Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_023434027.1 N177_RS18905 choline dehydrogenase
Query= BRENDA::Q76HN6 (526 letters) >NCBI__GCF_000496075.1:WP_023434027.1 Length = 563 Score = 396 bits (1017), Expect = e-114 Identities = 227/524 (43%), Positives = 310/524 (59%), Gaps = 6/524 (1%) Query: 2 EFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWA 61 EFD+++VGAGSAG VLA+RLSAD + V +LE G D S I P + L + +W Sbjct: 9 EFDFVVVGAGSAGSVLADRLSADGTNRVLVLEFGGRDNSIYIQMPTAFSIPLGMKRFDWG 68 Query: 62 FKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPY 121 + + P+PGL GR +Q RGKV+GGSSSING+ Y+RG+ DF++W+ G GWG+ VLPY Sbjct: 69 YHSEPEPGLKGRRIHQARGKVIGGSSSINGLAYVRGNAGDFDEWEEHGAAGWGYRHVLPY 128 Query: 122 FRKSEMHHGGSSEYHGGDGELYVSPAN--RHAASEAFVESALRAGHSYNPDFNGATQEGA 179 F ++E G+ EY G G L + N + AF+E+ +AG+ D+NG QEG Sbjct: 129 FVRAEDCLYGADEYRGAGGPLGTNNGNNMENPLYRAFIEAGRQAGYGETRDYNGYRQEGF 188 Query: 180 GYYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVH 239 D+T+R+G R STA A+LKP R+NL V TH I+ G++A GV+ G Sbjct: 189 CRMDMTVRNGVRCSTANAYLKPAMTRANLDVKTHALTTRILFEGRRAVGVEYRRGGETRR 248 Query: 240 LRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCYK 299 +AR EVILSA +F SP LLMLSG+G AA L+ GI H+LPGVG+NLQDH +V + Sbjct: 249 AKARGEVILSASSFNSPKLLMLSGVGPAAHLKSHGIDVLHDLPGVGRNLQDHLEVWVQQL 308 Query: 300 SNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQLHSVI 359 L L G V G + + G SN E+ +++T GL PD+Q H + Sbjct: 309 CTQPITLNRRL-GLVGQGLIGARWLLTKTGLGISNQFESNGYIRTRAGLRFPDLQYHFLA 367 Query: 360 GTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVATLLK 419 G + + G GF H+ +PKS G V L+S D P+I N+L+ ++D Sbjct: 368 GAISYDGKPATKGDGFQVHLGHNKPKSRGYVELSSRDAEAQPKIVFNYLSEEEDKEGFRA 427 Query: 420 GYRITRDIIAQTPMASFGLRDMYSAG--LHNDEQLIELLRKRTDTIYHPIGTCKMGQDEM 477 G R+TR+I AQ + D S G + D+++ + + + +T YHP G+C+MG DEM Sbjct: 428 GLRLTREIFAQGAFDPY-RGDELSPGRDVTTDDEIDDWVAETAETAYHPAGSCRMGTDEM 486 Query: 478 AVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAE 521 AVVD + RVHGIEGLRVVD+SIMPTL GN NA IMI E+ A+ Sbjct: 487 AVVDPECRVHGIEGLRVVDSSIMPTLTNGNINAPTIMIGEKGAD 530 Lambda K H 0.319 0.137 0.419 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: 865 Number of extensions: 39 Number of successful extensions: 4 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: 526 Length of database: 563 Length adjustment: 35 Effective length of query: 491 Effective length of database: 528 Effective search space: 259248 Effective search space used: 259248 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: 52 (24.6 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