Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate WP_011423771.1 RHE_RS01970 NADP-dependent malic enzyme
Query= curated2:Q8CJR5 (697 letters) >NCBI__GCF_000092045.1:WP_011423771.1 Length = 760 Score = 158 bits (400), Expect = 8e-43 Identities = 109/316 (34%), Positives = 162/316 (51%), Gaps = 5/316 (1%) Query: 371 LLEQARSDLRRVVLPEGTEERVLHAAEVLLRRGVCELTLLGPVEQIRKKAADLGIDLG-- 428 L E+ R +R+V E EE+VL AA + + LLG + IR A GIDL Sbjct: 443 LYERVRRRPKRIVFAEAEEEQVLRAALSYANQQLGTALLLGREDLIRATAERAGIDLNRP 502 Query: 429 GAELIDPAASELRDSFAEKYAALRAHKGVTVELAYDVV-SDVNYFGTLMVQEGFADGMVS 487 G E+++ S +++ + A +G A ++ +D N+F MV G ADGMV+ Sbjct: 503 GLEIVNARISTRVEAYIDYLYARLQRQGYLHRDAQRLIHNDRNHFAATMVALGDADGMVT 562 Query: 488 GSVHSTAATIRPAFEIIKTKPDAAIVSSVFFMCLADKVLVYGDCAVNPDPDAEQLADIAT 547 G + + + I KP ++ +C V V D AV+ P AEQLADIA Sbjct: 563 GITRNYSTALEDVRRCIDEKPGHRVIGVSLALCRGRTVFV-ADTAVHDMPTAEQLADIAE 621 Query: 548 QSASTAAQFGVEPRIAMLSYSTGTSGSGADVDKVREATELVRSRRPDLSVEGPIQYDAAV 607 ++A A + G PR+AML+YST SG ++VREA +++ RR D +G + D A+ Sbjct: 622 EAAGLARRMGYPPRVAMLAYSTFGHPSGERSERVREAVKILDRRRVDFEYDGEMAADVAL 681 Query: 608 EPSVAATKLPGSAVAGQASVLIFPDLNTGNNTYKAVQRSAGAIAVGPVLQGLRKPVNDLS 667 V + P ++G A+VL+ P ++ + + K +Q G+ +GP+L GL KPV S Sbjct: 682 NRKV-MEQYPFCRLSGPANVLVMPAFHSASISTKMLQELGGSTVIGPILVGLDKPVQITS 740 Query: 668 RGALVQDIVNTVAITA 683 GA DIVN AI A Sbjct: 741 MGAKDSDIVNMAAIAA 756 Lambda K H 0.318 0.134 0.378 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: 1161 Number of extensions: 60 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: 697 Length of database: 760 Length adjustment: 40 Effective length of query: 657 Effective length of database: 720 Effective search space: 473040 Effective search space used: 473040 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: 55 (25.8 bits)
This GapMind analysis is from Apr 09 2024. 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