Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_023432295.1 N177_RS10510 choline dehydrogenase
Query= BRENDA::Q76HN6 (526 letters) >NCBI__GCF_000496075.1:WP_023432295.1 Length = 554 Score = 413 bits (1061), Expect = e-119 Identities = 232/534 (43%), Positives = 318/534 (59%), Gaps = 19/534 (3%) Query: 1 MEFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNW 60 +E D++IVGAGSAGC LA+RLS D +V ++E G D P IH P L+ + +W Sbjct: 5 LEADFVIVGAGSAGCALAHRLSEDGRHSVLVIEGGGTDWGPFIHMPAALSYPMNMNRYDW 64 Query: 61 AFKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLP 120 F+T P+P LGGR PRGKVLGGSSSINGM+Y+RGH DF+ W+A G +GWGF D+LP Sbjct: 65 GFRTAPEPHLGGRRLAVPRGKVLGGSSSINGMVYVRGHACDFDGWEADGAKGWGFADILP 124 Query: 121 YFRKSEMHHGGSSEYHGGDGELYVSPA-NRHAASEAFVESALRAGHSYNPDFNGATQEGA 179 Y+ K E HGG + + G DG L+V+ R+ AFVE+ AG+ D+NG QEG Sbjct: 125 YYLKLETSHGGEAGWRGSDGPLHVTRGPRRNPLYHAFVEAGKEAGYGETADYNGHRQEGF 184 Query: 180 GYYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVH 239 G ++T+ GRRWS A A+L+ R N+ V+ ++ V +V+ +ATGV+ +G Sbjct: 185 GPMEMTVWGGRRWSAANAYLRRAWKRKNVRVMANSFVRRVVIENGRATGVEIGARGVERT 244 Query: 240 LRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCYK 299 +RAR+EVILSA + SP LLMLSGIG A L GI + + PGVG+NLQDH ++ L + Sbjct: 245 VRARREVILSASSINSPKLLMLSGIGGADALRKLGIEVKADRPGVGRNLQDHLEIYLQAE 304 Query: 300 S-------NDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPD 352 S +LLG +L G + + G ASN E+ AF+++ G+ PD Sbjct: 305 SLKPVTLYRYNNLLGKALVGA--------QWLFTKTGLGASNQFESAAFIRSKAGVSYPD 356 Query: 353 IQLHSVIGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDD 412 IQ H + V HGF HV +R KS G V L SP+P AP I N+++H + Sbjct: 357 IQYHFLPLAVRYDGTSAVKAHGFQVHVGPMRSKSRGHVALTSPEPEAAPEILFNYMSHAE 416 Query: 413 DVATLLKGYRITRDIIAQTPMASF-GLRDMYSAGLHNDEQLIELLRKRTDTIYHPIGTCK 471 D R+TR+I+ Q M + G M +DE L E +R+ ++ YHP GTC+ Sbjct: 417 DWEDFRACIRLTREILRQPAMKDYLGREIMPGPDATDDEALDEFVREEVESAYHPCGTCR 476 Query: 472 MG--QDEMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523 MG +D +AVVD + RV G+EGLRVVD+SI P + GN NA +IM+ E+AA+ I Sbjct: 477 MGAAEDPLAVVDPECRVIGVEGLRVVDSSIFPRITNGNLNAPSIMVGEKAADHI 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: 853 Number of extensions: 49 Number of successful extensions: 6 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: 554 Length adjustment: 35 Effective length of query: 491 Effective length of database: 519 Effective search space: 254829 Effective search space used: 254829 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