Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate BWI76_RS13720 BWI76_RS13720 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2119 (272 letters) >FitnessBrowser__Koxy:BWI76_RS13720 Length = 257 Score = 132 bits (331), Expect = 1e-35 Identities = 90/264 (34%), Positives = 136/264 (51%), Gaps = 27/264 (10%) Query: 18 RLKNKVVLLTGAAQGIGEAIVATFASQQARLIISDIQGEKVEKVAAHWRDQGADVVAIKA 77 R NKVV +TGAAQGIG A + ARL++ D + V ++AA D G++ +A++A Sbjct: 2 RFSNKVVAITGAAQGIGRQTAEQAAREGARLLLID-RSRYVHELAAALNDSGSEALALEA 60 Query: 78 DVSRQQDLHAMARLAIDLHGRIDVLVNCAGVNVFRDPL-----EMTEEDWRRCFAIDLDG 132 D+ + + + GR+DVL+N G ++ P + E++ RR L Sbjct: 61 DLEQWESTERAFAEGVAHFGRLDVLINNVGGTIWARPFAEYQPQQIEKEIRRSLFPTL-- 118 Query: 133 AWYGCKAVLPQMIEQGIGSIINIASTHSTHIIPGCFPYPVAKHGLLGLTRALGIEYAPKG 192 +GC+A LP M+ QG GSI+NI+S + + PY AK G+ LTR+L +EY+ G Sbjct: 119 --WGCRAALPWMLRQGKGSIVNISSVATAGV--NRVPYSAAKGGVNALTRSLALEYSANG 174 Query: 193 VRVNAIAPGYIETQLNVDYWNGFADPHAERQRAFD-----------LHPPRRIGQPIEVA 241 +R+NA+APG E + N P A+ Q+ + +H R G E A Sbjct: 175 IRINAVAPGGTEAPARLTPRNE-EQPTAQEQKWYQQVVDQTVASSLMH---RYGTLAEQA 230 Query: 242 MTAVFLASDEAPFINASCITIDGG 265 +FLASDEA +I + + GG Sbjct: 231 NAILFLASDEASYITGVTLPVAGG 254 Lambda K H 0.322 0.138 0.426 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: 148 Number of extensions: 8 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: 257 Length adjustment: 25 Effective length of query: 247 Effective length of database: 232 Effective search space: 57304 Effective search space used: 57304 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