Align protein-Npi-phosphohistidine-D-fructose phosphotransferase (subunit 2/2) (EC 2.7.1.202) (characterized)
to candidate BWI76_RS24865 BWI76_RS24865 PTS family enzyme IIB'BC, fructose-specific
Query= BRENDA::Q8DWE7 (466 letters) >FitnessBrowser__Koxy:BWI76_RS24865 Length = 470 Score = 511 bits (1315), Expect = e-149 Identities = 257/450 (57%), Positives = 331/450 (73%), Gaps = 2/450 (0%) Query: 5 KLIAATGCPTGIAHTFMAQEALEQAAKEKGVSIKVETHGQVGVENELTPAEIAGAKAVII 64 K+IA TGCPTGIAHTFMA+EAL+ AAK+ + IKVET+G GVEN +TPA++ VII Sbjct: 3 KIIAVTGCPTGIAHTFMAEEALKTAAKKLNIEIKVETNGASGVENAITPADLKDIYGVII 62 Query: 65 AADKDVQAERFAGKRVIEVSVADGIKKADQLIADALAGKGQIKGGTKIESAELSSDTEGE 124 AADKDV AERF G VIEV V + I LI ++G+ + G S + + E E Sbjct: 63 AADKDVNAERFNGLPVIEVPVKEAIHHPADLINKFISGQAARRQGISA-SDDSTEKYERE 121 Query: 125 SFGRQVYRHLMNGVSHMLPFVVAGGVLVAISFLFGIYSFDPKSEQYNWFAALLKTDIGGV 184 SFGRQVY+HLM+GVS+MLPFVVAGG+L+AISFL+GIYS DP S QYN AA L +G Sbjct: 122 SFGRQVYKHLMSGVSNMLPFVVAGGILIAISFLWGIYSADPNSPQYNVIAATLMK-VGQQ 180 Query: 185 AMGVMTPILAAYIAESIAKRPGFVAGFVGGMMAVNGGSGFLGGIIAGFAAGYIVLGLMKL 244 A +M PI AYIA SI+ RPG VAGFVGG++A G+GFLGGIIAGFAAGY +L + + Sbjct: 181 AFSIMVPIFTAYIAWSISGRPGMVAGFVGGLLANATGAGFLGGIIAGFAAGYFMLLIRNM 240 Query: 245 FEKLPKSLDGLKAIFLYPVFGVFLTGMVMAVVNSPMAWVNKSLMAWLGAFENANPLVLGV 304 LP+ +GLK+IF+ P+ GV + G++M ++ P+A +N ++M WL + + ANP++LG+ Sbjct: 241 LNGLPRQYEGLKSIFIMPLVGVLVIGVMMVLLGQPVAAINNAMMNWLSSLQEANPILLGI 300 Query: 305 IVGCMCAFDMGGPVNKAAYVTGTALLAQGNTTFMAGVSAACIAPPLITFVATTAFRKYYD 364 +VG MC+FD GGPVNKAAYVTGT LL QGN FMAGVSAACI PPL+ +ATT F K + Sbjct: 301 VVGAMCSFDFGGPVNKAAYVTGTLLLGQGNYFFMAGVSAACITPPLVIALATTFFPKGFS 360 Query: 365 ENDRNAGLANLILGSTHITEGAIPFAAKDPLRMLPTFMLGSSIAAILTYMWKVKVPAPHG 424 E +R AG+ N ILG THITEGAIPFAAKDPLR++P M+ SSI+A+L+Y +++VPAPHG Sbjct: 361 EEERAAGMVNYILGCTHITEGAIPFAAKDPLRVIPMMMIASSISAVLSYSLQIQVPAPHG 420 Query: 425 GFLVLPVVTHAFLWVLAIAIGAIVAGIIMG 454 GFL+LP+V+ +WVL I G+ +++G Sbjct: 421 GFLILPLVSKPLMWVLCILAGSACGAVMLG 450 Lambda K H 0.322 0.138 0.406 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: 637 Number of extensions: 21 Number of successful extensions: 3 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: 466 Length of database: 470 Length adjustment: 33 Effective length of query: 433 Effective length of database: 437 Effective search space: 189221 Effective search space used: 189221 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 (21.9 bits) S2: 51 (24.3 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