Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate NP_350239.1 CA_C3657 NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
Query= BRENDA::P42412 (487 letters) >NCBI__GCF_000008765.1:NP_350239.1 Length = 482 Score = 255 bits (651), Expect = 3e-72 Identities = 161/476 (33%), Positives = 258/476 (54%), Gaps = 15/476 (3%) Query: 8 KNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVPR 67 KN +G+WVESKT++ + +P ++ +V +KE++D +++ A K W + + Sbjct: 12 KNLFDGKWVESKTNKTIETHSPYDGSLIGKVQALSKEEVDEIFKSSRTAQKKWGETPINE 71 Query: 68 RARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGDSL 127 RARI+ +L + E +A +++ E K+ K +L EV R + + F A + M G+++ Sbjct: 72 RARIMRKAADILDDNAEYIAKILSNEIAKDLKSSLSEVKRTADFIRFTANEGTHMEGEAI 131 Query: 128 AS-----IATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTP 182 S D + R P+G+V I+PFN+P+ + A+ GN+ +LKPS Sbjct: 132 NSDNFPGSKKDKLSLVERVPLGIVLAISPFNYPVNLSGSKVAPALIAGNSVVLKPSTTGA 191 Query: 183 LLTEKLVELFEKAGLPKGVFNVVYG-AHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGS 241 + L E+F AGLP GV N V G ++ + ++ H E+ I+F GS VG+++ K Sbjct: 192 ISALHLAEIFNAAGLPAGVLNTVTGKGSEIGDYLITHEEVNFINFTGSSAVGKHISKIAG 251 Query: 242 ENLKRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFM 301 + V L G K+ IVL DANLE T +IV A+G +G+RC A V V + +ADE + Sbjct: 252 M-IPMVLEL-GGKDAAIVLEDANLETTAKSIVSGAYGYSGQRCTAVKRVLVMDKVADELV 309 Query: 302 AKLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSDDG 361 + +KV ++K+GN DD V + P+I + I+ +E+GA L+ + + Sbjct: 310 ELVTKKVKELKVGNPFDD-VTITPLIDNKAADYVQTLIDDAIEKGATLIVGNKRKEN--- 365 Query: 362 YFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNA 421 + PT+FDNVT +M I +E F PVL +IRVK++ EAIE+AN+SE+ + +FT N + Sbjct: 366 -LMYPTLFDNVTADMRIAWEEPFGPVLPIIRVKSMDEAIELANRSEYGLQSAVFTENMHD 424 Query: 422 IRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKKVV 477 Y +D G + +N FPF G KSS GT + S++ TR K + Sbjct: 425 AFYIANKLDVGTVQVNNKPERGPDHFPFLGTKSSGMGT--QGIRYSIEAMTRHKSI 478 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: 626 Number of extensions: 29 Number of successful extensions: 6 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: 482 Length adjustment: 34 Effective length of query: 453 Effective length of database: 448 Effective search space: 202944 Effective search space used: 202944 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 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