Align malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate BPHYT_RS28150 BPHYT_RS28150 methylmalonate-semialdehyde dehydrogenase
Query= BRENDA::A0A081YAY7 (498 letters) >FitnessBrowser__BFirm:BPHYT_RS28150 Length = 505 Score = 599 bits (1544), Expect = e-176 Identities = 293/493 (59%), Positives = 368/493 (74%), Gaps = 3/493 (0%) Query: 4 IKHLIGGELIAD-TGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTPPA 62 + H I G A +GR DVF+P+ G +VP+A+ + A+ AAKAAFPAW T P Sbjct: 12 LSHFIDGRRAAGASGRFGDVFDPAQGRVAARVPVANATEVDAAVAAAKAAFPAWSETAPL 71 Query: 63 KRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKGEY 122 KRA+++FRFK+LLEA+ + + +LI+ +HGK + DA GE+ RGIE VE+A P +LK ++ Sbjct: 72 KRARLMFRFKELLEAHSDELAELITRDHGKLLSDAKGEVVRGIEIVEFACGIPNLLKTDF 131 Query: 123 SRNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSSTL 182 + + ID W+ QP+GV AG+TPFNFP +VP WM+ +A ACGNTF+LKPSER PS+++ Sbjct: 132 TDQISGGIDNWNLRQPLGVAAGVTPFNFPMVVPCWMFVMAAACGNTFVLKPSERTPSASI 191 Query: 183 LIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRGKR 242 +AELF EAG PKGV NVVHG K VDALIE P+V A+S VGSTP+AEYIYSE KRGKR Sbjct: 192 RLAELFIEAGFPKGVFNVVHGGKAVVDALIEHPDVAAISVVGSTPVAEYIYSESAKRGKR 251 Query: 243 VQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQKLV 302 VQALG AKNH V+MPDADLD AV AL+ ++YGS GERCMA SVAV VG +I D L+++L Sbjct: 252 VQALGSAKNHLVVMPDADLDQAVDALIASSYGSAGERCMATSVAVAVG-RIGDELIERLA 310 Query: 303 PQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHENGF 362 P+++ L+IG G LDMGPL++ A R KV GYID GVA GA LVVDGRG+ V GHE GF Sbjct: 311 PRVRSLRIGGGMEPDLDMGPLISAAHRAKVLGYIDAGVAAGARLVVDGRGHSVPGHEAGF 370 Query: 363 FLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGEAA 422 FLGG+LFD V P+M+IY+EEIFGPVL +VRV L A+ L+N HE GN +FT DG AA Sbjct: 371 FLGGSLFDDVKPDMSIYREEIFGPVLSVVRVPDLASAIALVNAHELGNCVSLFTSDGGAA 430 Query: 423 RLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAITQRWP 482 R F +I++GMVG+NVP PVP A+HSFGGWKRSLFGD HAYG + VRFYT K++ QRWP Sbjct: 431 RAFSRQIQIGMVGINVPSPVPPAWHSFGGWKRSLFGDHHAYGEEAVRFYTHYKSVMQRWP 490 Query: 483 QRKSHEAAQFAFP 495 + + A+FA P Sbjct: 491 DSIA-KGAEFAMP 502 Lambda K H 0.319 0.137 0.411 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: 737 Number of extensions: 27 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: 498 Length of database: 505 Length adjustment: 34 Effective length of query: 464 Effective length of database: 471 Effective search space: 218544 Effective search space used: 218544 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 (21.7 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