Align The fructose porter, FruA (fructose-1-P forming IIABC) (Delobbe et al. 1975) FruA is 39% identical to 4.A.2.1.1). fructose can be metabolized to Fru-1-P via this system as well as Fru-6-P by another PTS system (characterized)
to candidate BWI76_RS24865 BWI76_RS24865 PTS family enzyme IIB'BC, fructose-specific
Query= TCDB::P71012 (635 letters) >FitnessBrowser__Koxy:BWI76_RS24865 Length = 470 Score = 426 bits (1095), Expect = e-123 Identities = 215/456 (47%), Positives = 301/456 (66%), Gaps = 8/456 (1%) Query: 171 KILAVTACPTGIAHTFMAADALKEKAKELGVEIKVETNGSSGIKHKLTAQEIEDAPAIIV 230 KI+AVT CPTGIAHTFMA +ALK AK+L +EIKVETNG+SG+++ +T +++D +I+ Sbjct: 3 KIIAVTGCPTGIAHTFMAEEALKTAAKKLNIEIKVETNGASGVENAITPADLKDIYGVII 62 Query: 231 AADKQVEMERFKGKRVLQVPVTAGIRRPQELIEKAMNQDAPIYQGSGGGSAASNDDEEAK 290 AADK V ERF G V++VPV I P +LI K ++ A QG +++DD K Sbjct: 63 AADKDVNAERFNGLPVIEVPVKEAIHHPADLINKFISGQAARRQG-----ISASDDSTEK 117 Query: 291 GKSGSGIGNTFYKHLMSGVSNMLPFVVGGGILVAISFFWGIHSADPNDPSYNTFAAALNF 350 + S G YKHLMSGVSNMLPFVV GGIL+AISF WGI+SADPN P YN AA L Sbjct: 118 YERES-FGRQVYKHLMSGVSNMLPFVVAGGILIAISFLWGIYSADPNSPQYNVIAATLMK 176 Query: 351 IGGDNALKLIVAVLAGFIAMSIADRPGFAPGMVGGFMATQANAGFLGGLIAGFLAGYVVI 410 +G A ++V + +IA SI+ RPG G VGG +A AGFLGG+IAGF AGY ++ Sbjct: 177 VG-QQAFSIMVPIFTAYIAWSISGRPGMVAGFVGGLLANATGAGFLGGIIAGFAAGYFML 235 Query: 411 LLKKVFTFIPQSLDGLKPVLIYPLFGIFITGVLMQFVVNTPVAAFMNFLTNWLESLGTGN 470 L++ + +P+ +GLK + I PL G+ + GV+M ++ PVAA N + NWL SL N Sbjct: 236 LIRNMLNGLPRQYEGLKSIFIMPLVGVLVIGVMM-VLLGQPVAAINNAMMNWLSSLQEAN 294 Query: 471 LVLMGIILGGMMAIDMGGPLNKAAFTFGIAMIDAGNYAPHAAIMAGGMVPPLGIALATTI 530 +L+GI++G M + D GGP+NKAA+ G ++ GNY A + A + PPL IALATT Sbjct: 295 PILLGIVVGAMCSFDFGGPVNKAAYVTGTLLLGQGNYFFMAGVSAACITPPLVIALATTF 354 Query: 531 FRNKFTQRDREAGITCYFMGAAFVTEGAIPFAAADPLRVIPAAVVGAAVAGGLTEFFRVT 590 F F++ +R AG+ Y +G +TEGAIPFAA DPLRVIP ++ ++++ L+ ++ Sbjct: 355 FPKGFSEEERAAGMVNYILGCTHITEGAIPFAAKDPLRVIPMMMIASSISAVLSYSLQIQ 414 Query: 591 LPAPHGGVFVAFITNHPMLYLLSIVIGAVVMAIILG 626 +PAPHGG + + + P++++L I+ G+ A++LG Sbjct: 415 VPAPHGGFLILPLVSKPLMWVLCILAGSACGAVMLG 450 Lambda K H 0.320 0.137 0.390 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: 708 Number of extensions: 35 Number of successful extensions: 5 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: 635 Length of database: 470 Length adjustment: 35 Effective length of query: 600 Effective length of database: 435 Effective search space: 261000 Effective search space used: 261000 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: 52 (24.6 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