Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate RR42_RS24385 RR42_RS24385 hypothetical protein
Query= BRENDA::Q76HN6 (526 letters) >FitnessBrowser__Cup4G11:RR42_RS24385 Length = 541 Score = 451 bits (1161), Expect = e-131 Identities = 244/528 (46%), Positives = 333/528 (63%), Gaps = 7/528 (1%) Query: 2 EFDYLIVGAGSAGCVLANRLSADPSVTVCLLEAGPEDRSPLIHTPLGLAAILPTRHVNWA 61 EFDY++VGAGSAGCVLANRLSA P+V+V LLEAG + + TP G+ + +NW Sbjct: 9 EFDYIVVGAGSAGCVLANRLSASPNVSVLLLEAGKDAEPFWVRTPAGVGNLFFNERLNWK 68 Query: 62 FKTTPQPGLGGRVGYQPRGKVLGGSSSINGMIYIRGHQDDFNDWQALGNEGWGFDDVLPY 121 F T P+ LG R Y PRGK+LGGSSSINGM+Y+RG D++ WQA GN GW + DVLPY Sbjct: 69 FFTEPEANLGDRQVYWPRGKILGGSSSINGMVYVRGFASDYDRWQAQGNPGWAWSDVLPY 128 Query: 122 FRKSEMHHGGSSEYHGGDGELYVS-PANRHAASEAFVESALRAGHSYNPD-FNGATQEGA 179 F+++E + G+SE G G L+VS P +H +EAFV + G + + D G EG Sbjct: 129 FKRAEHNDYGASESRGVGGPLHVSFPHRQHPTTEAFVRAGAAVGLTRHDDVVAGGDAEGV 188 Query: 180 GYYDVTIRDGRRWSTATAFLKPVRHRSNLTVLTHTHVESIVLLGKQATGVQALIKGSRVH 239 GY TI +GRRWS+A A+++PVR R+NL + + V + L G+ GV+ + +G Sbjct: 189 GYLQHTIGEGRRWSSAHAYVRPVRQRTNLAIESEAVVTRLHLDGRCVVGVEYIRRGQSRT 248 Query: 240 LRARKEVILSAGAFGSPHLLMLSGIGSAAELEPQGIAPRHELPGVGQNLQDHADVVLCYK 299 +RAR+EVILSAGA GSPHLLMLSGIG L+ G+ RH LPGVG NLQDH + CY+ Sbjct: 249 IRARREVILSAGAIGSPHLLMLSGIGPPDHLQEMGVRVRHALPGVGCNLQDHLAINACYE 308 Query: 300 SNDTSLLGFSLSGGVKMGKAMFDYARHRNGPVASNCAEAGAFLKTDPGLERPDIQL--HS 357 + L +LSG K + DY HR GP+A + A AF+ + ++ PDIQL Sbjct: 309 VRKDASLNAALSGWHKYLNGV-DYLLHRRGPLAIGASHAVAFVCSSTSIKVPDIQLSFRP 367 Query: 358 VIGTVDDHNR-KLHWGHGFSCHVCVLRPKSIGSVGLASPDPRKAPRIDPNFLAHDDDVAT 416 + D N+ ++H G +LRP+S G + L SP+P AP I N+L DD+ Sbjct: 368 LSFAFDSKNKLRMHTFAGVQFASAMLRPRSRGQILLRSPNPFDAPVIHANYLTDPDDMRV 427 Query: 417 LLKGYRITRDIIAQTPMASFGLRD-MYSAGLHNDEQLIELLRKRTDTIYHPIGTCKMGQD 475 ++ TR + A P+A +R+ + + + +++E +R+ + T++HP GTCKMG D Sbjct: 428 MVATLEWTRRLAATAPLADMVVREYLPGENVRSASEVVEFIRRSSQTLFHPAGTCKMGSD 487 Query: 476 EMAVVDSQLRVHGIEGLRVVDASIMPTLVGGNTNAAAIMIAERAAEWI 523 +AVVD +LRV GIE LRVVDAS+MPT+V GNTNA IMIAE+A++ I Sbjct: 488 SLAVVDERLRVRGIENLRVVDASVMPTIVSGNTNAPTIMIAEKASDMI 535 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: 779 Number of extensions: 26 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: 541 Length adjustment: 35 Effective length of query: 491 Effective length of database: 506 Effective search space: 248446 Effective search space used: 248446 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