Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate WP_150110902.1 ACIX8_RS16850 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-15203 (503 letters) >NCBI__GCF_000178955.2:WP_150110902.1 Length = 789 Score = 239 bits (609), Expect = 3e-67 Identities = 156/476 (32%), Positives = 251/476 (52%), Gaps = 34/476 (7%) Query: 8 HYINGHKTNGVADSHQEVTNPATGQVTGQVALASQADVDSAVAAAQAAFPAWSDTPPIRR 67 HYI+G T V+ S E NPATG+V ++A A +DVD AV AA+AA PAW +R Sbjct: 26 HYIDGAWTQ-VSGSSFETRNPATGEVLAKIATADASDVDRAVKAARAALPAWQALTGHQR 84 Query: 68 ARVMFKFLELLNAHKDELAEAITREHGKVFTDAQGEVARGIDIVEFA------CGIPQLL 121 AR ++ F + H LA T ++GK ++ R IDI A G QLL Sbjct: 85 ARYLYAFARQVQKHARRLAVLETLDNGKSIRES-----RDIDIPLVARHFYHHAGWAQLL 139 Query: 122 KGDYTEQVSTGIDNWTTRQPLGVVAGITPFNFPVMVPMWMFPLAIAAGNSFVLKPSPLDP 181 ++ S +GVV I P+NFP+++ W A+AAGN+ V+KP+ P Sbjct: 140 DEEFPGYTS-----------VGVVGQIIPWNFPLLMFAWKVAPALAAGNTVVIKPAEFTP 188 Query: 182 SASLMMADLLKQAGLPDGVFNVVQGDKDSVEALIDHPDVKALSFVGSTPIANLIYERGAR 241 ++L +A++ ++ GLP GV NV+ GD + A+++H D+ ++F GST + +I + A+ Sbjct: 189 LSALALAEIAQEIGLPKGVLNVINGDGKTGAAIVEHTDIDKIAFTGSTEVGRIIRKATAK 248 Query: 242 SGKRIQALGGAKNHMVVMPDANLDKAVDALIGAAYGSAGERCMAISVAVLVGDVADKIVP 301 + K++ G K+ +V DA+LD V+ L+ + + G+ C A S ++ VA+K+ Sbjct: 249 TSKKLSLELGGKSPFIVFDDADLDSTVEGLVDGIWFNQGQVCCAGSRLLVQERVAEKLYD 308 Query: 302 RLAERARDLKIKNGLELDAEMGPIVTSQAHQRITGYIEKGVAEGAEMVVDGRDFDSSVTG 361 ++ R L++ + L+ ++G IV + RI G +E GV EGA + VT Sbjct: 309 KIRSRMETLRVGSPLDKAIDIGAIVDQIQYDRIKGLVETGVKEGATC------WQPEVTM 362 Query: 362 EGCADGFWMGGTLFDHVTPEMTIYREEIFGPVLACVRVPDVATAIQLINDHEFGNGVSCF 421 G + TL +V P T+ +EEIFGPVL + A A++L N+ +G + Sbjct: 363 P--EKGLFFKPTLLTNVHPASTVAQEEIFGPVLVSMTFRTPAEAVELANNTTYGLAACVW 420 Query: 422 TESGSVAREFGRRIQVGMVGINVPIPVPMAWHGFGGWKRSMFGDTHAYGEEGVRFY 477 +E+ +VA + +++ G+V +N A GFGG++ S +G G+EG+ Y Sbjct: 421 SENINVALDVAAQVKAGVVWVNATNLFDAAC-GFGGYRESGYG--REGGKEGMYEY 473 Score = 51.2 bits (121), Expect = 1e-10 Identities = 46/197 (23%), Positives = 88/197 (44%), Gaps = 10/197 (5%) Query: 31 GQVTGQVALASQADVDSAVAAAQAAFPAWSDTPPIRRARVMFKFLELLNAHKDELAEAIT 90 GQ+ G+ L ++ D+ +AV AA+ W+ T RA++++ E + + E+ + Sbjct: 539 GQLVGEAPLGNRKDIRNAVEAARNISAKWAKTTAHGRAQILYYIAENMVQRRAEIVAKLA 598 Query: 91 REHGKVFTDAQGEVARGIDIVEFACGIPQLLKGDYTEQVSTGIDNWTTRQPLGVVAGITP 150 G A E+ G++ +G + ++ +G V + P Sbjct: 599 AFVGP--EQAAIELDYGVERTFAYAAWADKFEGS-VHNPPMRMVTLAMKEAIGTVGILCP 655 Query: 151 FNFPVMVPMWMFPLAIAAGNSFVLKPSPLDPSASLMMADLLK---QAGLPDGVFNVVQGD 207 + P++ + + AIA GN+ V PS + +M+DL + + LP GV N+V G Sbjct: 656 DDAPLLGFLSLVLPAIAMGNAVVAVPS---ERCATLMSDLYQVFDTSDLPGGVVNIVAGK 712 Query: 208 KDSV-EALIDHPDVKAL 223 + + L +H D+ A+ Sbjct: 713 ASELGKTLAEHDDIDAI 729 Lambda K H 0.319 0.136 0.406 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: 919 Number of extensions: 48 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 503 Length of database: 789 Length adjustment: 38 Effective length of query: 465 Effective length of database: 751 Effective search space: 349215 Effective search space used: 349215 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: 54 (25.4 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