Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate Ac3H11_4331 NADP-dependent malic enzyme (EC 1.1.1.40)
Query= curated2:P39197 (318 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4331 Length = 781 Score = 163 bits (412), Expect = 1e-44 Identities = 126/334 (37%), Positives = 176/334 (52%), Gaps = 26/334 (7%) Query: 1 MKPL-DRIHEAAKALDRHIILPEGEDPRVAEAARRLLAAGLARVTLMGGPEIPGAGRIDP 59 MKP+ D AAK + + EGE+ RV AA+ ++ +AR TL+G P I A RI+ Sbjct: 445 MKPIFDAARNAAK---KRVAYAEGEEERVLRAAQIVVDEKVARPTLIGRPAII-AQRIEK 500 Query: 60 AG-----GPDLAELA--------DHW---HRMRAARGMTAERALTEMRDPIRQ-AAMRVR 102 G G D + D W HRM +G+T + A EMR + +M + Sbjct: 501 FGLRLKEGVDYDVVNTDFDHRYNDFWQTYHRMTERKGITQQVAKIEMRRRLTLIGSMMLH 560 Query: 103 LGQADGTVGGAVATTADTVRAALQIIGK-APGAGIVSSFFLMLSCGPGAPVRGGMIF-AD 160 G+ DG + G TTA+ + Q+IGK A GA + + +C G + G +F D Sbjct: 561 KGEVDGLICGTWGTTANHLLYIDQVIGKHAGGADSTAQDVPVYACMNGLMLPGRQVFLVD 620 Query: 161 CGLVIQPDARELAAIALSAADSCRRILAEEPRVALLSFSTAGSAEHPSLGRIREALALIR 220 + P +ELA I AA+ R +P+ ALLS S G++ HPS ++R+ L L+R Sbjct: 621 THVNYDPTPQELAEITALAAEEMMRF-GIKPKAALLSHSNFGTSNHPSAVKMRQTLELLR 679 Query: 221 AAAPGLEVDGEMQFDAALDEAIRARKAPESPLTGRPNVFVFPDLADGNIGYKIAERLA-G 279 AP LEVDGEM D ALD RA P S LTG N+ VFP++ NI Y + + A G Sbjct: 680 QQAPWLEVDGEMHGDVALDGKARAALMPSSELTGDANLLVFPNIDAANIAYNLLKTAAGG 739 Query: 280 LTAIGPILQGLAKPANDLSRACSVKDIVNATAIT 313 AIGP+L G AKP + L+ + +V+ IVN TA+T Sbjct: 740 GIAIGPVLLGAAKPVHILTPSATVRRIVNMTALT 773 Lambda K H 0.320 0.136 0.391 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: 454 Number of extensions: 18 Number of successful extensions: 4 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: 318 Length of database: 781 Length adjustment: 34 Effective length of query: 284 Effective length of database: 747 Effective search space: 212148 Effective search space used: 212148 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 (21.8 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