Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate HSERO_RS16825 HSERO_RS16825 NADP-dependent malic enzyme oxidoreductase
Query= SwissProt::P77844 (329 letters) >FitnessBrowser__HerbieS:HSERO_RS16825 Length = 770 Score = 182 bits (462), Expect = 2e-50 Identities = 107/321 (33%), Positives = 177/321 (55%), Gaps = 9/321 (2%) Query: 12 KRARAEHSHIVLPEGDDDRILMAAHQLLDQDICDITILGDPVKIKERATELGLHLNTAY- 70 K+A IV EG+++R+L A ++D+++ ++G P +++R + GL L Sbjct: 448 KKAAEAKKRIVYAEGEEERVLRAVQVIVDENLAKPILVGRPEVLEQRIQKFGLRLRAGTD 507 Query: 71 --LVNPLTDPRLEEFAEQFAELRKSKSVTIDEAR-EIMKDISYFGTMMVHNGDADGMVSG 127 ++NP D R ++ + F E+ + K VT A+ E+ + + G+M +H GDADGM+ G Sbjct: 508 FEVINPNFDNRYRDYWQTFLEMSRRKGVTEQYAKLEMRRRHTLIGSMAIHKGDADGMICG 567 Query: 128 AANTTAHTIKPSFQIIKTVPEASVVSSIFLMVLRGRLWAFGDCAVNPNPTAEQLGEIAVV 187 TT + Q++ +V +++ ++L R D VN NP A +L EI ++ Sbjct: 568 TYGTTQLHLHYIDQVLGKREGVNVYAAMNAVILPNRQLVMVDTHVNENPNARELAEITML 627 Query: 188 SAKTAAQFGIDPRVAILSYSTGNSGGGSDVDRAIDALAEARRLNPELCVDGPLQFDAAVD 247 +A+ +FG+ PR A+LS+S S + +ALA R + PEL VDG + D A+D Sbjct: 628 AAEEMRRFGLHPRAALLSHSNFGSSNSESARKMREALAILREIAPELEVDGEMHGDTALD 687 Query: 248 PGVARKKMPDSDVAGQANVFIFPDLEAGNIGY---KTAQRTGHALAVGPILQGLNKPVND 304 + +PDS + G AN+ + P+++A NI Y KTA +G+ +A+GPIL G KPV+ Sbjct: 688 SKLLNAVIPDSPLKGDANLLVMPNIDAANIAYNLLKTA--SGNGVAIGPILLGCAKPVHI 745 Query: 305 LSRGATVPDIVNTVAITAIQA 325 L+ ATV I+N A+ + A Sbjct: 746 LTPSATVRRIINMTALCVMDA 766 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: 591 Number of extensions: 26 Number of successful extensions: 3 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: 329 Length of database: 770 Length adjustment: 34 Effective length of query: 295 Effective length of database: 736 Effective search space: 217120 Effective search space used: 217120 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