Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate N515DRAFT_0465 N515DRAFT_0465 aldehyde dehydrogenase (NAD+)
Query= BRENDA::Q97UA1 (478 letters) >FitnessBrowser__Dyella79:N515DRAFT_0465 Length = 511 Score = 228 bits (581), Expect = 4e-64 Identities = 148/462 (32%), Positives = 234/462 (50%), Gaps = 16/462 (3%) Query: 22 INPADKDHVLAKIRLYTKDDVKEAINKAVAKFDEWSRTPAPKRGSILLKAGELMEQEAQE 81 +NPA + V+ + + D + + +A F W TPAP+RG + GE + + Sbjct: 37 VNPATGE-VIGTVHASSAADYETIVKRAQEAFKTWRTTPAPRRGEAVRLCGEALRKHKDA 95 Query: 82 FALLMTLEEGKTLKDSMFEVTRSYNLLKFYGALAFKISGKTLPSADPNTRIFTVKEPLGV 141 L+ LE GK + EV ++ F + + G T+ S P R++ PLG+ Sbjct: 96 LGSLVALEMGKIKPEGDGEVQEMIDIADFAVGQSRMLYGYTMHSERPGHRMYEQYHPLGL 155 Query: 142 VALITPWNFPLSIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVEVLSKA----GLPEGV 197 V +I+ +NFP+++ W A G+ + KP+ KTPL +++ ++A G P+ + Sbjct: 156 VGIISAFNFPVAVWAWNAFLAAICGDICIWKPSPKTPLSAIATMKICNEALKAGGFPD-I 214 Query: 198 VNLVVGKGSEVGDTIVSDDNIAAVSFTGSTEVGKRIYKLVGNKNRMTRIQLELGGKNALY 257 L G+++ V D I +SFTGST+VG+ + + V RM R LELGG NA+ Sbjct: 215 FFLFNDAGTDLSQGFVDDKRIPLISFTGSTKVGRMVGERVA--RRMGRSLLELGGNNAII 272 Query: 258 VDKSADLTLAAELAVRGGFGLTGQSCTATSRLIINKDVYTQFKQRLLERVK--KWRVG-P 314 +D SADL LA V G G GQ CT T RL +++ + + +L+ K + ++G P Sbjct: 273 LDASADLKLAIPAIVFGAVGTAGQRCTTTRRLFVHESIVGEVTDKLVAAYKQVEGKIGDP 332 Query: 315 GTEDVDMGPVVDEGQFKKDLEYIEYGKNVGAKLIYGGNIIPG-KGYFLEPTIFEGVTSDM 373 MGP+ + + L +E K G K++ GG + KG F+ PTI GV + Sbjct: 333 TLATTLMGPLNSQDAVQAYLGAVEKAKASGGKVLTGGAALSDRKGNFVLPTIVTGVKNSD 392 Query: 374 RLFKEEIFGPVLSVTEAKDLDEAIRLVNAVDYGHTAGIVASDIKAINEFVSRV--EAGVI 431 + + E F P+L + K LDEAI L N V G ++ I D+KA +++S + G+ Sbjct: 393 EVVQTETFAPILYIMPFKSLDEAIELQNDVPQGLSSAIFTRDLKAAEQYLSSAGSDCGIA 452 Query: 432 KVNKPTVGLELQAPFGGFKNSGATTWKEMGEDALEFYLKEKT 473 VN T G E+ FGG K +G +E G DA + Y++ +T Sbjct: 453 NVNIGTSGAEIGGAFGGEKETGG--GRESGSDAWKVYMRRQT 492 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: 594 Number of extensions: 35 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: 478 Length of database: 511 Length adjustment: 34 Effective length of query: 444 Effective length of database: 477 Effective search space: 211788 Effective search space used: 211788 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