Align L-lactaldehyde reductase (EC 1.1.1.77) (characterized)
to candidate 207896 DVU2405 alcohol dehydrogenase, iron-containing
Query= metacyc::STM4044-MONOMER (382 letters) >lcl|MicrobesOnline__882:207896 DVU2405 alcohol dehydrogenase, iron-containing Length = 393 Score = 323 bits (827), Expect = 7e-93 Identities = 181/382 (47%), Positives = 238/382 (62%), Gaps = 6/382 (1%) Query: 7 LPKISLHGAGAIADMVNLVANKQWGKALIVTDGQLVKLGLLDSLFSALDEHQMSYHLFDE 66 +P+++L G GA + + K LIVTD +VK G+L + LD +M+Y ++DE Sbjct: 12 IPRVTLIGIGASKAIPEKIKALGGSKPLIVTDMGIVKAGILKQITDLLDAAKMAYSVYDE 71 Query: 67 VFPNPTEELVQKGFAAYQSAECDYIIAFGGGSPIDTAKAVKILTANPGPSTAYSGVGKVK 126 PNPT++ V KG Y+ +CD +I GGGS D K + ++ AN G + GV K Sbjct: 72 TIPNPTDDNVHKGVDVYKKNKCDSLITLGGGSSHDCGKGIGLVVANGGKIHDFEGVDKST 131 Query: 127 NAGVPLVAINTTAGTAAEMTSNAVIIDSARKVKEVIIDPNIIPDIAVDDASVMLEIPASV 186 P +A+NTTAGTA+EMT +I D++RKVK I+D + P+IA+DD +ML +P ++ Sbjct: 132 QRMPPYLAVNTTAGTASEMTRFCIITDTSRKVKMAIVDWRVTPNIALDDPLLMLGMPPAL 191 Query: 187 TAATGMDALTHAVEAYVSVGAHPLTDANALEAIRLINLWLPKAVDDGHNLEAREQMAFGQ 246 TAATGMDALTHAVEAYVS A P+TDA A +AI LI +L +AV +G +LEARE+M F Q Sbjct: 192 TAATGMDALTHAVEAYVSTIATPMTDACAEQAITLIATFLRRAVANGQDLEARERMCFAQ 251 Query: 247 YLAGMAFNSAGLGLVHALAHQPGATHNLPHGVCNAILLPIVENFNRPNAVARFARIAQAM 306 YLAGMAFN+A LG VHA+AHQ G ++LPHG CNAILLP V FN + R+ARIAQ M Sbjct: 252 YLAGMAFNNASLGHVHAMAHQLGGFYDLPHGECNAILLPHVSKFNLIAKLDRYARIAQLM 311 Query: 307 GVETRGMSDEAASQEAINAIRTLSKRVGIPEGFSKLG------VTKEDIEGWLDKALADP 360 G G+S A++ AI+AI+ LS VGIP G LG V DI A D Sbjct: 312 GENIAGLSTREAAERAISAIKCLSTDVGIPAGLVALGKRYGKDVKAADIAIMTKNAQKDA 371 Query: 361 CAPCNPRTASRDEVRGLYLEAL 382 C NPR + +V +Y AL Sbjct: 372 CGLTNPRCPTDADVAAIYEAAL 393 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: 372 Number of extensions: 15 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: 393 Length adjustment: 30 Effective length of query: 352 Effective length of database: 363 Effective search space: 127776 Effective search space used: 127776 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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