Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate Ac3H11_2257 Short-chain dehydrogenase/reductase SDR
Query= reanno::pseudo1_N1B4:Pf1N1B4_412 (272 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2257 Length = 267 Score = 152 bits (383), Expect = 1e-41 Identities = 90/248 (36%), Positives = 140/248 (56%), Gaps = 8/248 (3%) Query: 22 KVVLLTGAAQGIGEAIVATFASQQARLVISDIQGEKVEKVAAHWREQGADVVAIKADVSR 81 +V ++TG AQGIGEA V FA++ A+ VI D+ + + +AA E GA + ++ DV Sbjct: 21 RVCIVTGGAQGIGEACVRRFAAEGAKPVIVDVDDARGQALAA---ELGA--LYVRCDVGD 75 Query: 82 QQDLHAMARLAIELHGRIDVLVNCAGVNVFRDPLQMTEEDWHRCFAIDLDGAWYGCKAVL 141 + + A+ + HGRIDVLVN AG+ D L++TE D+ ++L G++ +AV Sbjct: 76 KAQVDALVAQVLAAHGRIDVLVNNAGIFRAADFLEVTEADFDAVLRVNLKGSFLVGQAVA 135 Query: 142 PQMIEQGIGSIINIASTHSTHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGIRVNAIAPG 201 M+ G G+I+N++S + IP Y V+K G+ LTR + + A K IRVNA+APG Sbjct: 136 RAMVTSGGGAIVNMSSVNGVLAIPNIASYNVSKGGVNQLTRVMALALADKNIRVNAVAPG 195 Query: 202 YIETQLNVDYWNGFADPHAERQRAFDLHPPRRIGQPIEVAMTAVFLASDEAPFINASCIT 261 I T+L +++ P +R+GQP E+A +LASD A ++ +T Sbjct: 196 TIATELAA---KAVLTSDEAKRKIMSRTPMKRLGQPSEIADVVAWLASDAASYVTGEIVT 252 Query: 262 IDGGRSVM 269 +DGGR + Sbjct: 253 VDGGRMTL 260 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: 145 Number of extensions: 4 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: 272 Length of database: 267 Length adjustment: 25 Effective length of query: 247 Effective length of database: 242 Effective search space: 59774 Effective search space used: 59774 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