Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate BPHYT_RS16880 BPHYT_RS16880 malic enzyme
Query= SwissProt::P77844 (329 letters) >FitnessBrowser__BFirm:BPHYT_RS16880 Length = 779 Score = 179 bits (454), Expect = 2e-49 Identities = 107/318 (33%), Positives = 174/318 (54%), Gaps = 9/318 (2%) Query: 10 LLKRARAEHSHIVLPEGDDDRILMAAHQLLDQDICDITILGDPVKIKERATELGLHLNTA 69 L + E IV EG+++R+L A ++D+ + ++G P I++R GL L Sbjct: 455 LARGVEPEKKRIVFAEGEEERVLRAMQIIVDEKLAKPILIGRPAVIEQRIARYGLRLIAG 514 Query: 70 Y---LVNPLTDPRLEEFAEQFAELRKSKSVTIDEAR-EIMKDISYFGTMMVHNGDADGMV 125 +VN D R +F +++ ++ K ++ A+ E+ + + G M+V G+ADGM+ Sbjct: 515 QDYTVVNTDHDERYRDFWQEYHKMMSRKGISAQMAKLEMRRRTTLIGAMLVEKGEADGMI 574 Query: 126 SGAANTTAHTIKPSFQIIKTVPEASVVSSIFLMVLRGRLWAFGDCAVNPNPTAEQLGEIA 185 G +TT + Q+I A V +++ +VL R D VN +PT EQL EI Sbjct: 575 CGTVSTTHRHLHFIDQVIGKKEGAKVYAAMNALVLPNRQIFLVDTHVNVDPTPEQLAEIT 634 Query: 186 VVSAKTAAQFGIDPRVAILSYSTGNSGGGSDVDRAIDALAEARRLNPELCVDGPLQFDAA 245 +++A+ +FGI+P++A+LS+S + + D LA R P+L VDG + D A Sbjct: 635 IMAAEEVRRFGIEPKIALLSHSNFGTSNAPTAQKMRDTLAILRERAPDLQVDGEMHGDIA 694 Query: 246 VDPGVARKKMPDSDVAGQANVFIFPDLEAGNIGY---KTAQRTGHALAVGPILQGLNKPV 302 +D + R+ MPDS + G AN+ + P+++A NI Y KTA G+ +A+GP+L G KPV Sbjct: 695 LDANLRREVMPDSTLEGDANLLVLPNIDAANISYNLLKTA--AGNNIAIGPMLLGAAKPV 752 Query: 303 NDLSRGATVPDIVNTVAI 320 + L+ ATV IVN A+ Sbjct: 753 HVLTASATVRRIVNMTAL 770 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: 588 Number of extensions: 28 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: 779 Length adjustment: 34 Effective length of query: 295 Effective length of database: 745 Effective search space: 219775 Effective search space used: 219775 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