Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_101443621.1 BD749_RS04795 glucose 1-dehydrogenase
Query= reanno::pseudo1_N1B4:Pf1N1B4_412 (272 letters) >NCBI__GCF_002846395.1:WP_101443621.1 Length = 247 Score = 143 bits (360), Expect = 4e-39 Identities = 84/244 (34%), Positives = 135/244 (55%), Gaps = 7/244 (2%) Query: 22 KVVLLTGAAQGIGEAIVATFASQQARLVISDIQGEKVEKVAAHWREQGADVVAIKADVSR 81 KV L+TG + GIG + +A + A++V+SDI E +V + G+ + + ADVS+ Sbjct: 5 KVALVTGGSSGIGRSAALLYAREGAKVVVSDIHEESGMQVVREIEQLGSQAIFVAADVSK 64 Query: 82 QQDLHAMARLAIELHGRIDVLVNCAGVNVFRDPL-QMTEEDWHRCFAIDLDGAWYGCKAV 140 D M + A+E GR+DV N AG+ + + M+ E W + +I+L+ +Y Sbjct: 65 PADCERMVQQAVEKFGRLDVAFNNAGIGGESNTIGDMSIEGWDKVISINLNSVFYCMHFQ 124 Query: 141 LPQMIEQGIGSIINIASTHSTHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGIRVNAIAP 200 + QM++QG G+I+N +S Y AKHG++GLT+ G+EYA KGIR+NAI P Sbjct: 125 IRQMLQQGGGAIVNNSSILGQVGFANSAAYVAAKHGVVGLTKNGGLEYASKGIRINAIGP 184 Query: 201 GYIETQLNVDYWNGFADPHAERQRAFDLHPPRRIGQPIEVAMTAVFLASDEAPFINASCI 260 +I+T L +G + Q HP R+G P E+A ++L+S++A F++ + Sbjct: 185 AFIKTPL----LSGMGE--ETLQFLTSKHPIGRLGAPEEIAELVIWLSSNKASFVSGAYY 238 Query: 261 TIDG 264 DG Sbjct: 239 AADG 242 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: 148 Number of extensions: 7 Number of successful extensions: 4 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: 247 Length adjustment: 24 Effective length of query: 248 Effective length of database: 223 Effective search space: 55304 Effective search space used: 55304 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 24 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