Align Lactaldehyde reductase; Propanediol oxidoreductase; EC 1.1.1.77 (characterized)
to candidate CA265_RS24860 CA265_RS24860 alcohol dehydrogenase
Query= SwissProt::P0A9S1 (382 letters) >FitnessBrowser__Pedo557:CA265_RS24860 Length = 382 Score = 199 bits (507), Expect = 8e-56 Identities = 121/375 (32%), Positives = 198/375 (52%), Gaps = 10/375 (2%) Query: 10 TAWFGRGAVGALTDEVKRRGYQKALIVTDKTLVQCGVVAKVTDKMDAAGLAWAIYDGVVP 69 T FG GAV L + + LIVTD T+ Q ++ + + A G+A ++ + Sbjct: 14 TIRFGAGAVKELPAYLSEHNLKAPLIVTDPTIAQLPFFKRIAEDLKAKGIAVEVFSDIHK 73 Query: 70 NPTITVVKEGLGVFQNSGADYLIAIGGGSPQDTCKAIGI-ISNNPEFADVRSLEGLSPTN 128 NP + V +G V+ + D +I IGGG+ D +AI + +++ + L G Sbjct: 74 NPVKSDVYKGTEVWDATNRDSIIGIGGGAALDVARAIVLRVNHREDLFKYDDLIGGDIYV 133 Query: 129 KPSVP-ILAIPTTAGTAAEVTINYVITDEEKRRKFVCVDPHDIPQVAFIDADMMDGMPPA 187 VP + IPTT+GT +EV + +I D+E +K + P + Q+ F D ++ +PP Sbjct: 134 TNDVPHFITIPTTSGTGSEVGRSAIIADDETHQKKILFSPKLMAQIVFADPELTMDLPPF 193 Query: 188 LKAATGVDALTHAIEGYITRGAWALTDALHIKAIEIIAGAL-RGSVAGDKDAGEEMALGQ 246 + AATG+DALTH +E Y+ + + D + ++ I +I AL R + D ++ +M + Sbjct: 194 ITAATGMDALTHNMEAYLAKNFHPMCDGIALEGISLIKDALERATNNPDLESRSKMLMAS 253 Query: 247 YVAGMGFSNVGLGLVHGMAHPLGAFYNTPHGVANAILLPHVMRYNADFTGEKYRDIARVM 306 + + F GLG+VH +AHPL + +T HG+ANA+ +P+ M++N ++++ IAR + Sbjct: 254 MMGAIAFQK-GLGVVHSLAHPLSSLLDTHHGLANAVNIPYGMQFNIAGFEDRFKKIARTL 312 Query: 307 GVKVEGMSLEEARNAAVEAVFALNRDVGIPPHLRDVGVRKEDIPALAQAALDDVCTGGNP 366 +K +E A V+ +F LN V IP L D+GV+ E I LA A D NP Sbjct: 313 DLK------DENGEAVVKYLFDLNTKVNIPHKLSDIGVKNEHIETLADLAFADFAHPNNP 366 Query: 367 REATLEDIVELYHTA 381 + + D +LY TA Sbjct: 367 KPVSRADFKQLYLTA 381 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: 23 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: 382 Length adjustment: 30 Effective length of query: 352 Effective length of database: 352 Effective search space: 123904 Effective search space used: 123904 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