Align Tagatose-6-phosphate kinase; EC 2.7.1.144; Phosphotagatokinase (uncharacterized)
to candidate WP_013404313.1 CALHY_RS12555 1-phosphofructokinase
Query= curated2:Q5HM37 (310 letters) >NCBI__GCF_000166355.1:WP_013404313.1 Length = 315 Score = 154 bits (390), Expect = 2e-42 Identities = 94/282 (33%), Positives = 156/282 (55%), Gaps = 7/282 (2%) Query: 1 MILTLTLNPSVDISYPLDQFNLDTVNRVSQTSKTAGGKGLNVTRVLSEFGEDVIASGFLG 60 MI T+TLNP++D++ +D+ VNR + AGGKG+NV++V+ G IA GFLG Sbjct: 1 MIYTVTLNPAIDMTVYIDELKKGQVNRSNHCLIDAGGKGINVSKVIKSLGGKSIALGFLG 60 Query: 61 GALGQYIEEQIETTRIKQAFFKIKGETRNCIAILHEGQQ--TEILEKGPTIELKESEEFK 118 + + ++ +I F + G TR I I+ Q+ T++ + G ++ K+ Sbjct: 61 NDNKDWFLKYLKNMQIDYDFIFVDGLTRTNIKIVETAQKVYTDLNQNGFEVKKKDINLLF 120 Query: 119 SHLLKLFKETDVAVMSGSLPKGLNTDYYADIVRLAKEQGILTILDSSGQSLEEVLISNVK 178 + ++ K D+ V+SGSLP G + D Y +++R+ K +G I D+ G++LE ++ K Sbjct: 121 DKIDRIAKTDDIFVLSGSLPPGTDEDVYVELIRMLKRKGAKVIYDADGKALESGVLE--K 178 Query: 179 PTVIKPNIDELSQLLNYKVTNDIKELKAAVSQPIFNDIEWIIVSLGSEGA-FAKHNQKFY 237 P VIKPNI E L + + ND+ + ++ + I N I+ +++S+GS+GA F N + + Sbjct: 179 PDVIKPNIHEFKCLFDVE-ENDLNSIVSSAKKLIENGIKKVLISMGSKGAVFVTENMELF 237 Query: 238 KVNIPNIKVVNPVGSGDSTVAGIASGLIHQQTDEELLKKANA 279 +KV + G+GDS VA I+ GL D + K A A Sbjct: 238 -AKAAEVKVKSTTGAGDSMVAAISYGLSQNMDDVSIFKLALA 278 Lambda K H 0.314 0.134 0.363 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: 234 Number of extensions: 10 Number of successful extensions: 4 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: 310 Length of database: 315 Length adjustment: 27 Effective length of query: 283 Effective length of database: 288 Effective search space: 81504 Effective search space used: 81504 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 48 (23.1 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