Align Lactaldehyde reductase (characterized, see rationale)
to candidate WP_066328438.1 BLR17_RS00855 iron-containing alcohol dehydrogenase
Query= uniprot:Q8A199 (384 letters) >NCBI__GCF_900100165.1:WP_066328438.1 Length = 380 Score = 198 bits (503), Expect = 2e-55 Identities = 129/386 (33%), Positives = 193/386 (50%), Gaps = 15/386 (3%) Query: 4 IILNETSY-FGAGCRSVIAVEAARRGFKKAFFVTDKDLIKFGVAAEIIKVFDDNHIPYEL 62 +ILN FG G + G K+ F + +L I+ +N + + Sbjct: 5 VILNPNRVVFGEGSMQRFVDDFVASGLKRMFLIGISELAN--TLVPYIEKLKENGVAVFV 62 Query: 63 YSDVKANPTIANVQNGVAAYKASGADFIVALGGGSSIDTAKGIGIVVNNPDFADVKSLEG 122 +K PT + + A AD +V +GGGS +D AK + + N D ++G Sbjct: 63 DESIKGEPTFDDFNEVLEKAIAFNADSVVGVGGGSVLDVAKLVAAQLKNTQSLD--EIKG 120 Query: 123 VADTKHKAVPTFALPTTAGTAAEVTINYVIIDEDARKKMVCVDPNDIPAVAIVDPELMYS 182 + + K + +PTT+GT +EV+ N + ++ + +K+ + P +P A +DP L Sbjct: 121 IGNLKERQTYVACIPTTSGTGSEVSPNAIFVN-NLGEKVGVISPYLVPDAAYIDPVLTVL 179 Query: 183 MPKGLTAATGMDALTHAIESYITPGAWAMSDMFELKAIEMIAQNLKAAVDNGKDTVAREA 242 +PK +TAATG+DALTH +E+Y A D++ L+ + +IA+ LK A D+G D AR Sbjct: 180 LPKSVTAATGIDALTHCLEAYTNKFAHPFVDLYALEGVRLIAKYLKRACDDGTDIEARTQ 239 Query: 243 MSQAQYIAGMGFSNVGLGIVHSMAHPLGAFYDTPHGVANALLLPYVMEYNAESPAAPKYI 302 ++ GM V VH++++PLG Y PHG++NALLLPYVMEYN E A+ KY Sbjct: 240 VALGSMYGGMCLGPVNTAAVHALSYPLGVEYHIPHGLSNALLLPYVMEYNIEEDAS-KYE 298 Query: 303 HIAKAMGV---NTDGMTETEGVKAAIEAVKALSLSIGIPQKLHEINVKEEDIPALAVAAF 359 IA+ +G NT T EGVK +K L G+P L VKEE I LA A Sbjct: 299 RIAEVLGAEKKNTSRETALEGVK----IMKQLIADCGLPTSLAHAGVKEESITKLAEGAI 354 Query: 360 N-DVCTGGNPRPTSVAEIEVLYRKAF 384 N R +V + +Y+ AF Sbjct: 355 KVQRLLKNNIREIAVEDAVAIYQSAF 380 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: 371 Number of extensions: 22 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: 380 Length adjustment: 30 Effective length of query: 354 Effective length of database: 350 Effective search space: 123900 Effective search space used: 123900 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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