Align The fructose inducible fructose/xylitol porter, FruI (characterized)
to candidate BWI76_RS27570 BWI76_RS27570 phosphotransferase system, fructose-specific IIC component
Query= TCDB::Q1LZ59 (655 letters) >FitnessBrowser__Koxy:BWI76_RS27570 Length = 363 Score = 210 bits (535), Expect = 8e-59 Identities = 123/372 (33%), Positives = 194/372 (52%), Gaps = 38/372 (10%) Query: 283 SSEKAGLGSAFYKHLMSGVSQMLPFVIGGGIMIALSFLIDQFMGVPKSSLSHLGNYHEIA 342 S K + KHL++G+S M+P ++ GI IAL ++ K+ I Sbjct: 2 SENKTPVSQEIKKHLLTGISWMIPLIVAAGICIALGQVLGGTNVGEKTGT--------IP 53 Query: 343 AIFNQVGNAAFGFMIPVFAAYIAYSIAEKPGLVAGFVAGSMATTGLAFNKVAFFEFGEKA 402 + NQ+G G ++P+ A IAYSIA++PG G + G F G+ Sbjct: 54 WMLNQIGGWGMGLIVPLICAAIAYSIADRPGFAPGLIVG--------------FVCGQ-- 97 Query: 403 SQASLTGIPSGFLGALAGGFLAGGVILVLKKALAFVPRSLEGIKSILLYPLLGVLVTGFL 462 I +GF+G + GGFL G +L LK + +P+S++G+ I++ P+L +++G L Sbjct: 98 -------IHTGFIGGMLGGFLVGYTVLALKHYIR-LPKSMQGLMPIMVLPVLSTIISGLL 149 Query: 463 ML-FVNIPMAAINTALYNFLGNLSGGSAVLLGLIVGGMMAIDMGGPFNKAAYVFGTSTLT 521 M+ + P+A + AL + L ++ GGS LLG I+G M D GGP NK +F L Sbjct: 150 MMTLIGKPIAWLQDALIHLLESMQGGSRFLLGAILGAMATFDFGGPVNKTMSLFADGLLV 209 Query: 522 AAALAKGGSVVMASVMAGGMVPPLAVFVATLLFKNKFTQEEHDAGLTNIVMGLSFITEGA 581 + A G ++PP + ++ LL ++K+T+ E +A MG+ ITEG Sbjct: 210 SGVYGPE-----AVKFVGSIIPPFGITLSFLLTRHKYTRAEREALKAAFPMGICMITEGV 264 Query: 582 IPFGAGDPARAIPSFIVGSAVTGALVGLSGIKLMAPHGGIFVIALTSNPLLYLLYIAVGA 641 IP A D R + S +V SAV G L+ G++ PHGG+FV+ L ++PLL+ L +A+G Sbjct: 265 IPIAARDLLRVVGSCVVASAVAGGLIMTWGVESPVPHGGMFVVPLFTHPLLFCLSLAIGT 324 Query: 642 VIAGILFGSLRK 653 VI G++ +K Sbjct: 325 VICGVMLSLWKK 336 Lambda K H 0.320 0.137 0.381 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: 578 Number of extensions: 36 Number of successful extensions: 6 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: 655 Length of database: 363 Length adjustment: 34 Effective length of query: 621 Effective length of database: 329 Effective search space: 204309 Effective search space used: 204309 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