Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate BWI76_RS07610 BWI76_RS07610 choline dehydrogenase
Query= BRENDA::Q76HN6 (526 letters) >FitnessBrowser__Koxy:BWI76_RS07610 Length = 554 Score = 377 bits (968), Expect = e-109 Identities = 230/533 (43%), Positives = 310/533 (58%), Gaps = 12/533 (2%) Query: 1 MEFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHT--PLGLAAILPTRHV 58 M+FDY+I+GAGSAG VLA RL+ DP TV LLEAG D T P LA L R Sbjct: 1 MQFDYIIIGAGSAGNVLATRLTEDPDTTVLLLEAGGPDYRFDFRTQMPAALAFPLQGRRY 60 Query: 59 NWAFKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDW-QALGNEGWGFDD 117 NWA++T P+P + R RGK LGGSS INGM YIRG+ D ++W A G E W + D Sbjct: 61 NWAYETEPEPHMNHRRMECGRGKGLGGSSLINGMCYIRGNAMDLDNWASAPGLEHWSYLD 120 Query: 118 VLPYFRKSEMHHGGSSEYHGGDGELYVSPANR--HAASEAFVESALRAGHSYNPDFNGAT 175 LPY+RK+E G+++YHGGDG + V+ + + A +E+ ++AG+ D NG Sbjct: 121 CLPYYRKAETRDIGANDYHGGDGPVSVTTPKQGNNPLFHAMIEAGVQAGYPRTDDLNGYQ 180 Query: 176 QEGAGYYDVTIR-DGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIK 234 QEG G D T+ GRR STA +L R R NLT+ TH + I+ GK+A GV+ L Sbjct: 181 QEGFGPMDRTVTPQGRRASTARGYLDQARARPNLTIRTHALTDHIIFAGKRAVGVEWLEG 240 Query: 235 GSRVHLRA--RKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHA 292 S +A KEV+L AGA SP +L SG+GS L I+ H LPGVG+NLQDH Sbjct: 241 DSTAPSKATANKEVLLCAGAIASPQILQRSGVGSPELLRQFDISLVHALPGVGENLQDHL 300 Query: 293 DVVLCYKSNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPD 352 ++ L Y+ + L +L K ++ G ASN EAG F+++ P+ Sbjct: 301 EMYLQYECKEPVSLYPALQWW-NQPKIGAEWLFGGTGIGASNQFEAGGFIRSREAFAWPN 359 Query: 353 IQLHSVIGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDD 412 IQ H + ++ + HGF CHV +R S G V L S DP + P I N+++H+ Sbjct: 360 IQYHFLPVAINYNGSNAVKEHGFQCHVGSMRSPSRGHVRLKSRDPHQHPAILFNYMSHEQ 419 Query: 413 DVATLLKGYRITRDIIAQTPMASFGLRDMYSAGLH--NDEQLIELLRKRTDTIYHPIGTC 470 D RITR+I++Q + ++ R++ S G+ +D +L E +R +T +HP GTC Sbjct: 420 DWQEFRDAIRITREIMSQPALDNYRGREI-SPGIECQSDAELDEFVRNHAETAFHPCGTC 478 Query: 471 KMGQDEMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523 KMG DEMAVVD + RVHG+EGLRVVDASIMP ++ GN NA IMI E+ A+ I Sbjct: 479 KMGYDEMAVVDGEGRVHGLEGLRVVDASIMPQIITGNLNATTIMIGEKMADAI 531 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: 867 Number of extensions: 43 Number of successful extensions: 8 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 17 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