Align homoserine kinase (EC 2.7.1.39) (characterized)
to candidate WP_092482868.1 BM299_RS07580 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase
Query= reanno::Cola:Echvi_2001 (311 letters) >NCBI__GCF_900115975.1:WP_092482868.1 Length = 284 Score = 70.9 bits (172), Expect = 3e-17 Identities = 69/209 (33%), Positives = 97/209 (46%), Gaps = 16/209 (7%) Query: 76 DYKGGLEVELYKGLPLGSGMGSSAASSVAALEAANQLLGNPLDKKALLPFAMKAEGVACG 135 +Y GG E+ L K +PL +G+ +A + A L N+L L AE A G Sbjct: 76 EYAGGAEIRLVKRIPLAAGLAGGSADAAAVLRGLNKLWHLGLGP---------AELAALG 126 Query: 136 AEHADNVAPSLLGGFVLIRSYHPLDVTKLHVPKGLYCALVHPHLELNTADSRSVLRQQVP 195 AE +V L GG L+R VT L L LV P ++TA+ V R+ Sbjct: 127 AEIGSDVPFCLYGGTALVRGRGEA-VTPLRDLPPLGVVLVKPPFGVSTAE---VYRRYDA 182 Query: 196 LKDAITQSGNIAGLVAGLYQEDMGLISRSLQDVIAEPSRSVLIPGFDEIKSAIKEVGALG 255 L + Q G ++A + D ++ L + + EP L P IK + GALG Sbjct: 183 LVNP-PQPG-CRRMLAAAKRGDAADLAACLVNSL-EPVTMSLHPVIGAIKRELSAAGALG 239 Query: 256 VGISGSGPTTFILAPSREVAERASEICQE 284 V +SGSGPT F L SR AERA+ + ++ Sbjct: 240 VLMSGSGPTVFGLFKSRASAERAAGMIRQ 268 Lambda K H 0.317 0.136 0.383 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: 188 Number of extensions: 11 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: 311 Length of database: 284 Length adjustment: 26 Effective length of query: 285 Effective length of database: 258 Effective search space: 73530 Effective search space used: 73530 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: 48 (23.1 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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