Align D-xylose 1-dehydrogenase (NADP+) (EC 1.1.1.179) (characterized)
to candidate BPHYT_RS20760 BPHYT_RS20760 oxidoreductase domain-containing protein
Query= BRENDA::D4GP30 (325 letters) >FitnessBrowser__BFirm:BPHYT_RS20760 Length = 322 Score = 132 bits (333), Expect = 9e-36 Identities = 101/316 (31%), Positives = 143/316 (45%), Gaps = 8/316 (2%) Query: 3 FGILGTAGIGVKSVIPAVQASEH-EAAAIASRDEARASAVADELGIPTAYGSYEALLADD 61 +G+LG A I V+PA+Q S + +ASRD ARA A A + I SYE ++A Sbjct: 7 WGVLGAAKIANNFVVPALQRSRNGRVTMVASRDLARAQAFATKHDIARVSASYEEVIASQ 66 Query: 62 SLDAVYIPLPNGLHADWVRAAADRGLHVLCEKPLTASADETAAVFDYCEDAGVTLMEAFM 121 +DA+YIPLP H +W + A G HVLCEKP+ + E + + G+ EAFM Sbjct: 67 DVDAIYIPLPTASHFEWCKKALLGGKHVLCEKPIAMNTAEVEELIALRDQTGLVCGEAFM 126 Query: 122 YRFHPLTERAAELVASEL-GAVVSVTSNFSFRLPDGADDIRIDPDLAGGSVMDVGCYAVS 180 HP + +A L G + V +F++ D ++ + L GG V D+G Y V Sbjct: 127 VAHHPQWAYVRDSLAQGLIGELKLVEGSFTY-FNDDPGALKNNLALGGGGVRDIGVYPVV 185 Query: 181 AARLFLG-TPDRVYATTTDTRDCGVDTRMSGVLEYDSGATARVESSFDTPETQYYRVQTT 239 ARL G PDR+ + G D V ++ G T Q+ T Sbjct: 186 TARLATGLEPDRIQSEIVLDPRFGTDRFARCVADF-PGFTLSFYCGTQMARRQHMMFHGT 244 Query: 240 DGRLEANPAFNVDPTAAAELTYATD--GRVVTETFDPTDSYRREVEAFARAVETGETPRV 297 G L + FN A++ + D G T+ F D Y+ VE F+ V G V Sbjct: 245 KGWLSVDAPFNPGSYGPAKVRHRRDATGSEHTQEFSDVDQYQAMVEDFSNTVIGGTAGLV 304 Query: 298 -DREESVSVMRTIDAI 312 E S++ R ID I Sbjct: 305 FSLESSLANQRVIDQI 320 Lambda K H 0.316 0.131 0.371 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: 218 Number of extensions: 7 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: 325 Length of database: 322 Length adjustment: 28 Effective length of query: 297 Effective length of database: 294 Effective search space: 87318 Effective search space used: 87318 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: 48 (23.1 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