Align Phosphotransferase system transporter fructose-specific IIBC component, FruA, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized)
to candidate 14863 b0731 fused 2-O-a-mannosyl-D-glycerate specific PTS enzymes: IIA component/IIB component/IIC component (NCBI)
Query= TCDB::Q9HY57 (585 letters) >FitnessBrowser__Keio:14863 Length = 658 Score = 295 bits (754), Expect = 5e-84 Identities = 183/494 (37%), Positives = 275/494 (55%), Gaps = 16/494 (3%) Query: 90 RAFLQRAAALASVEVAGDEAGLVAPEAGA--APRIVAVTACPTGVAHTFMAAEALQLAAG 147 RA +Q A + A D+ G P A AP IV VTACP G+AHT+MAAE L+ A Sbjct: 152 RARIQSATTPDELLSALDDKGGTQPSASFSNAPTIVCVTACPAGIAHTYMAAEYLEKAGR 211 Query: 148 QLGFALQVETQGSVGARNPLDPADIAAADVVLLAADIDV-DTARFAGKKIYRCGTGVALK 206 +LG + VE QG+ G L + +A + AA++ + ++ RF G ++ Sbjct: 212 KLGVNVYVEKQGANGIEGRLTADQLNSATACIFAAEVAIKESERFNGIPALSVPVAEPIR 271 Query: 207 QARATLERALAEGQVESAGAASAVV--ARDEKRGVYKHLLTGVSFMLPMVVAGGLLIA-- 262 A A +++AL + + + K + + LL+G+SF +P++VAGG ++A Sbjct: 272 HAEALIQQALTLKRSDETRTVQQDTQPVKSVKTELKQALLSGISFAVPLIVAGGTVLAVA 331 Query: 263 --LSLAFGI-DAYKQPGSLAAVLRTVGDTAF-VLMVPMLAGYIAYSIADRPGLAPGMLGG 318 LS FG+ D + + S + R +G +LMVP+LA Y AYS+AD+P LAPG G Sbjct: 332 VLLSQIFGLQDLFNEENSWLWMYRKLGGGLLGILMVPVLAAYTAYSLADKPALAPGFAAG 391 Query: 319 LLAGTLGAGFIGGIVAGFIAGYAARAISHGLRLPASLEALKPILVIPLLASLVTGLLMLY 378 L A +G+GF+G +V G IAGY R + + LRL + + P+L +L G LML+ Sbjct: 392 LAANMIGSGFLGAVVGGLIAGYLMRWVKNHLRLSSKFNGFLTFYLYPVLGTLGAGSLMLF 451 Query: 379 VVGKPVAGMLAALTGFLDGMGTSNAILLGLLLGGMMCVDLGGPVNKAAYAFSVGLLSSHS 438 VVG+PVA + +LT +L+G+ SNA+LLG +LG M DLGGPVNKAAYAF +G +++ Sbjct: 452 VVGEPVAWINNSLTAWLNGLSGSNALLLGAILGFMCSFDLGGPVNKAAYAFCLGAMANGV 511 Query: 439 YAPMAAVMAAGMVPPIGMGLATLLARRKFAESERQAGKAASVLGLCFISEGAIPFAAKDP 498 Y P A + MV + +T+LA R F E E + GK+ +LGL I+EGAIP A +DP Sbjct: 512 YGPYAIFASVKMVSAFTVTASTMLAPRLFKEFEIETGKSTWLLGLAGITEGAIPMAIEDP 571 Query: 499 LRVIPASIAGGALTGALSMYFGCKLQAPHGGLFVMLV-----PNAINHALAYLLAIVAGS 553 LRVI + + G +TGA+ L P G+F + + + A+ + A + G+ Sbjct: 572 LRVIGSFVLGSMVTGAIVGAMNIGLSTPGAGIFSLFLLHDNGAGGVMAAIGWFGAALVGA 631 Query: 554 LLTGLLYAVLKRGA 567 ++ + + +R A Sbjct: 632 AISTAILLMWRRHA 645 Score = 46.2 bits (108), Expect = 4e-09 Identities = 31/98 (31%), Positives = 44/98 (44%), Gaps = 1/98 (1%) Query: 3 LAIVTACPGGQVTSVLAARLLRGAAERLGWETCVEANAGSRPEGELSAEQIAEAD-WVLL 61 + VTACP G + +AA L A +LG VE + EG L+A+Q+ A + Sbjct: 186 IVCVTACPAGIAHTYMAAEYLEKAGRKLGVNVYVEKQGANGIEGRLTADQLNSATACIFA 245 Query: 62 VGVEPLAAARFVGKPVYRARPAEALADPRAFLQRAAAL 99 V + RF G P AE + A +Q+A L Sbjct: 246 AEVAIKESERFNGIPALSVPVAEPIRHAEALIQQALTL 283 Lambda K H 0.321 0.137 0.392 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: 778 Number of extensions: 32 Number of successful extensions: 5 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: 585 Length of database: 658 Length adjustment: 37 Effective length of query: 548 Effective length of database: 621 Effective search space: 340308 Effective search space used: 340308 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 (21.9 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