Align Malonate-semialdehyde dehydrogenase 1; MSA dehydrogenase 1; EC 1.2.1.-; Methylmalonate-semialdehyde dehydrogenase 1; MMSA dehydrogenase 1; MSDH 1; EC 1.2.1.27 (uncharacterized)
to candidate CA265_RS19780 CA265_RS19780 aldehyde dehydrogenase family protein
Query= curated2:Q5L025 (488 letters) >FitnessBrowser__Pedo557:CA265_RS19780 Length = 513 Score = 202 bits (513), Expect = 3e-56 Identities = 148/482 (30%), Positives = 234/482 (48%), Gaps = 17/482 (3%) Query: 16 GGQWVASSGTETLEVPNPATGEVLARVPISTKEDVDQAVQAAKKAFATWKDVPVPKRARI 75 G W TLE +P G+++A I+T +D D V A++AF W+ VP PKR I Sbjct: 24 GSNWGGELNVNTLESFSPVDGKLIASAKIATADDYDAVVLKAQEAFTAWRSVPAPKRGEI 83 Query: 76 MFSFHHLLNQHHEELAELVVQENGKAYKEAYGEIQRGIECVEFAAGAPTLLMGESLSNIA 135 + F L ++ + L LV E GK+ +E +GE+Q I+ +FA G L G L+ + Sbjct: 84 VRQFGDALRENKDALGTLVSYEMGKSLQEGFGEVQEMIDICDFAVGLSRQLYG--LTMHS 141 Query: 136 EEIDSEMFR--YPLGVVAGITPFNFPMMVPLWMFPLAIVCGNTFVLKPSERTPILA---- 189 E M+ +PLG+V I+ FNFP+ V W LA+VCGN + KPSE+TP+ A Sbjct: 142 ERPSHRMYEQWHPLGIVGIISAFNFPVAVWSWNTALALVCGNVCIWKPSEKTPLTAIACQ 201 Query: 190 NKLAELFTEAGAPPGVLNVVHGAHEVVNALIDHEDIRAISFVGSQPVAKYVYERTAAQ-G 248 + +A++F + GV N++ G EV + + I IS GS + K V A+ G Sbjct: 202 HIIAKVFKDNDIAEGVCNLILGDREVGERMTNDGRIPLISATGSTRMGKAVGAAVGARLG 261 Query: 249 KRVQALSGAKNHHIVMPDADVETAVQHVISSAFGSAGQRCMACSAVVI-VGENETFVRRL 307 K + L G N I+ AD++ ++ + A G+AGQRC + ++I + F +L Sbjct: 262 KSLLEL-GGNNAIIISEHADLDMSLIGAVFGAVGTAGQRCTSTRRLIIHESVYDAFTAKL 320 Query: 308 KQKADELIIGNGMDPEVLLTPVIRQSHREKVLGYIQK-GIEEGAVLLRDGRKEMDDRPEG 366 + +L IG+ +D + P+I L I K E G ++ G D G Sbjct: 321 VKAYGQLRIGDPLDQNNHVGPLIDTDAVAAYLDSIAKCKAEGGNFVVEGGVLSGDAYTSG 380 Query: 367 NFLGPTIFDYVTPDMTIAKEEIFAPVLSLLRANDLDEALSYIRKSRYGNGATIYTKDAKA 426 ++ P I + V D I + E FAP+L L++ LDEA++ G + I T + + Sbjct: 381 CYVKPCIAE-VQNDFKIVQHETFAPILYLIKYKTLDEAIALQNGVPQGLSSAIMTLNLRE 439 Query: 427 VRKF--REEADAGMLGINVGVPATMAFFPFSGWKDSFYGDLHVNGKDGVNFYTRKKMITS 484 +F + +D G+ +N+G F G K++ G +G D Y R++ T Sbjct: 440 AEQFLSAKGSDCGIANVNIGTSGAEIGGAFGGEKET--GGGRESGSDAWRAYMRRQTNTI 497 Query: 485 RF 486 + Sbjct: 498 NY 499 Lambda K H 0.319 0.136 0.396 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: 549 Number of extensions: 31 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: 488 Length of database: 513 Length adjustment: 34 Effective length of query: 454 Effective length of database: 479 Effective search space: 217466 Effective search space used: 217466 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