Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_013449840.1 SULKU_RS12970 phenylacetaldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_000183725.1:WP_013449840.1 Length = 481 Score = 286 bits (732), Expect = 1e-81 Identities = 166/471 (35%), Positives = 258/471 (54%), Gaps = 9/471 (1%) Query: 24 FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVR 83 FIN + S K V+P+T E +V+ A +EDI++A+ A AA W+ + P+ + Sbjct: 7 FINGQNKPSHPGKVIDDVNPATGEVFAKVHLASAEDIEEAISTAYAA-SKLWAKTTPREK 65 Query: 84 MKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKGDVALTAAYFRSCAGWTDKIKGSVIE 143 VL K AD+ + D + I ++G + ++ L A R AG ++ G Sbjct: 66 EAVLLKAADIFESRTDEIRTILMRESGSVYAKAMFEIGLVADILRVAAGEARRVFGQTFT 125 Query: 144 TGDTH-FNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYL 202 + D +Y+ R P+GV I P+N P+++++ K + G VLK + TP+ L Sbjct: 126 SNDPGVLSYSTRRPLGVIAGISPFNAPMILSTKKFAMAIAAGNAFVLKPSSHTPICGLIF 185 Query: 203 ASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKK 262 + KEAG P GV+N++ G + P+I + TGST G+ ++ A+A +LKK Sbjct: 186 GEIFKEAGLPDGVLNIIPCSSGDLGETFQTDPRIAMITLTGSTRVGK-LVAASAAMHLKK 244 Query: 263 VTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEFKN 322 T+ELGGKSP IV DADV + IF + G++C AGSRI V+E IYD+ +F Sbjct: 245 CTVELGGKSPTIVLGDADVDYAVDTATFSIFLHQGQICMAGSRIIVEENIYDEFCEKFAA 304 Query: 323 AAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNKGYFIKPT 382 ++LK+G+P T +G + Q I ID +GAT+++G E ++G F KPT Sbjct: 305 KVKTLKVGNPEDPSTIIGPLIEEAQCRFIDGLIDDAVAKGATLLSGRE---HEGCFYKPT 361 Query: 383 IFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAISVSN 442 + +V E+ I +E FGP I K + ++ VI LAN+S YGL++ + T NLS A+ +S Sbjct: 362 VVSNVTEEMVIFHEEAFGPAAAIIKARDLDHVIELANNSNYGLSSSIITDNLSAALRLSE 421 Query: 443 KINSGTIWVN--TYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRI 491 +I SG + +N T D +PFGG +SG+GRE G A++ T++K V + Sbjct: 422 EIESGMVHINGPTIQD-EAHIPFGGVKESGMGREGGHFAIEEMTELKWVTV 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: 602 Number of extensions: 34 Number of successful extensions: 6 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: 481 Length adjustment: 34 Effective length of query: 461 Effective length of database: 447 Effective search space: 206067 Effective search space used: 206067 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