Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_011383248.1 AMB_RS04115 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_000009985.1:WP_011383248.1 Length = 485 Score = 323 bits (828), Expect = 8e-93 Identities = 180/467 (38%), Positives = 260/467 (55%), Gaps = 13/467 (2%) Query: 31 QSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVRMKVLYKL 90 Q +S T ++P+ E I Q+ ++ AV AA AF W+ R K+L K+ Sbjct: 10 QVESASTIANLNPANNEVICQIAAGGEAEVAQAVAAAKEAF-PKWAGLPASQRAKLLRKV 68 Query: 91 ADLIDEHADTLAHIEALDNGKSLMCSKGDVALTAA-YFRSCAGWTDKIKGSVIETGDTHF 149 DLI++H D +A +E+LD G+S +K + AA F A + G T D H Sbjct: 69 GDLINQHVDEIAKLESLDTGQSYWRTKKMLVPRAADNFYFFADTCCHVDGETYPTND-HL 127 Query: 150 NYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYLASLIKEA 209 NYT +P+GV G I PWN P + A+WK P L G T VLK +E +PLSA L LI EA Sbjct: 128 NYTLYQPVGVVGLISPWNVPFMTATWKTAPCLAFGNTAVLKMSELSPLSADRLGQLILEA 187 Query: 210 GAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKKVTLELGG 269 G P GV N+V G+G G + HP ++ V+FTGSTATG I+++ LKK ++ELGG Sbjct: 188 GIPAGVFNIVHGYGSAVGEALVKHPDVRGVSFTGSTATGNRIIQS---GGLKKYSMELGG 244 Query: 270 KSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEFKNAAESLKI 329 KSPNI+FDD D + + + ++ N GE C G+RI VQ+G+YD+ V+ + + Sbjct: 245 KSPNIIFDDCDFERAVDAAIVAVYGNNGESCTNGTRILVQDGLYDRFVAALAERTRKVVV 304 Query: 330 GDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGG-------ERFGNKGYFIKPT 382 GDP E T +G ++ K+ YI++G EGA V+ GG G F++PT Sbjct: 305 GDPLDEATNVGPMITRDHWKKVTSYIELGISEGARVVAGGLGTPEGLAPHLKNGNFVRPT 364 Query: 383 IFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAISVSN 442 + DV ++ ++EIFGPV + +FK E + +AN + YGLA+ V T N + AI ++ Sbjct: 365 VLADVDNSWRVAQEEIFGPVACVIRFKDEAEALKIANATSYGLASYVWTENGARAIRMAE 424 Query: 443 KINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAV 489 I +G ++VN+ N PFGG SG GRE G + + + +VK V Sbjct: 425 GIEAGLVFVNSQNVRDLRQPFGGIKGSGTGREGGHYSYEAFLEVKNV 471 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: 630 Number of extensions: 39 Number of successful extensions: 4 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: 485 Length adjustment: 34 Effective length of query: 461 Effective length of database: 451 Effective search space: 207911 Effective search space used: 207911 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