Align The fructose inducible fructose/xylitol porter, FruI (characterized)
to candidate Pf1N1B4_1144 PTS system, fructose-specific IIB component (EC 2.7.1.69) / PTS system, fructose-specific IIC component (EC 2.7.1.69)
Query= TCDB::Q1LZ59 (655 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1144 Length = 579 Score = 338 bits (866), Expect = 5e-97 Identities = 205/503 (40%), Positives = 296/503 (58%), Gaps = 51/503 (10%) Query: 156 ATPAAPVADSHDFLVAVTACTTGIAHTYMAEEALKKQAAEMGVGIKVETNGASGVGNKLT 215 A PAA V S LVAVTAC TG+AHT+MA EAL++ A +G ++VET G+ G N L+ Sbjct: 110 AEPAAAVK-SAPRLVAVTACPTGVAHTFMAAEALQQAAKRLGYDLQVETQGSVGARNPLS 168 Query: 216 ADDIKRAKGVIIAADKAVEMDRFNGKPLISRPVAEGIKKPEELINIIL-DGKAEAYVADN 274 A+ I A V++AAD V +RF GK + +K+ E +N L +GK E+ Sbjct: 169 AEAIADADVVLLAADIEVATERFAGKKIYRCGTGIALKQAEATLNKALAEGKQESA---- 224 Query: 275 SDLSSEASSSEKAGLGSAFYKHLMSGVSQMLPFVIGGGIMIALSFLIDQFMGVPKSSLSH 334 S + + EK G+ YKHL++GVS MLP V+ GG+MIALSF+ + +L+ Sbjct: 225 STGAKGPAKQEKTGI----YKHLLTGVSFMLPMVVAGGLMIALSFVFGITAFKEEGTLA- 279 Query: 335 LGNYHEIAAIFNQVGNAAFGFMIPVFAAYIAYSIAEKPGLVAGFVAGSMATTGLAFNKVA 394 AA+ G+ AF M+P+ A YIAYSIA++PGL G + G +A+T Sbjct: 280 -------AALMQIGGDTAFKLMVPLLAGYIAYSIADRPGLAPGMIGGLLAST-------- 324 Query: 395 FFEFGEKASQASLTGIPSGFLGALAGGFLAGGVILVLKKALAFVPRSLEGIKSILLYPLL 454 + +GF+G + GF+AG + + A +P+SLE +K IL+ PLL Sbjct: 325 ---------------LGAGFIGGIIAGFIAGYAAQAINR-YARLPQSLEALKPILIIPLL 368 Query: 455 GVLVTGFLMLFV-NIPMAAINTALYNFLGNLSGGSAVLLGLIVGGMMAIDMGGPFNKAAY 513 L TG +M++V P+A + L +FL ++ +A+LLG+++GGMM +D+GGP NKAAY Sbjct: 369 ASLFTGLVMIYVVGKPVAGMLAGLTHFLDSMGTTNAILLGVLLGGMMCVDLGGPINKAAY 428 Query: 514 VFGTSTLTAAALAKGGSVVMASVMAGGMVPPLAVFVATLLFKNKFTQEEHDAGLTNIVMG 573 F L + + A MA+ MA GMVPP+ + +AT + + KF Q E +AG +V+G Sbjct: 429 AFSVGLLASQSYAP-----MAATMAAGMVPPIGLGIATFIARRKFAQTEREAGKAALVLG 483 Query: 574 LSFITEGAIPFGAGDPARAIPSFIVGSAVTGALVGLSGIKLMAPHGGIFVIAL---TSNP 630 L FI+EGAIPF A DP R IP+ I G A+TGAL G KLMAPHGG+FV+ + ++ Sbjct: 484 LCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKLMAPHGGLFVMLIPNAINHA 543 Query: 631 LLYLLYIAVGAVIAGILFGSLRK 653 LLYLL I G+++ + + L++ Sbjct: 544 LLYLLAIVAGSLLTAVTYALLKR 566 Score = 46.2 bits (108), Expect = 4e-09 Identities = 32/119 (26%), Positives = 60/119 (50%), Gaps = 3/119 (2%) Query: 169 LVAVTACTTGIAHTYMAEEALKKQAAEMGVGIKVETNGASGVGNKLTADDIKRAKGVIIA 228 L VTAC G+ + + L A G VE A+ +L+A I+ A+ V++ Sbjct: 3 LAIVTACPNGMVTSVLCARLLDAAAQRQGWSTSVEVVDAAHPERQLSAATIEAAEWVLLV 62 Query: 229 ADKAVEMDRFNGKPLISRPVAEGIKKPEELINIILDGKAEAYVADNSDLSSEASSSEKA 287 V+M RF GK + A+ ++ E ++ ++ +AE YVA ++++E +++ K+ Sbjct: 63 TSAPVDMSRFVGKRVFQSTPAQALQDVEAVLRRGVE-EAEVYVA--PEVAAEPAAAVKS 118 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: 843 Number of extensions: 42 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 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