Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate 353297 BT3771 3-oxoacyl-[acyl-carrier protein] reductase (NCBI ptt file)
Query= reanno::pseudo1_N1B4:Pf1N1B4_412 (272 letters) >FitnessBrowser__Btheta:353297 Length = 248 Score = 130 bits (326), Expect = 4e-35 Identities = 86/254 (33%), Positives = 130/254 (51%), Gaps = 13/254 (5%) Query: 19 LKNKVVLLTGAAQGIGEAIVATFASQQARLVISDIQ-GEKVEKVAAHWREQGADVVAIKA 77 L K ++TGAA+GIG+AI FA++ A + +D+ E EK G V K Sbjct: 4 LDGKTAIVTGAARGIGKAIALKFAAEGANIAFTDLVIDENAEKTRVELEAMG---VKAKG 60 Query: 78 DVSRQQDLHAMARLAIELH---GRIDVLVNCAGVNVFRDPLQMTEEDWHRCFAIDLDGAW 134 S + A++ E+H GRID+LVN AG+ ++M+E+ W ++L A+ Sbjct: 61 YASNAANFEDTAKVVEEIHKDFGRIDILVNNAGITRDGLMMRMSEQQWDMVINVNLKSAF 120 Query: 135 YGCKAVLPQMIEQGIGSIINIASTHSTHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGIR 194 A P M+ Q GSIIN+AS H G Y +K G++ L +++ E +GIR Sbjct: 121 NFIHACTPVMMRQKAGSIINMASVVGVHGNAGQANYAASKAGMIALAKSIAQELGSRGIR 180 Query: 195 VNAIAPGYIETQLNVDYWNGFADPHAERQRAFDLHPPRRIGQPIEVAMTAVFLASDEAPF 254 NAIAPG+I T + + A++ P RR G P +VA A FLASD + + Sbjct: 181 ANAIAPGFILTDMTAALSDEVRAEWAKK------IPLRRGGTPEDVANIATFLASDMSSY 234 Query: 255 INASCITIDGGRSV 268 ++ I +DGG ++ Sbjct: 235 VSGQVIQVDGGMNM 248 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: 149 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: 272 Length of database: 248 Length adjustment: 24 Effective length of query: 248 Effective length of database: 224 Effective search space: 55552 Effective search space used: 55552 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