Align Lactaldehyde reductase (characterized, see rationale)
to candidate AZOBR_RS32240 AZOBR_RS32240 acetaldehyde dehydrogenase
Query= uniprot:Q8A199 (384 letters) >FitnessBrowser__azobra:AZOBR_RS32240 Length = 886 Score = 220 bits (561), Expect = 1e-61 Identities = 149/403 (36%), Positives = 216/403 (53%), Gaps = 34/403 (8%) Query: 6 LNETSYFGAGCRSVIAVEAARRGFKKAFFVTDKDLIKFGVAAEIIKVFDDNHIPYELYSD 65 L ++ YF GC E RG K+ VTD+ L + G E +++ + E + + Sbjct: 456 LPKSIYFRRGCLPFALEEL--RGKKRCLIVTDRFLFENGHVDETVRILKGLGLAVETFFE 513 Query: 66 VKANPTIANVQNGVAAYKASGADFIVALGGGSSIDTAKGIGIVVNNPDFADVKSLEGVAD 125 V A+PT+A V+ G+A A D I+ALGGGS +D AK + ++ PD A D Sbjct: 514 VAADPTLAVVRRGLALANAFQPDVILALGGGSPMDAAKIMWVMYEAPDVAFEDLALRFMD 573 Query: 126 TKHKAVPTF----------ALPTTAGTAAEVTINYVIIDEDARKKMVCVDPNDIPAVAIV 175 + K + TF A+PTT+GT +EVT V+ DE K D P +AI+ Sbjct: 574 IR-KRIYTFPKLGVKAQFVAVPTTSGTGSEVTPFAVVTDERTGIKYPIADYELTPNMAII 632 Query: 176 DPELMYSMPKGLTAATGMDALTHAIESYITPGAWAMSDMFELKAIEMIAQNLKAAVDN-G 234 D L+ MPKGLTAA G+DA+THA+E+Y++ A +D L+A++++ ++L +A N G Sbjct: 633 DANLVMDMPKGLTAAGGIDAVTHALEAYVSVLANEYTDGQALQALKLLKEHLPSAYANGG 692 Query: 235 KDTVAREAMSQAQYIAGMGFSNVGLGIVHSMAHPLGAFYDTPHGVANALLLPYVMEYNA- 293 KD ARE + A +AG+ F+N LG+ HSMAH LGA + PHGVANALL+ V+ YNA Sbjct: 693 KDPKAREQVHSAATLAGIAFANAFLGVCHSMAHKLGAEFHLPHGVANALLIANVIRYNAA 752 Query: 294 -------------ESPAAPKYIHIAKAMGVNTDGMTETEGVKAAIEAVKALSLSIGIPQK 340 +Y IA+ +G+ G + E V+ + V+ L ++ IP Sbjct: 753 DIPTKQTAFSQYDRPKGVARYAEIARHLGLG--GSRDHERVETLVAWVEELKRTLDIPAS 810 Query: 341 LHEINVKEED----IPALAVAAFNDVCTGGNPRPTSVAEIEVL 379 + V E + + A+A AAF+D CTG NPR VAEI L Sbjct: 811 IQAAGVPEAEFLARLDAIAEAAFDDQCTGANPRFPLVAEIRQL 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: 861 Number of extensions: 50 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: 886 Length adjustment: 36 Effective length of query: 348 Effective length of database: 850 Effective search space: 295800 Effective search space used: 295800 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