Align Alcohol dehydrogenase; EC 1.1.1.1; EC 1.1.1.4; EC 1.2.1.3 (characterized)
to candidate WP_025331133.1 SALWKB2_RS07905 zinc-dependent alcohol dehydrogenase family protein
Query= SwissProt::Q0KDL6 (366 letters) >NCBI__GCF_000600005.1:WP_025331133.1 Length = 356 Score = 199 bits (506), Expect = 1e-55 Identities = 125/365 (34%), Positives = 195/365 (53%), Gaps = 32/365 (8%) Query: 5 MKAAVFVEPGRIELADKPIPDI-GPNDALVRITTTTICGTDVHILKGEYPVAK------- 56 MKA V+ G I ++ P I P DA++R+T TTICGTD+ I KG+ P + Sbjct: 1 MKAMVYYGAGDIRFEERTKPVIIEPTDAIIRLTRTTICGTDLGIWKGKNPEIEQTAIQKD 60 Query: 57 ----GLTVGHEPVGIIEKLGSAVTGYREGQRVIAGAICPNFNSYAAQDGVASQDGSYLMA 112 G +GHE +GIIE+ GSAV +++G +VI + ++ G L A Sbjct: 61 GQFNGRILGHEGIGIIEETGSAVKNFKKGDKVIISCV--------SRCGTCENCQKQLYA 112 Query: 113 SGQCGCHGYKATAGWRFGNMIDGTQAEYVLVPDAQANLTPIPDGLTDEQVLMCPDIMSTG 172 Q G GW G MIDGTQAEYV P A +L +P L ++ ++ D + T Sbjct: 113 HCQSG-------GGWIMGYMIDGTQAEYVRTPFADNSLYRLPANLNEDVAVLLSDALPTA 165 Query: 173 FK-GAENANIRIGDTVAVFAQGPIGLCATAGARLCGATTIIAIDGNDHRLEIARKMGADV 231 + G + +++ GDTVA+ GP+G+ A+L + II ID +D+RL +A+++GA Sbjct: 166 HEIGVQYGDVKPGDTVAIVGAGPVGMSCLLTAQLYSPSQIIMIDMDDNRLHMAKELGATQ 225 Query: 232 VLNFRNCDVVDEVMKLTGGRGVDASIEALGTQATFEQSLRVLKPGGTLSSLGVYSSDLTI 291 ++N + D V V++ TGGRGVD ++EA+G +AT+ RV+K GG L+++GV+ + Sbjct: 226 IINSASEDAVARVLEYTGGRGVDCAMEAVGLEATWNICQRVVKEGGHLANVGVHGQSVNF 285 Query: 292 PLSAFAAGLGDHKINTALCPGGKERMRRLINVIESGRVDLGALVTHQYRLDDIVAAYDLF 351 L + + I T L M L+ SG++ + L TH + +++ AYD+F Sbjct: 286 ELEKL--WIKNLTITTGLVNANTTGM--LLKTCCSGKLPMEKLATHHFHFNELEKAYDVF 341 Query: 352 ANQRD 356 + D Sbjct: 342 KHAAD 346 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: 346 Number of extensions: 16 Number of successful extensions: 5 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: 356 Length adjustment: 29 Effective length of query: 337 Effective length of database: 327 Effective search space: 110199 Effective search space used: 110199 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