Align methylmalonate-semialdehyde dehydrogenase subunit (EC 1.2.1.27) (characterized)
to candidate GFF3484 PS417_17840 betaine-aldehyde dehydrogenase
Query= metacyc::MONOMER-13339 (508 letters) >FitnessBrowser__WCS417:GFF3484 Length = 486 Score = 223 bits (569), Expect = 9e-63 Identities = 153/439 (34%), Positives = 221/439 (50%), Gaps = 11/439 (2%) Query: 15 VKLLIDGKFVDSNTTEWLDDVNPATQAVLSRVPMATAEEVNAAVAAAKRAFASWRHAPIG 74 +K I+G+ V+S T + NPAT + V AEEV AVAAAK AF W + P Sbjct: 2 IKHWINGREVESKDT--FINYNPATGEAIGEVASGGAEEVALAVAAAKEAFPKWANTPAK 59 Query: 75 TRARIFLKYQQLIRENMGELAALLTAEQGKTRLDAEGDIF-RGLEVVEHAAAIGNLQLGE 133 RAR+ K +LI +N+ LA L T + G + + R + A + G Sbjct: 60 ERARLMRKLGELIEQNVPHLAELETLDTGLPIHQTKNVLIPRASHNFDFFAEVCTRMDGH 119 Query: 134 LANNVAKMVDTYTRLQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVLKPSEQDPMVT 193 + V + YT QP+GVC ++P+N P M W +A GNT VLK SE P+ Sbjct: 120 -SYPVDDQMLNYTLYQPVGVCGLVSPWNVPFMTATWKTAPCLALGNTAVLKMSELSPLTA 178 Query: 194 MRLVELALEAGVPSGVLNVVHG-GAQVVDAICDHPDIKAISFVGSTRVGTHVYNRATLAG 252 L LA+EAG+P+GVLNV+ G GA DA+ HPD++AISF G T G + A L Sbjct: 179 NELGRLAVEAGIPNGVLNVIQGYGATAGDALVRHPDVRAISFTGGTATGKKIMQTAGL-- 236 Query: 253 KRVQCMMGAKNHAILMPDANREQSLNAIAGAAFGAAGQRCMA-LPVLVMVGEAQRWLPDL 311 K+ +G K+ ++ DA+ E++L++ F G+RC A + + +++ + Sbjct: 237 KKYSMELGGKSPVLIFEDADLERALDSALFTIFSLNGERCTAGSRIFIQESVYPQFVAEF 296 Query: 312 VAKAKALTVNAGDAAGADVGPLISPSACGRVRELIGEGVEAGAKL---ELDGRAVSVSGY 368 A+AK L V VG +I+ + +V I G+E GA L LD A + Sbjct: 297 AARAKRLIVGDPQDPKTQVGSMITQAHYDKVTGYIKIGIEEGATLLAGGLDRPANLPAHL 356 Query: 369 EKGNFVGPTIFSGVKPGMSIYDIEIFGPVLCVIAADNLDEAIEIINANPSGNGTAIFTQS 428 KG F+ PT+F+ V M I EIFGPV+C+I + EA+++ N G + I+TQ Sbjct: 357 SKGQFIQPTVFADVNNKMRIAQEEIFGPVVCLIPFKDEAEALQLANDTEYGLASYIWTQD 416 Query: 429 GAAARRFEEDIDVGQVGIN 447 A R I+ G V IN Sbjct: 417 IGKAHRLARGIEAGMVFIN 435 Lambda K H 0.319 0.135 0.395 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: 498 Number of extensions: 20 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: 508 Length of database: 486 Length adjustment: 34 Effective length of query: 474 Effective length of database: 452 Effective search space: 214248 Effective search space used: 214248 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