Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_041097806.1 SUTH_RS05840 aldehyde dehydrogenase family protein
Query= BRENDA::Q97YT9 (492 letters) >NCBI__GCF_000828635.1:WP_041097806.1 Length = 479 Score = 238 bits (607), Expect = 3e-67 Identities = 149/476 (31%), Positives = 249/476 (52%), Gaps = 14/476 (2%) Query: 14 KLKLYINGEFIDSKTDTIGKAYNPAKDEIIAEVPFSAKDEVEEAIQSAQEAFEKWREVPI 73 + + YI+G+++ + ++P ++A VP + ++A+ +A+ AF+ W P Sbjct: 4 RTQFYIDGQWVSPAGQGTIEVFSPTDGALLATVPQGNAADADKAVTAARGAFDAWSVTPA 63 Query: 74 TTRIQYLFALKNRLEEYSETIARIIVQNHGKTIQEARGDMRRTIENVEAAI-SAAYTLYK 132 R YL ++ L+ ++ IA KTI G + + ++ +A++ +Y Sbjct: 64 AERAAYLKKIQESLKARADEIA--------KTITLEMGMPYKFSQRIQVGSPTASFGMYS 115 Query: 133 GEHLDQVSQEV--DETVVREPLGVFGIITPFNFPTMVPFWFLPYAIVLGNTVVVKPSEIT 190 D +E + VVRE +GV ITP+N+P + A+ G TVV+KPSE+ Sbjct: 116 KMLADFPFEEKVGNSKVVREAVGVVAAITPWNYPLHQIAAKVAAALAAGCTVVLKPSEVA 175 Query: 191 PVPMDFIIRIFDEIKLPRGVVNVVHGAKDVVDE-FLTNKLVQGVTFVGSTRVGKYIYENA 249 P+ + I +P GV N++ G VV E +T++ V V+F GSTR G + E A Sbjct: 176 PLNAFLLAEIIHAAGVPAGVFNLITGYGPVVGEAMVTHREVDMVSFTGSTRAGTRVSELA 235 Query: 250 GKNGKKAIVQAGAKNFVVVMPDADLNKAIPSIVSAFFGNAGQRCLAAANLVAVGNIYDEV 309 K+ ++ G K+ +++ DAD N A+ +V + N+GQ C A ++ Y E Sbjct: 236 SATVKRVALELGGKSAAIILDDADFNVAVKGVVGNCYLNSGQTCTAHTRMLVPATRYAEA 295 Query: 310 KRKFIEASKQLKIGYGLDESVDMGPVVTKDAKKRIIGYIEKGIEEGAKLLLDGRDVKVPE 369 + +EA++ ++G + E V +GP+ +K + R+ YI KGI EG +LL G D+ Sbjct: 296 AKLAVEAAQAYRVGDPMAEGVTLGPLASKMQQDRVRDYIGKGIAEGCELLTGGADLPEGV 355 Query: 370 YPNGYFLGPTVFDEVTPEMVIAKEEIFGPVASIIHVKNLDEAINIINRSNYGNASSIFTT 429 P+GY++ PT+F +V P+ IA+EEIFGPV SII + ++A++I N + YG A +++ Sbjct: 356 NPDGYYVKPTIFGKVKPDSSIAQEEIFGPVLSIISYADEEDAVSIANGTVYGLAGGVWSA 415 Query: 430 SGYYARKFRREVNTGNIGINIGVAAPMAFFPFGGRKESFFGILHGQIDSVDFFTDK 485 + +A + R + TG + IN G A PFGG K+S G G+ DF K Sbjct: 416 TDEHAEQVARRMRTGQVEINGGTFNMYA--PFGGYKQSGNGRELGKYGLEDFLEFK 469 Lambda K H 0.319 0.139 0.398 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: 554 Number of extensions: 26 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: 492 Length of database: 479 Length adjustment: 34 Effective length of query: 458 Effective length of database: 445 Effective search space: 203810 Effective search space used: 203810 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 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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