Align L-lactaldehyde reductase (EC 1.1.1.77) (characterized)
to candidate PfGW456L13_1214 Alcohol dehydrogenase (EC 1.1.1.1)
Query= metacyc::STM4044-MONOMER (382 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1214 Length = 382 Score = 248 bits (633), Expect = 2e-70 Identities = 150/381 (39%), Positives = 217/381 (56%), Gaps = 5/381 (1%) Query: 2 SFMLALPKISLHGAGAIADMVNLVANKQWGKALIVTDGQLVKLGLLDSLFSALDEHQMSY 61 SF +A I+ GAGAI + + LIVTD LVK G ++ + L SY Sbjct: 5 SFKIAHKLIT--GAGAIEQLAAELTRLDIDNPLIVTDVALVKSGTVELALAQLGGR--SY 60 Query: 62 HLFDEVFPNPTEELVQKGFAAYQSAECDYIIAFGGGSPIDTAKAVKILTANPGPSTAYSG 121 +FD V P+P +V+ Y+ D +I GGGS ID AK+V G G Sbjct: 61 EIFDRVLPDPEIAIVEDCMQVYRDGGHDGLIGLGGGSAIDIAKSVAAYAGYHGALEDLFG 120 Query: 122 VGKVKNAGVPLVAINTTAGTAAEMTSNAVIIDSARKVKEVIIDPNIIPDIAVDDASVMLE 181 + +V G PL+AI TTAGT +E+T+ A++ D ++K+ I+ ++PD+A+ + L Sbjct: 121 IDQVPRKGPPLIAIPTTAGTGSEVTNVAILSDKVAQLKKGIVSDYLLPDVALVSPQMTLT 180 Query: 182 IPASVTAATGMDALTHAVEAYVSVGAHPLTDANALEAIRLINLWLPKAVDDGHNLEAREQ 241 P SVTAA+G+DAL HA+E+Y+SV A P+TD+ A+ AI+LI LPKA + NL+ARE Sbjct: 181 CPRSVTAASGVDALVHAIESYLSVNASPITDSLAIGAIKLIAKALPKAYANPSNLQARED 240 Query: 242 MAFGQYLAGMAFNSAGLGLVHALAHQPGATHNLPHGVCNAILLPIVENFNRPNAVARFAR 301 MA +AGMAF +AG+G VHALA+ G N+ HGV NA+LLP V +N+ + R Sbjct: 241 MATASLMAGMAFGNAGVGAVHALAYPLGGRFNIAHGVSNALLLPYVMTWNKMACIERMQD 300 Query: 302 IAQAMGVETRGMSDEAASQEAINAIRTLSKRVGIPEGFSKLGVTKEDIEGW-LDKALADP 360 IA+AMGV+T +S A+ +A+ A+ L V IP+G GV ++ I ++ A + Sbjct: 301 IAEAMGVKTAHLSLNEAADKAVQAMTELCAAVEIPQGLRSFGVPEDAIPSMAVEAAGIER 360 Query: 361 CAPCNPRTASRDEVRGLYLEA 381 NPR S ++ +Y A Sbjct: 361 LMRNNPRKLSAVDIEKIYRAA 381 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: 396 Number of extensions: 16 Number of successful extensions: 2 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: 382 Length adjustment: 30 Effective length of query: 352 Effective length of database: 352 Effective search space: 123904 Effective search space used: 123904 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 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