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_RS27570 BWI76_RS27570 phosphotransferase system, fructose-specific IIC component
Query= TCDB::P71012 (635 letters) >FitnessBrowser__Koxy:BWI76_RS27570 Length = 363 Score = 265 bits (678), Expect = 2e-75 Identities = 139/333 (41%), Positives = 204/333 (61%), Gaps = 5/333 (1%) Query: 303 KHLMSGVSNMLPFVVGGGILVAISFFWGIHSADPNDPSYNTFAAALNFIGGDNALKLIVA 362 KHL++G+S M+P +V GI +A+ G + T LN IGG + LIV Sbjct: 14 KHLLTGISWMIPLIVAAGICIALGQVLGGTNVGEKT---GTIPWMLNQIGGWG-MGLIVP 69 Query: 363 VLAGFIAMSIADRPGFAPGMVGGFMATQANAGFLGGLIAGFLAGYVVILLKKVFTFIPQS 422 ++ IA SIADRPGFAPG++ GF+ Q + GF+GG++ GFL GY V+ LK + +P+S Sbjct: 70 LICAAIAYSIADRPGFAPGLIVGFVCGQIHTGFIGGMLGGFLVGYTVLALKH-YIRLPKS 128 Query: 423 LDGLKPVLIYPLFGIFITGVLMQFVVNTPVAAFMNFLTNWLESLGTGNLVLMGIILGGMM 482 + GL P+++ P+ I+G+LM ++ P+A + L + LES+ G+ L+G ILG M Sbjct: 129 MQGLMPIMVLPVLSTIISGLLMMTLIGKPIAWLQDALIHLLESMQGGSRFLLGAILGAMA 188 Query: 483 AIDMGGPLNKAAFTFGIAMIDAGNYAPHAAIMAGGMVPPLGIALATTIFRNKFTQRDREA 542 D GGP+NK F ++ +G Y P A G ++PP GI L+ + R+K+T+ +REA Sbjct: 189 TFDFGGPVNKTMSLFADGLLVSGVYGPEAVKFVGSIIPPFGITLSFLLTRHKYTRAEREA 248 Query: 543 GITCYFMGAAFVTEGAIPFAAADPLRVIPAAVVGAAVAGGLTEFFRVTLPAPHGGVFVAF 602 + MG +TEG IP AA D LRV+ + VV +AVAGGL + V P PHGG+FV Sbjct: 249 LKAAFPMGICMITEGVIPIAARDLLRVVGSCVVASAVAGGLIMTWGVESPVPHGGMFVVP 308 Query: 603 ITNHPMLYLLSIVIGAVVMAIILGIVKKPVTEK 635 + HP+L+ LS+ IG V+ ++L + KKPVTE+ Sbjct: 309 LFTHPLLFCLSLAIGTVICGVMLSLWKKPVTER 341 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: 570 Number of extensions: 25 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: 635 Length of database: 363 Length adjustment: 34 Effective length of query: 601 Effective length of database: 329 Effective search space: 197729 Effective search space used: 197729 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: 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