Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_052473627.1 SUTH_RS13000 GMC family oxidoreductase N-terminal domain-containing protein
Query= BRENDA::Q76HN6 (526 letters) >NCBI__GCF_000828635.1:WP_052473627.1 Length = 531 Score = 562 bits (1448), Expect = e-164 Identities = 278/524 (53%), Positives = 360/524 (68%), Gaps = 2/524 (0%) Query: 2 EFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWA 61 EFDY++VG G+ GC +A RLS DP+V+VCLLEAG D LI P A +LPT NWA Sbjct: 3 EFDYIVVGGGAGGCAVAGRLSEDPAVSVCLLEAGKGDDQLLIKVPFCTALMLPTPINNWA 62 Query: 62 FKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPY 121 F+T PQPGL GR GY PRGK +GGS+SIN M+Y RGH D++ W ALGNEGW + DVLPY Sbjct: 63 FETVPQPGLNGRRGYVPRGKAMGGSTSINAMVYTRGHPWDYDHWAALGNEGWSWKDVLPY 122 Query: 122 FRKSEMHHGGSSEYHGGDGELYVSPA-NRHAASEAFVESALRAGHSYNPDFNGATQEGAG 180 FRKSE + EYHG G L V+ + + E + E+A + G DFNGA QEG G Sbjct: 123 FRKSEHNENFDGEYHGQGGPLNVANLRSMNPFQEIYREAARQTGFKLIDDFNGADQEGIG 182 Query: 181 YYDVTIRDGRRWSTATAFLKP-VRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVH 239 Y V ++G RW+ A A++ P + R NLTV+T ++ GK+A+ V+ L G+ Sbjct: 183 IYQVMQKNGERWNAARAYVTPHLASRPNLTVITQARARRVLFTGKRASAVEFLQGGAVQA 242 Query: 240 LRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCYK 299 +A++EVIL+AGA SP LLMLSG+G+ AEL+ GI H+LPGVG+NLQDH D V Y+ Sbjct: 243 FQAKREVILAAGALQSPQLLMLSGVGAGAELQQFGIPVIHDLPGVGKNLQDHPDYVFNYR 302 Query: 300 SNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQLHSVI 359 + LLG SL G ++M K + Y R R G + SN AE G FL+ P P+ QLH V+ Sbjct: 303 AKSLDLLGISLGGSLQMMKEIGRYRRERTGMMTSNGAEGGGFLRRYPDSPAPEFQLHFVV 362 Query: 360 GTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVATLLK 419 G +D H RKLH GHG+SCH+C+LRPKSIG++GLAS DP AP IDP F H DD+ ++ Sbjct: 363 GMIDSHARKLHMGHGYSCHICLLRPKSIGTLGLASADPHAAPSIDPKFFDHPDDLDAMVD 422 Query: 420 GYRITRDIIAQTPMASFGLRDMYSAGLHNDEQLIELLRKRTDTIYHPIGTCKMGQDEMAV 479 G+++TR I+ +A ++Y+AG+H+D+ + E L+ R+DTIYHP+GTCKMG D MAV Sbjct: 423 GFKLTRKIMDAPVLAGIRTGEVYTAGIHSDDAIREELKNRSDTIYHPVGTCKMGSDAMAV 482 Query: 480 VDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523 VD++LRVHG+EGLRVVDASIMPTL+GGNT A +MI E+AAE I Sbjct: 483 VDARLRVHGLEGLRVVDASIMPTLIGGNTTAPTLMIGEKAAEMI 526 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: 28 Number of successful extensions: 3 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 Apr 09 2024. 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