Align Alcohol dehydrogenase; EC 1.1.1.1; EC 1.1.1.4; EC 1.2.1.3 (characterized)
to candidate WP_086510909.1 BZY95_RS16090 NAD(P)-dependent alcohol dehydrogenase
Query= SwissProt::Q0KDL6 (366 letters) >NCBI__GCF_002151265.1:WP_086510909.1 Length = 359 Score = 573 bits (1478), Expect = e-168 Identities = 280/364 (76%), Positives = 319/364 (87%), Gaps = 7/364 (1%) Query: 1 MTAMMKAAVFVEPGRIELADKPIPDIGPNDALVRITTTTICGTDVHILKGEYPVAKGLTV 60 M AMMKAA+FVEPGRIE+ DKPIPDIGPNDAL+R+TTTTICGTDVHILKGEYPVA+GLT+ Sbjct: 1 MPAMMKAAIFVEPGRIEIDDKPIPDIGPNDALIRVTTTTICGTDVHILKGEYPVARGLTI 60 Query: 61 GHEPVGIIEKLGSAVTGYREGQRVIAGAICPNFNSYAAQDGVASQDGSYLMASGQCGCHG 120 GHEPVG+IEKLG+ V GY+EGQRVIAGAICP+F SYA QDG +QDG + HG Sbjct: 61 GHEPVGVIEKLGANVRGYQEGQRVIAGAICPSFTSYACQDGCCAQDGGH-------HAHG 113 Query: 121 YKATAGWRFGNMIDGTQAEYVLVPDAQANLTPIPDGLTDEQVLMCPDIMSTGFKGAENAN 180 YK GWRFGN IDG QAEY+LVPDAQANL P+PDGLTDEQVLMCPDIMSTGF GAE+A Sbjct: 114 YKPMGGWRFGNTIDGAQAEYLLVPDAQANLAPVPDGLTDEQVLMCPDIMSTGFAGAESAG 173 Query: 181 IRIGDTVAVFAQGPIGLCATAGARLCGATTIIAIDGNDHRLEIARKMGADVVLNFRNCDV 240 I+IGD+VAVFAQGPIGLCATAGARL GA IIA+DG D RL +AR+MGADV L+FR DV Sbjct: 174 IKIGDSVAVFAQGPIGLCATAGARLRGAGLIIAVDGVDERLAMARQMGADVTLDFRKVDV 233 Query: 241 VDEVMKLTGGRGVDASIEALGTQATFEQSLRVLKPGGTLSSLGVYSSDLTIPLSAFAAGL 300 V+E++++TGGRGVDASIEALG Q+TFE +LRV+KPGGTLSSLGVYSSDLTIPL AF AGL Sbjct: 234 VEEILRITGGRGVDASIEALGLQSTFEAALRVVKPGGTLSSLGVYSSDLTIPLGAFCAGL 293 Query: 301 GDHKINTALCPGGKERMRRLINVIESGRVDLGALVTHQYRLDDIVAAYDLFANQRDGVLK 360 GDHKI T+LCPGGKERMRRL+ VIE+GR+DLG +VTH+Y L DIV AYDLF++QRDGVLK Sbjct: 294 GDHKIVTSLCPGGKERMRRLMQVIETGRIDLGPMVTHRYALADIVEAYDLFSHQRDGVLK 353 Query: 361 IAIK 364 +AI+ Sbjct: 354 VAIQ 357 Lambda K H 0.320 0.138 0.408 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: 603 Number of extensions: 18 Number of successful extensions: 2 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: 366 Length of database: 359 Length adjustment: 29 Effective length of query: 337 Effective length of database: 330 Effective search space: 111210 Effective search space used: 111210 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: 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