Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate PfGW456L13_3453 Short-chain dehydrogenase/reductase SDR
Query= reanno::pseudo1_N1B4:Pf1N1B4_412 (272 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3453 Length = 272 Score = 136 bits (343), Expect = 4e-37 Identities = 86/259 (33%), Positives = 130/259 (50%), Gaps = 19/259 (7%) Query: 17 ERLKNKVVLLTGAAQGIGEAIVATFASQQARLVISDIQGEKVEKVAAHWREQGADVVAIK 76 +RL KV ++TGA GIG A FA + A +V++D+ E + VAA E G + + ++ Sbjct: 6 KRLDGKVCVITGAGSGIGRASALRFAREGATVVVTDLFAESAQAVAA---EIGVNALVLQ 62 Query: 77 ADVSRQQDLHAMARLAIELHGRIDVLVNCAGVNVFRDP--------LQMTEEDWHRCFAI 128 DV ++ L M + GRIDVL N A V+R+P + E +H C + Sbjct: 63 VDVGQEDALREMVEQTVRTFGRIDVLFNNA---VYRNPATTRDIDFINFNTELFHNCMRV 119 Query: 129 DLDGAWYGCKAVLPQMIEQGIGSIINIASTHSTHIIPGCFPYPVAKHGLLGLTRALGIEY 188 ++ G CK LP M+ QG GSI+ +ST S F Y +K L + + + Sbjct: 120 NVLGGVLACKYALPHMLAQGSGSILFTSSTSSIAGEISQFSYGASKAALNWYVQTIAATF 179 Query: 189 APKGIRVNAIAPGYIETQLNVDYWNGFADPHAERQRAFDLHPPRRIGQPIEVAMTAVFLA 248 +GIR N I PG I T + N A + DL ++G+P ++A A FLA Sbjct: 180 GKRGIRCNGILPGVIRTPAMESWAN-----EAMKSAFLDLQNVPQLGEPEDIAAMAAFLA 234 Query: 249 SDEAPFINASCITIDGGRS 267 SD+A ++N + + +DGG S Sbjct: 235 SDDAAYVNGTLMRVDGGMS 253 Lambda K H 0.321 0.138 0.424 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: 139 Number of extensions: 9 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: 272 Length of database: 272 Length adjustment: 25 Effective length of query: 247 Effective length of database: 247 Effective search space: 61009 Effective search space used: 61009 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 (21.9 bits) S2: 47 (22.7 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