Align Putative alcohol dehydrogenase D; EC 1.1.1.1 (characterized)
to candidate WP_043767718.1 U743_RS09715 alcohol dehydrogenase catalytic domain-containing protein
Query= SwissProt::P9WQB9 (368 letters) >NCBI__GCF_000733765.1:WP_043767718.1 Length = 379 Score = 249 bits (637), Expect = 7e-71 Identities = 150/374 (40%), Positives = 205/374 (54%), Gaps = 13/374 (3%) Query: 3 TTAAVLFEAG--------KPFELMELDLDGPGPGEVLVKYTAAGLCHSDLHLTDGDLPPR 54 T AVL E G +P ++ L+L PGPGE+ V+ AAG+CHSDL + +G P Sbjct: 5 TRGAVLREMGAAQPYAETRPLKIETLELAPPGPGEIQVRVRAAGICHSDLSVVNGSRPRP 64 Query: 55 FPIVGGHEGSGVIEEVGAGVTRVKPGDHVVCSFIPNCGTCRYCCTGRQNLCDMGATI-LE 113 P+V GHE +G +E VG V PGD VV SF+P CGTC YC GR LC GA Sbjct: 65 MPMVLGHEAAGDVEAVGPDVADFAPGDRVVFSFVPACGTCSYCAEGRPVLCVPGAAANSA 124 Query: 114 GCMPDGSFRFH-SQGTDFGAMCMLGTFAERATVSQHSVVKVDDWLPLETAVLVGCGVPSG 172 G + G+ R+ S G + + FAER VS S V++D LP+E A L GC V +G Sbjct: 125 GTLLSGARRWRDSDGAECHHHLGVSAFAERTVVSTRSAVRIDPDLPVEIAALFGCAVMTG 184 Query: 173 WGTAVNAGNLRAGDTAVIYGVGGLGINAVQGATAAGCKYVVVVDPVAFKRETALKFGATH 232 G AVN +R G++ ++G+GG+G+ A+ GA AAG VV VDPVA KRE AL GATH Sbjct: 185 VGAAVNTAAVRPGESVAVFGMGGVGLAALLGAIAAGAWPVVAVDPVAAKRELALSLGATH 244 Query: 233 AFADAASAAAKVDELTWGQGADAALILVGTVDDEVVSAATAVIGKGGTVVITGLADPAKL 292 A A + G GA A+ VG+ ++V+ A +GG V GL P ++ Sbjct: 245 VVDPTAEDAVEAVRAHTGGGAAHAVETVGS--EKVLEQAYFATVRGGQTVTVGLPHPERM 302 Query: 293 TVHVSGTDLTLHEKTIKGSLFGSCNPQYDIVRLLRLYDAGQLMLDELVTTTYNLEQVNQG 352 + + L E+T++GS GS D+ R L LY AG+L +D+L+T L+ +N Sbjct: 303 -LSIPAVSLVAEERTLRGSYMGSAVVSRDVPRFLSLYRAGRLPVDKLLTHELALDGINAA 361 Query: 353 YQDLRDGKNIRGVI 366 + L + +R VI Sbjct: 362 FDRLARAEAVRQVI 375 Lambda K H 0.320 0.138 0.422 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: 327 Number of extensions: 21 Number of successful extensions: 3 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: 368 Length of database: 379 Length adjustment: 30 Effective length of query: 338 Effective length of database: 349 Effective search space: 117962 Effective search space used: 117962 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 (21.8 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