Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate RR42_RS01280 RR42_RS01280 GMC family oxidoreductase
Query= BRENDA::Q76HN6 (526 letters) >FitnessBrowser__Cup4G11:RR42_RS01280 Length = 559 Score = 533 bits (1372), Expect = e-156 Identities = 282/542 (52%), Positives = 358/542 (66%), Gaps = 18/542 (3%) Query: 3 FDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHV-NWA 61 FDYL+VG GSAGC LA RL+ S +V +LE G D L+ TP G AA+LP N+ Sbjct: 5 FDYLVVGGGSAGCALAGRLADSGSDSVAVLETGGHDHHVLVSTPAGCAAMLPRAGSHNYG 64 Query: 62 FKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPY 121 ++T PQPGL GR GYQPRG+ LGGSSS+N MIY RG D++ W + G +GW +DDVLPY Sbjct: 65 YRTVPQPGLNGRRGYQPRGRGLGGSSSLNAMIYTRGTPADYDRWASAGCDGWAWDDVLPY 124 Query: 122 FRKSEMHHGGSSE----YHGGDGELYVSPANR-HAASEAFVESALRAGHSYNPDFNGATQ 176 FR++E + + +HGG G L+VS + + F+E+A +AG+ N DFNG Q Sbjct: 125 FRRAECNERVAGRDDDPWHGGSGPLHVSDLRTPNPFGQRFIEAAQQAGYRRNDDFNGVDQ 184 Query: 177 EGAGYYDVTIRDGRRWSTATAFLK---PVRH-----RSNLTVLTHTHVESIVLLGKQATG 228 EGAG+Y VT G RW+ A A+L H R NL V+T T V I G+ A G Sbjct: 185 EGAGWYQVTQHGGERWNAARAYLHRGDAADHASNGGRENLAVMTGTQVLRIAFEGRHAVG 244 Query: 229 VQALIKGSRVHLRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNL 288 V + G LRAR+EVI+SAGAFGSP LLM+SG+G A+ L GI H+LPGVG NL Sbjct: 245 VVVRLDGRETLLRARREVIVSAGAFGSPQLLMVSGVGPASHLRELGIPVVHDLPGVGANL 304 Query: 289 QDHADVVLCYKSNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGL 348 QDH D+++ + + L G S+ G ++ + Y R R G + SN AEAGAFLK+ GL Sbjct: 305 QDHLDIIVHKRVAASELFGVSVGGAFRLLAEILRYRRERTGMLTSNFAEAGAFLKSHAGL 364 Query: 349 ERPDIQLHSVIGTVDDHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFL 408 + PD+QLH V+G DDH R++ GHG+SCHVCVLRPKS G V LASPD R+AP IDP FL Sbjct: 365 DEPDLQLHFVVGMADDHMRRIRLGHGYSCHVCVLRPKSRGEVRLASPDIREAPMIDPCFL 424 Query: 409 AHDDDVATLLKGYRITRDIIAQTPMASFGLRDMYSAGL----HNDEQLIELLRKRTDTIY 464 + D+ L+ G RI R I+AQ +A+FG +++YSA L +D + ++R DTIY Sbjct: 425 SDPRDLDGLVAGVRIVRRILAQPQLAAFGGKELYSAHLPADGGDDSAIRAMIRAHADTIY 484 Query: 465 HPIGTCKMGQDEMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWIA 524 HP+GTC+MG DE AVVD QLRV G+EGLRVVDASIMPTL+GGNTNA AIMI ERA + I Sbjct: 485 HPVGTCRMGMDEYAVVDPQLRVRGVEGLRVVDASIMPTLIGGNTNAPAIMIGERAHDLIR 544 Query: 525 HG 526 HG Sbjct: 545 HG 546 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: 965 Number of extensions: 45 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: 559 Length adjustment: 35 Effective length of query: 491 Effective length of database: 524 Effective search space: 257284 Effective search space used: 257284 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