Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate HSERO_RS24005 HSERO_RS24005 methylmalonate-semialdehyde dehydrogenase
Query= reanno::pseudo5_N2C3_1:AO356_23175 (500 letters) >FitnessBrowser__HerbieS:HSERO_RS24005 Length = 503 Score = 729 bits (1882), Expect = 0.0 Identities = 350/500 (70%), Positives = 418/500 (83%), Gaps = 4/500 (0%) Query: 5 PVVGHYIDGRIQASDNARLSNVFNPATGAVQARVALAEPSTVDAAVASALAAFPAWSEQS 64 P + H+I+G+I S++ R +VFNPATGA A+VALA V+AAVA+A AA PAW+E + Sbjct: 4 PHIDHFINGQISRSESGRSQDVFNPATGAATAKVALASVQEVNAAVAAASAAAPAWAETA 63 Query: 65 SLRRSRVMFKFKELLDRHHDELAQIISREHGKVLSDAHGEVTRGIEIVEYACGAPNLLKT 124 L+R+RV+FKFKEL++++HD LA+ I+ EHGKV SDA GEVTRG+EIVE+A G P LLKT Sbjct: 64 PLKRARVLFKFKELIEQNHDALAKAITLEHGKVFSDAKGEVTRGLEIVEFATGIPQLLKT 123 Query: 125 DFSDNIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSERDPSA 184 F+DNIGGGIDNWNLRQPLGV AG+TPFNFPVMVPLWM P+A+ GN F+LKPSERDPS Sbjct: 124 QFTDNIGGGIDNWNLRQPLGVTAGITPFNFPVMVPLWMAPIAIATGNSFVLKPSERDPSP 183 Query: 185 SLLMARLLTEAGLPDGVFNVVQGDKVAVDALLQHPDIEAISFVGSTPIAEYIHQQGTAQG 244 SL++A L AGLPDGVFNVVQGDKVAVDALL+HP+++A+SFVGSTPIAEYI+++ T + Sbjct: 184 SLMLAELFKRAGLPDGVFNVVQGDKVAVDALLEHPEVQAVSFVGSTPIAEYIYRKATERA 243 Query: 245 K----RVQALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAVAVGDVGDEL 300 R QALGGAKNH++VMPDA+LDQA DALIGAAYGSAGERCMAIS+AVAVG V D+L Sbjct: 244 GTFPLRAQALGGAKNHLVVMPDANLDQAVDALIGAAYGSAGERCMAISVAVAVGSVADKL 303 Query: 301 IAKLLPRIDQLKIGNGQQPGTDMGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRGFKVPG 360 + L+PR+ LK+ NG + +MGPLVTA HKAKVEG+I +GV GA+L+VDGRG KVPG Sbjct: 304 VEALIPRVKALKVKNGMEDDAEMGPLVTAAHKAKVEGYIQSGVDAGAKLLVDGRGLKVPG 363 Query: 361 AEQGFFVGATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCFTR 420 E+GFF+G TLFD VT EM IYQ+EIFGPVL +VRVPDFA+AV LINAHE+GNGVS FT Sbjct: 364 HEEGFFIGGTLFDHVTTEMKIYQEEIFGPVLCVVRVPDFASAVQLINAHEYGNGVSLFTA 423 Query: 421 DGGIARAFARSIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGLRFYSRYKSV 480 DG A F+R I+VGMVGINVPIPVPMAWHSFGGWKRSLFGD HAYGEEG+RFY+RYKS+ Sbjct: 424 DGNTAHEFSRRIQVGMVGINVPIPVPMAWHSFGGWKRSLFGDTHAYGEEGIRFYTRYKSI 483 Query: 481 MQRWPDSIAKGPEFSMPTAQ 500 MQRW +I KG EF+MP A+ Sbjct: 484 MQRWSATIGKGAEFTMPVAK 503 Lambda K H 0.320 0.137 0.412 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: 783 Number of extensions: 20 Number of successful extensions: 2 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: 503 Length adjustment: 34 Effective length of query: 466 Effective length of database: 469 Effective search space: 218554 Effective search space used: 218554 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