Align Lactaldehyde reductase (characterized, see rationale)
to candidate 6937537 Sama_1693 bifunctional acetaldehyde-CoA/alcohol dehydrogenase (RefSeq)
Query= uniprot:Q8A199 (384 letters) >FitnessBrowser__SB2B:6937537 Length = 867 Score = 213 bits (541), Expect = 2e-59 Identities = 149/408 (36%), Positives = 215/408 (52%), Gaps = 34/408 (8%) Query: 6 LNETSYFGAGCRSVIAVEAARRGFKKAFFVTDKDLIKFGVAAEIIKVFDDNHIPYELYSD 65 L + YF G + E + G K+A VTDK L G E I++ + E++ + Sbjct: 456 LPSSIYFRRGSLPIALEELS--GKKRALIVTDKFLFNNGYCDETIRILKSQGLETEVFYE 513 Query: 66 VKANPTIANVQNGVAAYKASGADFIVALGGGSSIDTAKGIGIVVNNPD--FADV------ 117 V+A+PT+A V+ G + D IVALGGGS +D AK I ++ +PD FAD+ Sbjct: 514 VEADPTLAVVRAGAKVATSFQPDVIVALGGGSPMDAAKIIWVMYEHPDVDFADLALRFMD 573 Query: 118 --KSLEGVADTKHKAVPTFALPTTAGTAAEVTINYVIIDEDARKKMVCVDPNDIPAVAIV 175 K + KA+ A+PTT+GT +EVT V+ DE K D P +AIV Sbjct: 574 IRKRIYKFPKLGAKAMMV-AIPTTSGTGSEVTPFAVVTDEQTGAKYPIADYELTPNMAIV 632 Query: 176 DPELMYSMPKGLTAATGMDALTHAIESYITPGAWAMSDMFELKAIEMIAQNLKAAVDNGK 235 DP L+ MPK LTA G+DA+THA+E+Y++ A SD L+A++++ + L + G Sbjct: 633 DPNLVMDMPKSLTAFGGIDAITHALEAYVSVMANEYSDGQALQALDLLFKYLPDSYARGA 692 Query: 236 DT-VAREAMSQAQYIAGMGFSNVGLGIVHSMAHPLGAFYDTPHGVANALLLPYVMEYNA- 293 +ARE + IAG+ F+N LGI HSMAH LGA + PHG+ANALL+ V+ +NA Sbjct: 693 QAPLAREKVHNGATIAGIAFANAFLGICHSMAHKLGAEFHLPHGLANALLISNVIRFNAT 752 Query: 294 -------------ESPAAPKYIHIAKAMGVNTDGMTETEGVKAAIEAVKALSLSIGIPQK 340 A +Y IA +G+ G + V+A I ++ L +IGIP Sbjct: 753 DLPTKQAAFSQYDRPKALCRYAAIASHLGL--AGNNDEAKVEALIAKIEELKAAIGIPVS 810 Query: 341 LHEINVKEEDIPA----LAVAAFNDVCTGGNPRPTSVAEIEVLYRKAF 384 + + V E D A LA AF+D CTG NPR ++E++ L +F Sbjct: 811 IKDAGVNEADFMAKLDELAEDAFDDQCTGANPRYPLISELKQLLIDSF 858 Lambda K H 0.317 0.133 0.379 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: 755 Number of extensions: 39 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: 384 Length of database: 867 Length adjustment: 36 Effective length of query: 348 Effective length of database: 831 Effective search space: 289188 Effective search space used: 289188 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Apr 09 2024. 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