Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate Ac3H11_1079 NADP-dependent malic enzyme (EC 1.1.1.40)
Query= SwissProt::P77844 (329 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1079 Length = 768 Score = 142 bits (357), Expect = 4e-38 Identities = 99/315 (31%), Positives = 154/315 (48%), Gaps = 7/315 (2%) Query: 21 IVLPEGDDDRILMAAHQLLDQDICDITILGDPVKIKERATELGLHLNTAYLV---NPLTD 77 + +G+D+R L AA +D I ++G P I R + GL + V NP D Sbjct: 454 VAYADGEDERALRAAQMAIDDKIATPILIGRPAVIAARIAKAGLRMQLGKDVEVCNPEDD 513 Query: 78 PRLEEFAEQFAELRKSKSVTIDEARE-IMKDISYFGTMMVHNGDADGMVSGAANTTAHTI 136 PR ++ E + +L K T + A+ + + + ++MV GDAD M+ G T + Sbjct: 514 PRFRQYWEHYHQLMKRNGATPEVAKAAVRRSNTIIASLMVKLGDADAMICGLVGTYETHL 573 Query: 137 KPSFQIIKTVPEASVVSSI-FLMVLRGRLWAFGDCAVNPNPTAEQLGEIAVVSAKTAAQF 195 + II A +++ LM RG L+ D VN +PTA+QL +IA +S + +F Sbjct: 574 ERIHSIIGRQEGARDYAALNALMTNRGTLF-IADTYVNEDPTAQQLADIAWMSVQEVQRF 632 Query: 196 GIDPRVAILSYSTGNSGGGSDVDRAIDALAEARRLNPELCVDGPLQFDAAVDPGVARKKM 255 G+ P+VA LS+S+ S + + +A +PE+ DG L DAA++P + M Sbjct: 633 GLPPKVAFLSHSSYGSSKRASARKMREARDLFVAAHPEIECDGELHGDAALEPNIRNAYM 692 Query: 256 PDSDVAGQANVFIFPDLEAGNIGYKTAQ-RTGHALAVGPILQGLNKPVNDLSRGATVPDI 314 DS + AN+ I P+L+A NI Y + T + VGPIL G L+ ATV + Sbjct: 693 ADSTLTDSANLLICPNLDAANILYNVLKTTTSGGVTVGPILMGGAATAYILTPAATVRRV 752 Query: 315 VNTVAITAIQAGGRS 329 N A+ A R+ Sbjct: 753 FNMTALAVASAAARA 767 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: 539 Number of extensions: 29 Number of successful extensions: 5 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: 768 Length adjustment: 34 Effective length of query: 295 Effective length of database: 734 Effective search space: 216530 Effective search space used: 216530 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