Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate BPHYT_RS18310 BPHYT_RS18310 malic enzyme
Query= SwissProt::P77844 (329 letters) >FitnessBrowser__BFirm:BPHYT_RS18310 Length = 760 Score = 159 bits (403), Expect = 2e-43 Identities = 107/321 (33%), Positives = 170/321 (52%), Gaps = 13/321 (4%) Query: 14 ARAEHSHIVLPEGDDDRILMAAHQLLDQDICDITILGDPVKIKERATELGLHLNTA---Y 70 A++E + IV EG+D+R+L AA +L + I ++G P I+ R ++G L Sbjct: 437 AKSEPARIVFAEGEDERVLRAAQFVLLEKIAKPILVGRPSVIEMRLKKMGSKLKCGDDFE 496 Query: 71 LVNPLTDPRLEEFAEQFAELRKSKSVTIDEAREIMKDIS-YFGTMMVHNGDADGMVSGAA 129 +V+P DPR ++ + + EL + VT D A+ M+ + G ++V G+ADGM+ G Sbjct: 497 IVDPEDDPRYQQSWQAYHELGAREGVTPDVAKAAMRKFNTLIGAILVRLGEADGMICGMI 556 Query: 130 NTTAHTIKPSFQIIKTVPEASVVSSIFLMVLRGRLWAFGDCAVNPNPTAEQLGEIAVVSA 189 +K Q++ +++ L++L GR D VN PTAEQL ++ +++A Sbjct: 557 GQYHAHLKFIEQVLGKADNVQNFAAMNLLMLPGRNLFICDTYVNETPTAEQLADMTMLAA 616 Query: 190 KTAAQFGIDPRVAILSYSTGNSGGGSDVDRAIDALAEARRL----NPELCVDGPLQFDAA 245 +FGI P+VA+LS NS GS + +A AR+L P L +DG + DAA Sbjct: 617 GEIEKFGITPKVALLS----NSNFGSAPSSSSQRMAAARKLIVERAPSLEIDGEMHGDAA 672 Query: 246 VDPGVARKKMPDSDVAGQANVFIFPDLEAGNIGYKTAQRT-GHALAVGPILQGLNKPVND 304 + V + P + + G+AN+ I P++EA NI Y + G + VGP L G KPV+ Sbjct: 673 LSEVVRKAAFPGTTLTGEANLLIMPNVEAANITYNLLKMIGGEGVTVGPFLLGAEKPVHI 732 Query: 305 LSRGATVPDIVNTVAITAIQA 325 L+ ATV I+N A+ + A Sbjct: 733 LTPAATVRRIINMTAVASANA 753 Lambda K H 0.318 0.134 0.386 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: 531 Number of extensions: 33 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 329 Length of database: 760 Length adjustment: 34 Effective length of query: 295 Effective length of database: 726 Effective search space: 214170 Effective search space used: 214170 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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