Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_011425015.1 RHE_RS08800 aldehyde dehydrogenase family protein
Query= BRENDA::Q97YT9 (492 letters) >NCBI__GCF_000092045.1:WP_011425015.1 Length = 506 Score = 221 bits (562), Expect = 6e-62 Identities = 146/476 (30%), Positives = 248/476 (52%), Gaps = 10/476 (2%) Query: 16 KLYINGEFIDSKTDTIGKAYNPAKDEIIAEVPFSAKDEVEEAIQSAQEAFEK--WREVPI 73 K+ I+G++ + I + P+ ++ P + + E AI +A++AF++ W + Sbjct: 19 KMLIDGKWEAGASHPIERIA-PSHGVTVSRFPAGSATDAERAIAAARKAFDEGPWPRMTA 77 Query: 74 TTRIQYLFALKNRLEEYSETIARIIVQNHGKTIQEARGDMRRTIENVEAAISAAYTLYKG 133 + R L + + +E +A + GK I + RG++ +++ A + A L+ G Sbjct: 78 SERSAILLKAADLIAARAEELAFLDAIEAGKPITQVRGEIAGSVDIWRYAAALARDLH-G 136 Query: 134 EHLDQVSQEVDETVVREPLGVFGIITPFNFPTMVPFWFLPYAIVLGNTVVVKPSEITPVP 193 E + + V+RE +GV IITP+NFP ++ LP+A+ G T VVKPSE+T Sbjct: 137 ESYNTLGDGTVGVVLREAIGVVSIITPWNFPFLIVGQKLPFALAAGCTTVVKPSELTSGS 196 Query: 194 MDFIIRIFDEIKLPRGVVNVVHGAKDVVDEFLTNKL-VQGVTFVGSTRVGKYIYENAGKN 252 + I + +P GVVN+V G V +T+ V ++F GST VGK +NA + Sbjct: 197 TLVLGEILQQAGVPDGVVNIVTGTGPEVGAVMTSHPDVDMISFTGSTGVGKLTMKNAAQT 256 Query: 253 GKKAIVQAGAKNFVVVMPDADLNKAIPSIVSAFFGNAGQRCLAAANLVAVGNIYDEVKRK 312 KK ++ G KN +V PDADL+ I + V + NAG+ C A + L+ +I +V R+ Sbjct: 257 LKKVSLELGGKNPQIVFPDADLDAFIDAAVFGAYFNAGECCNAGSRLILHKSIASDVVRR 316 Query: 313 FIEASKQLKIGYGLDESVDMGPVVTKDAKKRIIGYIEKGIEEGAKLLLDGRDVKVPEYPN 372 E SK +K+G LD +G ++T ++I GY+ GA++ G + + Sbjct: 317 VAELSKGVKVGDPLDPQTQVGAIITPQHLEKISGYVAGARSNGARVTHGGETL---DLGM 373 Query: 373 GYFLGPTVFDEVTPEMVIAKEEIFGPVASIIHVKNLDEAINIINRSNYGNASSIFTTSGY 432 G F+ PT+ + VTP+M +A+EE+FGPV S++ + EA+ I N +YG ++ +++ Sbjct: 374 GQFMSPTILEAVTPDMAVAREEVFGPVLSVLTFETTAEAVRIANSIDYGLSAGVWSRDFD 433 Query: 433 YARKFRREVNTGNIGINIGVAAPMAFFPFGGRKESFFGILHGQIDSVDFFTDKKVV 488 R V G I +N + + PFGG K+S G G+ +V+ +T+ K + Sbjct: 434 TCLTIGRSVRAGTIWMNTFMDG-ASELPFGGYKQSGLGRELGR-HAVEDYTETKTL 487 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: 550 Number of extensions: 21 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: 492 Length of database: 506 Length adjustment: 34 Effective length of query: 458 Effective length of database: 472 Effective search space: 216176 Effective search space used: 216176 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