Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate CCNA_02704 CCNA_02704 NADP-dependent malic enzyme
Query= curated2:P39197 (318 letters) >FitnessBrowser__Caulo:CCNA_02704 Length = 758 Score = 137 bits (346), Expect = 6e-37 Identities = 109/327 (33%), Positives = 159/327 (48%), Gaps = 26/327 (7%) Query: 7 IHEAAKALDRHIILPEGEDPRVAEAARRLLAAGLARVTLMGGPEIPG----------AGR 56 + E A+ + E ED RV A + ++ GLA L+G E+ AG+ Sbjct: 433 VFERARKQPVKVAYAEAEDERVLRAVQTVVDEGLAYPVLVGRREVITGKIEELGLRLAGK 492 Query: 57 ---IDPAGGPDL-AELADHWHRMRAARGM---TAERALTEMRDPIRQAAMRVRLGQADGT 109 IDP DL A L + R+ RG+ AER +T R A+M + G + Sbjct: 493 VEIIDPQADKDLFAPLIADYQRLVGRRGVPPIAAERRVTGRRTVA--ASMLLATGYVEAA 550 Query: 110 VGGAVATTADTVRAALQIIGKAPGAGIVSSFFLMLSCGPGAPVRGGMIFADCGLVIQPDA 169 + G ++ AL II P VS + M S +G + F D + + P A Sbjct: 551 LVGGSGDWWQHMKYALPII---PRRDNVSRVYAMSSL---ILDKGTLFFCDTHVNVDPTA 604 Query: 170 RELAAIALSAADSCRRILAEEPRVALLSFSTAGSAEHPSLGRIREALALIRAAAPGLEVD 229 ++A AA++ RR P+ ALLS S+ G+++ P+ ++REALAL+R AP LEVD Sbjct: 605 EQIAECTQLAAEAVRRF-GLTPKAALLSHSSFGASDSPTARKMREALALLRTQAPDLEVD 663 Query: 230 GEMQFDAALDEAIRARKAPESPLTGRPNVFVFPDLADGNIGYKIAERLAGLTAIGPILQG 289 GEM DAAL + +R R +SPL G N+ V P L NIG + +GP+L G Sbjct: 664 GEMHADAALSQHLRDRMVADSPLKGSANLLVMPTLDAANIGLTLLSAATESLLVGPVLLG 723 Query: 290 LAKPANDLSRACSVKDIVNATAITAMQ 316 +AKP + L + + + IVN TA+ Q Sbjct: 724 MAKPLHVLIPSVTARGIVNLTALAVNQ 750 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: 440 Number of extensions: 15 Number of successful extensions: 1 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: 758 Length adjustment: 34 Effective length of query: 284 Effective length of database: 724 Effective search space: 205616 Effective search space used: 205616 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