Align The fructose inducible fructose/xylitol porter, FruI (characterized)
to candidate GFF3289 Psest_3353 PTS system, fructose-specific, IIB component/PTS system, fructose subfamily, IIC component
Query= TCDB::Q1LZ59 (655 letters) >FitnessBrowser__psRCH2:GFF3289 Length = 579 Score = 335 bits (859), Expect = 3e-96 Identities = 195/489 (39%), Positives = 288/489 (58%), Gaps = 45/489 (9%) Query: 169 LVAVTACTTGIAHTYMAEEALKKQAAEMGVGIKVETNGASGVGNKLTADDIKRAKGVIIA 228 LVAVTAC TG+AHT+MA EAL++ A G ++VET G+ G N L AD I A V++A Sbjct: 120 LVAVTACPTGVAHTFMAAEALQQAAIRKGYDLQVETRGSVGARNVLEADVIAAADVVLLA 179 Query: 229 ADKAVEMDRFNGKPLISRPVAEGIKKPEELINIILDGKAEAYVADNSDLSSEASSSEKAG 288 AD V++ RF GK + +K+PE ++ L+ E V + +++ AS EK G Sbjct: 180 ADIEVDVARFAGKRVFRCGTGVALKQPEATLDRALE---EGAVLSGNAVATSASG-EKKG 235 Query: 289 LGSAFYKHLMSGVSQMLPFVIGGGIMIALSFLIDQFMGVPKSSLSHLGNYHEIAAIFNQV 348 + YKH+++GVS MLP V+ GG++IALSF+ + +L+ AA+ Sbjct: 236 EKTGVYKHMLTGVSYMLPMVVAGGLLIALSFVFGIEAFKEEGTLA--------AALMKIG 287 Query: 349 GNAAFGFMIPVFAAYIAYSIAEKPGLVAGFVAGSMATTGLAFNKVAFFEFGEKASQASLT 408 G AF M+P+ A YIAYSIA++PGL G + G +A T Sbjct: 288 GETAFQLMVPLLAGYIAYSIADRPGLAPGMIGGLLAGT---------------------- 325 Query: 409 GIPSGFLGALAGGFLAGGVILVLKKALAFVPRSLEGIKSILLYPLLGVLVTGFLMLF-VN 467 + +GF+G + GF+AG + + + +P S+E +K IL+ PLL LVTG +M++ V Sbjct: 326 -LGAGFIGGIIAGFVAGYAAKAVSRWIP-LPASIESLKPILIIPLLASLVTGLVMIYIVG 383 Query: 468 IPMAAINTALYNFLGNLSGGSAVLLGLIVGGMMAIDMGGPFNKAAYVFGTSTLTAAALAK 527 P+A + L FL + +A+LLGL++G MM +D+GGP NKAAY F L + + A Sbjct: 384 TPVAKLLAGLTEFLDTMGTSNAILLGLLLGTMMCVDLGGPVNKAAYAFSVGLLASQSYAP 443 Query: 528 GGSVVMASVMAGGMVPPLAVFVATLLFKNKFTQEEHDAGLTNIVMGLSFITEGAIPFGAG 587 MA+ MA GMVPP+ + +ATL+ + KF Q E +AG +V+G FI+EGAIPF A Sbjct: 444 -----MAATMAAGMVPPIGMGIATLIARRKFAQTEREAGKAALVLGCCFISEGAIPFAAK 498 Query: 588 DPARAIPSFIVGSAVTGALVGLSGIKLMAPHGGIFVIAL---TSNPLLYLLYIAVGAVIA 644 DP R IP+ I G A+TGAL G KL+APHGG+FV+ + ++ LLYL+ I G+++ Sbjct: 499 DPLRVIPASIAGGALTGALSMAFGAKLLAPHGGLFVLLIPNAINHALLYLVAILAGSLVT 558 Query: 645 GILFGSLRK 653 G+++ +++ Sbjct: 559 GVIYAVIKQ 567 Score = 49.7 bits (117), Expect = 4e-10 Identities = 28/108 (25%), Positives = 48/108 (44%) Query: 169 LVAVTACTTGIAHTYMAEEALKKQAAEMGVGIKVETNGASGVGNKLTADDIKRAKGVIIA 228 L+ VTAC G+ + + L+ A +G VE + +G+ LT I A V++ Sbjct: 3 LLIVTACPNGMVTSVLTSRLLEAAAHRLGWSTAVEVHDPKAIGSPLTPAQIANADLVVVV 62 Query: 229 ADKAVEMDRFNGKPLISRPVAEGIKKPEELINIILDGKAEAYVADNSD 276 + + RF GK + +E + PE + D +E AD ++ Sbjct: 63 KTGPLSLQRFVGKRVAQSTPSEALLDPEAFLRSAADTASELQQADEAE 110 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: 831 Number of extensions: 41 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 655 Length of database: 579 Length adjustment: 37 Effective length of query: 618 Effective length of database: 542 Effective search space: 334956 Effective search space used: 334956 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