Align Phosphate acetyltransferase; EC 2.3.1.8; Phosphotransacetylase (uncharacterized)
to candidate SMc00169 SMc00169 malic enzyme
Query= curated2:P39197 (318 letters) >FitnessBrowser__Smeli:SMc00169 Length = 770 Score = 155 bits (392), Expect = 3e-42 Identities = 111/333 (33%), Positives = 161/333 (48%), Gaps = 25/333 (7%) Query: 1 MKPLDRIHEAAKALDRHIILPEGEDPRVAEAARRLLAAGLARVTLMGGPEIPGAGR---- 56 MKP+ A A +I EGED RV AA+ LL G A+ L+G P+I Sbjct: 443 MKPV--FAAAKNAAKNRVIFAEGEDERVLRAAQVLLEEGTAKPILIGRPQIIETRLRRYG 500 Query: 57 -----------IDPAGGPDLAELADHWHRMRAARGMTAERALTEMRDPIRQ-AAMRVRLG 104 ++P G P + D + + G+ E A T +R A+ V+ G Sbjct: 501 LRIRPDVDFEVVNPEGDPRYRDYVDDYFALVGRLGVIPEAARTIVRTNTTVIGALAVKRG 560 Query: 105 QADGTVGGAVATTADTVRAALQIIGKAPGAGIVSSFFLMLSCGPGAPVRGGMIFADCGLV 164 +AD + G + +R QIIGK G S+ L++S RG F D + Sbjct: 561 EADALICGVEGRYSRHLRDVSQIIGKRSGVLDFSALSLLIS------QRGATFFTDTYVS 614 Query: 165 IQPDARELAAIALSAADSCRRILAEEPRVALLSFSTAGSAEHPSLGRIREALALIRAAAP 224 P A E+A + AA+ RR PR AL+S S GS + S ++R AL L+R AP Sbjct: 615 FSPSAEEIAQTTVMAANEIRRF-GITPRAALVSHSNFGSRDSESAFKMRTALQLVRELAP 673 Query: 225 GLEVDGEMQFDAALDEAIRARKAPESPLTGRPNVFVFPDLADGNIGYKIAERLAGLTAIG 284 LEVDGEM D+A+ E +R R P+S L G N+ VFP+L NI + + + +G Sbjct: 674 DLEVDGEMHGDSAISEVLRQRVMPDSTLNGEANLLVFPNLDAANITLGVVKTMTDSLHVG 733 Query: 285 PILQGLAKPANDLSRACSVKDIVNATAITAMQT 317 PIL G A PA+ LS + + + +VN A+ +++ Sbjct: 734 PILLGSALPAHILSPSVTSRGVVNMAALAVVES 766 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: 471 Number of extensions: 22 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: 318 Length of database: 770 Length adjustment: 34 Effective length of query: 284 Effective length of database: 736 Effective search space: 209024 Effective search space used: 209024 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