Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate BPHYT_RS19500 BPHYT_RS19500 methylmalonate-semialdehyde dehydrogenase
Query= reanno::pseudo6_N2E2:Pf6N2E2_515 (500 letters) >FitnessBrowser__BFirm:BPHYT_RS19500 Length = 512 Score = 758 bits (1958), Expect = 0.0 Identities = 362/499 (72%), Positives = 424/499 (84%) Query: 2 SDAPVVGHYLNGHVQDHDSTRFSNVFNPATGAVQARVALAEPGTVDAAVASALAAFPAWS 61 + A + H++NG + S RF +VFNPA G+V ARV LA VDAAVA+A AAFPAWS Sbjct: 14 TSARALTHFINGKTFEGTSGRFGDVFNPAQGSVSARVPLASVAEVDAAVAAAKAAFPAWS 73 Query: 62 EQSSLRRSRVMFKFKELLDRHHDELAQIISREHGKVLSDAHGEVTRGIEIVEYACGAPNL 121 E + ++R+RV+FKFKELLDRHHDELA++I+REHGKV SDA GEV RGIEIVE+ACG PNL Sbjct: 74 ETAPIKRARVLFKFKELLDRHHDELAELITREHGKVFSDAKGEVMRGIEIVEFACGIPNL 133 Query: 122 LKTDFSDNIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSERD 181 LKTDF+D IGGGIDNWNLRQPLGV AG+TPFNFP+MVP WM P+A+ GN F+LKPSERD Sbjct: 134 LKTDFTDQIGGGIDNWNLRQPLGVVAGITPFNFPMMVPCWMFPVAIACGNTFVLKPSERD 193 Query: 182 PSASLLMARLLTEAGLPDGVFNVVQGDKVAVDALLQHPDIEAISFVGSTPIAEYIHQQGT 241 PS S +A LL EAGLPDGVFNVV GDKVAVDALL HP++ A+SFVGSTPIAEYI+ +GT Sbjct: 194 PSCSNRLAELLKEAGLPDGVFNVVHGDKVAVDALLVHPEVSALSFVGSTPIAEYIYTEGT 253 Query: 242 AHGKRVQALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAVAVGDVGDELI 301 HGKRVQALGGAKNH++VMPDADLDQA DALIGAAYGSAGERCMAIS+AVAVG + DELI Sbjct: 254 KHGKRVQALGGAKNHLVVMPDADLDQAVDALIGAAYGSAGERCMAISVAVAVGHIADELI 313 Query: 302 AKLLPRIDQLKIGNGQQPGTDMGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRSFKVPGA 361 +L PR+ LKI NG + +MGPLVTA H+ KV G+ID+GV GA+L+VDGR +V G Sbjct: 314 ERLTPRVKSLKILNGMESDAEMGPLVTAVHREKVVGYIDSGVEAGAKLVVDGRGHQVSGH 373 Query: 362 EQGFFVGATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCFTRD 421 E+GFF+G TLFD V+ +M IY++EIFGPVL +VRVPDFA+AV LINA+EF NGVS FT D Sbjct: 374 EKGFFLGGTLFDNVSTDMKIYREEIFGPVLCVVRVPDFASAVELINANEFANGVSLFTSD 433 Query: 422 GGIARAFARSIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGLRFYSRYKSVM 481 GG+ARAF+R I++GMVGINVPIPVPMAWHSFGGWK+SLFGDHHAYGEEG+RFY+RYKS+M Sbjct: 434 GGVARAFSRQIQIGMVGINVPIPVPMAWHSFGGWKKSLFGDHHAYGEEGVRFYTRYKSIM 493 Query: 482 QRWPDSIAKGPEFSMPTAQ 500 QRWPDSIAKG EF+MP A+ Sbjct: 494 QRWPDSIAKGAEFTMPVAK 512 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: 821 Number of extensions: 27 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: 512 Length adjustment: 34 Effective length of query: 466 Effective length of database: 478 Effective search space: 222748 Effective search space used: 222748 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