Align The fructose inducible fructose/xylitol porter, FruI (characterized)
to candidate PP_0795 PP_0795 fructose PTS permease - IIBC component
Query= TCDB::Q1LZ59 (655 letters) >FitnessBrowser__Putida:PP_0795 Length = 580 Score = 333 bits (855), Expect = 1e-95 Identities = 206/514 (40%), Positives = 297/514 (57%), Gaps = 52/514 (10%) Query: 148 ATEEEKKEATPAAPVADSHDF--LVAVTACTTGIAHTYMAEEALKKQAAEMGVGIKVETN 205 A E A AP A S +VAVTAC TG+AHT+MA EAL++ A ++G + VET Sbjct: 97 AANAELLAAVTGAPAAASSAGARIVAVTACPTGVAHTFMAAEALQQAAQQLGYQLTVETQ 156 Query: 206 GASGVGNKLTADDIKRAKGVIIAADKAVEMDRFNGKPLISRPVAEGIKKPEELINIILDG 265 G+ G N L+A+ I A V++AAD V RF GK + +K+ ++ L Sbjct: 157 GSVGARNPLSAEAIAAADVVLLAADIEVPTARFAGKRIYRCGTGIALKQARATLDKAL-- 214 Query: 266 KAEAYVADNSDLSSEAS--SSEKAGLGSAFYKHLMSGVSQMLPFVIGGGIMIALSFLIDQ 323 A+A V + +D ++ + SEK G+ YKHL++GVS MLP V+ GG++IALSF+ Sbjct: 215 -AQATVENGADAAAATTPTKSEKTGV----YKHLLTGVSFMLPMVVAGGLLIALSFVFGI 269 Query: 324 FMGVPKSSLSHLGNYHEIAAIFNQVGNAAFGFMIPVFAAYIAYSIAEKPGLVAGFVAGSM 383 +L AA+ G AAF M+P+ A YIA+SIA++PGL G + G + Sbjct: 270 EAYKEAGTLP--------AALMQIGGEAAFKLMVPLLAGYIAWSIADRPGLAPGMIGGLL 321 Query: 384 ATTGLAFNKVAFFEFGEKASQASLTGIPSGFLGALAGGFLAGGVILVLKKALAFVPRSLE 443 A+T + +GF+G + GFLAG + + A +P SLE Sbjct: 322 AST-----------------------LGAGFIGGIVAGFLAGYSAKAIAR-WARLPSSLE 357 Query: 444 GIKSILLYPLLGVLVTGFLMLFV-NIPMAAINTALYNFLGNLSGGSAVLLGLIVGGMMAI 502 +K IL+ PLL L TG +M++V P+AA+ L +FL ++ +A+LLGL++GGMM + Sbjct: 358 ALKPILIIPLLASLFTGLVMIYVVGQPVAAMLEGLTHFLDSMGTTNAILLGLLLGGMMCV 417 Query: 503 DMGGPFNKAAYVFGTSTLTAAALAKGGSVVMASVMAGGMVPPLAVFVATLLFKNKFTQEE 562 D+GGP NKAAY F L +++ A MA+ MA GMVPP+ + +AT L + KF Q E Sbjct: 418 DLGGPINKAAYAFSVGLLASSSYAP-----MAATMAAGMVPPIGLGIATFLARRKFAQSE 472 Query: 563 HDAGLTNIVMGLSFITEGAIPFGAGDPARAIPSFIVGSAVTGALVGLSGIKLMAPHGGIF 622 +AG + +GL FI+EGAIPF A DP R IP+ I G A+TGAL G KLMAPHGG+F Sbjct: 473 REAGKAALALGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKLMAPHGGLF 532 Query: 623 VIAL---TSNPLLYLLYIAVGAVIAGILFGSLRK 653 V+ + ++ LLYLL I G+++ +++ ++K Sbjct: 533 VLLIPNAINHALLYLLAIVAGSLVTAVVYAVIKK 566 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: 810 Number of extensions: 31 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: 580 Length adjustment: 37 Effective length of query: 618 Effective length of database: 543 Effective search space: 335574 Effective search space used: 335574 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