Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate Pf1N1B4_2416 Choline dehydrogenase (EC 1.1.99.1)
Query= BRENDA::Q76HN6 (526 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2416 Length = 567 Score = 379 bits (972), Expect = e-109 Identities = 232/534 (43%), Positives = 315/534 (58%), Gaps = 16/534 (2%) Query: 2 EFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHT--PLGLAAILPTRHVN 59 EFDY+I+GAGSAG LA RL+ D VTV LLEAG D T P LA L R N Sbjct: 4 EFDYIIIGAGSAGNTLATRLTEDEGVTVLLLEAGGPDYRLDFRTQMPAALAFPLQGRRYN 63 Query: 60 WAFKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQAL-GNEGWGFDDV 118 WA++T P+P + GR RGK LGGSS INGM YIRG+ D+++W L G E W + D Sbjct: 64 WAYETDPEPHMDGRRMECGRGKGLGGSSLINGMCYIRGNAMDYDNWSKLPGLEDWTYLDC 123 Query: 119 LPYFRKSEMHHGGSSEYHGGDGELYVSP--ANRHAASEAFVESALRAGHSYNPDFNGATQ 176 LPYFRK+E G ++YHGGDG + V+ A + A VE+ ++AG+ D NG Q Sbjct: 124 LPYFRKAETRDIGPNDYHGGDGPVSVTTPKAGNNPLFHAMVEAGVQAGYPRTEDLNGYQQ 183 Query: 177 EGAGYYDVTIR-DGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKG 235 EG G D T+ +GRR STA +L + RS LT++TH + I+ GK+A GV+ LI Sbjct: 184 EGFGPMDRTVTPNGRRASTARGYLDVAKKRSTLTIVTHALTDKILFEGKRAVGVRYLIGA 243 Query: 236 S--RVHLRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHAD 293 + RV +RARKEV+L +GA SP +L SG+G A L+ I H+LPGVG+NLQDH + Sbjct: 244 AEERVEVRARKEVLLCSGAIASPQILQRSGVGPAELLKKLDIPVVHDLPGVGENLQDHLE 303 Query: 294 VVLCYKSNDTSLL--GFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERP 351 + L Y L L +G ++ + G ASN EAG F++T P + P Sbjct: 304 LYLQYACTQPVSLYPSLLLHNQPAIGA---EWLFNGTGIGASNQFEAGGFIRTRPEFDWP 360 Query: 352 DIQLHSVIGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHD 411 +IQ H + ++ + HGF H+ +R S G + S DPR+ P I N++A + Sbjct: 361 NIQYHFLPVAINYNGSNGVKEHGFQAHMGSMRSPSRGRIQAKSKDPREYPSILFNYMATE 420 Query: 412 DDVATLLKGYRITRDIIAQTPMASFGLRDMYSAGL--HNDEQLIELLRKRTDTIYHPIGT 469 D G R+TR+I+ Q + +F R++ S G+ DEQL + +R+ +T +HP + Sbjct: 421 QDWQEFRDGIRLTREIMQQPALDAFRGREI-SPGIDVQTDEQLDKFIREHAETAFHPSCS 479 Query: 470 CKMGQDEMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523 CKMG DEMAVVD + RVHG++ LRVVDASIMP + GN NA IM+AE+ A+ I Sbjct: 480 CKMGTDEMAVVDGEGRVHGMQALRVVDASIMPIITTGNLNAPTIMMAEKIADKI 533 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: 861 Number of extensions: 47 Number of successful extensions: 9 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: 567 Length adjustment: 36 Effective length of query: 490 Effective length of database: 531 Effective search space: 260190 Effective search space used: 260190 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