
Sbjct: 56  YGYPTDTLPGSTVSLEAALAKNDIQVIGEEWAGRSPAWVKAASEGKVFGLGDTVKGATEG 115

Query: 120 WYVPRYVVEGDAKRKLEAKAPGLKNIADLGQYAAVFKDPEEPSKGRFYNCPAGWTCELDN 179
           W+VP YV++GD +R ++  AP LK++ADL +Y  VF+DPE+PS+GRF N P GWT E+ N
Sbjct: 116 WWVPEYVIKGDPERGIKPLAPELKSVADLARYKDVFRDPEDPSRGRFLNSPTGWTSEIVN 175

Query: 180 SEMLKSYGLEKTYTNFRPGTGPALDAAVLSSYKRGEPILFYYWSPTPLMGQVDLVKLEEK 239
           S+ LK+Y L  +Y NFR G+G ALDA V SS +RG+P+LFYYWSPTPL+G+  LVKLEE 
Sbjct: 176 SQKLKAYDLTASYVNFRTGSGAALDAEVASSIRRGKPVLFYYWSPTPLLGRFKLVKLEEP 235

Query: 240 PGVDKS-------------------VSIKVGLSKTFHDEAPELVAVLEKVNLPIDILNQN 280
           P   ++                    S+ +G+S  F  + P+LVA  EKV+LPID+LNQ 
Sbjct: 236 PFDAQAWKTLADANNPNPKGTRSMPASLAIGVSAPFKAQYPDLVAFFEKVDLPIDLLNQT 295

Query: 281 LGRMAKERIESPKLAKIFLKEHPEVWHAWVSEDAAKKIDAAL 322
           LG+M+++R    ++A+ FL++ P+VW AWV  + A K+  +L
Sbjct: 296 LGQMSEKRQPPRQVAEAFLRDQPQVWKAWVPGEVATKVSESL 337


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: 337
Number of extensions: 9
Number of successful extensions: 2
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: 337
Length adjustment: 28
Effective length of query: 294
Effective length of database: 309
Effective search space:    90846
Effective search space used:    90846
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: 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:

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