GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mt2d in Burkholderia phytofirmans PsJN

Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Allergen Cla h 8; EC 1.1.1.138 (characterized)
to candidate BPHYT_RS28235 BPHYT_RS28235 short-chain dehydrogenase

Query= SwissProt::P0C0Y5
         (267 letters)



>FitnessBrowser__BFirm:BPHYT_RS28235
          Length = 260

 Score =  121 bits (303), Expect = 2e-32
 Identities = 90/257 (35%), Positives = 128/257 (49%), Gaps = 16/257 (6%)

Query: 18  LKGKVVVVTGASGPKGMGIEAARGCAEMGAAVAITY-------ASRAQGAEENVKELEKT 70
           LK KVV+VTG  G +G+G   A  CA  GA VAI Y         R     E V E+E  
Sbjct: 3   LKDKVVIVTG--GSRGIGRAIAVACAAEGADVAINYWGDNDVSYGRRSAVAEVVAEIE-A 59

Query: 71  YGIKAKAYKCQVDSYESCEKLVKDVVADFGQIDAFIANAGATADSGILDGSVEAWNHVVQ 130
            G +  A +  V + E+ ++LV+  V  FG++D   +NAG       LD   E     V 
Sbjct: 60  LGRRVIAIEGNVAARETGQQLVRHTVEAFGKVDVLASNAGICPFHAFLDMPPEVLESTVA 119

Query: 131 VDLNGTFHCAKAVGHHFKERGT-GSLVITASMSGHIANFPQEQTSYNVAKAGCIHMARSL 189
           V+LNG F+  +A     K +GT G++V T+S+S  +      QT Y   KAG   + +S 
Sbjct: 120 VNLNGAFYVTQAAAQQMKLQGTGGAIVATSSISALVGG--GMQTHYTPTKAGVHSLMQSC 177

Query: 190 ANEWRDFA-RVNSISPGYIDTGLS--DFVPKETQQLWHSMIPMGRDGLAKELKGAYVYFA 246
           A     +  R NS+ PG I T L+  D   +  +  +   IP+GR G  +++     + A
Sbjct: 178 AVALGPYGIRCNSVMPGTIATDLNAQDLADEAKKAYFEKRIPLGRLGRPEDVADCVTFLA 237

Query: 247 SDASTYTTGADLLIDGG 263
           SD + Y TGA LL+DGG
Sbjct: 238 SDRARYVTGAALLVDGG 254


Lambda     K      H
   0.316    0.131    0.383 

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: 178
Number of extensions: 13
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: 267
Length of database: 260
Length adjustment: 25
Effective length of query: 242
Effective length of database: 235
Effective search space:    56870
Effective search space used:    56870
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: 41 (21.6 bits)
S2: 47 (22.7 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