Align L-lactaldehyde reductase (EC 1.1.1.77) (characterized)
to candidate GFF3193 HP15_3135 iron-containing alcohol dehydrogenase
Query= metacyc::STM4044-MONOMER (382 letters) >FitnessBrowser__Marino:GFF3193 Length = 387 Score = 265 bits (677), Expect = 2e-75 Identities = 149/369 (40%), Positives = 218/369 (59%) Query: 14 GAGAIADMVNLVANKQWGKALIVTDGQLVKLGLLDSLFSALDEHQMSYHLFDEVFPNPTE 73 GAG+ + N +N +V+D + G +D + + L + + ++ V PNP Sbjct: 19 GAGSRKSVANFASNFGARHVFLVSDPGVAAAGWVDEIVTLLTDAGIRSTVYTGVSPNPKV 78 Query: 74 ELVQKGFAAYQSAECDYIIAFGGGSPIDTAKAVKILTANPGPSTAYSGVGKVKNAGVPLV 133 + V G Y+S ECD I+A GGGSP+D AK + I+ + + GV + N PL+ Sbjct: 79 DEVMTGAELYKSNECDVIVAIGGGSPMDCAKGIGIVATHGRSILEFEGVDTITNPSPPLI 138 Query: 134 AINTTAGTAAEMTSNAVIIDSARKVKEVIIDPNIIPDIAVDDASVMLEIPASVTAATGMD 193 I TTAGT+A+++ A+I D R+ K II ++PD+++ D V + A +TA TG+D Sbjct: 139 LIPTTAGTSADVSQFAIISDPNRRFKFSIISKAVVPDVSLIDPEVTETMDAYLTACTGVD 198 Query: 194 ALTHAVEAYVSVGAHPLTDANALEAIRLINLWLPKAVDDGHNLEAREQMAFGQYLAGMAF 253 AL HA+EAYVS G+ PLTD +ALEAIRLIN L VD+ + REQ+ AG+AF Sbjct: 199 ALVHAIEAYVSTGSGPLTDTHALEAIRLINRNLEPLVDNTADPYLREQIMLASMQAGLAF 258 Query: 254 NSAGLGLVHALAHQPGATHNLPHGVCNAILLPIVENFNRPNAVARFARIAQAMGVETRGM 313 ++A LG VHA++H G +LPHG+CNA+LL V +N +A RF R+A+AM ++TRGM Sbjct: 259 SNAILGAVHAMSHSLGGFLDLPHGLCNALLLEHVVAYNFQSAEDRFRRVAEAMDIDTRGM 318 Query: 314 SDEAASQEAINAIRTLSKRVGIPEGFSKLGVTKEDIEGWLDKALADPCAPCNPRTASRDE 373 + + +N I L +RVG+ ++LGV+ DI AL DPC NPR +S + Sbjct: 319 AKPEIKKRLMNRIVELKRRVGLEARLAQLGVSVSDIPHLSGFALQDPCILTNPRKSSLRD 378 Query: 374 VRGLYLEAL 382 V+ +Y EAL Sbjct: 379 VQVVYEEAL 387 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: 438 Number of extensions: 16 Number of successful extensions: 1 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: 387 Length adjustment: 30 Effective length of query: 352 Effective length of database: 357 Effective search space: 125664 Effective search space used: 125664 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