Align L-lactaldehyde reductase (EC 1.1.1.77) (characterized)
to candidate 8499551 DvMF_0321 iron-containing alcohol dehydrogenase (RefSeq)
Query= metacyc::STM4044-MONOMER (382 letters) >FitnessBrowser__Miya:8499551 Length = 393 Score = 318 bits (815), Expect = 2e-91 Identities = 179/382 (46%), Positives = 237/382 (62%), Gaps = 6/382 (1%) Query: 7 LPKISLHGAGAIADMVNLVANKQWGKALIVTDGQLVKLGLLDSLFSALDEHQMSYHLFDE 66 +P ++L G GA + + K LIVTD +VK G+L + LD +M+Y ++DE Sbjct: 12 IPSVTLIGIGASKAIPEKIKALGGSKPLIVTDMGIVKAGILKQITDLLDAAKMAYSVYDE 71 Query: 67 VFPNPTEELVQKGFAAYQSAECDYIIAFGGGSPIDTAKAVKILTANPGPSTAYSGVGKVK 126 PNPT++ V KG Y+ +CD +I GGGS D K + ++ AN G + GV K Sbjct: 72 TIPNPTDDNVHKGVEVYKKNKCDSLITLGGGSSHDCGKGIGLVIANGGKIHDFEGVDKSF 131 Query: 127 NAGVPLVAINTTAGTAAEMTSNAVIIDSARKVKEVIIDPNIIPDIAVDDASVMLEIPASV 186 P VA+NTTAGTA+EMT +I D++RKVK I+D + P IA+DD +M+ +P ++ Sbjct: 132 KPMPPYVAVNTTAGTASEMTRFCIITDTSRKVKMAIVDWRVTPSIALDDPLLMMGMPPAL 191 Query: 187 TAATGMDALTHAVEAYVSVGAHPLTDANALEAIRLINLWLPKAVDDGHNLEAREQMAFGQ 246 TAATGMDALTHAVEAYVS A P+TDA A +AI LI +L +AV +G ++EARE+M F Q Sbjct: 192 TAATGMDALTHAVEAYVSTIATPMTDACAEQAITLIATFLRRAVANGRDIEARERMCFAQ 251 Query: 247 YLAGMAFNSAGLGLVHALAHQPGATHNLPHGVCNAILLPIVENFNRPNAVARFARIAQAM 306 YLAGMAFN+A LG VHA+AHQ G ++LPHG CNAILLP V FN + RFARIA+ M Sbjct: 252 YLAGMAFNNASLGHVHAMAHQLGGFYDLPHGECNAILLPHVSQFNLIAKLDRFARIAELM 311 Query: 307 GVETRGMSDEAASQEAINAIRTLSKRVGIPEGFSKLG------VTKEDIEGWLDKALADP 360 G G+S A+++AI AI+ LS VGIP G LG V +DI A D Sbjct: 312 GENISGLSVRDAAEKAICAIKRLSADVGIPAGLVALGKRYGKDVKAKDIAIMTKNAQKDA 371 Query: 361 CAPCNPRTASRDEVRGLYLEAL 382 C NPR + +V +Y A+ Sbjct: 372 CGLTNPRCPTDADVAAIYEAAM 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: 380 Number of extensions: 18 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:
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