Align acetate kinase (EC 2.7.2.15) (characterized)
to candidate 16559 b2460 hypothetical protein (NCBI)
Query= metacyc::STM2468-MONOMER (229 letters) >FitnessBrowser__Keio:16559 Length = 233 Score = 409 bits (1050), Expect = e-119 Identities = 205/233 (87%), Positives = 216/233 (92%), Gaps = 4/233 (1%) Query: 1 MKKLITANDIRAAHARGEQAMSVVLRASIITPEAREVAELLGFTITECDESVPASTSAQA 60 MKKLITANDIR AHARGEQAMSVVLRASIITPEAREVA+LLGFTITECDES+P + S A Sbjct: 1 MKKLITANDIREAHARGEQAMSVVLRASIITPEAREVADLLGFTITECDESIPVTASVPA 60 Query: 61 C----KSESQRIREAIIAQLPEGQFTESLVAQLMEKVLKEKQSLELGTMQPSFTSVTGKG 116 K+ESQRIRE IIAQLPEGQFTESLVAQLMEKV+KEKQSLE G MQPSF SVTGKG Sbjct: 61 SVPADKTESQRIRETIIAQLPEGQFTESLVAQLMEKVMKEKQSLEQGAMQPSFKSVTGKG 120 Query: 117 GVKVIDGSSVKFGRFDGAEPHCVGLTDLVTEQDGSSMAAGFMQWDNAFFPWTLNYDEIDM 176 G+KVIDGSSVKFGRFDGAEPHCVGLTDLVT DGSSMAAGFMQW+NAFFPWTLNYDEIDM Sbjct: 121 GIKVIDGSSVKFGRFDGAEPHCVGLTDLVTGDDGSSMAAGFMQWENAFFPWTLNYDEIDM 180 Query: 177 VLEGELHVRHEGETMIAKAGDVMFIPKGSSIEFGTPTSVRFLYVAWPANWQSV 229 VLEGELHVRHEG+TMIAKAGDVMFIPKGSSIEFGT +SV+FLYVAWPANWQS+ Sbjct: 181 VLEGELHVRHEGQTMIAKAGDVMFIPKGSSIEFGTTSSVKFLYVAWPANWQSL 233 Lambda K H 0.317 0.131 0.379 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: 304 Number of extensions: 8 Number of successful extensions: 2 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: 229 Length of database: 233 Length adjustment: 23 Effective length of query: 206 Effective length of database: 210 Effective search space: 43260 Effective search space used: 43260 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: 46 (22.3 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