Align Acetate kinase; EC 2.7.2.1; Acetokinase (uncharacterized)
to candidate WP_011798194.1 PNAP_RS22350 acetate kinase
Query= curated2:Q1J2C9 (395 letters) >NCBI__GCF_000015505.1:WP_011798194.1 Length = 356 Score = 231 bits (589), Expect = 2e-65 Identities = 149/345 (43%), Positives = 193/345 (55%), Gaps = 30/345 (8%) Query: 4 LVVNCGSSSLKFALLNPATGETPLTGLAERLGSDLAAVRVDRGEERGTVPLPQGSYSEAF 63 L +N GSSSLKF +G+ + V + EE T+ PQ + + Sbjct: 10 LALNAGSSSLKFGFF--------------MVGASGSRVLLSGAEE--TLAKPQAAVAR-- 51 Query: 64 GVLLAELDALGLRQEVRAVGHRVVHGGDRFNAPVRITPEVLEVIRTCIPLAPLHNPANLA 123 + ++A GL + AVGHR+VHGG + I V+ + APLH P LA Sbjct: 52 --IAQRMEAQGLPAPI-AVGHRIVHGGPQCRRHTLIDAAVMWQLEAATAFAPLHVPPALA 108 Query: 124 GIEAALAAFPELPQVAVFDTAFHQSMPPVAYRYAVPTVWYTCYGVRRYGFHGISHAYVAE 183 + AA A F + QVA DTAFH MP VA +P G+ RYGFHG+S E Sbjct: 109 LVRAAQACFSGIAQVACLDTAFHAGMPDVARTLPLPRE-LRALGIERYGFHGLS----GE 163 Query: 184 EAARLLARDLTDLSLVTAHLGNGCSVTAVQGGRSLDTSMGLTPLEGLVMGTRSGDVDPGL 243 R L DL +V AHLG+G SVTAV G S+DTSMGLTP G++M TR GD+DPG+ Sbjct: 164 SIVRQLGSDLPP-RVVIAHLGHGASVTAVAQGASVDTSMGLTPTGGVIMSTRCGDIDPGV 222 Query: 244 PDYLAREAGLTLAEITAALNRESGLLGLSGLTNDMRELEAAAA---GGNTNAQLALEIFV 300 Y+ RE G A++ A +++ SGLLG+SGL+ DMREL AAAA +A+LA+ +F Sbjct: 223 LAYVVREHGYDAAQLEALIDQRSGLLGISGLSGDMRELHAAAASTSASGADARLAIAMFC 282 Query: 301 YRLAKTIAGMATVLGRLDALVFTGGIGENSATVRAATLARLGLLG 345 + K IA MA VLG +D LVFTGGIGEN A+ RA L +LG Sbjct: 283 ASVRKQIAAMAVVLGGVDLLVFTGGIGENDASTRAFICEGLEVLG 327 Lambda K H 0.319 0.135 0.390 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: 363 Number of extensions: 22 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: 395 Length of database: 356 Length adjustment: 30 Effective length of query: 365 Effective length of database: 326 Effective search space: 118990 Effective search space used: 118990 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 (21.7 bits) S2: 50 (23.9 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