Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_073950325.1 RH94_RS25575 gamma-aminobutyraldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_001906585.1:WP_073950325.1 Length = 511 Score = 322 bits (826), Expect = 1e-92 Identities = 183/474 (38%), Positives = 274/474 (57%), Gaps = 14/474 (2%) Query: 24 FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVR 83 +I + S +T V P+T EE+ A +D+D AV AA AF W+ + P R Sbjct: 24 YIAGRLTKGTSGRTHAVVDPATGEEVHTYELAGPDDVDAAVAAAREAF-PGWAGATPGDR 82 Query: 84 MKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKG-DVALT---AAYFRSCAGWTDKIKG 139 L++ A+++ + A+ A E+L GK L ++ DV T AA+F AG ++G Sbjct: 83 SDALHRFAEVLADRAEDFARAESLQCGKPLKLTREFDVPGTIDNAAFF---AGAARHLQG 139 Query: 140 -SVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLS 198 S E H +Y RREPIGV G I PWN+PL MA+WK+ P + G T VLK AE TPL+ Sbjct: 140 QSAGEYSGDHTSYVRREPIGVVGSIAPWNYPLQMAAWKVLPAIAAGNTIVLKPAELTPLT 199 Query: 199 ALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAES 258 +L A EAG P GV+N+V+G G AG + HP + V+FTGSTA G+ + + A S Sbjct: 200 SLLFAQAATEAGIPDGVINIVTGTGKEAGEHLVGHPDVAMVSFTGSTAVGKRVAEIATAS 259 Query: 259 NLKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVS 318 +K++ LELGGK+P +VFDDAD+++ + V G NTG+ C A +R YVQ +Y++ V+ Sbjct: 260 -VKRLHLELGGKAPFVVFDDADLEAAVNGAVAGALINTGQDCTAATRAYVQRPLYEEFVA 318 Query: 319 EFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNK--- 375 E++++GDPF T +G S + D++ ++D + A V+TGGE + Sbjct: 319 RTAALMETVRLGDPFAPGTDLGPLISHVHRDRVAGFVDRARAY-ARVVTGGEAPQGELKN 377 Query: 376 GYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLS 435 G + +PT+ +D +IV+ EIFGPV+ + F + +E I LAND+ YGLAA + ++ Sbjct: 378 GAYYRPTLIAGAAQDSEIVQSEIFGPVLVVLPFDSDDEGIRLANDTAYGLAASAWSRDVY 437 Query: 436 TAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAV 489 A + +I +G +WVN + +P GG QSG G++M + + YTQ+K V Sbjct: 438 RANRATREIKAGCVWVNDHIPIISEMPHGGSKQSGFGKDMSSYSFEEYTQIKHV 491 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: 636 Number of extensions: 34 Number of successful extensions: 5 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: 511 Length adjustment: 34 Effective length of query: 461 Effective length of database: 477 Effective search space: 219897 Effective search space used: 219897 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