Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_104913707.1 C3B54_RS06115 gamma-aminobutyraldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_002950575.1:WP_104913707.1 Length = 478 Score = 313 bits (802), Expect = 8e-90 Identities = 177/469 (37%), Positives = 274/469 (58%), Gaps = 8/469 (1%) Query: 24 FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVR 83 FIN ++V SK +T V P+TEE + + D+DDA +AA+ AF WS + P R Sbjct: 9 FINGQYVDSKGSETIPLVDPATEEVYAHSPISSAADVDDAYQAASKAFEG-WSETTPAER 67 Query: 84 MKVLYKLADLIDEHADTLAHIEALDNGKS-LMCSKGDVALTAAYFRSCAGWTDKIKG-SV 141 L+++AD +++ + A +E+ D GK + +++L+ R AG ++G S Sbjct: 68 QLALFRIADELEKRGEEFADLESQDAGKPRASLVEDEISLSVDQIRFFAGAARNLEGKSA 127 Query: 142 IETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALY 201 E H ++ RREPIGV GQ+ PWN+PL MA WK P + G TTVLK +++TP S L Sbjct: 128 GEYMKDHTSFIRREPIGVVGQVAPWNYPLNMAVWKFAPAVAAGNTTVLKPSDTTPQSTLL 187 Query: 202 LASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLK 261 LA + P GVVNV++G T GA I H + V+ TGS G + KAAA ++LK Sbjct: 188 LAEICA-MHLPEGVVNVITGDRTTGGAMID-HKIPEMVSITGSVRAGLEVAKAAA-TDLK 244 Query: 262 KVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEFK 321 +V LELGGK+P IVFDDAD+ S I+ + ++N G+ C A +R+ V E I+D+ ++E K Sbjct: 245 RVHLELGGKAPVIVFDDADIPSAIEGIGIAGYFNAGQDCTAATRVVVHESIHDEFIAELK 304 Query: 322 N-AAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNKGYFIK 380 A ++ G P +TF G + Q+D+++ + +TV GG R G +GYFI+ Sbjct: 305 KWVAANVTTGLPSDPNTFYGPVNNANQMDRVMGILG-ELPSHSTVEAGGVRQGERGYFIE 363 Query: 381 PTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAISV 440 PTI +K++ ++ EIFGPV+T+ F+T EE + +AN YGL++ V T + + A+ Sbjct: 364 PTIVSGLKQNDAAIQTEIFGPVITVQPFRTEEEAMTMANGVPYGLSSSVWTKDHARAMRF 423 Query: 441 SNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAV 489 + ++ G +W+N + +P GG+ SG G+++ + + YT+VK V Sbjct: 424 AKGLDFGAVWINCHIPLVAEMPHGGFKHSGHGKDLSQYGFEEYTRVKHV 472 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: 572 Number of extensions: 33 Number of successful extensions: 7 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: 478 Length adjustment: 34 Effective length of query: 461 Effective length of database: 444 Effective search space: 204684 Effective search space used: 204684 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