Align Sugar amine kinase; EC 2.7.1.- (characterized, see rationale)
to candidate 3609413 Dshi_2797 PfkB domain protein (RefSeq)
Query= uniprot:Q92VI2 (311 letters) >FitnessBrowser__Dino:3609413 Length = 308 Score = 62.4 bits (150), Expect = 1e-14 Identities = 74/243 (30%), Positives = 104/243 (42%), Gaps = 21/243 (8%) Query: 39 GGCAGNNALAWDSLGVDYVIAANVGNDQFGTWLKEAFGERSRNWPVEAVG---TTLS-VG 94 GG N A+A LG D + + D FG L A + + + TTL+ V Sbjct: 29 GGAVFNTAVALGRLGADVGLVTGLSRDLFGEVLMTALAAADVDSDMAVLSDRPTTLAFVT 88 Query: 95 ITHPDGERTFF---TTRGHLPLFSFPEVHSMLDGNRLRGGYALLSGSFLTDALTLAYDAL 151 +T + F+ T L P+ + G GG +L + AY+AL Sbjct: 89 LTDGHAQYAFYDENTAGRMLAPADMPDPGPEV-GTLFFGGISLA-----VEPCAAAYEAL 142 Query: 152 FDWADAHEIAVA---LDTGWPLDGWTETNRLRTLGWLKRCHCALFNEVETTTLTGLSDPA 208 A A + + + G+ D T R+ + L ++ + L G D A Sbjct: 143 CLKAAAGRVVMLDPNIRPGFIKDETTFRARIDRM--LAVTDIVKVSDEDLAWLMGPGDLA 200 Query: 209 EAALSLKGEMPAEAIVVVKRGPHGALAIDRDGGTFSVPAPQVQVVDTIGAGDVFNAGFLA 268 E+A +L+ PA +V V RG G A G T V A V+VVDT+GAGD FNAGFLA Sbjct: 201 ESAAALRARGPA--VVCVTRGGAGVEAHTATGITH-VAAEAVEVVDTVGAGDTFNAGFLA 257 Query: 269 ALA 271 LA Sbjct: 258 GLA 260 Lambda K H 0.319 0.137 0.426 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: 248 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: 311 Length of database: 308 Length adjustment: 27 Effective length of query: 284 Effective length of database: 281 Effective search space: 79804 Effective search space used: 79804 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: 48 (23.1 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