Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_011778592.1 MVAN_RS06715 aldehyde dehydrogenase
Query= BRENDA::Q97UA1 (478 letters) >NCBI__GCF_000015305.1:WP_011778592.1 Length = 483 Score = 359 bits (922), Expect = e-103 Identities = 199/472 (42%), Positives = 280/472 (59%), Gaps = 12/472 (2%) Query: 11 WIKG-SGEEYLDINPADKDHVLAKIRLYTKDDVKEAINKAVAKFDEWSRTPAPKRGSILL 69 W+ SG + NPAD V+ DDV+ A++ EW+ T +R SIL Sbjct: 12 WVPAQSGRTFTRANPADPADVIGTFPASDADDVRNAVDALEKAAPEWAATAPERRASILE 71 Query: 70 KAGELMEQEAQEFALLMTLEEGKTLKDSMFEVTRSYNLLKFYGALAFKISGKTLPSADPN 129 A +E ++ + EEGKT+ ++ EVTR+ + L+FY A A + +G T P+A + Sbjct: 72 SAAAQLESRSEALIAELVREEGKTVAEATMEVTRTPSNLRFYAAEATRAAGMTFPAAG-D 130 Query: 130 TRIFTVKEPLGVVALITPWNFPLSIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVEVLS 189 T ++TV+EP+G+V ITPWNFPL+IP KL PALA G+ + KP+ TPLM +LVE L Sbjct: 131 TMVYTVREPVGIVGAITPWNFPLNIPSRKLGPALAVGDPVLFKPSELTPLMGQRLVEALL 190 Query: 190 KAGLPEGVVNLVVGKGSEVGDTIVSDDNIAAVSFTGSTEVGKRIYKLVGNKNRMTRIQLE 249 GLP GV+ LV G G G + +D+ +AAV+FTGST VG+ I++ VG R +QLE Sbjct: 191 AGGLPPGVLALVHGDGV-AGAAVAADERVAAVTFTGSTAVGRSIHRAVGPHRR---VQLE 246 Query: 250 LGGKNALYVDKSADLTLAAELAVRGGFGLTGQSCTATSRLIINKDVYTQFKQRLLERVKK 309 +GGKN + V ADL AA L V+G FGL+GQ+CT TSR+I + +R++ R + Sbjct: 247 MGGKNPVVVADDADLDRAAALIVKGAFGLSGQACTGTSRVIATDATHDGLVERVVARAEA 306 Query: 310 WRVGPGTED-VDMGPVVDEGQFKKDLEYIEYGKNVGAKLIYGGNI--IPGK--GYFLEPT 364 RVGPG + +DMG + Q +K Y+ G + GA L GG +PG G+F+ P Sbjct: 307 LRVGPGAQPGIDMGALASAAQAEKFAHYVGVGVDEGASLRCGGTRLDVPGHAGGFFVRPA 366 Query: 365 IFEGVTSDMRLFKEEIFGPVLSVTEAKDLDEAIRLVNAVDYGHTAGIVASDIKAINEFVS 424 +F MR+ EE+FGP+L+ A L EAI L NA ++G +A IV D+ +F Sbjct: 367 VFTDTEPTMRIVSEEVFGPLLAFQRAGSLTEAIELANATEFGLSAAIVTGDLATAAQFAR 426 Query: 425 RVEAGVIKVNKPTVGLELQAPFGGFKNSGATTWKEM-GEDALEFYLKEKTVY 475 G++K+N+PT G+ + APFGG+K S TT+KE G +EFYL EKTVY Sbjct: 427 ESRTGLVKINQPTTGMAMNAPFGGYKASSTTTFKEQAGASMMEFYLTEKTVY 478 Lambda K H 0.316 0.135 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: 595 Number of extensions: 36 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: 478 Length of database: 483 Length adjustment: 34 Effective length of query: 444 Effective length of database: 449 Effective search space: 199356 Effective search space used: 199356 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: 51 (24.3 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