Align Short-chain dehydrogenase (characterized, see rationale)
to candidate CA265_RS08605 CA265_RS08605 short-chain dehydrogenase
Query= uniprot:A0A2E7P8M8 (258 letters) >FitnessBrowser__Pedo557:CA265_RS08605 Length = 262 Score = 268 bits (686), Expect = 6e-77 Identities = 137/259 (52%), Positives = 179/259 (69%), Gaps = 2/259 (0%) Query: 1 MDLNLQDKVVIVTGGASGIGGAISLQLAAEGAIPVVFARSEPDPQFWARLTGLQP-RAAL 59 MDL L++KV+++TG A GIG +I+ A E AI V+ R D Q +AA Sbjct: 1 MDLQLKEKVIVITGAAKGIGRSIAEVFAKENAIAVIVGRKAEDNQIVVDAIATNGGKAAQ 60 Query: 60 FQLELQDEARCGEAVAETVRRFGRLDGLVNNAGVNDSVGLDAGR-NEFVASLERNLIHYY 118 F EL + C V V +FGR+DGLVNNAGVND VGL++G +F+ASL +N++HYY Sbjct: 61 FVAELSNPEDCETVVKNIVAQFGRIDGLVNNAGVNDGVGLESGNYKDFMASLHKNVVHYY 120 Query: 119 VMAHYCVPHLKATRGAILNVSSKTALTGQGNTSGYCASKGAQLSLTREWAAALRDDGVRV 178 +MAH+ +P L ++GAI+N++SKTA TGQGNTS Y A+ G + +LTREWA L G+RV Sbjct: 121 LMAHHVLPELIKSKGAIVNITSKTAETGQGNTSAYAAANGGRNALTREWAVELLKYGIRV 180 Query: 179 NALIPAEVMTPLYEKWIATFENPQEKLDAITSKIPLGKRFTTSEEMADMAVFLLSGRSSH 238 NA++ AE TP YE WI T +N +EKL IT+KIPL R TT+EE+A+M FL+S +SSH Sbjct: 181 NAVVVAECWTPAYETWIETLDNAEEKLKEITAKIPLENRMTTAEEIANMTAFLMSSKSSH 240 Query: 239 TTGQWVFVDGGYTHLDRAL 257 TTGQ + VDGGY HLDRAL Sbjct: 241 TTGQIIHVDGGYVHLDRAL 259 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: 200 Number of extensions: 9 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: 262 Length adjustment: 24 Effective length of query: 234 Effective length of database: 238 Effective search space: 55692 Effective search space used: 55692 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: 47 (22.7 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