Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate PfGW456L13_1795 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= reanno::pseudo5_N2C3_1:AO356_23175 (500 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1795 Length = 482 Score = 232 bits (592), Expect = 2e-65 Identities = 153/479 (31%), Positives = 245/479 (51%), Gaps = 11/479 (2%) Query: 8 GHYIDGRIQASDNARLSNVFNPATGAVQARVALAEPSTVDAAVASALAAFPAWSEQSSLR 67 G YI+G+ A N L V NPAT A+ V + VD AV++A AF WS+ S Sbjct: 9 GLYINGQWSAG-NEHL-RVINPATEALLTTVNGGDERAVDQAVSAATQAFADWSKTSGAE 66 Query: 68 RSRVMFKFKELLDRHHDELAQIISREHGKVLSDAHGEVTRGIEIVEYACGAPNLLKTDFS 127 R ++ K + + ++L + S +GK +A +V I EY G L Sbjct: 67 RGAILRKIATGVQANREKLMHLQSSNNGKPQFEAAIDVDDVIATFEYYAGLAEGLDAKQD 126 Query: 128 DNIGGGIDNWNLR---QPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSERDPSA 184 + D+++ R +P GV + P+NFP++ W + AL AG C +LKPSE P Sbjct: 127 SAVELPTDDFSARLRREPCGVVGLIVPWNFPMVTTAWKLAPALAAGCCVVLKPSEVTPLP 186 Query: 185 SLLMARLLTEAGLPDGVFNVVQGDKVAVDALLQ-HPDIEAISFVGSTPIAEYIHQQGTAQ 243 L +A ++ EAG+P GVFN+V G +AV A L P I +SF GS + + Q+ Sbjct: 187 ELELAAIIAEAGVPAGVFNLVCGTGLAVGAPLSADPRIAKVSFTGSNAVGVQVMQRAAET 246 Query: 244 GKRVQALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAVAVGDVGDELIAK 303 K V G K+ ++V+ DAD + A + G + +AG+ C A S + ++ DE + + Sbjct: 247 VKGVSLELGGKSSLLVLADADPELAVEVACGGGFFNAGQMCSATSRVLVADELADEFLNR 306 Query: 304 LLPRIDQLKIGNGQQPGTDMGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRGFKVPGAEQ 363 + R + +++ + P +MG LV +V G ID G++ GA+L+ G + + Sbjct: 307 VKARAEAIRVADPFDPNVEMGALVNQAQYQRVLGHIDRGLSAGAKLVCGGN--RPADLPR 364 Query: 364 GFFVGATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCFTRDGG 423 G+F+ T+F +V + +++ +EIFGPV+ + R A A+AL N +FG S TR+ Sbjct: 365 GYFLQPTVFTEVPLDSALWNEEIFGPVICVRRFASEAEAIALANDSQFGLVASVVTRNAQ 424 Query: 424 IARAFARSIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGLRFYSRYKSVMQ 482 A A +++ G+V IN P V ++GG+K+S G G GL+ + K V++ Sbjct: 425 TADRVANALQAGLVWINAP-QVIFPQTAWGGYKQSSIG--RELGPWGLQAFQEIKHVIR 480 Lambda K H 0.320 0.137 0.412 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: 523 Number of extensions: 29 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: 500 Length of database: 482 Length adjustment: 34 Effective length of query: 466 Effective length of database: 448 Effective search space: 208768 Effective search space used: 208768 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: 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