Align The fructose inducible fructose/xylitol porter, FruI (characterized)
to candidate GFF782 PS417_03975 FruA
Query= TCDB::Q1LZ59 (655 letters) >FitnessBrowser__WCS417:GFF782 Length = 569 Score = 330 bits (847), Expect = 8e-95 Identities = 200/517 (38%), Positives = 291/517 (56%), Gaps = 51/517 (9%) Query: 141 DVINLFNATEEEKKEATPAAPVADSHDFLVAVTACTTGIAHTYMAEEALKKQAAEMGVGI 200 DV + EE + A++ +VA+TAC TG+AHT+MA EAL++ A +G + Sbjct: 88 DVDAVLRRGAEEAQVYVATQQAAENAPRIVAITACPTGVAHTFMAAEALQQTAKRLGYDL 147 Query: 201 KVETNGASGVGNKLTADDIKRAKGVIIAADKAVEMDRFNGKPLISRPVAEGIKKPEELIN 260 +VET G+ G L+ I A V++AAD V +RF GK + +K+ E +N Sbjct: 148 QVETQGSVGARTPLSPQAIAEADVVLLAADIEVATERFAGKKIYRCGTGIALKQSEATLN 207 Query: 261 IILDGKAEAYVADNSDLSSEASSSEKAGLGSAFYKHLMSGVSQMLPFVIGGGIMIALSFL 320 KA A A S S + EK G+ YKHL++GVS MLP V+ GG++IALSF+ Sbjct: 208 -----KALAEGAVESAASGAVAKKEKTGV----YKHLLTGVSFMLPMVVAGGLLIALSFM 258 Query: 321 IDQFMGVPKSSLSHLGNYHEIAAIFNQVGNAAFGFMIPVFAAYIAYSIAEKPGLVAGFVA 380 K +L AA VG+ AF M+P+ A YIAYSIA++P L G + Sbjct: 259 FGITAFEEKGTL---------AAALKTVGDQAFMLMVPLLAGYIAYSIADRPALAPGMIG 309 Query: 381 GSMATTGLAFNKVAFFEFGEKASQASLTGIPSGFLGALAGGFLAGGVILVLKKALAFVPR 440 G +ATT + +GF+G + GFLAG + ++ +A+ +P+ Sbjct: 310 GLLATT-----------------------LGAGFIGGIFAGFLAGYCVKLITRAVQ-LPQ 345 Query: 441 SLEGIKSILLYPLLGVLVTGFLMLF-VNIPMAAINTALYNFLGNLSGGSAVLLGLIVGGM 499 SL+ +K IL+ PLL L TG M++ V P+A + L FL + +AVLLG+++GGM Sbjct: 346 SLDALKPILIIPLLASLFTGLAMIYLVGPPVARMLVGLTEFLNTMGTTNAVLLGILLGGM 405 Query: 500 MAIDMGGPFNKAAYVFGTSTLTAAALAKGGSVVMASVMAGGMVPPLAVFVATLLFKNKFT 559 M +D+GGP NKAAY F L A + A +A+ MA GMVPP+ + +AT L + KF Sbjct: 406 MCVDLGGPINKAAYAFSVGMLAAHSGAP-----IAATMAAGMVPPIGMGIATFLARRKFA 460 Query: 560 QEEHDAGLTNIVMGLSFITEGAIPFGAGDPARAIPSFIVGSAVTGALVGLSGIKLMAPHG 619 Q E +AG I++G+ FI+EGAIPF A DP R IP+ I G A+ GAL G KL APHG Sbjct: 461 QTEREAGKAAIILGMVFISEGAIPFAAKDPLRVIPASIAGGALAGALSMYFGCKLAAPHG 520 Query: 620 GIFVIAL---TSNPLLYLLYIAVGAVIAGILFGSLRK 653 G+ V+ + ++ LLYLL I G+++ G+++ +++ Sbjct: 521 GLAVLVIPNAMNHALLYLLAIVAGSLLTGLVYALIKR 557 Score = 37.0 bits (84), Expect = 2e-06 Identities = 26/104 (25%), Positives = 45/104 (43%), Gaps = 1/104 (0%) Query: 169 LVAVTACTTGIAHTYMAEEALKKQAAEMGVGIKVETNGASGVGNKLTADDIKRAKGVIIA 228 L VTAC G+ + + L A G VE +L+ I A+ V++ Sbjct: 3 LAIVTACPNGMVTSVLCARLLDAAAQRQGWSTSVEVVDVQRPERQLSQATIDDAEWVLLV 62 Query: 229 ADKAVEMDRFNGKPLISRPVAEGIKKPEELINIILDGKAEAYVA 272 + V+M RF GK + A+ + + ++ + +A+ YVA Sbjct: 63 SSTPVDMQRFVGKRVFQSTPAQALADVDAVLRRGAE-EAQVYVA 105 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: 838 Number of extensions: 49 Number of successful extensions: 7 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: 569 Length adjustment: 37 Effective length of query: 618 Effective length of database: 532 Effective search space: 328776 Effective search space used: 328776 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