Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_012592396.1 MSIL_RS17445 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_000021745.1:WP_012592396.1 Length = 474 Score = 319 bits (818), Expect = 1e-91 Identities = 177/456 (38%), Positives = 263/456 (57%), Gaps = 6/456 (1%) Query: 34 SKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVRMKVLYKLADL 93 S TF +P+TEE I +A E ++ AV AA AF +WS R ++ ++ DL Sbjct: 20 SAATFEAFNPATEEVIAAAPDASREQLEAAVAAAKRAF-PAWSARPIAERQALVARIGDL 78 Query: 94 IDEHADTLAHIEALDNGKSLMCSKGDVALTAAYFRSCAGWTDKIKGSVIETGDTHFNYTR 153 I+ HA+ + + GK ++ ++ +A + R A ++ + E T TR Sbjct: 79 IEAHAEDFMRLLTREQGKPRKGAEWEIFGSAIWCREIA--KQELPVHISEESQTRRVETR 136 Query: 154 REPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYLASLIKEAGAPP 213 REP+GV I PWNFP+L+A WK+ P L G T VLK + TPL L L L++E PP Sbjct: 137 REPLGVIAGITPWNFPVLLAIWKIAPALVAGNTMVLKPSPYTPLCTLKLGELVREL-LPP 195 Query: 214 GVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKKVTLELGGKSPN 273 GV+N+VSG G G +++H I+K++FTGST TGR IM AAA N+K++TLELGG P Sbjct: 196 GVLNIVSG-GNELGVWMTTHSDIRKISFTGSTETGRKIM-AAASGNIKRITLELGGNDPA 253 Query: 274 IVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEFKNAAESLKIGDPF 333 IV D DVK T + L F N+ + C A R+Y+ IYD + +E A+++K+GD Sbjct: 254 IVLPDVDVKETAEKLFWAAFQNSAQFCVAAKRLYIHADIYDDLAAELVAYAKTVKVGDGS 313 Query: 334 KEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNKGYFIKPTIFGDVKEDHQI 393 + T +G +++Q +K+ + K G + GG+ KG+F+ TI + E+ ++ Sbjct: 314 LQGTDLGPIQNRMQFEKLKNLLADAKTNGLRFLLGGDVTDAKGFFVPVTIIDNPPENSRV 373 Query: 394 VRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAISVSNKINSGTIWVNT 453 V +E FGP++ + KF ++ VIA AND+EYGLAA V ++ A V+ +I++GT+WVN Sbjct: 374 VAEEAFGPILPLLKFDDIDGVIARANDTEYGLAASVWGKDIKAARRVAERIDAGTVWVNE 433 Query: 454 YNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAV 489 + F P V FGG+ QSG+G E E L YT K + Sbjct: 434 VHTFSPHVAFGGHKQSGLGIENALEGLAEYTNAKTL 469 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: 510 Number of extensions: 20 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: 474 Length adjustment: 34 Effective length of query: 461 Effective length of database: 440 Effective search space: 202840 Effective search space used: 202840 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 Apr 09 2024. 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