Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate N515DRAFT_2488 N515DRAFT_2488 succinate-semialdehyde dehydrogenase / glutarate-semialdehyde dehydrogenase
Query= reanno::WCS417:GFF2142 (499 letters) >FitnessBrowser__Dyella79:N515DRAFT_2488 Length = 463 Score = 197 bits (501), Expect = 7e-55 Identities = 140/443 (31%), Positives = 211/443 (47%), Gaps = 19/443 (4%) Query: 25 NPATGEKTGRVALASRQTVSEAVAAAQAAFAGWADTPPIRRARVLFEYLHLLRERKDDLA 84 NP TGE A+ V++A+ AQA F W D R +VL + LLRE A Sbjct: 7 NPYTGETVKTFPSATDAEVTQALDQAQAMFEAWKDVGVAARVKVLQKAADLLRESHTQYA 66 Query: 85 RIIVAEHGKVFTDAQGEVDRGIDILEFACG------IPNLLKGEHSDQVSRGMDNWTMRQ 138 +++ E GKV +A+GEV+ ILE+ P L H +W Sbjct: 67 KVLTLEMGKVIGEAEGEVELCAQILEYYADHAEQLLAPEKLSSRHPSYTQ----SWVEHV 122 Query: 139 PLGVVAGVTPFNFPVMVPMWMYPIAIAAGNTFILKPSPTDPSASLFMAELLREAGLPKGV 198 P G++ V P+NFP + + +AAGN ILK + P + L REAGLP+G Sbjct: 123 PQGILLAVEPWNFPYYQIVRIAAPQLAAGNVLILKHASNVPQCAAAFERLFREAGLPQGG 182 Query: 199 FNVVQGDKESVDALIEHPDVKAVSFVGSTPIAQYI-YETGARNGKRVQGLGGAKNHMVVM 257 F + ++ + A+IE P V+ V+ GS + + G K LGGA + VV+ Sbjct: 183 FTNLYATRDQLKAIIEDPRVQGVALTGSEGAGAVVAAQAGQALKKSTMELGGA-DAFVVL 241 Query: 258 PDADIEKTVDALMGAAYGSAGERCMAISVAVLVGDVGDKVIAALTERAKHLRITDGRDLK 317 DAD++K V + + +AG+ C + ++V ++ D + LR D + Sbjct: 242 ADADLDKAVQWAVTGRHWNAGQVCCSSKRIIVVDEIYDAFLEKYKAGVARLRAGDPMEPS 301 Query: 318 AEMGPIVSRAALERISGYIEQGVQAGAQLLLDGRDYVPTEPGLENGFWLGATLFDHVTEE 377 + P+ SR A++ + +EQ V GA++ + G + VP+ G + L HV+++ Sbjct: 302 TTLAPMSSRGAVDDLKKQLEQAVAHGAKVEVIGAE-VPS-----RGAFFRPVLLSHVSDD 355 Query: 378 MSIYREEIFGPVLACVRVNDFAEAIKLVNAHEFGNGVSCFTRDGNIAREFARRIEVGMVG 437 E FGPV +R D A+AI++ N FG G S FT D E A++I GMV Sbjct: 356 NPARYWEFFGPVSQVIRARDEADAIRIANDSPFGLGGSVFTTDIKHGIEVAKKISTGMVY 415 Query: 438 INVPISVPMAWHGFGGWKKSLFG 460 IN P V A FGG ++S +G Sbjct: 416 INHPTGV-AADLPFGGVRRSGYG 437 Lambda K H 0.320 0.136 0.407 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: 511 Number of extensions: 24 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: 499 Length of database: 463 Length adjustment: 34 Effective length of query: 465 Effective length of database: 429 Effective search space: 199485 Effective search space used: 199485 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 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