Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate 7025959 Shewana3_3107 methylmalonate-semialdehyde dehydrogenase [acylating] (RefSeq)
Query= reanno::pseudo6_N2E2:Pf6N2E2_515 (500 letters) >FitnessBrowser__ANA3:7025959 Length = 496 Score = 635 bits (1637), Expect = 0.0 Identities = 304/490 (62%), Positives = 381/490 (77%), Gaps = 1/490 (0%) Query: 9 HYLNGHVQDHDSTRFSNVFNPATGAVQARVALAEPGTVDAAVASALAAFPAWSEQSSLRR 68 HY+NG STR +F PATG + +V+LA V AA+A A +AF WS+ + L R Sbjct: 6 HYVNGE-HTAASTRSQEIFEPATGECRGQVSLASRDEVSAAIAIAKSAFDTWSQVTPLNR 64 Query: 69 SRVMFKFKELLDRHHDELAQIISREHGKVLSDAHGEVTRGIEIVEYACGAPNLLKTDFSD 128 +RV+FKFK L+++H DELAQ+I+ EHGKVL DA GE+ RG+E+VE+ACG P+LLK + ++ Sbjct: 65 ARVLFKFKALVEQHMDELAQLITLEHGKVLDDARGELIRGLEVVEFACGIPHLLKGEHTE 124 Query: 129 NIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSERDPSASLLM 188 +GGG+D W++ Q LGV AG+ PFNFPVMVP+WM P+A+ GN FI+KPSE+DPSA + + Sbjct: 125 QVGGGVDAWSVNQALGVVAGIAPFNFPVMVPMWMFPIAIACGNTFIMKPSEKDPSAVMRI 184 Query: 189 ARLLTEAGLPDGVFNVVQGDKVAVDALLQHPDIEAISFVGSTPIAEYIHQQGTAHGKRVQ 248 A LLT+AGLP GVFNVV GDK AVD LL H DI+A+SFVGSTPIAEYI+ + HGKRVQ Sbjct: 185 AELLTQAGLPAGVFNVVNGDKEAVDTLLSHEDIQAVSFVGSTPIAEYIYSTASKHGKRVQ 244 Query: 249 ALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAVAVGDVGDELIAKLLPRI 308 ALGGAKNHM++MPDADLDQA AL+GAAYGSAGERCMAIS+ +AVGDVGD+L+ KLLP+I Sbjct: 245 ALGGAKNHMLLMPDADLDQAVSALMGAAYGSAGERCMAISVVLAVGDVGDKLVDKLLPQI 304 Query: 309 DQLKIGNGQQPGTDMGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRSFKVPGAEQGFFVG 368 QLK+GNG P +MGPL++ +H AKV F+DAGV EGA L+VDGR V +QG+F+G Sbjct: 305 QQLKVGNGLTPEMEMGPLISRQHLAKVTEFVDAGVKEGATLVVDGRQLTVADHQQGYFLG 364 Query: 369 ATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCFTRDGGIARAF 428 A LFD VT EM IY++EIFGPVL IVRV D+A+A+ALIN HEFGNG + FT+ G AR F Sbjct: 365 ACLFDNVTPEMRIYREEIFGPVLSIVRVKDYASALALINQHEFGNGTAIFTQSGEAARHF 424 Query: 429 ARSIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGLRFYSRYKSVMQRWPDSI 488 ++VGMVG+NVPIPVPMA+HSFGGWKRSLFG H +G +G+RFY++ K++ RWP Sbjct: 425 CHHVQVGMVGVNVPIPVPMAFHSFGGWKRSLFGPLHMHGPDGVRFYTKRKAITARWPVGK 484 Query: 489 AKGPEFSMPT 498 EF MPT Sbjct: 485 QTQAEFVMPT 494 Lambda K H 0.321 0.137 0.415 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: 686 Number of extensions: 21 Number of successful extensions: 1 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: 500 Length of database: 496 Length adjustment: 34 Effective length of query: 466 Effective length of database: 462 Effective search space: 215292 Effective search space used: 215292 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 (21.8 bits) S2: 52 (24.6 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