Align L-lactaldehyde reductase (EC 1.1.1.77) (characterized)
to candidate BWI76_RS23175 BWI76_RS23175 propanediol utilization protein
Query= metacyc::STM4044-MONOMER (382 letters) >FitnessBrowser__Koxy:BWI76_RS23175 Length = 370 Score = 210 bits (535), Expect = 5e-59 Identities = 143/379 (37%), Positives = 204/379 (53%), Gaps = 31/379 (8%) Query: 14 GAGAIADMVNLVANKQWGKALIVTDGQLVKLGLLDSLFSALD-EHQMSYHLFDEVFPNPT 72 G G++A + W I+ DG L + LL++L +AL ++++S +F E+ P+PT Sbjct: 13 GQGSLAALKRFTNKHIW----IICDGFLARSPLLETLRNALPADNRIS--VFSEITPDPT 66 Query: 73 EELVQKGFAAYQSAECDYIIAFGGGSPIDTAKAVKILTANPGPSTAYSGVGKVKNAGVPL 132 V +G A Q+ + +I FGGGS +D AKA+ + G S Sbjct: 67 IHTVVQGIAQMQALQPQVVIGFGGGSAMDAAKAIVWFSQQSGISIE------------TC 114 Query: 133 VAINTTAGTAAEMTSNAVIIDSARKVKEVIIDPNIIPDIAVDDASVMLEIPASVTAATGM 192 VAI TT+GT +E+TS VI D + +K + + + PD+A+ D +++ +P +TA TGM Sbjct: 115 VAIPTTSGTGSEVTSACVISDPDKGIKYPLFNNALYPDMAILDPELVVSVPPQITANTGM 174 Query: 193 DALTHAVEAYVSVGAHPLTDANALEAIRLINLWLPKAVDDGHNLEAREQMAFGQYLAGMA 252 D LTHA+EA+VS A TDA A +A +L+ +LP AV+ G + R +M LAGMA Sbjct: 175 DVLTHALEAWVSPHASDFTDALAEKAAKLVFQYLPTAVEKGDCVATRGKMHNASTLAGMA 234 Query: 253 FNSAGLGLVHALAHQPGATHNLPHGVCNAILLPIVENFNR--PNAVARFARIAQAMGVET 310 F+ AGLGL HA+AHQ G +LPHG+ NA+LL V FN P A R+AR+A+A G Sbjct: 235 FSQAGLGLNHAIAHQLGGQFHLPHGLANALLLTTVIRFNAAVPRAGKRYARLAKACGFCP 294 Query: 311 RGMSDEAASQEAINAIRTLSKRVGIP-------EGFSKLGVTKEDIEGWLDKALADPCAP 363 +D A I I L +R +P EG S+ I + ALAD Sbjct: 295 AEANDVTAINALIQQIERLKQRCALPSLAIALKEGRSEFSAR---IPAMVQAALADVTLR 351 Query: 364 CNPRTASRDEVRGLYLEAL 382 NPR AS +E+R L E L Sbjct: 352 TNPRPASAEEIRELLEELL 370 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: 368 Number of extensions: 18 Number of successful extensions: 4 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: 370 Length adjustment: 30 Effective length of query: 352 Effective length of database: 340 Effective search space: 119680 Effective search space used: 119680 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