Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate WP_108358580.1 B9Z44_RS13785 3-oxoacyl-ACP reductase FabG
Query= reanno::Burk376:H281DRAFT_00644 (263 letters) >NCBI__GCF_003063475.1:WP_108358580.1 Length = 255 Score = 118 bits (296), Expect = 1e-31 Identities = 81/248 (32%), Positives = 124/248 (50%), Gaps = 17/248 (6%) Query: 17 VSAGAAGIGLAIAEAFIEAQAEVYICDVNQAAIDEATSRFPKLHAG----IADVSKQAQV 72 ++ A GIGLA A F A V +CDV QAA+DEA + L A + DV+++ V Sbjct: 19 ITGAAQGIGLATALKFAREGAIVIVCDVKQAAVDEAVKQCQALGAQALGFVVDVTQRDMV 78 Query: 73 DQIIDDARRKLGGLDVLVNNAGIAGPTGAVEELDPAQWESTVSTNLNSQFYFLRKAVPVL 132 D + K G +DVLVNNAGI ++++ Q++ + NL F+ +AV Sbjct: 79 DATVKAVLDKFGRIDVLVNNAGIT-QDARLQKMTLEQFDRVIDVNLRGVFH-CAQAVTEA 136 Query: 133 KETSDCASIIAMSSVAGRLGYPFRTPYASTKWAIVGLVKSLAAELGPSNVRVNAILPGVV 192 I+ SSV G G +T YA+TK+ ++G K+ + ELGP +RVNA+ PG + Sbjct: 137 MVAQGSGVILNASSVVGIYGNFGQTNYAATKFGVIGFTKTWSRELGPKGIRVNAVAPGFI 196 Query: 193 EGERMDRVISARADALGIPFNAMREEYLKKISLRRMVTVDDIAAMALFLASPAGSNVTGQ 252 + + IP + E ++ L+R+ +DIA + FLAS + + G Sbjct: 197 QTPILST----------IPEKVI-HEMTDRVPLKRLGQPEDIANVYAFLASDEAAYINGT 245 Query: 253 AISVDGNV 260 I V G + Sbjct: 246 VIEVAGGL 253 Lambda K H 0.318 0.134 0.375 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: 138 Number of extensions: 9 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: 263 Length of database: 255 Length adjustment: 24 Effective length of query: 239 Effective length of database: 231 Effective search space: 55209 Effective search space used: 55209 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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