Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate CCNA_00994 CCNA_00994 oxidoreductase, GMC family
Query= BRENDA::Q76HN6 (526 letters) >FitnessBrowser__Caulo:CCNA_00994 Length = 555 Score = 415 bits (1066), Expect = e-120 Identities = 239/542 (44%), Positives = 316/542 (58%), Gaps = 20/542 (3%) Query: 1 MEFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDR----------SPLIHTPLGLA 50 +E DY+IVGAGSAGCVLA RLS + V LLEAG +DR + +IH P+G + Sbjct: 5 IEADYVIVGAGSAGCVLAARLSENGRYKVVLLEAGGDDRPTKNLSQFASNMMIHIPVGYS 64 Query: 51 AILPTRHVNWAFKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGN 110 + L VNW F T P PG GGR PRGKVLGGSSSIN M+Y+RG D++ W+ LG Sbjct: 65 STLKDPKVNWLFTTEPDPGTGGRSHVWPRGKVLGGSSSINAMLYVRGQAADYDGWRQLGC 124 Query: 111 EGWGFDDVLPYFRKSEMHHGGSSEYHGGDGELYVSPA-NRHAASEAFVESALRAGHSYNP 169 EGW +DDVLPYFRK++ G+ + H G L V+ + H SEA +E+ +AG P Sbjct: 125 EGWAWDDVLPYFRKAQNQERGACDLHATGGPLNVADMRDAHPISEALIEACDQAGIPRYP 184 Query: 170 DFNGATQEGAGYYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGV 229 D NGA QEGA +Y VT ++G R S+A A+L P R NL V T+ ++ GK+A GV Sbjct: 185 DLNGADQEGATWYQVTQKNGARCSSAVAYLHPAMKRPNLRVETNALAGRVLFEGKRAVGV 244 Query: 230 QALIKGSRVHLRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQ 289 + + G R AR EVIL+ GA SP LL LSG+G+ L GI +LPGVG+NLQ Sbjct: 245 EFMQNGERRAAMARGEVILAGGAINSPQLLQLSGVGAGGLLREHGIEVVADLPGVGENLQ 304 Query: 290 DHADVVLCYKSNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLE 349 DH V Y+ ++ S G ++ Y R G + + A AF K+ P L Sbjct: 305 DHYIVAARYRLKSGTVSVNEQSKGGRLAAEAMKYLLFRKGLLTLSAAHVAAFCKSRPDLA 364 Query: 350 RPDIQLHSVIGTVD------DHNRKLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRI 403 PDIQ H + T+D + +L G + C LRP+S G + + S DP P I Sbjct: 365 GPDIQFHILPATMDLDKLFNEQKMELEGAPGMTIAPCQLRPESRGYIRIKSADPSVYPAI 424 Query: 404 DPNFLAHDDDVATLLKGYRITRDIIAQTPMASFGLRDMYSAGL--HNDEQLIELLRKRTD 461 N+LA D ++ G + R I Q +A + +M + GL DEQL++ R+ Sbjct: 425 FANYLADPLDQEVIVAGLKWARKIGQQPAIAQYVESEM-NPGLEVQTDEQLLDFARQTGS 483 Query: 462 TIYHPIGTCKMGQDEMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAE 521 T+YHP+G+C+MG MAVVD+QLRV G+EGLRVVDASIMP L+ GNTNA +IMI E+ A+ Sbjct: 484 TLYHPVGSCQMGTGPMAVVDAQLRVRGVEGLRVVDASIMPRLISGNTNAPSIMIGEKGAD 543 Query: 522 WI 523 I Sbjct: 544 MI 545 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: 762 Number of extensions: 35 Number of successful extensions: 5 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: 555 Length adjustment: 35 Effective length of query: 491 Effective length of database: 520 Effective search space: 255320 Effective search space used: 255320 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