Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate BPHYT_RS21100 BPHYT_RS21100 methylmalonate-semialdehyde dehydrogenase
Query= reanno::pseudo5_N2C3_1:AO356_23175 (500 letters) >FitnessBrowser__BFirm:BPHYT_RS21100 Length = 501 Score = 672 bits (1735), Expect = 0.0 Identities = 317/498 (63%), Positives = 396/498 (79%), Gaps = 1/498 (0%) Query: 1 MSDAPVVGHYIDGRIQAS-DNARLSNVFNPATGAVQARVALAEPSTVDAAVASALAAFPA 59 M++ + H+I+G+ AS NA VFNPA G A+VA+ + AAV +A AAFPA Sbjct: 1 MTNLETISHFINGQRTASLRNAETQAVFNPALGEAVAQVAMGSAEDIHAAVGAAAAAFPA 60 Query: 60 WSEQSSLRRSRVMFKFKELLDRHHDELAQIISREHGKVLSDAHGEVTRGIEIVEYACGAP 119 WS + L R+R++ K+ +L+ +H D LAQ+++REHGK L DA GEV RG+E+VE+A G P Sbjct: 61 WSARPPLARARILAKYLQLMQQHTDTLAQMLTREHGKTLDDARGEVARGLEVVEFAVGIP 120 Query: 120 NLLKTDFSDNIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSE 179 +LLK +FSD I GID W++RQPLGV AG+TPFNFP MVP+WM P+AL GN F+LKPSE Sbjct: 121 HLLKGEFSDQISRGIDAWSIRQPLGVVAGITPFNFPAMVPMWMFPIALACGNTFVLKPSE 180 Query: 180 RDPSASLLMARLLTEAGLPDGVFNVVQGDKVAVDALLQHPDIEAISFVGSTPIAEYIHQQ 239 RDPS SLL A LL EAGLPDGVFNVVQGDK VDALL HP+++A+SFVGSTPIAEY++ + Sbjct: 181 RDPSCSLLHAELLKEAGLPDGVFNVVQGDKAVVDALLDHPEVQAVSFVGSTPIAEYVYAR 240 Query: 240 GTAQGKRVQALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAVAVGDVGDE 299 +A GKR QALGGAKNH++VMPDAD+ A DALIGAA+GSAGERCMAIS+AVAVGDVGD Sbjct: 241 ASANGKRAQALGGAKNHLVVMPDADMAMATDALIGAAFGSAGERCMAISVAVAVGDVGDR 300 Query: 300 LIAKLLPRIDQLKIGNGQQPGTDMGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRGFKVP 359 L+A L R LKI +G PG +MGP++TA + ++E I AGVA+GA L+VDGR ++VP Sbjct: 301 LVAALAERTRALKIDDGTAPGAEMGPVITAAARERIESLIGAGVADGATLVVDGRDYRVP 360 Query: 360 GAEQGFFVGATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCFT 419 G E GFFVG TLFD VT EM++Y++EIFGPVL +VRVP+ A AV LINAHE+GNGV+ FT Sbjct: 361 GRESGFFVGGTLFDHVTPEMTVYREEIFGPVLCVVRVPNVAAAVELINAHEYGNGVAVFT 420 Query: 420 RDGGIARAFARSIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGLRFYSRYKS 479 RDGG+AR F R +++GMVG+NVP+PVPMA++SFGGWKRSLFGDHH YG EG+RFY+R+K+ Sbjct: 421 RDGGVAREFTRQVQIGMVGVNVPVPVPMAFNSFGGWKRSLFGDHHIYGPEGVRFYTRHKA 480 Query: 480 VMQRWPDSIAKGPEFSMP 497 VMQRWPD+I G EF+ P Sbjct: 481 VMQRWPDTITAGAEFAFP 498 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: 753 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: 501 Length adjustment: 34 Effective length of query: 466 Effective length of database: 467 Effective search space: 217622 Effective search space used: 217622 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