Align furfuryl alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_043917880.1 jaqu_RS05220 alcohol dehydrogenase AdhP
Query= metacyc::MONOMER-17184 (342 letters) >NCBI__GCF_000877395.1:WP_043917880.1 Length = 340 Score = 434 bits (1116), Expect = e-126 Identities = 221/340 (65%), Positives = 258/340 (75%), Gaps = 2/340 (0%) Query: 1 MPAMMKAAVVRAFGAPLTIDEVPVPQPGPGQVQVKIEASGVCHTDLHAADGDWPVKPTLP 60 MP+ MKAAVV F PL I EV P G++ VKIEA GVCHTDLHAA GDWPVKP P Sbjct: 1 MPSTMKAAVVTDFSKPLEIKEVERPTVSDGKILVKIEACGVCHTDLHAARGDWPVKPEPP 60 Query: 61 FIPGHEGVGYVSAVGSGVSRVKEGDRVGVPWLYSACGYCEHCLQGWETLCEKQ-QNTGYS 119 FIPGHEGVG V+ VG GV+ VKEGDRVGVPWL+ ACG+C C+ GWETLC + Q TGY+ Sbjct: 61 FIPGHEGVGIVAEVGRGVASVKEGDRVGVPWLHHACGHCTACVTGWETLCRTEPQYTGYT 120 Query: 120 VNGGYGEYVVADPNYVGLLPDKVGFVEIAPILCAGVTVYKGLKVTDTRPGQWVVISGIGG 179 VNGG+ EYV ADP YVG LP + F APILCAGVTVYKGLK D RPGQ VVISGIGG Sbjct: 121 VNGGFAEYVEADPAYVGHLPGALDFAPAAPILCAGVTVYKGLKECDLRPGQSVVISGIGG 180 Query: 180 LGHVAVQYARAMGLRVAAVDIDDAKLNLARRLGAEVAVNARDTDPAAWLQKEIGGAHGVL 239 LGH+AVQYARAMGL V AVDI + KL LAR LGAE +NA DTDP + + +GGA GVL Sbjct: 181 LGHLAVQYARAMGLHVIAVDIAEDKLRLARDLGAETTINAGDTDPVDEVTR-LGGADGVL 239 Query: 240 VTAVSPKAFSQAIGMVRRGGTIALNGLPPGDFGTPIFDVVLKGITIRGSIVGTRSDLQES 299 VTAVS AF+QA+GM+ GGT++L GLPPGDF IFDVVL TIRGSIVGTR+DL ES Sbjct: 240 VTAVSNSAFTQAVGMLAPGGTMSLVGLPPGDFSLNIFDVVLNRKTIRGSIVGTRADLAES 299 Query: 300 LDFAAHGDVKATVSTAKLDDVNDVFGRLREGKVEGRVVLD 339 L FAA G V + +T +LD++N +F + +GK++GR+V++ Sbjct: 300 LSFAAEGTVASHYATDRLDNINGIFEAMEQGKIDGRIVME 339 Lambda K H 0.319 0.139 0.427 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: 412 Number of extensions: 15 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: 342 Length of database: 340 Length adjustment: 29 Effective length of query: 313 Effective length of database: 311 Effective search space: 97343 Effective search space used: 97343 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 (21.7 bits) S2: 49 (23.5 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