Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate 14450 b0312 betaine aldehyde dehydrogenase, NAD-dependent (NCBI)
Query= reanno::Smeli:SMc00781 (498 letters) >FitnessBrowser__Keio:14450 Length = 490 Score = 242 bits (618), Expect = 2e-68 Identities = 163/487 (33%), Positives = 252/487 (51%), Gaps = 20/487 (4%) Query: 1 MYELGHFIDGKRVAGTSGRVSNIFNPATGEVQGTVALASDADLAAAVESAKAAQPKWAAT 60 M E +I G + TSGR NPA G V TV A D+ AV+SA+ Q WA+ Sbjct: 4 MAEQQLYIHGGYTSATSGRTFETINPANGNVLATVQAAGREDVDRAVKSAQQGQKIWASM 63 Query: 61 NPQRRARVFMKFVQLLNDNMNELAEMLSREHGKTIDDAKG-DIVRGLEVCEFVIG-IPHL 118 R+R+ + V +L + +ELA++ + + GK + DIV G +V E+ G IP L Sbjct: 64 TAMERSRILRRAVDILRERNDELAKLETLDTGKAYSETSTVDIVTGADVLEYYAGLIPAL 123 Query: 119 QKSEFTEGAGPGIDMYSIRQPVGIGAGITPFNFPGMIPMWMFAPAIACGNAFILKPSERD 178 + S+ + Y+ R+P+G+ AGI +N+P I +W APA+A GNA I KPSE Sbjct: 124 EGSQIPLRETSFV--YTRREPLGVVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVT 181 Query: 179 PSVPIRLAELMIEAGLPAGILNVVNGDKGAVDAILT-HPDIAAVSFVGSTPIARYVY-GT 236 P ++LAE+ EAGLP G+ NV+ G LT HP IA VSF G + V + Sbjct: 182 PLTALKLAEIYSEAGLPDGVFNVLPGVGAETGQYLTEHPGIAKVSFTGGVASGKKVMANS 241 Query: 237 AAMNGKRAQCFGGAKNHMIIMPDADLDQAANALIGAGYGSAGERCM-AISVAVPVGEETA 295 AA + K G K+ +I+ DADLD AA+ + A + S+G+ C V VP + A Sbjct: 242 AASSLKEVTMELGGKSPLIVFDDADLDLAADIAMMANFFSSGQVCTNGTRVFVPAKCKAA 301 Query: 296 NRLIDKLVPMVESLRIGPYTDEKADMGPVVTKEAEQRIRSLIDSGIEQGAKLVVDGRDFK 355 K++ VE +R G D + + GP+V+ + I G E+GA+++ G K Sbjct: 302 --FEQKILARVERIRAGDVFDPQTNFGPLVSFPHRDNVLRYIAKGKEEGARVLCGGDVLK 359 Query: 356 LQGYENGHFIGGCLFDDVTPDMDIYKTEIFGPVLSVVRARNYEEALSLPMKHEYGNGVAI 415 G++NG ++ +F D + DM I + EIFGPV+S++ + +E + +YG I Sbjct: 360 GDGFDNGAWVAPTVFTDCSDDMTIVREEIFGPVMSILTYESEDEVIRRANDTDYGLAAGI 419 Query: 416 YTRDGDAARDFASRINIGMVGVNV----PIPVPLAYHSFGGWKSSSFGDLNQHGTDSIKF 471 T D + A ++ G+ +N P +P+ GG+K S G ++G +++ Sbjct: 420 VTADLNRAHRVIHQLEAGICWINTWGESPAEMPV-----GGYKHSGIG--RENGVMTLQS 472 Query: 472 WTRTKTI 478 +T+ K+I Sbjct: 473 YTQVKSI 479 Lambda K H 0.319 0.137 0.409 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: 588 Number of extensions: 29 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: 498 Length of database: 490 Length adjustment: 34 Effective length of query: 464 Effective length of database: 456 Effective search space: 211584 Effective search space used: 211584 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 (21.7 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