Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_013843459.1 DESRU_RS17700 aldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_000215085.1:WP_013843459.1 Length = 491 Score = 393 bits (1010), Expect = e-114 Identities = 217/478 (45%), Positives = 296/478 (61%), Gaps = 8/478 (1%) Query: 23 LFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQV 82 LFI ++V+ + TF T P+ E + +A D+D AV+AA A+ +SW PQ Sbjct: 11 LFIGGKWVEGQEGNTFKTYCPANGELLATCVDAGQADVDMAVDAAWKAY-ASWKDVSPQE 69 Query: 83 RMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKG-DVALTAAYFRSCAGWTDKIKGSV 141 R +L K+ADLID +A+ LA +E+LDNGK + + DV L++ +FR A G Sbjct: 70 RAGMLLKIADLIDANAEKLALVESLDNGKPIRETMAVDVPLSSDHFRYFASAVRTEVGEA 129 Query: 142 IETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALY 201 + + REPIGV GQIIPWNFPLLM +WK+ P L G V+K + +TPLS L Sbjct: 130 VMIDKDTMSLVLREPIGVVGQIIPWNFPLLMGAWKIAPALAAGDCVVIKPSSTTPLSLLE 189 Query: 202 LASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLK 261 LA L+ E PPGVVNV++G G +G + H K+AFTGST G I +AAA+ L Sbjct: 190 LAKLLAEV-LPPGVVNVITGRGSVSGNYMLEHKGFAKLAFTGSTEIGHTIAEAAAKK-LI 247 Query: 262 KVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEFK 321 TLELGGKS NI F D ++ L GI +N G+VCCAGSR+++ E IYDK ++E Sbjct: 248 PATLELGGKSANIYFPDCPWDKAMEGLQIGILFNQGQVCCAGSRVFIHEDIYDKFLAEAV 307 Query: 322 NAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGG----ERFGNKGY 377 A E +K+G P+++DT MG Q ++ QL KIL YI+IG++EGATV GG E +KG Sbjct: 308 KAFEKVKVGLPWEQDTQMGCQVNENQLKKILNYIEIGRQEGATVACGGYKITENGLDKGS 367 Query: 378 FIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTA 437 F++PTI +V ++ ++EIFGPVV KFK EVI +ANDSEYGL V T +++ A Sbjct: 368 FLQPTILANVNNKMRVAQEEIFGPVVCFIKFKDEAEVIKMANDSEYGLGGAVWTRDINRA 427 Query: 438 ISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIGLSQ 495 V+ I +G +WVN YN+ PFGGY +SGIGRE + LD+Y+Q K + I L++ Sbjct: 428 FRVARSIETGRMWVNNYNNLPAHAPFGGYKKSGIGRETHKMMLDHYSQKKNIFISLTE 485 Lambda K H 0.316 0.133 0.389 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: 607 Number of extensions: 27 Number of successful extensions: 6 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: 495 Length of database: 491 Length adjustment: 34 Effective length of query: 461 Effective length of database: 457 Effective search space: 210677 Effective search space used: 210677 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 (21.6 bits) S2: 52 (24.6 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