Align Alcohol dehydrogenase; EC 1.1.1.1; EC 1.1.1.4; EC 1.2.1.3 (characterized)
to candidate WP_009763936.1 MICLODRAFT_RS21540 NAD(P)-dependent alcohol dehydrogenase
Query= SwissProt::Q0KDL6 (366 letters) >NCBI__GCF_000262405.1:WP_009763936.1 Length = 357 Score = 509 bits (1310), Expect = e-149 Identities = 256/361 (70%), Positives = 294/361 (81%), Gaps = 7/361 (1%) Query: 5 MKAAVFVEPGRIELADKPIPDIGPNDALVRITTTTICGTDVHILKGEYPVAKGLTVGHEP 64 M+AA+FVEPGRI L +KPIP+IGP DALVRI+TTTICGTD+HILKGEYPVA GLT+GHEP Sbjct: 4 MRAAIFVEPGRIVLDEKPIPNIGPLDALVRISTTTICGTDIHILKGEYPVAPGLTIGHEP 63 Query: 65 VGIIEKLGSAVTGYREGQRVIAGAICPNFNSYAAQDGVASQDGSYLMASGQCGCHGYKAT 124 VGIIEKLGSAV GYREGQRVIAGAI P+ S A G SQDG+ HG+KA Sbjct: 64 VGIIEKLGSAVQGYREGQRVIAGAITPSGYSEACLCGCHSQDGAGTK-------HGWKAM 116 Query: 125 AGWRFGNMIDGTQAEYVLVPDAQANLTPIPDGLTDEQVLMCPDIMSTGFKGAENANIRIG 184 GW+FGN IDG QAEY+ VPDA ANL P+PDGLTDEQVLMCPDI+STGF GAE+ IRIG Sbjct: 117 GGWKFGNTIDGCQAEYLRVPDAMANLAPVPDGLTDEQVLMCPDILSTGFSGAESGRIRIG 176 Query: 185 DTVAVFAQGPIGLCATAGARLCGATTIIAIDGNDHRLEIARKMGADVVLNFRNCDVVDEV 244 DTVAVFAQGPIGLCATAGA+L GATTIIA++ R++++R+MGAD V++F D V+E+ Sbjct: 177 DTVAVFAQGPIGLCATAGAKLMGATTIIAVESLPERIDMSRRMGADHVIDFTKADPVEEI 236 Query: 245 MKLTGGRGVDASIEALGTQATFEQSLRVLKPGGTLSSLGVYSSDLTIPLSAFAAGLGDHK 304 +LT GRGVD SIEALG Q TFE +LRVL+PGGTLSSLGVYS DL IPL F AGLGD+ Sbjct: 237 RRLTDGRGVDVSIEALGRQQTFEAALRVLRPGGTLSSLGVYSGDLRIPLDGFLAGLGDYT 296 Query: 305 INTALCPGGKERMRRLINVIESGRVDLGALVTHQYRLDDIVAAYDLFANQRDGVLKIAIK 364 I T LCPGGKERMRRLI+ I SGRVD LVTH+++LD I AYDLF++QRDGVLK+AI Sbjct: 297 IRTTLCPGGKERMRRLISAIASGRVDTRPLVTHRFKLDQIEEAYDLFSHQRDGVLKVAIA 356 Query: 365 P 365 P Sbjct: 357 P 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: 542 Number of extensions: 17 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: 357 Length adjustment: 29 Effective length of query: 337 Effective length of database: 328 Effective search space: 110536 Effective search space used: 110536 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