Align Lactaldehyde reductase; Propanediol oxidoreductase; EC 1.1.1.77 (characterized)
to candidate AZOBR_RS28580 AZOBR_RS28580 alcohol dehydrogenase
Query= SwissProt::P0A9S1 (382 letters) >FitnessBrowser__azobra:AZOBR_RS28580 Length = 387 Score = 209 bits (533), Expect = 8e-59 Identities = 124/373 (33%), Positives = 197/373 (52%), Gaps = 5/373 (1%) Query: 13 FGRGAVGALTDEVKRRGYQKALIVTDKTLVQCGVVAKVTDKMDAAGLAWAIYDGVVPNPT 72 FG GA L D ++ + ++ D L + ++ + + G+A +++ G+ P P Sbjct: 17 FGVGAHEQLPDVLREWNATRLFVLLDPALADSAIFRRIEGLLTSNGVALSVFTGIEPEPG 76 Query: 73 ITVVKEGLGVFQNSGADYLIAIGGGSPQDTCKAIGIISNNPEFADVRSLEGLSPTNKPSV 132 V+ + A L+AIGGGS D KA+GI+ N + EG+ + Sbjct: 77 DRTVQAAYERCREQDAQALLAIGGGSTIDVAKAVGILMTNG--GRIADYEGIEKFAIRPL 134 Query: 133 PILAIPTTAGTAAEVTINYVITDEEKRRKFVCVDPHDIP-QVAFIDADMMDGMPPALKAA 191 P++A+PTTAGT +EV+ VITD ++ K P QVA +D + MP + A Sbjct: 135 PLIAVPTTAGTGSEVSGACVITDTARKTKMAIRHAAFSPAQVAILDPLAVGSMPAHVAAH 194 Query: 192 TGVDALTHAIEGYITRGAWALTDALHIKAIEIIAGALRGSVAGDKD--AGEEMALGQYVA 249 G+DA HA E Y+++ A +DA+++ A+ +IAG++R VA + A +M G +A Sbjct: 195 AGIDAFVHAFESYLSKRATVFSDAVNLHAMTLIAGSIRPFVADRTNVPAALDMLCGSALA 254 Query: 250 GMGFSNVGLGLVHGMAHPLGAFYNTPHGVANAILLPHVMRYNADFTGEKYRDIARVMGVK 309 M F GLG VH MA +GA + PHG+ANA+ LP+ +N E+ IA ++GV Sbjct: 255 AMSFGVTGLGNVHCMAMSVGALFPVPHGLANAVCLPYAAAFNVSAKPERMARIAEILGVD 314 Query: 310 VEGMSLEEARNAAVEAVFALNRDVGIPPHLRDVGVRKEDIPALAQAALDDVCTGGNPREA 369 G+ L++A AAV+ + L D+GIPP LRDVGV ++ + +A+ + NPR Sbjct: 315 TAGLPLDQAAEAAVDGLRTLCADLGIPPRLRDVGVTEDRLDEMARRSYAADYNRWNPRHT 374 Query: 370 TLEDIVELYHTAW 382 + D +L+ A+ Sbjct: 375 SEPDFQDLFRAAF 387 Lambda K H 0.319 0.136 0.404 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: 378 Number of extensions: 24 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: 382 Length of database: 387 Length adjustment: 30 Effective length of query: 352 Effective length of database: 357 Effective search space: 125664 Effective search space used: 125664 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: 50 (23.9 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