Align PTS system fructose-specific EIIB'BC component; EIIB'BC-Fru; EC 2.7.1.202 (characterized)
to candidate BWI76_RS19725 BWI76_RS19725 PTS fructose transporter subunit EIIBC
Query= SwissProt::P20966 (563 letters) >FitnessBrowser__Koxy:BWI76_RS19725 Length = 558 Score = 973 bits (2516), Expect = 0.0 Identities = 495/558 (88%), Positives = 527/558 (94%), Gaps = 1/558 (0%) Query: 1 MKTLLIIDANLGQARAYMAKTLLGAAARKAKLEIIDNPNDAEMAIVLGDSIPNDSALNGK 60 MKTLLIIDA LGQARAYMAKTLL AA+KA+LE+IDNPNDAE+AIVLG ++P DSALNGK Sbjct: 1 MKTLLIIDAGLGQARAYMAKTLLSTAAQKAQLELIDNPNDAELAIVLGTALPADSALNGK 60 Query: 61 NVWLGDISRAVAHPELFLSEAKGHAKPYTAPVAATAPVAASGPKRVVAVTACPTGVAHTF 120 V+LGDI+RAVAHPELFL EAK HA PY AP AA P AA+GPKR+VAVTACPTGVAHTF Sbjct: 61 KVYLGDINRAVAHPELFLGEAKSHATPYAAPTAAALPTAANGPKRIVAVTACPTGVAHTF 120 Query: 121 MAAEAIETEAKKRGWWVKVETRGSVGAGNAITPEEVAAADLVIVAADIEVDLAKFAGKPM 180 MAAEAIETEAKKRGWWVKVETRGSVGAGNAITPEEV ADLV+VAADIEVDLAKFAGKPM Sbjct: 121 MAAEAIETEAKKRGWWVKVETRGSVGAGNAITPEEVEQADLVVVAADIEVDLAKFAGKPM 180 Query: 181 YRTSTGLALKKTAQELDKAVAEATPYEPAGKAQTATTESKKESAGAYRHLLTGVSYMLPM 240 YRT+TGLALKKTAQELDKAV EA PY+PAGK+Q A E KKESAGAYRHLLTGVSYMLPM Sbjct: 181 YRTTTGLALKKTAQELDKAVVEAKPYQPAGKSQAAA-EGKKESAGAYRHLLTGVSYMLPM 239 Query: 241 VVAGGLCIALSFAFGIEAFKEPGTLAAALMQIGGGSAFALMVPVLAGYIAFSIADRPGLT 300 VVAGGLCIALSFAFGI+AF+ TLAAALMQIGGGSAFALMVPVLAG+IAFSIADRPGLT Sbjct: 240 VVAGGLCIALSFAFGIKAFEVKDTLAAALMQIGGGSAFALMVPVLAGFIAFSIADRPGLT 299 Query: 301 PGLIGGMLAVSTGSGFIGGIIAGFLAGYIAKLISTQLKLPQSMEALKPILIIPLISSLVV 360 PGLIGGMLAVSTGSGFIGGIIAGFLAGY+AK IST+LKLPQSMEALKPILIIPL+SSL+V Sbjct: 300 PGLIGGMLAVSTGSGFIGGIIAGFLAGYVAKAISTKLKLPQSMEALKPILIIPLVSSLIV 359 Query: 361 GLAMIYLIGKPVAGILEGLTHWLQTMGTANAVLLGAILGGMMCTDMGGPVNKAAYAFGVG 420 GLAMIYLIGKPVAGILEGLTHWLQTMGTANAVLLGAILGGMMCTDMGGPVNKAAYAFGVG Sbjct: 360 GLAMIYLIGKPVAGILEGLTHWLQTMGTANAVLLGAILGGMMCTDMGGPVNKAAYAFGVG 419 Query: 421 LLSTQTYGPMAAIMAAGMVPPLAMGLATMVARRKFDKAQQEGGKAALVLGLCFISEGAIP 480 LLSTQTY PMAAIMAAGMVPPLA+GLAT++AR+KFDKAQQEGGKAALVLGLCFI+EGAIP Sbjct: 420 LLSTQTYAPMAAIMAAGMVPPLALGLATLIARKKFDKAQQEGGKAALVLGLCFITEGAIP 479 Query: 481 FAARDPMRVLPCCIVGGALTGAISMAIGAKLMAPHGGLFVLLIPGAITPVLGYLVAIIAG 540 FAARDPMRVLPCCIVGGA+TGA+SM +GAKLMAPHGGLFVLLIPGAITPVLGYL+AI+ G Sbjct: 480 FAARDPMRVLPCCIVGGAVTGAMSMWVGAKLMAPHGGLFVLLIPGAITPVLGYLMAIVVG 539 Query: 541 TLVAGLAYAFLKRPEVDA 558 TLVAGL+YA LKRPEV A Sbjct: 540 TLVAGLSYAVLKRPEVQA 557 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: 1152 Number of extensions: 62 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: 563 Length of database: 558 Length adjustment: 36 Effective length of query: 527 Effective length of database: 522 Effective search space: 275094 Effective search space used: 275094 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