Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate BPHYT_RS28150 BPHYT_RS28150 methylmalonate-semialdehyde dehydrogenase
Query= reanno::pseudo5_N2C3_1:AO356_23175 (500 letters) >FitnessBrowser__BFirm:BPHYT_RS28150 Length = 505 Score = 717 bits (1850), Expect = 0.0 Identities = 341/493 (69%), Positives = 405/493 (82%) Query: 7 VGHYIDGRIQASDNARLSNVFNPATGAVQARVALAEPSTVDAAVASALAAFPAWSEQSSL 66 + H+IDGR A + R +VF+PA G V ARV +A + VDAAVA+A AAFPAWSE + L Sbjct: 12 LSHFIDGRRAAGASGRFGDVFDPAQGRVAARVPVANATEVDAAVAAAKAAFPAWSETAPL 71 Query: 67 RRSRVMFKFKELLDRHHDELAQIISREHGKVLSDAHGEVTRGIEIVEYACGAPNLLKTDF 126 +R+R+MF+FKELL+ H DELA++I+R+HGK+LSDA GEV RGIEIVE+ACG PNLLKTDF Sbjct: 72 KRARLMFRFKELLEAHSDELAELITRDHGKLLSDAKGEVVRGIEIVEFACGIPNLLKTDF 131 Query: 127 SDNIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSERDPSASL 186 +D I GGIDNWNLRQPLGV AGVTPFNFP++VP WM +A GN F+LKPSER PSAS+ Sbjct: 132 TDQISGGIDNWNLRQPLGVAAGVTPFNFPMVVPCWMFVMAAACGNTFVLKPSERTPSASI 191 Query: 187 LMARLLTEAGLPDGVFNVVQGDKVAVDALLQHPDIEAISFVGSTPIAEYIHQQGTAQGKR 246 +A L EAG P GVFNVV G K VDAL++HPD+ AIS VGSTP+AEYI+ + +GKR Sbjct: 192 RLAELFIEAGFPKGVFNVVHGGKAVVDALIEHPDVAAISVVGSTPVAEYIYSESAKRGKR 251 Query: 247 VQALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAVAVGDVGDELIAKLLP 306 VQALG AKNH++VMPDADLDQA DALI ++YGSAGERCMA S+AVAVG +GDELI +L P Sbjct: 252 VQALGSAKNHLVVMPDADLDQAVDALIASSYGSAGERCMATSVAVAVGRIGDELIERLAP 311 Query: 307 RIDQLKIGNGQQPGTDMGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRGFKVPGAEQGFF 366 R+ L+IG G +P DMGPL++A H+AKV G+IDAGVA GARL+VDGRG VPG E GFF Sbjct: 312 RVRSLRIGGGMEPDLDMGPLISAAHRAKVLGYIDAGVAAGARLVVDGRGHSVPGHEAGFF 371 Query: 367 VGATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCFTRDGGIAR 426 +G +LFD V +MSIY++EIFGPVL +VRVPD A+A+AL+NAHE GN VS FT DGG AR Sbjct: 372 LGGSLFDDVKPDMSIYREEIFGPVLSVVRVPDLASAIALVNAHELGNCVSLFTSDGGAAR 431 Query: 427 AFARSIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGLRFYSRYKSVMQRWPD 486 AF+R I++GMVGINVP PVP AWHSFGGWKRSLFGDHHAYGEE +RFY+ YKSVMQRWPD Sbjct: 432 AFSRQIQIGMVGINVPSPVPPAWHSFGGWKRSLFGDHHAYGEEAVRFYTHYKSVMQRWPD 491 Query: 487 SIAKGPEFSMPTA 499 SIAKG EF+MP A Sbjct: 492 SIAKGAEFAMPVA 504 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: 782 Number of extensions: 23 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: 505 Length adjustment: 34 Effective length of query: 466 Effective length of database: 471 Effective search space: 219486 Effective search space used: 219486 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