Align Short-chain dehydrogenase (characterized, see rationale)
to candidate GFF2911 HP15_2855 short-chain dehydrogenase/reductase SDR
Query= uniprot:A0A2E7P8M8 (258 letters) >FitnessBrowser__Marino:GFF2911 Length = 256 Score = 104 bits (259), Expect = 2e-27 Identities = 81/241 (33%), Positives = 113/241 (46%), Gaps = 6/241 (2%) Query: 10 VIVTGGASGIGGAISLQLAAEGAIPVVFARSEPDPQFWARLTGLQPRAA-LFQLELQDEA 68 VIV GG+ GIG AI+L A GA V AR + A + A + ++ D+A Sbjct: 17 VIVAGGSKGIGRAIALGFARAGASVSVCARGQASLDALAEEVASEGLALHVTPCDIGDKA 76 Query: 69 RCGEAVAETVRRFGRLDGLVNNAGVNDSVGLDAGRNEFVASLERNLIHYYVMAHYCVPHL 128 + + G LD LVN A + G + +++S+E +L+ H C+P L Sbjct: 77 ELEAYLQNAMGELGGLDVLVNCAS---AFGREDNEEGWLSSVEVDLMGTVRAGHICLPAL 133 Query: 129 KATRGAILNVSSKTALTGQGNTSGYCASKGAQLSLTREWAAALRDDGVRVNALIPAEVMT 188 K T G I+N++S AL T+ Y A K A T A + VRVN + P + Sbjct: 134 KETGGTIINIASIAALHASTRTAPYAAIKAAVAHYTGSLAVTMAPHKVRVNGIAPGSIEF 193 Query: 189 PLYEKWIATFENPQEKLDAITSKIPLGKRFTTSEEMADMAVFLLSGRSSHTTGQWVFVDG 248 P W +N E I IP G R T EE+AD+A+FL S + TGQ + VDG Sbjct: 194 P-GGVWDQARQNNPELYQRIREGIPFG-RLGTPEEVADVALFLASDLARWITGQTLVVDG 251 Query: 249 G 249 G Sbjct: 252 G 252 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: 145 Number of extensions: 7 Number of successful extensions: 2 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: 256 Length adjustment: 24 Effective length of query: 234 Effective length of database: 232 Effective search space: 54288 Effective search space used: 54288 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