Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate YP_004141818.1 Mesci_2633 aldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_000185905.1:YP_004141818.1 Length = 496 Score = 371 bits (952), Expect = e-107 Identities = 205/473 (43%), Positives = 287/473 (60%), Gaps = 6/473 (1%) Query: 24 FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSS-WSTSDPQV 82 FI+ + V ++S +TF +V+P+T E + +V EDID AV AA +F++ WS + P Sbjct: 23 FIDGKTVAARSGRTFASVNPATGEVLAEVASCGEEDIDLAVAAARRSFNAGVWSRTSPAH 82 Query: 83 RMKVLYKLADLIDEHADTLAHIEALDNGKSLM-CSKGDVALTAAYFRSCAGWTDKIKGSV 141 R +VL +LA L+ ++ LA +E+LD GK + + DV +AA F+ DKI G V Sbjct: 83 RKEVLLRLAQLLRDNLHELALLESLDMGKLVRDAASVDVPGSAAIFQWYGEAIDKIYGEV 142 Query: 142 IETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALY 201 TG+ RREP+GV G ++PWNFPL MA+WK P L G + VLK AE +PLSAL Sbjct: 143 APTGEGDLVLVRREPLGVVGAVVPWNFPLDMATWKCAPALAAGNSVVLKPAEQSPLSALL 202 Query: 202 LASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLK 261 LA L EAG P GV+NVV G G TAG + H + +AFTGSTA G+ ++ + +SN+K Sbjct: 203 LAELAMEAGLPAGVLNVVPGLGETAGQALGRHMDVDCLAFTGSTAVGKMFLQYSGQSNMK 262 Query: 262 KVTLELGGKSPNIVFDD-ADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEF 320 +V LE GGKSPN+VF D D+ GIF+N GEVC A SR+ VQ GI D +V + Sbjct: 263 QVWLETGGKSPNLVFADCGDLDVVADMAAFGIFFNQGEVCSANSRLLVQRGIKDALVEKL 322 Query: 321 KNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGE--RFGNKGYF 378 A + + GDP + MGA ++++++ GKK A ++ GG+ +G F Sbjct: 323 VQRAAATQPGDPLDPISKMGAMVDSRHAANVMRFVEAGKKT-ARLVAGGDMVTVNGRGSF 381 Query: 379 IKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAI 438 ++PTIF DV I RDEIFGPV+++ F + I +ANDS YGLAA + T +LS A Sbjct: 382 VQPTIFDDVAPADPIARDEIFGPVLSVIAFDDEADAIRIANDSPYGLAASLWTDSLSRAH 441 Query: 439 SVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRI 491 ++ ++ +GT+ VNT + PM PFGG+ QSG GR++ ALD YT +K I Sbjct: 442 RIAGRLQAGTVSVNTVDALSPMTPFGGFKQSGFGRDLSLHALDKYTALKTTWI 494 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: 553 Number of extensions: 35 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: 496 Length adjustment: 34 Effective length of query: 461 Effective length of database: 462 Effective search space: 212982 Effective search space used: 212982 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