Align The fructose inducible fructose/xylitol porter, FruI (characterized)
to candidate 16276 b2167 fused fructose-specific PTS enzymes: IIBcomponent/IIC components (NCBI)
Query= TCDB::Q1LZ59 (655 letters) >FitnessBrowser__Keio:16276 Length = 563 Score = 332 bits (852), Expect = 2e-95 Identities = 207/531 (38%), Positives = 300/531 (56%), Gaps = 51/531 (9%) Query: 131 DKLRQVTNPDDVINLFNATEEEKKEATPAA---PVADSHDF-LVAVTACTTGIAHTYMAE 186 D R V +P+ + L A K P A PVA S +VAVTAC TG+AHT+MA Sbjct: 66 DISRAVAHPE--LFLSEAKGHAKPYTAPVAATAPVAASGPKRVVAVTACPTGVAHTFMAA 123 Query: 187 EALKKQAAEMGVGIKVETNGASGVGNKLTADDIKRAKGVIIAADKAVEMDRFNGKPLISR 246 EA++ +A + G +KVET G+ G GN +T +++ A VI+AAD V++ +F GKP+ Sbjct: 124 EAIETEAKKRGWWVKVETRGSVGAGNAITPEEVAAADLVIVAADIEVDLAKFAGKPMYRT 183 Query: 247 PVAEGIKKPEELINIILDGKAEAYVADNSDLSSEASSSEKAGLGSAFYKHLMSGVSQMLP 306 +KK + ++ + A + ++ S E AG Y+HL++GVS MLP Sbjct: 184 STGLALKKTAQELDKAVAEATPYEPAGKAQTATTESKKESAGA----YRHLLTGVSYMLP 239 Query: 307 FVIGGGIMIALSFLIDQFMGVPKSSLSHLGNYHEIAAIFNQVGNAAFGFMIPVFAAYIAY 366 V+ GG+ IALSF +L+ AA+ G +AF M+PV A YIA+ Sbjct: 240 MVVAGGLCIALSFAFGIEAFKEPGTLA--------AALMQIGGGSAFALMVPVLAGYIAF 291 Query: 367 SIAEKPGLVAGFVAGSMATTGLAFNKVAFFEFGEKASQASLTGIPSGFLGALAGGFLAGG 426 SIA++PGL G + G +A + TG SGF+G + GFLAG Sbjct: 292 SIADRPGLTPGLIGGMLAVS---------------------TG--SGFIGGIIAGFLAGY 328 Query: 427 VILVLKKALAFVPRSLEGIKSILLYPLLGVLVTGFLMLF-VNIPMAAINTALYNFLGNLS 485 + ++ L +P+S+E +K IL+ PL+ LV G M++ + P+A I L ++L + Sbjct: 329 IAKLISTQLK-LPQSMEALKPILIIPLISSLVVGLAMIYLIGKPVAGILEGLTHWLQTMG 387 Query: 486 GGSAVLLGLIVGGMMAIDMGGPFNKAAYVFGTSTLTAAALAKGGSVVMASVMAGGMVPPL 545 +AVLLG I+GGMM DMGGP NKAAY FG L+ MA++MA GMVPPL Sbjct: 388 TANAVLLGAILGGMMCTDMGGPVNKAAYAFGVGLLSTQTYGP-----MAAIMAAGMVPPL 442 Query: 546 AVFVATLLFKNKFTQEEHDAGLTNIVMGLSFITEGAIPFGAGDPARAIPSFIVGSAVTGA 605 A+ +AT++ + KF + + + G +V+GL FI+EGAIPF A DP R +P IVG A+TGA Sbjct: 443 AMGLATMVARRKFDKAQQEGGKAALVLGLCFISEGAIPFAARDPMRVLPCCIVGGALTGA 502 Query: 606 LVGLSGIKLMAPHGGIFVIALTS--NPLL-YLLYIAVGAVIAGILFGSLRK 653 + G KLMAPHGG+FV+ + P+L YL+ I G ++AG+ + L++ Sbjct: 503 ISMAIGAKLMAPHGGLFVLLIPGAITPVLGYLVAIIAGTLVAGLAYAFLKR 553 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: 907 Number of extensions: 59 Number of successful extensions: 8 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: 563 Length adjustment: 37 Effective length of query: 618 Effective length of database: 526 Effective search space: 325068 Effective search space used: 325068 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