Align PTS system fructose-specific EIIB'BC component; EIIB'BC-Fru; EC 2.7.1.202 (characterized)
to candidate 16276 b2167 fused fructose-specific PTS enzymes: IIBcomponent/IIC components (NCBI)
Query= SwissProt::P20966 (563 letters) >FitnessBrowser__Keio:16276 Length = 563 Score = 1087 bits (2811), Expect = 0.0 Identities = 563/563 (100%), Positives = 563/563 (100%) Query: 1 MKTLLIIDANLGQARAYMAKTLLGAAARKAKLEIIDNPNDAEMAIVLGDSIPNDSALNGK 60 MKTLLIIDANLGQARAYMAKTLLGAAARKAKLEIIDNPNDAEMAIVLGDSIPNDSALNGK Sbjct: 1 MKTLLIIDANLGQARAYMAKTLLGAAARKAKLEIIDNPNDAEMAIVLGDSIPNDSALNGK 60 Query: 61 NVWLGDISRAVAHPELFLSEAKGHAKPYTAPVAATAPVAASGPKRVVAVTACPTGVAHTF 120 NVWLGDISRAVAHPELFLSEAKGHAKPYTAPVAATAPVAASGPKRVVAVTACPTGVAHTF Sbjct: 61 NVWLGDISRAVAHPELFLSEAKGHAKPYTAPVAATAPVAASGPKRVVAVTACPTGVAHTF 120 Query: 121 MAAEAIETEAKKRGWWVKVETRGSVGAGNAITPEEVAAADLVIVAADIEVDLAKFAGKPM 180 MAAEAIETEAKKRGWWVKVETRGSVGAGNAITPEEVAAADLVIVAADIEVDLAKFAGKPM Sbjct: 121 MAAEAIETEAKKRGWWVKVETRGSVGAGNAITPEEVAAADLVIVAADIEVDLAKFAGKPM 180 Query: 181 YRTSTGLALKKTAQELDKAVAEATPYEPAGKAQTATTESKKESAGAYRHLLTGVSYMLPM 240 YRTSTGLALKKTAQELDKAVAEATPYEPAGKAQTATTESKKESAGAYRHLLTGVSYMLPM Sbjct: 181 YRTSTGLALKKTAQELDKAVAEATPYEPAGKAQTATTESKKESAGAYRHLLTGVSYMLPM 240 Query: 241 VVAGGLCIALSFAFGIEAFKEPGTLAAALMQIGGGSAFALMVPVLAGYIAFSIADRPGLT 300 VVAGGLCIALSFAFGIEAFKEPGTLAAALMQIGGGSAFALMVPVLAGYIAFSIADRPGLT Sbjct: 241 VVAGGLCIALSFAFGIEAFKEPGTLAAALMQIGGGSAFALMVPVLAGYIAFSIADRPGLT 300 Query: 301 PGLIGGMLAVSTGSGFIGGIIAGFLAGYIAKLISTQLKLPQSMEALKPILIIPLISSLVV 360 PGLIGGMLAVSTGSGFIGGIIAGFLAGYIAKLISTQLKLPQSMEALKPILIIPLISSLVV Sbjct: 301 PGLIGGMLAVSTGSGFIGGIIAGFLAGYIAKLISTQLKLPQSMEALKPILIIPLISSLVV 360 Query: 361 GLAMIYLIGKPVAGILEGLTHWLQTMGTANAVLLGAILGGMMCTDMGGPVNKAAYAFGVG 420 GLAMIYLIGKPVAGILEGLTHWLQTMGTANAVLLGAILGGMMCTDMGGPVNKAAYAFGVG Sbjct: 361 GLAMIYLIGKPVAGILEGLTHWLQTMGTANAVLLGAILGGMMCTDMGGPVNKAAYAFGVG 420 Query: 421 LLSTQTYGPMAAIMAAGMVPPLAMGLATMVARRKFDKAQQEGGKAALVLGLCFISEGAIP 480 LLSTQTYGPMAAIMAAGMVPPLAMGLATMVARRKFDKAQQEGGKAALVLGLCFISEGAIP Sbjct: 421 LLSTQTYGPMAAIMAAGMVPPLAMGLATMVARRKFDKAQQEGGKAALVLGLCFISEGAIP 480 Query: 481 FAARDPMRVLPCCIVGGALTGAISMAIGAKLMAPHGGLFVLLIPGAITPVLGYLVAIIAG 540 FAARDPMRVLPCCIVGGALTGAISMAIGAKLMAPHGGLFVLLIPGAITPVLGYLVAIIAG Sbjct: 481 FAARDPMRVLPCCIVGGALTGAISMAIGAKLMAPHGGLFVLLIPGAITPVLGYLVAIIAG 540 Query: 541 TLVAGLAYAFLKRPEVDAVAKAA 563 TLVAGLAYAFLKRPEVDAVAKAA Sbjct: 541 TLVAGLAYAFLKRPEVDAVAKAA 563 Lambda K H 0.320 0.136 0.392 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: 1216 Number of extensions: 57 Number of successful extensions: 1 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: 563 Length of database: 563 Length adjustment: 36 Effective length of query: 527 Effective length of database: 527 Effective search space: 277729 Effective search space used: 277729 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 (21.8 bits) S2: 53 (25.0 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