Align L-rhamnose-1-dehydrogenase; EC 1.1.1.173 (characterized)
to candidate WP_052668841.1 NITAL_RS24290 3-oxoacyl-ACP reductase
Query= SwissProt::A3LZU7 (258 letters) >NCBI__GCF_000969705.1:WP_052668841.1 Length = 253 Score = 139 bits (349), Expect = 7e-38 Identities = 88/256 (34%), Positives = 137/256 (53%), Gaps = 17/256 (6%) Query: 5 LNGKVVAITGGVTGIGRAIAIEMARNGAKVVVNHLPSEEQAQLAKELKEEISDGENNVLT 64 L+GKV +TG +G+G A A +A GA V + + + + ++ + + L Sbjct: 9 LDGKVAIVTGASSGLGVAFAQALAEAGADVAL----AARRVEKLEQTRALVEATGRRALV 64 Query: 65 IPGDISLPETGRRIVELAVEKFGEINVFVSNAGVCGFREFLEITPETLFQTVNINLNGAF 124 + D+++PE +VE V + G +++ V+NAG+ TPE Q +++NLNG + Sbjct: 65 VATDVAIPEDATELVERTVAELGRVDILVNNAGIGTAVPATRETPEQFRQVIDVNLNGCY 124 Query: 125 FAIQAAAQQMVKQGKGGSIIGISSISALV-GGAHQTHYTPTKAGILSLMQSTACA-LGKY 182 + QA + M G+G SII ISS+ L G Q Y +KAG++ L + A G+ Sbjct: 125 WMAQACGRVM---GEGSSIINISSVLGLTTAGLPQAAYAASKAGLIGLTRDLAQQWTGRK 181 Query: 183 GIRCNAILPGTISTALNEEDLKDPEKRKYMEGRIPL---GRVGDPKDIAGPAIFLASDMS 239 GIR NA+ PG + + E L D Y+E + P GR GDP ++A A+FLASD + Sbjct: 182 GIRVNALAPGFFPSEMTGE-LPDG----YLESQAPRLVSGRTGDPMELAATAVFLASDAA 236 Query: 240 NYVNGAQLLVDGGLFV 255 +Y+ G L VDGGL + Sbjct: 237 SYITGQTLAVDGGLTI 252 Lambda K H 0.317 0.136 0.382 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: 153 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: 258 Length of database: 253 Length adjustment: 24 Effective length of query: 234 Effective length of database: 229 Effective search space: 53586 Effective search space used: 53586 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 (21.6 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