Align The fructose inducible fructose/xylitol porter, FruI (characterized)
to candidate BWI76_RS19725 BWI76_RS19725 PTS fructose transporter subunit EIIBC
Query= TCDB::Q1LZ59 (655 letters) >FitnessBrowser__Koxy:BWI76_RS19725 Length = 558 Score = 342 bits (876), Expect = 3e-98 Identities = 209/516 (40%), Positives = 299/516 (57%), Gaps = 56/516 (10%) Query: 151 EEKKEATP-AAPVA-------DSHDFLVAVTACTTGIAHTYMAEEALKKQAAEMGVGIKV 202 E K ATP AAP A + +VAVTAC TG+AHT+MA EA++ +A + G +KV Sbjct: 80 EAKSHATPYAAPTAAALPTAANGPKRIVAVTACPTGVAHTFMAAEAIETEAKKRGWWVKV 139 Query: 203 ETNGASGVGNKLTADDIKRAKGVIIAADKAVEMDRFNGKPLISRPVAEGIKKP-EELINI 261 ET G+ G GN +T +++++A V++AAD V++ +F GKP+ +KK +EL Sbjct: 140 ETRGSVGAGNAITPEEVEQADLVVVAADIEVDLAKFAGKPMYRTTTGLALKKTAQELDKA 199 Query: 262 ILDGKAEAYVADNSDLSSEASSSEKAGLGSAFYKHLMSGVSQMLPFVIGGGIMIALSFLI 321 +++ K Y ++ E AG Y+HL++GVS MLP V+ GG+ IALSF Sbjct: 200 VVEAKP--YQPAGKSQAAAEGKKESAGA----YRHLLTGVSYMLPMVVAGGLCIALSFAF 253 Query: 322 DQFMGVPKSSLSHLGNYHEIAAIFNQVGNAAFGFMIPVFAAYIAYSIAEKPGLVAGFVAG 381 K +L+ AA+ G +AF M+PV A +IA+SIA++PGL G + G Sbjct: 254 GIKAFEVKDTLA--------AALMQIGGGSAFALMVPVLAGFIAFSIADRPGLTPGLIGG 305 Query: 382 SMATTGLAFNKVAFFEFGEKASQASLTGIPSGFLGALAGGFLAGGVILVLKKALAFVPRS 441 +A + TG SGF+G + GFLAG V + L +P+S Sbjct: 306 MLAVS---------------------TG--SGFIGGIIAGFLAGYVAKAISTKLK-LPQS 341 Query: 442 LEGIKSILLYPLLGVLVTGFLMLF-VNIPMAAINTALYNFLGNLSGGSAVLLGLIVGGMM 500 +E +K IL+ PL+ L+ G M++ + P+A I L ++L + +AVLLG I+GGMM Sbjct: 342 MEALKPILIIPLVSSLIVGLAMIYLIGKPVAGILEGLTHWLQTMGTANAVLLGAILGGMM 401 Query: 501 AIDMGGPFNKAAYVFGTSTLTAAALAKGGSVVMASVMAGGMVPPLAVFVATLLFKNKFTQ 560 DMGGP NKAAY FG L+ A MA++MA GMVPPLA+ +ATL+ + KF + Sbjct: 402 CTDMGGPVNKAAYAFGVGLLSTQTYAP-----MAAIMAAGMVPPLALGLATLIARKKFDK 456 Query: 561 EEHDAGLTNIVMGLSFITEGAIPFGAGDPARAIPSFIVGSAVTGALVGLSGIKLMAPHGG 620 + + G +V+GL FITEGAIPF A DP R +P IVG AVTGA+ G KLMAPHGG Sbjct: 457 AQQEGGKAALVLGLCFITEGAIPFAARDPMRVLPCCIVGGAVTGAMSMWVGAKLMAPHGG 516 Query: 621 IFVIALTS--NPLL-YLLYIAVGAVIAGILFGSLRK 653 +FV+ + P+L YL+ I VG ++AG+ + L++ Sbjct: 517 LFVLLIPGAITPVLGYLMAIVVGTLVAGLSYAVLKR 552 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: 910 Number of extensions: 59 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 655 Length of database: 558 Length adjustment: 37 Effective length of query: 618 Effective length of database: 521 Effective search space: 321978 Effective search space used: 321978 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