Align Lactaldehyde reductase; Propanediol oxidoreductase; EC 1.1.1.77 (characterized)
to candidate GFF2063 HP15_2019 iron-containing alcohol dehydrogenase
Query= SwissProt::P0A9S1 (382 letters) >FitnessBrowser__Marino:GFF2063 Length = 385 Score = 217 bits (552), Expect = 5e-61 Identities = 125/372 (33%), Positives = 208/372 (55%), Gaps = 8/372 (2%) Query: 16 GAVGALTDEVKRRGYQKALIVTDKTLVQCGVVAKVTDKMDAAGLAWAIYDGVVPNPTITV 75 G L VK +K L+VTD LV+ G++ T+ ++ AG+ + ++DGVV +P ++V Sbjct: 17 GVTHRLGQIVKEHMGKKVLLVTDPGLVKAGLLDVATNSLNEAGVKYELFDGVVADPPVSV 76 Query: 76 VKEGLGVFQNSGADYLIAIGGGSPQDTCKAIGIISNNPEFADVRSLEGLSPTNKPSVPIL 135 V+ L + +G D +I GGGS D K I ++ E D + G+ +P++ Sbjct: 77 VEAALADAREAGVDGVIGFGGGSSMDVAKLIALLIGGEEKLD--DVYGVGQAKGKRLPLI 134 Query: 136 AIPTTAGTAAEVTINYVITDEEKRRKFVCVDPHDIPQVAFIDADMMDGMPPALKAATGVD 195 IPTTAGT +EVT +IT E +K V V P +P +A +DA++ G+P + AATG+D Sbjct: 135 QIPTTAGTGSEVTPISIITVGETEKKGV-VAPQLLPDIALLDAELTLGLPAHVTAATGID 193 Query: 196 ALTHAIEGYITRGAW--ALTDALHIKAIEIIAGALRGSVAGDKD--AGEEMALGQYVAGM 251 A+ HAIE Y + A ++ AL +A+ ++ + +V + A +M LG +AG Sbjct: 194 AMVHAIESYTSASANNNPVSKALAREALRLLGANIETAVKDGSNVKARSDMLLGAMLAGQ 253 Query: 252 GFSNVGLGLVHGMAHPLGAFYNTPHGVANAILLPHVMRYNADFTGEKYRDIARVMGVKVE 311 F+N + VH +A+P+G ++ PHG++NA++LPHVMR+N + GE Y +A + + Sbjct: 254 AFANSPVAAVHALAYPIGGIFHVPHGLSNALVLPHVMRFNTEICGEAYSILATDVFPDLA 313 Query: 312 GMSLEEARNAAVEAVFALNRDVGIPPHLRDVGVRKEDIPALAQAALDDV-CTGGNPREAT 370 G + N ++ + AL+ D+G+ LR+VG+ + D+ LA ++ NPRE + Sbjct: 314 GTPAAKRANQFIDRLEALSADLGLEQTLREVGIGEADLATLASDSMKQTRLLVNNPREVS 373 Query: 371 LEDIVELYHTAW 382 D + +Y A+ Sbjct: 374 ETDALAIYKAAF 385 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: 388 Number of extensions: 25 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: 385 Length adjustment: 30 Effective length of query: 352 Effective length of database: 355 Effective search space: 124960 Effective search space used: 124960 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