Align Short-chain dehydrogenase (characterized, see rationale)
to candidate N515DRAFT_1583 N515DRAFT_1583 NAD(P)-dependent dehydrogenase, short-chain alcohol dehydrogenase family
Query= uniprot:A0A2E7P8M8 (258 letters) >FitnessBrowser__Dyella79:N515DRAFT_1583 Length = 334 Score = 114 bits (284), Expect = 3e-30 Identities = 88/252 (34%), Positives = 125/252 (49%), Gaps = 12/252 (4%) Query: 5 LQDKVVIVTGGASGIGGAISLQLAAEGA-IPVVFARSEPDPQFWARLTGLQP-RAALFQL 62 L+ ++TGG SGIG A+++ A EGA + +V+ S D + R + R L Q Sbjct: 89 LKGMATLITGGDSGIGRAVAVLFAREGADVGIVYLESSDDAEETRRHVEQEGGRCLLIQG 148 Query: 63 ELQDEARCGEAVAETVRRFGRLDGLVNNAGVNDSVGL--DAGRNEFVASLERNLIHYYVM 120 ++ D C +AV ETV FG LD LVNNA + D + NL Y+ M Sbjct: 149 DVTDPDFCQQAVEETVEEFGHLDVLVNNAAFQEHADTLEDITEEHMDLTFRTNLYGYFHM 208 Query: 121 AHYCVPHLKATRGAILNVSSKTALTGQGNTSGYCASKGAQLSLTREWAAALRDDGVRVNA 180 A +PH+KA +I+N S+T L G Y A+KGA + TR +A L G+RVNA Sbjct: 209 ARAALPHMKAG-ASIINTGSETGLFGNPKLLDYSATKGAIHAFTRSLSANLVKKGIRVNA 267 Query: 181 LIPAEVMTPLYEKWIATFENPQEKLDAITSKIPLGKRFTTSEEMADMAVFLLS-GRSSHT 239 + P V TPL + P + + S P+G R EE+A VFL + +S+ Sbjct: 268 VAPGPVWTPLNPA-----DQPAKSVAKFGSSNPMG-RPAQPEEVAPAYVFLAAPSCASYI 321 Query: 240 TGQWVFVDGGYT 251 +G + V GG T Sbjct: 322 SGAILPVMGGPT 333 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: 175 Number of extensions: 14 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: 334 Length adjustment: 26 Effective length of query: 232 Effective length of database: 308 Effective search space: 71456 Effective search space used: 71456 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: 48 (23.1 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