Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate Echvi_3928 Echvi_3928 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
Query= uniprot:B2T9V3 (247 letters) >FitnessBrowser__Cola:Echvi_3928 Length = 252 Score = 140 bits (353), Expect = 2e-38 Identities = 92/252 (36%), Positives = 135/252 (53%), Gaps = 24/252 (9%) Query: 5 LAGKTALITAAGQGIGLATAELFAREGARVIAT------------DIRIDGLAGKPVEAR 52 L GK A++T GIG +TA+ EGA+VI T ++ + G+ +E Sbjct: 4 LNGKVAVVTGGNSGIGYSTAKKLKEEGAQVIITGRSAEKVNVAAAELGVTGITADVLELA 63 Query: 53 KLDVRDDAAIKALAAEIGAVDVLFNCAGFVHAGNILECSEEDWDFAFDLNVKAMYRMIRA 112 +D AA+ + A+ G VD+LF AG I + +E+ +D D+N+K I Sbjct: 64 AID----AAVNQVKADFGHVDILFVNAGIFLPAPIGQTTEDLFDQQMDINLKGAVFTIEK 119 Query: 113 FLPAMLDKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFITRGVRCNAI 172 FLP + D GGSIIN+SS ++ G+PN Y ASKAA+ T++ A + R +R NA+ Sbjct: 120 FLPILKD--GGSIINLSSI-NAYTGMPNTSIYGASKAALNSYTRTAATELAPRKIRVNAV 176 Query: 173 CPGTVASPSLEQRIVAQAQAQGATLDAVQAAFVARQPMGRIGKPEEIAALALYLGSDESS 232 PG V +P + +++ Q G + AA R P+ R GKPE+IA L +L SD +S Sbjct: 177 NPGPVYTPIFSKTGMSEDQLNG-----MAAAMQNRIPLKRYGKPEDIAELVAFLASDRAS 231 Query: 233 FTTGHAHVIDGG 244 F TG + IDGG Sbjct: 232 FITGAEYNIDGG 243 Lambda K H 0.320 0.133 0.381 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: 129 Number of extensions: 8 Number of successful extensions: 5 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: 247 Length of database: 252 Length adjustment: 24 Effective length of query: 223 Effective length of database: 228 Effective search space: 50844 Effective search space used: 50844 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 (21.8 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