Align PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit DhaK; EC 2.7.1.121 (characterized)
to candidate H281DRAFT_05885 H281DRAFT_05885 dihydroxyacetone kinase DhaK subunit
Query= SwissProt::Q9CIV8 (332 letters) >FitnessBrowser__Burk376:H281DRAFT_05885 Length = 329 Score = 292 bits (747), Expect = 9e-84 Identities = 157/331 (47%), Positives = 216/331 (65%), Gaps = 6/331 (1%) Query: 4 EKIINQPQDVVSEMLDGLTYAYGDLIEKVPDFEIIQRKSPKSGKVALVSGGGSGHKPAHA 63 +K IN D ++E L G A+GDL+ + ++RK K GKVAL+SGGGSGH+P H+ Sbjct: 2 KKFINHVDDFLAESLAGFAAAHGDLVVLNREPVFVRRKDLKPGKVALISGGGSGHEPLHS 61 Query: 64 GFVGEGMLSAAVCGAIFTSPTPDQIYEAIKSADEGAGVLLIIKNYLGDVMNFEMAREMAE 123 GFVG GML AA G IFTSPTPDQ+ A K+ D GAGVL I+KNY GD+MNFEMA EM+E Sbjct: 62 GFVGHGMLDAACPGQIFTSPTPDQMMAAAKAVDTGAGVLFIVKNYSGDLMNFEMASEMSE 121 Query: 124 MEEIKVEQIIVDDDIAVENSLYTQGRRGVAGTVLVHKILGAAAHQEASLDEIKDLADKVV 183 + V +++DD+AVENS YT GRRGVAG V+V K++G+ A ASLDE K +++ Sbjct: 122 VPNAMV---LINDDVAVENSSYTTGRRGVAGAVIVEKLVGSLAESGASLDECKAFGNRIN 178 Query: 184 KNIKTIGLALSAATVPEVGKPGFVLDDNEIEYGVGIHSEPGYRREKMKTSYELATELVGK 243 K ++G+A S+ TVP G F + D+EIE GVGIH EPG RR K ++ +A EL+ Sbjct: 179 KRTASMGVAFSSCTVPAAGTLTFKIGDDEIEVGVGIHGEPGRRRAKFASADTIAAELLTA 238 Query: 244 LKEEFKFEAGQKYGILVNGMGATPLMEQFIFMNDVAKLLTEENIEILFKKVGNYMTSIDM 303 + ++ K AG +LVNG+G TPL E ++ N L + +++I +VG+ TS++M Sbjct: 239 IVDDLKPAAGAGVLVLVNGLGGTPLGELYLLFNSTRAWLEKRDLKIARVQVGSLTTSLEM 298 Query: 304 AGLSLTMIKLEDDQWLKNLNEDVKT--ISWG 332 AG S+T+ L D+Q K+ + V T + WG Sbjct: 299 AGASITLCML-DEQMTKHWDSAVHTPALRWG 328 Lambda K H 0.315 0.135 0.375 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: 320 Number of extensions: 15 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: 332 Length of database: 329 Length adjustment: 28 Effective length of query: 304 Effective length of database: 301 Effective search space: 91504 Effective search space used: 91504 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: 42 (22.0 bits) S2: 49 (23.5 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