Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate SMa1414 SMa1414 Dehydrogenase, FAD-dependent
Query= BRENDA::Q76HN6 (526 letters) >FitnessBrowser__Smeli:SMa1414 Length = 531 Score = 400 bits (1028), Expect = e-116 Identities = 231/531 (43%), Positives = 307/531 (57%), Gaps = 18/531 (3%) Query: 3 FDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWAF 62 FDY+IVG GS+GCVLA RLS +PSV VCL+EAG DR PLIH P+G A + + W Sbjct: 5 FDYVIVGGGSSGCVLAARLSENPSVRVCLIEAGGRDRHPLIHMPVGFAK-MTAGPMTWGL 63 Query: 63 KTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPYF 122 T PQ R + +VLGG SSIN +Y RGH D++ W G +GW F +V PYF Sbjct: 64 TTAPQKHANNREIPYAQARVLGGGSSINAEVYTRGHPRDYDRWVEEGADGWSFQEVKPYF 123 Query: 123 RKSEMHHGGSSEYHGGDGELYVSPA-NRHAASEAFVESALRAGHSYNPDFNGATQEGAGY 181 +SE + S E+HG DG L VS + + AFV+S G YNPDFNG QEGAG Sbjct: 124 LRSEGNTILSGEWHGTDGPLGVSNLPDPQPMTRAFVQSCQELGIPYNPDFNGPVQEGAGV 183 Query: 182 YDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVHLR 241 Y TIR+ RR S A +L+P R NL ++T V IV G++A GV+ G+ R Sbjct: 184 YQTTIRNSRRCSAAVGYLRPALARKNLMLITGALVLRIVFQGRRAVGVEYSTGGAAKIAR 243 Query: 242 ARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDH--ADVVLCYK 299 A EV++++GA G+P L+MLSG+G AA L GI ++ GVGQNL DH D+V K Sbjct: 244 AESEVLVTSGAIGTPKLMMLSGVGPAASLRSHGIDVVQDMAGVGQNLHDHFGVDIVAELK 303 Query: 300 SNDT----SLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQL 355 +D+ + + L G+ +YA ++GPVASN E GAF D PD+Q Sbjct: 304 GHDSLDKYNKFHWMLLAGI-------EYALFKSGPVASNVVEGGAFWYGDRASPYPDLQF 356 Query: 356 HSVIGTVDDHN--RKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDD 413 H + G + G + + +RPKS GSV L S DPR P +DPNFL DD Sbjct: 357 HFLAGAGAEAGVPSVPKGSSGVTLNSYTVRPKSRGSVTLRSADPRALPIVDPNFLDDPDD 416 Query: 414 VATLLKGYRITRDIIAQTPMASFGLRDMY-SAGLHNDEQLIELLRKRTDTIYHPIGTCKM 472 + ++G RI+R+I Q + + + + R+ T YHP TCKM Sbjct: 417 LRISVEGIRISREIFGQPSLQKYIKTIRFPDESVRTQADFEAYARQYGRTSYHPTCTCKM 476 Query: 473 GQDEMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523 G+D+M+VVD QLRVHG++G+R+ D+S+MP+LVG NTNAA IMI E+AA+ I Sbjct: 477 GRDDMSVVDPQLRVHGLDGIRICDSSVMPSLVGSNTNAATIMIGEKAADLI 527 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: 798 Number of extensions: 29 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: 531 Length adjustment: 35 Effective length of query: 491 Effective length of database: 496 Effective search space: 243536 Effective search space used: 243536 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