Align L-lactaldehyde reductase (EC 1.1.1.77) (characterized)
to candidate WP_086508352.1 BZY95_RS02010 alcohol dehydrogenase
Query= metacyc::STM4044-MONOMER (382 letters) >NCBI__GCF_002151265.1:WP_086508352.1 Length = 389 Score = 203 bits (517), Expect = 6e-57 Identities = 131/382 (34%), Positives = 199/382 (52%), Gaps = 14/382 (3%) Query: 8 PKISLHGAGAIADMVNLVANKQWGKALIVTDGQLVKLGLLDSLFSALDEHQMSYHLFDEV 67 P L GAG I D+ G L+VTD L L ++ + A + + +F ++ Sbjct: 11 PSNILTGAGRIRDLPAACKALGMGAPLLVTDPGLAALPMVQACVQACQDAGLRTAVFSQI 70 Query: 68 FPNPTEELVQKGFAAYQSAECDYIIAFGGGSPIDTAKAVKILTANPGPSTAYS--GVG-K 124 NPT V G AA++ D +IAFGGGS +D AKAV ++ + +S +G Sbjct: 71 KGNPTGRNVLDGIAAFRGGSHDGVIAFGGGSGLDAAKAVALMANQREGLSLWSLEDIGDN 130 Query: 125 VKNAGV----PLVAINTTAGTAAEMTSNAVIIDSARKVKEVIIDPNIIPDIAVDDASVML 180 KNA P+VA+ TTAGT +E+ +VI D A VK +I P ++P + D + + Sbjct: 131 WKNADARAIAPVVAVPTTAGTGSEVGRASVITDEAEHVKRIIFHPGMVPATVILDPELTV 190 Query: 181 EIPASVTAATGMDALTHAVEAYVSVGAHPLTDANALEAIRLINLWLPKAVDDGHNLEARE 240 +P +VTAATGMDAL+H +EA+ S HP+ + A+E +R I+L+L +A DG +LEAR Sbjct: 191 GLPPAVTAATGMDALSHCMEAWCSPLYHPMAEGIAVEGMRRIDLYLQRAYSDGADLEARM 250 Query: 241 QMAFGQYLAGMAFNSAGLGLVHALAHQPGATHNLPHGVCNAILLPIVENFNRPNAVARFA 300 M + AF GLG +HALAH GA ++ HG NA+L+P V N Sbjct: 251 NMLVASSMGATAF-QRGLGAMHALAHPLGALYDAHHGTLNAVLMPYVLRANERAIGEPMV 309 Query: 301 RIAQAMGVETRGMSDEAASQEAINAIRTLSKRVGIPEGFSKLGVTKEDIEGWLDKALADP 360 R+ + + + D+ + I + L +R+GIP ++LG+ + A+ADP Sbjct: 310 RLGRYLNL------DQPGTAAVIEWVLGLRERLGIPHTLAELGIDTRQADKVGRMAVADP 363 Query: 361 CAPCNPRTASRDEVRGLYLEAL 382 + NP DE G+++ A+ Sbjct: 364 SSGTNPVAFDADEYCGIFVAAV 385 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: 423 Number of extensions: 30 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: 389 Length adjustment: 30 Effective length of query: 352 Effective length of database: 359 Effective search space: 126368 Effective search space used: 126368 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