Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate Ga0059261_3374 Ga0059261_3374 NAD-dependent aldehyde dehydrogenases
Query= BRENDA::P42412 (487 letters) >FitnessBrowser__Korea:Ga0059261_3374 Length = 474 Score = 231 bits (589), Expect = 4e-65 Identities = 158/467 (33%), Positives = 242/467 (51%), Gaps = 28/467 (5%) Query: 7 LKNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVP 66 LK+YI GEWVES+ DV+NPAT+ + ++ + ++ D D A A AF ++S+ +V Sbjct: 5 LKHYIGGEWVESEGGTRHDVINPATEAPVTEITLGSEADADKAVAAAKAAFDSFSRTSVD 64 Query: 67 RRARILFNFQQLLSQHKE---ELAHLITIENGKNTKEA-LGEVGRGIENVEFAAGAP--- 119 R +L + +L+++K +LA I E G A +VG GI ++ A Sbjct: 65 ERIALL---EAILAEYKNRAGDLADAIAAEMGAPISLAKTAQVGSGIGHLMSTINALKAF 121 Query: 120 --SLMMGDSLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKP 177 S +G SL PIGVV I P+N+P+ A+A GNT +LKP Sbjct: 122 EFSEQIGQSLV----------VHEPIGVVALITPWNWPLNQIVAKVAPALAAGNTMVLKP 171 Query: 178 SERTPLLTEKLVELFEKAGLPKGVFNVVYGAHDVVNGILE-HPEIKAISFVGSKPVGEYV 236 SE P E+ +KAG+P GVFN+V G +V L H ++ +SF GS G V Sbjct: 172 SEEAPGSAAIFAEIMDKAGVPAGVFNLVQGDGPIVGTALSRHRDVDMVSFTGSTRAGIQV 231 Query: 237 YKKGSENLKRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGI 296 K +E +KRV G K+ ++L A+L V + + ++G+ C+A A + V E Sbjct: 232 AKNAAETVKRVHQELGGKSPNVILPGADLSRAVQVGLFSVVMNSGQSCIAPARMLVHESQ 291 Query: 297 ADEFMAKLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVC--DGR 354 A E + ++ G+ +G +GPV+ + ++ I KG+EEGA+L GR Sbjct: 292 AAEAAQIASGLMKAVETGDPAQEGRHIGPVVNKAQWEKIQGLIRKGMEEGAKLETGGPGR 351 Query: 355 ENVSDDGYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACL 414 + + GYFV PT+F V +MTI ++EIF PV+++I ++ +EA+ IAN +++ A L Sbjct: 352 PDGIETGYFVKPTLFSGVRNDMTIAREEIFGPVITIIPYRDEEEAVRIANDTDYGLSAVL 411 Query: 415 FTSNSNAIRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLH 461 F S ++ + AGM+ IN G P P PF G+K S G H Sbjct: 412 FGS-PEEVKRVAPRLRAGMVYINGGQPDPS--LPFGGYKQSGNGREH 455 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: 513 Number of extensions: 24 Number of successful extensions: 5 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 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