Align galactonate dehydratase [EC: 4.2.1.6] (characterized)
to candidate CA265_RS13665 CA265_RS13665 galactonate dehydratase
Query= reanno::BFirm:BPHYT_RS16405 (382 letters) >FitnessBrowser__Pedo557:CA265_RS13665 Length = 388 Score = 171 bits (432), Expect = 4e-47 Identities = 123/381 (32%), Positives = 191/381 (50%), Gaps = 28/381 (7%) Query: 1 MKITKLETFIVPP---RWCFLKIETDEGIVGWGEPVVEGRAHTVAAAVEELSDYLIGKDP 57 MKIT ++ ++V W LKI TD G G GE + V A + + +IG DP Sbjct: 1 MKITDVKVWLVEGVKYNWTLLKIYTDTGHTGVGEATNWPGSPIVFEATKHVGQRIIGLDP 60 Query: 58 LLIEDHWQVMYRSGFYRGG-PITMSAIAGVDQALWDIKGKHHGVPIHALLGGQVRDKIKV 116 + + W +YR + G +M AI+G+D AL D+K K GVP + LLGG R I + Sbjct: 61 MKTDFIWTKLYRDLNWMGPFGASMCAISGIDMALLDLKAKVLGVPCYELLGGAFRKDILL 120 Query: 117 YS--WI--GGDRPSDVANNARAVVERGFKAVKMNG------------SEELQIIDTFDKV 160 Y+ W GG +D A A+ V E GF +K + S LQ+ T + Sbjct: 121 YANYWFTGGGHNTADYAAQAKKVKEAGFTGLKFDPFAHTNYLYGEDLSSNLQL--TAPQQ 178 Query: 161 QGVINNVAAVREAVGPNIGIGVDFHGRVHKPMAKVLAKELDPYKLLFIEEPVLSENAEAL 220 N AVR+AVGP I ++ H ++ +A +A+ L + + EEP ENA L Sbjct: 179 DLAFNVSKAVRDAVGPEFDIMIETHAMLNYRVAVTMAQRLSELNITWYEEPAGPENANTL 238 Query: 221 RDIVNQ--TNTPIALGERLYSRWDFKHILSGGYVDIIQPDASHAGGITECRKIASMAEAY 278 + + ++ +N I +GER Y+R + +L DI+ PD + GG +E +++A+M EAY Sbjct: 239 KAMRDRIPSNVSICVGERHYTRHGIRDVLEKHICDIMMPDITRCGGPSEMKRMATMMEAY 298 Query: 279 DVALALHCPLGPIALATCLQIDAVSYNAFIQEQSLGIHYNQGNDLLDYIKNPEVFKYEDG 338 +V LA H P GP++ Q+ A N F QE +N + I +P ++G Sbjct: 299 NVLLAPHNPNGPLSTLASAQVCASVPNFFRQE----FMFNDVPWRDEVISHPIADMVQNG 354 Query: 339 FVSIPQGPGLGIEVNEEKVRE 359 + + PGLG+++ EE++ + Sbjct: 355 HLKLSDRPGLGVDLIEEEMEK 375 Lambda K H 0.319 0.139 0.428 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: 429 Number of extensions: 22 Number of successful extensions: 6 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: 382 Length of database: 388 Length adjustment: 30 Effective length of query: 352 Effective length of database: 358 Effective search space: 126016 Effective search space used: 126016 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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