Align Short-chain dehydrogenase (characterized, see rationale)
to candidate GFF901 HP15_880 oxidoreductase, short chain dehydrogenase/reductase family
Query= uniprot:A0A2E7P8M8 (258 letters) >FitnessBrowser__Marino:GFF901 Length = 243 Score = 98.6 bits (244), Expect = 1e-25 Identities = 82/242 (33%), Positives = 123/242 (50%), Gaps = 12/242 (4%) Query: 12 VTGGASGIGGAISLQLAAEGAIPVVFARSEPDPQFWARLTGLQPRAALFQL-ELQDEARC 70 +TGGA GIG I L LAA G V F + D RL A F ++ E Sbjct: 1 MTGGAKGIGRGIVLHLAAAGW-KVAFC--DTDSAVGERLAAGADYALHFLPGDVASETDV 57 Query: 71 GEAVAETVRRFGRLDGLVNNAGV-NDSVGL--DAGRNEFVASLERNLIHYYVMAHYCVPH 127 VAE +R GRLD ++NNAG+ N G + +++ L+ NL +++ + VPH Sbjct: 58 ERIVAEALRWGGRLDAVINNAGIANPETGPIEELSLDQWQRRLDVNLTGPFLVTKHAVPH 117 Query: 128 LKATRGAILNVSSKTALTGQGNTSGYCASKGAQLSLTREWAAALRDDGVRVNALIPAEVM 187 L+ T+GAI+N++S AL + +T Y A+KG ++LT A +L D VRVN + P + Sbjct: 118 LRKTKGAIVNMASTRALQSEPDTEAYAATKGGIVALTHALAVSLGPD-VRVNCISPGWID 176 Query: 188 TPLYEKWIATFENPQEKLDAITSKIPLGKRFTTSEEMADMAVFLLSGRSSHTTGQWVFVD 247 T ++ E P + D + + P G R ++A + +L+S +S TGQ D Sbjct: 177 TRAWQGGAEPVE-PLSENDHL--QHPAG-RVGQPGDIASLVAYLISQEASFITGQNFVAD 232 Query: 248 GG 249 GG Sbjct: 233 GG 234 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: 159 Number of extensions: 8 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: 243 Length adjustment: 24 Effective length of query: 234 Effective length of database: 219 Effective search space: 51246 Effective search space used: 51246 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