Align phosphotransacetylase (EC 2.3.1.8) (characterized)
to candidate WP_066607556.1 V473_RS16165 NADP-dependent malic enzyme
Query= metacyc::MONOMER-13062 (328 letters) >NCBI__GCF_001046645.1:WP_066607556.1 Length = 753 Score = 145 bits (367), Expect = 2e-39 Identities = 98/306 (32%), Positives = 149/306 (48%), Gaps = 6/306 (1%) Query: 17 KLVFPEGEDERIISAASRLANDDLAIPVLLGNEAEIKKTADALNVSLDGIEIVDIENVPG 76 ++VF E E+E ++ AA + IPVL+G ++K + + E+ + N P Sbjct: 447 RVVFAEAEEEVVLRAAIQFRELGYGIPVLVGRGDVVEKLKELGVRDPESFELHNSVNSP- 505 Query: 77 EVRQQMVQAIVER--RKGKTTADQAAQWLKDPNYFGTTMVYMDDVDGMVSGAAHPTGDTV 134 + MV + R R+G D +D N FGT +V M D M++G P T+ Sbjct: 506 -LVPDMVDMLYARLQRRGYLRRDCERMVNRDRNIFGTLLVKMGVADAMITGMTRPYAQTL 564 Query: 135 RPALQIIKTKPGVNLISGSFVMQKGDQRYLFADCAININPNETQLAEIAVESGKTARLFD 194 R +++ G G VM D+ AD +N P ++LA+IA + AR Sbjct: 565 REVKRVMDPAAGRTPF-GIHVMVAKDKTVFLADTTVNERPTASELADIAEGTVAVARRMG 623 Query: 195 IDPRVALLSFSTNGSAKSPEVEKVHNATKLAQEMDPAMPIDGEMQFDAAFVPAVAKAKYS 254 +DPRVA LS+S G+ +E V A KL E +GEM D A PAV K Y Sbjct: 624 VDPRVAFLSYSNFGNPPGAFLENVRGAVKLLDERAVDFEYEGEMTADVALNPAVMK-NYP 682 Query: 255 DSKVAGHATVFVFPELQSGNIGYKIAQRMGGFEAIGPILQGLNKPVSDLSRGCNAEDVYK 314 S+++G A + V P LQS NI K+ + +GG IGP+L G+ K V + NA ++ Sbjct: 683 FSRLSGPANILVMPGLQSANISAKLLRELGGTSMIGPVLVGMEKSVQIATMSSNASELLT 742 Query: 315 VSIITA 320 ++++ A Sbjct: 743 LAVLAA 748 Lambda K H 0.315 0.133 0.369 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: 516 Number of extensions: 23 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: 328 Length of database: 753 Length adjustment: 34 Effective length of query: 294 Effective length of database: 719 Effective search space: 211386 Effective search space used: 211386 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 (21.6 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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