Align L-rhamnose-1-dehydrogenase; EC 1.1.1.173 (characterized)
to candidate WP_013721611.1 ALIDE2_RS05725 3-oxoacyl-ACP reductase
Query= SwissProt::A3LZU7 (258 letters) >NCBI__GCF_000204645.1:WP_013721611.1 Length = 253 Score = 143 bits (360), Expect = 4e-39 Identities = 90/251 (35%), Positives = 134/251 (53%), Gaps = 9/251 (3%) Query: 4 LLNGKVVAITGGVTGIGRAIAIEMARNGAKVVVNHLPSEEQAQLAKELKEEISDGENNVL 63 LL K+ +TG GIGRAIA+ A GA+V+V L A + + E+ Sbjct: 6 LLENKLALVTGAGRGIGRAIAVAYANAGARVIVTDLSEAACA----DTRAEVGAAGAQAW 61 Query: 64 TIPGDISLPETGRRIVELAVEKFGEINVFVSNAGVCGFREFLEI--TPETLFQTVNINLN 121 T D+ + R+ + + G++ V V+NAG+ RE ++ + Q + +N Sbjct: 62 TYALDVCDADACARLADTVARELGDLQVLVNNAGLM-IREKVDSPRAAHAVRQLMEVNYF 120 Query: 122 GAFFAIQAAAQQMVKQGKGGSIIGISSISALVGGAHQTHYTPTKAGILSLMQSTACALGK 181 G F + A + + G +I ++S +AL G Y+P+K + L Q+ A LG Sbjct: 121 GTFNVLHAFLPALRRSH--GCVINLASGAALTGLPGCVGYSPSKGAVKMLTQAMAADLGT 178 Query: 182 YGIRCNAILPGTISTALNEEDLKDPEKRKYMEGRIPLGRVGDPKDIAGPAIFLASDMSNY 241 GIR NAI PG I TA+ E +DP++ GRIP GR+G ++IAGPA+FLASD+++Y Sbjct: 179 DGIRVNAIAPGVIETAMTESTRQDPQRLGGFMGRIPAGRLGRAEEIAGPAVFLASDLASY 238 Query: 242 VNGAQLLVDGG 252 VNG L VDGG Sbjct: 239 VNGITLPVDGG 249 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: 150 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: 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