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 17939 b3899 PTS system, fructose-like enzyme IIBC component (VIMSS)
Query= TCDB::P71012 (635 letters) >FitnessBrowser__Keio:17939 Length = 483 Score = 237 bits (604), Expect = 1e-66 Identities = 147/472 (31%), Positives = 260/472 (55%), Gaps = 39/472 (8%) Query: 171 KILAVTACPTGIAHTFMAADALKEKAKELGVEIKVETNGSSGIKHKLTAQEIEDAPAIIV 230 +I+A+T CP GIAHT+M A+AL++KA+ LG IKVET GSSG++++L+++EI A +I+ Sbjct: 6 RIVAITNCPAGIAHTYMVAEALEQKARSLGHTIKVETQGSSGVENRLSSEEIAAADYVIL 65 Query: 231 AADKQV---EMERFKGKRVLQVPVTAGIRRPQELIEKAMNQDAPIYQGSGGGSAASNDDE 287 A + + + RF GK+V ++ ++ ++ ++ + + ++ ++ G + + Sbjct: 66 ATGRGLSGDDRARFAGKKVYEIAISQALKNIDQIFSE-LPTNSQLFAADSGVKLGKQEVQ 124 Query: 288 EAKGKSGSGIGNTFYKHLMSGVSNMLPFVVGGGILVAISFF---WGIHSADPND--PSYN 342 SGS + HLM+GVS LPFV+GGGILVA++ +G+ D + PS+ Sbjct: 125 -----SGSVMS-----HLMAGVSAALPFVIGGGILVALANMLVQFGLPYTDMSKGAPSFT 174 Query: 343 TFAAALNFIGGDNALKLIVAVLAGFIAMSIADRPGFAPGMVGGFMA-------TQANAGF 395 ++ ++G ++ ++ +IA SIAD+P FAP + ++A TQ+ AGF Sbjct: 175 WVVESIGYLG----FTFMIPIMGAYIASSIADKPAFAPAFLVCYLANDKALLGTQSGAGF 230 Query: 396 LGGLIAGFLAGYVVILLKKVFTFIPQSLDGLKPVLIYPLFGIFITGVLMQFVVNTPVAAF 455 LG ++ G GY V +KV + ++L L ++ P + + GVL +V+ ++ Sbjct: 231 LGAVVLGLAIGYFVFWFRKVR--LGKALQPLLGSMLIPFVTLLVFGVLTYYVIGPVMSDL 288 Query: 456 MNFLTNWLESLGTGNLVLMGIILGGMMAIDMGGPLNKAAFTFGIAMIDAGNYAPHAAIMA 515 M L ++L ++ ++G M+A DMGGP+NK A+ F ++++ Y +A + Sbjct: 289 MGGLLHFLNTIPPSMKFAAAFLVGAMLAFDMGGPINKTAWFFCFSLLEKHIYDWYAIVGV 348 Query: 516 GGMVPPLGIALATTIFRNKFTQRDREAGITCYFMGAAFVTEGAIPFAAADPLRVIPAAVV 575 ++PP+ LAT I FT++++EA + +GA TE AIP+A A PL +I A + Sbjct: 349 VALMPPVAAGLATFIAPKLFTRQEKEAASSAIVVGATVATEPAIPYALAAPLPMITANTL 408 Query: 576 GAAVAGGLTEFFRVTLPAPHGGVFVAFITNHPMLYLLSIVIGAVVMAIILGI 627 + G L F + AP G+F P++ L+S +G+ + + +G+ Sbjct: 409 AGGITGVLVIAFGIKRLAPGLGIF------DPLIGLMS-PVGSFYLVLAIGL 453 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: 718 Number of extensions: 39 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: 483 Length adjustment: 36 Effective length of query: 599 Effective length of database: 447 Effective search space: 267753 Effective search space used: 267753 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