Align Short-chain dehydrogenase (characterized, see rationale)
to candidate PfGW456L13_2522 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)
Query= uniprot:A0A2E7P8M8 (258 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2522 Length = 248 Score = 103 bits (256), Expect = 4e-27 Identities = 80/249 (32%), Positives = 119/249 (47%), Gaps = 16/249 (6%) Query: 5 LQDKVVIVTGGASGIGGAISLQLAAEGAIPVVFARSEPDPQFWARLTGLQPRAALFQLEL 64 LQ+KV +VTGGASGIG A + +AEGA + F GL L++ Sbjct: 4 LQNKVAVVTGGASGIGLACVRRFSAEGAQVIGLDIGSAPADF----PGL-----FMTLDV 54 Query: 65 QDEARCGEAVAETVRRFGRLDGLVNNAGVNDSVGL-DAGRNEFVASLERNLIHYYVMAHY 123 +DEA+ + + E + RFGR+D LVN AGV D + + ++ NL + + Y Sbjct: 55 RDEAQVQQVMQEVISRFGRIDVLVNAAGVADQGSVTQTTTANWQRVMDINLTGSMLTSKY 114 Query: 124 CVPHLKATR-GAILNVSSKTALTGQGNTSGYCASKGAQLSLTREWAAALRDDGVRVNALI 182 + + R G+I+NV S L G Y SKG LTR A +RVN L Sbjct: 115 ALASMVEQRNGSIINVGSIFGLQGCDGNVAYNVSKGGINQLTRSMAIDYGYANIRVNGLC 174 Query: 183 PAEVMTPLYEKWIATFENPQEKLDAITSKIPLGKRFTTSEEMADMAVFLLSGRSSHTTGQ 242 P + TP+ + + A + + R EE+A++A+FL S +S +GQ Sbjct: 175 PGLIETPM-----TSMVRDNDAFHAFFASQHMLNRSGQPEEVANVALFLASDEASFVSGQ 229 Query: 243 WVFVDGGYT 251 + VDGG++ Sbjct: 230 MIAVDGGFS 238 Lambda K H 0.318 0.134 0.394 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: 139 Number of extensions: 12 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: 248 Length adjustment: 24 Effective length of query: 234 Effective length of database: 224 Effective search space: 52416 Effective search space used: 52416 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 (21.7 bits) S2: 46 (22.3 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