Align xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate CA265_RS13665 CA265_RS13665 galactonate dehydratase
Query= BRENDA::D4GP40 (412 letters) >FitnessBrowser__Pedo557:CA265_RS13665 Length = 388 Score = 205 bits (521), Expect = 2e-57 Identities = 121/379 (31%), Positives = 202/379 (53%), Gaps = 18/379 (4%) Query: 37 EITDVQTTMVDG-NYPWILVRVYTDAGVVGTGEAYWGGGDTAIIERMKPF---LVGENPL 92 +ITDV+ +V+G Y W L+++YTD G G GEA G + E K ++G +P+ Sbjct: 2 KITDVKVWLVEGVKYNWTLLKIYTDTGHTGVGEATNWPGSPIVFEATKHVGQRIIGLDPM 61 Query: 93 DIDRLYEHLVQKMSGEGSVSGKVISAISGIEIALHDVAGKLLDVPAYQLVGGKYRDEVRV 152 D ++ L + ++ G G + AISGI++AL D+ K+L VP Y+L+GG +R ++ + Sbjct: 62 KTDFIWTKLYRDLNWMGPF-GASMCAISGIDMALLDLKAKVLGVPCYELLGGAFRKDILL 120 Query: 153 YCDLHTEDEANPQACAEEGVRVVEELGYDAIKFDLDVPSGH------EKDRANRHLRNPE 206 Y + + A + V+E G+ +KFD P H E +N L P+ Sbjct: 121 YANYWFTGGGHNTADYAAQAKKVKEAGFTGLKFD---PFAHTNYLYGEDLSSNLQLTAPQ 177 Query: 207 IDHKVEIVEAVTEAVGDRADVAFDCHWSFTGGSAKRLASELEDYDVWWLEDPVPPENHDV 266 D + +AV +AVG D+ + H A +A L + ++ W E+P PEN + Sbjct: 178 QDLAFNVSKAVRDAVGPEFDIMIETHAMLNYRVAVTMAQRLSELNITWYEEPAGPENANT 237 Query: 267 QKLVTQS--TTTPIAVGENVYRKFGQRTLLEPQAVDIIAPDLPRVGGMRETRKIADLADM 324 K + + I VGE Y + G R +LE DI+ PD+ R GG E +++A + + Sbjct: 238 LKAMRDRIPSNVSICVGERHYTRHGIRDVLEKHICDIMMPDITRCGGPSEMKRMATMMEA 297 Query: 325 YYIPVAMHNVSSPIGTMASAQVAAAIPNSLALEYHSYQLGWWEDLVEED--DLIQNGHME 382 Y + +A HN + P+ T+ASAQV A++PN E+ + W ++++ D++QNGH++ Sbjct: 298 YNVLLAPHNPNGPLSTLASAQVCASVPNFFRQEFMFNDVPWRDEVISHPIADMVQNGHLK 357 Query: 383 IPEKPGLGLTLDLDAVEAH 401 + ++PGLG+ L + +E H Sbjct: 358 LSDRPGLGVDLIEEEMEKH 376 Lambda K H 0.315 0.135 0.401 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: 24 Number of successful extensions: 5 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: 412 Length of database: 388 Length adjustment: 31 Effective length of query: 381 Effective length of database: 357 Effective search space: 136017 Effective search space used: 136017 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: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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:
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