Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate 3607155 Dshi_0577 aldehyde dehydrogenase (RefSeq)
Query= BRENDA::P42412 (487 letters) >FitnessBrowser__Dino:3607155 Length = 483 Score = 260 bits (665), Expect = 6e-74 Identities = 156/477 (32%), Positives = 240/477 (50%), Gaps = 4/477 (0%) Query: 10 YINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVPRRA 69 YI+G W E T Q E+ T +++ + +D A A A W + +R Sbjct: 8 YIDGAWTEG-TAQIENRNPSDTTDLIGMYAQADAGQLDTALAAARRAQPAWWAAGIQKRH 66 Query: 70 RILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGDSLAS 129 +L L +E+ L++ E GK E GEV R + + A GD S Sbjct: 67 DVLMAIGTELMARSDEIGRLLSREEGKPLAEGKGEVYRAGQFFTYFAAEALRQHGDLAES 126 Query: 130 IATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTEKLV 189 + +E R +GVV I+P+NFP+ P W A+A GN + KP+ TP L Sbjct: 127 VRPGIEIDVRREAVGVVAIISPWNFPVATPAWKIAPALAFGNAVVWKPANVTPASAIALT 186 Query: 190 ELFEKAGLPKGVFNVVYG-AHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSENLKRVQ 248 E+ + +PKG+FN+V G DV ++E E+ AISF GS PVG + +N+ +VQ Sbjct: 187 EIIARQDIPKGLFNLVAGPGRDVGQRLVESAEVDAISFTGSVPVGRGIAAAAVQNMTKVQ 246 Query: 249 SLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKLQEKV 308 G+KN IV++D +L+ V + +AFG G++C A + + V + D F+ KL Sbjct: 247 MEMGSKNPLIVMDDCDLDLAVAHAASSAFGGTGQKCTAASRLIVHSAVHDAFVEKLVAAA 306 Query: 309 ADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDG-RENVSDDGYFVGPT 367 +K+G+ L+DG LGPV+ E + + YI G +EGA L+C G R ++ DGYF+ P Sbjct: 307 RAMKVGHALEDGTQLGPVVSESQLNQNMEYIGVGKDEGAELLCGGDRLEMATDGYFMAPA 366 Query: 368 IFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIRYFRE 427 +F +M I ++E+FAP+ +V RV + EA+ AN ++F A + T++ +FR Sbjct: 367 VFAGTANDMRINREEMFAPITAVQRVDSYDEALARANDTQFGLTAGIMTTSLARASHFRA 426 Query: 428 NIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKKVVTARYPAP 484 ++ AG + +NL PF G +S FG G + +FYT K AP Sbjct: 427 HMRAGCVMVNLPTAGTDYHVPFGGRGASSFGP-REQGSYAAEFYTTVKTAYVAAGAP 482 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: 523 Number of extensions: 27 Number of successful extensions: 3 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: 483 Length adjustment: 34 Effective length of query: 453 Effective length of database: 449 Effective search space: 203397 Effective search space used: 203397 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