Align D-threo-aldose 1-dehydrogenase (EC 1.1.1.122) (characterized)
to candidate Pf1N1B4_4176 Alcohol dehydrogenase (EC 1.1.1.1)
Query= BRENDA::Q97YM2 (349 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4176 Length = 327 Score = 82.8 bits (203), Expect = 1e-20 Identities = 91/347 (26%), Positives = 148/347 (42%), Gaps = 28/347 (8%) Query: 10 KAALLKKFSEPLSIEDVNIPEPQGEEVLIRIGGAGVCRTDLRVWKGVEAKQGFRLPIILG 69 +A +L +PL E+ IP P ++LI++ GVCRTDL + G E Q LP + G Sbjct: 2 RAMVLHAPGQPLQREERAIPIPDAHQLLIKVLACGVCRTDLHLVDG-ELPQAV-LPRVPG 59 Query: 70 HENAGTIVEVG-ELAKVKKGDNV-VVYATWGDLTCRYCREGKFNICKNQIIPGQTTNGGF 127 HE G + VG +A G V V + W C +CR G+ N+C G +GG+ Sbjct: 60 HEIVGEVTAVGANVAPDWVGKRVGVPWLGWTCGECTFCRSGRENLCDRARFTGCHLDGGY 119 Query: 128 SEYMLVKSSRWLVKLNSLSPVEAAPLADAGTTSMGAIRQALPFISKFAEPVVIVNGIGGL 187 +EY + + ++LS EAAPL AG A++ A K A + + G G Sbjct: 120 AEYTVADAHFCFPIPDALSAAEAAPLLCAGLIGFRALQMA-----KGARHLGLY-GFGAA 173 Query: 188 AVYTIQILKALMKNITIVGISRSKKHRDFALELGADYV--SEMKDAESLINKLTDG-LGA 244 A IQ+ + + + + + +A LGA++ S+ L L +GA Sbjct: 174 AHLAIQVARGRGQQVYAFTRPDDSEGQAYARTLGAEWAGPSDQPPPHPLDASLIFAPVGA 233 Query: 245 SIAIDLVGTEETTYNLGKLLAQEGAIILVGMEGKRVSLEAFDTAVWNKKLLGSNYGSLND 304 + L T + G +I G+ + + +W ++ + S +L Sbjct: 234 LVPPALEAT-----------VKGGCVICAGIHMSDIPSFPY-RLLWGERSIRS-VANLTR 280 Query: 305 LEDVVRLSE--SGKIKPYIIKVPLDDINKAFTNLDEGRVDGRQVITP 349 + +E + + LDD N+A +L G+V G V+ P Sbjct: 281 EDGTAFFAELRHTPVHSDVTCFALDDANQALASLRAGQVKGAIVLIP 327 Lambda K H 0.317 0.136 0.389 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: 255 Number of extensions: 19 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 349 Length of database: 327 Length adjustment: 28 Effective length of query: 321 Effective length of database: 299 Effective search space: 95979 Effective search space used: 95979 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 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