Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_011385953.1 AMB_RS18195 DUF1487 domain-containing protein
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_000009985.1:WP_011385953.1 Length = 496 Score = 296 bits (758), Expect = 1e-84 Identities = 176/474 (37%), Positives = 265/474 (55%), Gaps = 13/474 (2%) Query: 25 INNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVRM 84 I + V + + F +P+T E I ED+D AV +A AA W+ + R Sbjct: 22 IGGKLVPAGCGEVFEVDNPATGEIIGTAAFGTKEDVDIAVISAKAA-QKDWAKQSARARG 80 Query: 85 KVLYKLADLIDEHADTLAHIEALDNGKSLMC-SKGDVALTAAYFRSCAGWTDKIKGSVIE 143 K++ + ++ H + L + AL+ GK+L S+ + + A F G ++KG I Sbjct: 81 KLVAECGRVLSAHVEELGRLVALETGKALRTESRVEAGVLADMFTFFGGLGSELKGETIP 140 Query: 144 TGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYLA 203 T REP+GV G IIPWN PLL+ + K L G + V+K+AE PL+ L +A Sbjct: 141 FNPDMLTVTVREPVGVVGCIIPWNVPLLLMAMKAAAALVAGNSVVVKSAEEAPLTVLRVA 200 Query: 204 SLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKKV 263 ++ PPG+ N++SGFGP GAP+ HP +KKV FTGS TGR + KAAAE L V Sbjct: 201 EIMNTV-LPPGLFNMLSGFGPECGAPLVEHPDVKKVTFTGSVETGRIVYKAAAEK-LIPV 258 Query: 264 TLELGGKSPNIVFDDADVKSTIQHLVTGI-FYNTGEVCCAGSRIYVQEGIYDKIVSEFKN 322 TLELGGKSP IV DAD+ + + G+ F G+ C A SR++V E I+D+ V++ K Sbjct: 259 TLELGGKSPMIVCADADMDQAVAGALAGMRFTRQGQSCTASSRLFVHESIHDEFVAKVKA 318 Query: 323 AAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKK-EGAT-----VITGGERFGNKG 376 +++ +GDP E T +G S QL+++ YI IG++ +GAT + + KG Sbjct: 319 KVDAMVMGDPLDEKTDIGTIVSDGQLERVRSYIKIGEETKGATKHVCSALPTDPKLA-KG 377 Query: 377 YFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLST 436 F++P IF +K ++ ++EIFGPV + K+ E+V+A ANDSEYGLAA + T + Sbjct: 378 RFVQPVIFTGMKNSDRLCQEEIFGPVCAVIKWSDYEDVLAQANDSEYGLAASIWTRDFKL 437 Query: 437 AISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMG-EEALDNYTQVKAV 489 A+ + ++ +G + VN P + +GG SGIG+E E L+++T K + Sbjct: 438 AMDATKRLEAGFVQVNQNLVVQPGLSYGGVKTSGIGKEASLESMLEHFTHKKTI 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: 593 Number of extensions: 39 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: 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 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