Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate GFF501 PGA1_c05130 aldehyde dehydrogenase
Query= BRENDA::P42412 (487 letters) >FitnessBrowser__Phaeo:GFF501 Length = 476 Score = 269 bits (687), Expect = 2e-76 Identities = 160/470 (34%), Positives = 245/470 (52%), Gaps = 5/470 (1%) Query: 8 KNYINGEWVESKTDQYEDVVNPA-TKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVP 66 KN I G+W S+T +NP+ T++VL S ED++ A A +A W+ Sbjct: 4 KNLIAGDW--SETVAAAANINPSDTQDVLGYAANSPAEDMERAIAAARDAAPGWASSTPQ 61 Query: 67 RRARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGDS 126 +R +L + K EL L++ E GK E +GE R + +F AG G+ Sbjct: 62 QRFDVLDAIGTEILARKAELGKLLSREEGKTLPEGIGEAARAGQIFKFFAGETLRQAGEI 121 Query: 127 LASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTE 186 L S+ V R P+GVVG I P+NFP+ +P W A+A G+ +LKP+E TP Sbjct: 122 LGSVRPGVGVEVTRSPVGVVGLITPWNFPIAIPAWKIAPALAYGDAVVLKPAELTPGCAH 181 Query: 187 KLVELFEKAGLPKGVFNVVYGAHDVVNGIL-EHPEIKAISFVGSKPVGEYVYKKGSENLK 245 L E+ ++GLP+GVFN+V+G V L + + AISF GS G + K Sbjct: 182 ALAEIINRSGLPEGVFNIVFGTGSTVGQTLVQSRHVDAISFTGSVETGSAIAAACGAQRK 241 Query: 246 RVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKLQ 305 ++Q G KN +VL+DA+LE V + AF S G+RC A + + V EGI D F+A L Sbjct: 242 KLQLEMGGKNPMVVLDDADLETAVDASLNGAFFSTGQRCTASSRLIVTEGIHDRFVAALG 301 Query: 306 EKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSDDGYFVG 365 E++ +++GN LDD +GPV+ E ++ L Y++ EG +++ S G+++ Sbjct: 302 ERMTGLRVGNALDDSTQIGPVVDERQLEKDLYYLDVAASEGGQVLGGQTLQRSTKGFYLA 361 Query: 366 PTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIRYF 425 P + + +M I ++E+F P+ SVIRV + EA+ +AN + F A + T + +F Sbjct: 362 PALVTETSNDMRINQEEVFGPLASVIRVADYDEALVVANDTPFGLSAGICTGSLKYATHF 421 Query: 426 RENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKK 475 + + +AGM +NL PF G K S FG G + +FYT+ K Sbjct: 422 KAHAEAGMAMVNLPTAGVDYHVPFGGTKGSSFGA-REQGSHAKEFYTKVK 470 Lambda K H 0.318 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: 526 Number of extensions: 27 Number of successful extensions: 2 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: 487 Length of database: 476 Length adjustment: 34 Effective length of query: 453 Effective length of database: 442 Effective search space: 200226 Effective search space used: 200226 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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