Align L-lactaldehyde reductase (EC 1.1.1.77) (characterized)
to candidate WP_011460576.1 DHAF_RS19580 alcohol dehydrogenase
Query= metacyc::STM4044-MONOMER (382 letters) >NCBI__GCF_000021925.1:WP_011460576.1 Length = 401 Score = 152 bits (383), Expect = 2e-41 Identities = 116/361 (32%), Positives = 182/361 (50%), Gaps = 21/361 (5%) Query: 3 FMLALPKISLHGAGAIADMVNLVANKQWGKALIVT--DGQLVKL-GLLDSLFSALDEHQM 59 F + +P + G+G + + L K GK ++T +G+ V+ G LD L + Sbjct: 14 FNMYVPTRFVFGSGRLRE---LHQQKMPGKKALITISNGKSVRENGALDRTQEQLRLAGV 70 Query: 60 SYHLFDEVFPNPTEELVQKGFAAYQSAECDYIIAFGGGSPIDTAKAVKILTANPGPSTAY 119 + +FD++ NPT+ V +G + + CD+I+A GGGS +D AKA+ ++ N G Y Sbjct: 71 AMVVFDKIGANPTKTAVMEGAKSARDHGCDFIVALGGGSVMDAAKAIAMMATNDGDLWDY 130 Query: 120 SG--VGK---VKNAGVPLVAINTTAGTAAEMTSNAVIIDSARKVKEVIIDPNI-IPDIAV 173 G GK +++ +PLV I TTAGT +E V+ + K + + P +++ Sbjct: 131 VGGKTGKGQALRHEPLPLVCITTTAGTGSEADQWGVVTNEETNEKIGVGGYDASFPVVSI 190 Query: 174 DDASVMLEIPASVTAATGMDALTHAVEAYVSVGAHPLTDANALEAIRLINLWLPKAVDDG 233 D +M+ +P TA G DAL HA E Y+S A P++D AL AI + +L +A DG Sbjct: 191 IDPELMVSVPPKFTAYQGFDALFHATEGYISKFASPMSDMYALTAIENVGNYLVRACRDG 250 Query: 234 HNLEAREQMAFGQYLAGMAFNSAGLGLVHALAHQPGATH-NLPHGV-CNAILLPIVENFN 291 ++EARE MAF L+G+ + H+L H A H LPHG I E F Sbjct: 251 RDMEAREGMAFANTLSGVVMTVSVTTAEHSLEHAMSAYHPELPHGAGLIMISRAFYEFFI 310 Query: 292 RPNAV-ARFARIAQAMGVETRGMSDEAASQEAINAIRTLSKRVGIPE-GFSKLGVTKEDI 349 +A RF R+AQA+ GM D A ++ I + L + G+ + S G+T ++ Sbjct: 311 EKHACDQRFVRMAQAL-----GMKDAARPEDFITMLVKLQENCGVADLKMSDYGMTPDEF 365 Query: 350 E 350 + Sbjct: 366 D 366 Lambda K H 0.317 0.133 0.384 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: 366 Number of extensions: 22 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: 382 Length of database: 401 Length adjustment: 31 Effective length of query: 351 Effective length of database: 370 Effective search space: 129870 Effective search space used: 129870 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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