Align Lactaldehyde reductase (characterized, see rationale)
to candidate 201293 SO2136 aldehyde-alcohol dehydrogenase (NCBI ptt file)
Query= uniprot:Q8A199 (384 letters) >FitnessBrowser__MR1:201293 Length = 866 Score = 210 bits (535), Expect = 1e-58 Identities = 140/402 (34%), Positives = 208/402 (51%), Gaps = 32/402 (7%) Query: 6 LNETSYFGAGCRSVIAVEAARRGFKKAFFVTDKDLIKFGVAAEIIKVFDDNHIPYELYSD 65 L + YF G + E + + K+A VTD L G E +K+ + E++ + Sbjct: 456 LPSSIYFRRGSLPIALEELSDK--KRALIVTDPFLFNQGYCDETLKILKAQGLETEVFYE 513 Query: 66 VKANPTIANVQNGVAAYKASGADFIVALGGGSSIDTAKGIGIVVNNPD---------FAD 116 V+A+PT+A V+ G + D I+ALGGGS +D AK I ++ +PD F D Sbjct: 514 VEADPTLATVRQGAKVANSFKPDVIIALGGGSPMDAAKIIWVMYEHPDVDFADLALRFMD 573 Query: 117 VKSLEGVADTKHKAVPTFALPTTAGTAAEVTINYVIIDEDARKKMVCVDPNDIPAVAIVD 176 ++ A+PTT+GT +EVT V+ DE KK D P +AIVD Sbjct: 574 IRKRIYKFPKMGVKATMVAIPTTSGTGSEVTPFAVVTDEQTGKKYPIADYQLTPNMAIVD 633 Query: 177 PELMYSMPKGLTAATGMDALTHAIESYITPGAWAMSDMFELKAIEMIAQNLKAAVDNG-K 235 P L+ MPK LTA G+DA+THA+E+Y++ A SD L+A++++ + L A G Sbjct: 634 PNLVMDMPKSLTAFGGIDAITHALEAYVSVMANEYSDGQALQALDLLCKYLPDAYQLGAA 693 Query: 236 DTVAREAMSQAQYIAGMGFSNVGLGIVHSMAHPLGAFYDTPHGVANALLLPYVMEYNA-- 293 +ARE + IAG+ F+N LGI HSMAH LGA + HG+ANALL+ V+ +NA Sbjct: 694 SPIAREKVHNGATIAGIAFANAFLGICHSMAHKLGAEFHLAHGLANALLISNVIRFNATD 753 Query: 294 ------------ESPAAPKYIHIAKAMGVNTDGMTETEGVKAAIEAVKALSLSIGIPQKL 341 A +Y IA + + G ++ + V+ +E ++ L ++GIP + Sbjct: 754 LPTKQAAFSQYDRPKALCRYAAIADHLALG--GNSDAQKVEKLLEKIEQLKKTLGIPASI 811 Query: 342 HEINVKEEDIPA----LAVAAFNDVCTGGNPRPTSVAEIEVL 379 E V E D A LA AF+D CTG NPR ++E++ L Sbjct: 812 QEAGVNEADFLAKLDMLAEDAFDDQCTGANPRYPLISELKQL 853 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: 746 Number of extensions: 37 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: 866 Length adjustment: 36 Effective length of query: 348 Effective length of database: 830 Effective search space: 288840 Effective search space used: 288840 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 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