Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate 5208453 Shew_0965 methylmalonate-semialdehyde dehydrogenase (RefSeq)
Query= reanno::pseudo6_N2E2:Pf6N2E2_515 (500 letters) >FitnessBrowser__PV4:5208453 Length = 496 Score = 628 bits (1620), Expect = 0.0 Identities = 303/493 (61%), Positives = 378/493 (76%), Gaps = 3/493 (0%) Query: 7 VGHYLNG-HVQDHDSTRFSNVFNPATGAVQARVALAEPGTVDAAVASALAAFPAWSEQSS 65 + HY+NG H Q S R + VF PATG +A V+LA VDAA+ A A WSE + Sbjct: 4 INHYINGQHTQP--SARSAAVFEPATGEHKANVSLASALEVDAAIELAKKAHGPWSEMTP 61 Query: 66 LRRSRVMFKFKELLDRHHDELAQIISREHGKVLSDAHGEVTRGIEIVEYACGAPNLLKTD 125 L R+R++FKFK L++ + DELA +I+REHGKVL DA GE+ RG+E+VE+ACG P+LLK + Sbjct: 62 LNRARILFKFKALVEANMDELAAMITREHGKVLDDAKGEIIRGLEVVEFACGIPHLLKGE 121 Query: 126 FSDNIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSERDPSAS 185 ++ +GGG+D W L Q LGV AG+ PFNFPVMVP+WM P+A+ AGN FI+KPSE+DP++ Sbjct: 122 HTEQVGGGVDAWTLNQSLGVVAGIAPFNFPVMVPMWMFPIAIAAGNTFIMKPSEKDPTSV 181 Query: 186 LLMARLLTEAGLPDGVFNVVQGDKVAVDALLQHPDIEAISFVGSTPIAEYIHQQGTAHGK 245 + MA LLTEAGLPDGVFNVV GDK AVD LL H DI+A+SFVGSTPIAEYI+Q AHGK Sbjct: 182 MRMAELLTEAGLPDGVFNVVNGDKEAVDTLLTHKDIQAVSFVGSTPIAEYIYQTAAAHGK 241 Query: 246 RVQALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAVAVGDVGDELIAKLL 305 RVQALGGAKNHM++MPDADLDQA AL+GAAYGSAGERCMAIS+ +AVG+VGD L+ KLL Sbjct: 242 RVQALGGAKNHMLLMPDADLDQAVSALMGAAYGSAGERCMAISVVLAVGEVGDALVEKLL 301 Query: 306 PRIDQLKIGNGQQPGTDMGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRSFKVPGAEQGF 365 P+I LK+GNG + +MGPL++A+H KV ++D GV+EGA L+ DGR V EQG+ Sbjct: 302 PQIQALKVGNGLEGEMEMGPLISAQHLDKVRSYVDTGVSEGASLLADGRQLTVADHEQGY 361 Query: 366 FVGATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCFTRDGGIA 425 F+G LFD VT EM+IY++EIFGPVL IVRV D+A A+ LIN HEFGNG + FT+ G A Sbjct: 362 FLGGCLFDHVTPEMTIYKEEIFGPVLTIVRVKDYAEALTLINEHEFGNGTAIFTQSGEAA 421 Query: 426 RAFARSIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGLRFYSRYKSVMQRWP 485 R F ++VGMVG+NVPIPVPMA+HSFGGWKRSLFG H +G +G+RFY++ K++ RWP Sbjct: 422 RHFCHHVQVGMVGVNVPIPVPMAFHSFGGWKRSLFGPLHMHGPDGVRFYTKRKAITARWP 481 Query: 486 DSIAKGPEFSMPT 498 EF MPT Sbjct: 482 KGKGSQAEFVMPT 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: 706 Number of extensions: 17 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