Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate H281DRAFT_06507 H281DRAFT_06507 NAD(P)-dependent dehydrogenase, short-chain alcohol dehydrogenase family
Query= uniprot:B2T9V3 (247 letters) >FitnessBrowser__Burk376:H281DRAFT_06507 Length = 249 Score = 143 bits (360), Expect = 4e-39 Identities = 96/255 (37%), Positives = 141/255 (55%), Gaps = 26/255 (10%) Query: 4 RLAGKTALITAAGQGIGLATAELFAREGARVIATDIR--------------IDGLAGKPV 49 +L+GK A+IT G+GLATA+LFA+EGA+VI T R +G+ G Sbjct: 3 KLSGKIAVITGGNSGMGLATAQLFAKEGAKVIITGRRQKELDEAVESIGANAEGVLGDVS 62 Query: 50 EARKLDVRDDAAIKALAAEIGAVDVLFNCAGFVHAGNILECSEEDWDFAFDLNVKAMYRM 109 LD +D + A+ G VDV+F AG I + +E +D F++NVK Y Sbjct: 63 RLSDLDKLNDH----VKAKYGRVDVIFANAGLGSLAPIDQVTEAQFDETFNVNVKGTYFT 118 Query: 110 IRAFLPAMLDKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFITRGVRC 169 ++ LP + D GGSII +S ASS KG+ YSA+KAAV L +++ D R +R Sbjct: 119 VQKLLPLVPD--GGSIILNTSIASS-KGMEAFSVYSATKAAVRSLARTLTTDLKARKIRV 175 Query: 170 NAICPGTVASPSLEQRIVAQAQAQGATLDAVQAAFVARQPMGRIGKPEEIAALALYLGSD 229 NAI PG + +P + + + + +G ++ ++ P+GRIG PEEIA AL+L SD Sbjct: 176 NAISPGPIDTPIFGKTGLTEQEIEG-----FKSGITSQVPLGRIGLPEEIAKPALFLASD 230 Query: 230 ESSFTTGHAHVIDGG 244 +SS+ +G +DGG Sbjct: 231 DSSYISGIELTVDGG 245 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: 147 Number of extensions: 7 Number of successful extensions: 4 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: 249 Length adjustment: 24 Effective length of query: 223 Effective length of database: 225 Effective search space: 50175 Effective search space used: 50175 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