Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_013450164.1 CALNI_RS00150 aldehyde dehydrogenase
Query= BRENDA::P42412 (487 letters) >NCBI__GCF_000183405.1:WP_013450164.1 Length = 474 Score = 216 bits (549), Expect = 2e-60 Identities = 150/479 (31%), Positives = 238/479 (49%), Gaps = 15/479 (3%) Query: 4 IRKLKNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKV 63 + K K +I G+WV+ T +Y DV NP ++ Q+ ++ E D A + + Sbjct: 1 MEKKKLFIEGKWVD--TGKYIDVRNPYDNSLIAQISMADAEWTDRGIDFAYSNRSIMASL 58 Query: 64 AVPRRARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMM 123 R IL L+ ++ ++LA I E+GK + A GEV R E +FAA + Sbjct: 59 TAKERGDILNKASLLIKENLDDLAITIARESGKALRFAKGEVLRSSETFQFAADEARRLS 118 Query: 124 GD--SLASIATDVEAANY--RYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSE 179 G+ L + AT Y RYP+GV+G I PFNFP+ + AIA GN +LKP+ Sbjct: 119 GELIPLDAAATGKNRFGYYKRYPLGVIGAITPFNFPLNLVSHKVAPAIAAGNCIVLKPAS 178 Query: 180 RTPLLTEKLVELFEKAGLPK-GVFNVVYGAHDVVNGILEHPEIKAISFVGSKPVGEYVYK 238 TPL KLVE+ +AGLPK G+ +V V N ++E + ISF GS VG + + Sbjct: 179 TTPLTAVKLVEILLEAGLPKEGITLLVGSGSSVGNRMVESDRLAMISFTGSPEVGLEIKR 238 Query: 239 KGSENLKRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIAD 298 K +K+V G + I+ DA++ + V F ++G+ C++ + V I D Sbjct: 239 KA--GMKKVTLELGNNSAVIIHKDADIASALPKCVVGGFANSGQVCISIQRIYVHREIYD 296 Query: 299 EFMAKLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVS 358 F ++ E V + G+ LD+ V +GP+I E R +I + + +GAR+ C G+ N Sbjct: 297 LFTSQFVEAVKNTSYGSQLDENVVVGPMIEEKEAIRVEEWINEAVNQGARIACGGKRN-- 354 Query: 359 DDGYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSN 418 G + PT+ + M + +EIF PV+ +++ L+EAIE AN S++ A +FT + Sbjct: 355 --GALLEPTVLLDTNETMKVVSEEIFGPVVCLMKYDTLEEAIEKANNSKYGLQAGIFTKD 412 Query: 419 SNAIRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKKVV 477 + + ++ G + +N + P+ G K S GT K +V+ T K V Sbjct: 413 IKSAFDAIDKLEVGGVMVNDMPTFRVDQMPYGGVKLS--GTGREGPKFAVEEMTEIKTV 469 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: 525 Number of extensions: 28 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: 487 Length of database: 474 Length adjustment: 34 Effective length of query: 453 Effective length of database: 440 Effective search space: 199320 Effective search space used: 199320 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: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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