Align L-lactaldehyde reductase (EC 1.1.1.77) (characterized)
to candidate WP_003942060.1 C1M55_RS09025 iron-containing alcohol dehydrogenase
Query= metacyc::STM4044-MONOMER (382 letters) >NCBI__GCF_002893965.1:WP_003942060.1 Length = 401 Score = 251 bits (641), Expect = 3e-71 Identities = 143/370 (38%), Positives = 208/370 (56%), Gaps = 2/370 (0%) Query: 14 GAGAIADMVNLVANKQWGKALIVTDGQLVKLGLLDSLFSALDEHQMSYHLFDEVFPNPTE 73 G G++ + + + +VTD L+ G + L L E ++ ++ + PNP + Sbjct: 33 GIGSLVEAAHATLRFGGFRPFLVTDPGLIDAGWVSELEDHLTEQGLTATVWSGLTPNPKD 92 Query: 74 ELVQKGFAAYQSAECDYIIAFGGGSPIDTAKAVKILTANPGPSTAYSGVGKVKNAGVPLV 133 + GF YQ ECD IIA GGGS ID AK V +L AN G Y GV + PLV Sbjct: 93 FEIAAGFEVYQEGECDVIIALGGGSVIDAAKGVAVLAANGGNILDYEGVDQATKPIPPLV 152 Query: 134 AINTTAGTAAEMTSNAVIIDSARKVKEVIIDPNIIPDIAVDDASVMLEIPASVTAATGMD 193 + TT+GT A+++ ++ D+ R K II ++PD+ V D ++ +P + AATG+D Sbjct: 153 MVPTTSGTGADVSQFCIVTDTTRGTKITIIGRALVPDVTVIDPRLLTTMPEWLNAATGLD 212 Query: 194 ALTHAVEAYVSVGAHPLTDANALEAIRLINLWLPKAVDDGHNLEAREQMAFGQYLAGMAF 253 ALTH +EA+VS+ +PLTD +AL A+ L+ L + D +EAR MA AG+AF Sbjct: 213 ALTHGIEAFVSLAHNPLTDHHALRAVGLVTENLVHTIQDPMEMEARSVMAQASLEAGLAF 272 Query: 254 NSAGLGLVHALAHQPGATHNLPHGVCNAILLPIVENFNRPNAVARFARIAQAMGV-ETRG 312 +A LG HA++HQ G +LPHGV N ILLP V FN A F IA A+ + E RG Sbjct: 273 TNAILGAAHAMSHQVGGMLDLPHGVINGILLPHVIRFNSTTDAAPFVAIAAALSLPEQRG 332 Query: 313 MSDEAASQEAINAIRTLSKRVGIPEGFSKLGVTKEDIEGWLDKALADPCAPCNPRTASRD 372 +EAA A + + L++ VG+P+G +LGV +ED+ AL D C NPR A+++ Sbjct: 333 TPEEAALAVA-DRVERLAREVGVPKGLGELGVREEDLSRLASFALLDACMSTNPREATQE 391 Query: 373 EVRGLYLEAL 382 ++ L+ AL Sbjct: 392 QMVALFRGAL 401 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: 452 Number of extensions: 23 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: 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