Align Phosphotransferase system transporter fructose-specific IIBC component, FruA, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized)
to candidate GFF3783 HP15_3725 PTS system, fructose-specific IIBC component
Query= TCDB::Q9HY57 (585 letters) >FitnessBrowser__Marino:GFF3783 Length = 587 Score = 634 bits (1636), Expect = 0.0 Identities = 349/578 (60%), Positives = 420/578 (72%), Gaps = 12/578 (2%) Query: 1 MKLAIVTACPGGQVTSVLAARLLRGAAERLGWETCVEANA-GSRPEGELSAEQIAEADWV 59 M L IVTACP G T LAAR L AA R GW + + + + S I +AD V Sbjct: 1 MNLIIVTACPQGVATRFLAARALERAANRRGWSVTTDTRGPDGKTDNKPSEAAIQQADLV 60 Query: 60 LLVGVEPLAAARFVGKPVYRARPAEALADPRAFLQRAAALASV---EVAGDEAGLVAPEA 116 + P+ + GK + + AL DP A L RA A A+ +A E+ + Sbjct: 61 IAAVGIPVNLDVYAGKRLLQIPVTAALPDPDAILTRAQAEATPWDPAMASQESIATSTAV 120 Query: 117 G---AAPRIVAVTACPTGVAHTFMAAEALQLAAGQLGFALQVETQGSVGARNPLDPADIA 173 G A RIVAVTACPTGVAHTFMAAEAL AA G ++VETQGSVGA++PL +IA Sbjct: 121 GSTSAGKRIVAVTACPTGVAHTFMAAEALTAAAQSAGHKIRVETQGSVGAQDPLTEEEIA 180 Query: 174 AADVVLLAADIDVDTARFAGKKIYRCGTGVALKQARATLERALAEGQVESAGA--ASAVV 231 AADVV+LA DI+VD RF+GK+++R TG ALK+ T+ AL + V +AG S Sbjct: 181 AADVVILACDIEVDPGRFSGKRVWRTSTGAALKKPADTIRDALEQAVVLNAGQKKTSGAS 240 Query: 232 ARDEKRGVYKHLLTGVSFMLPMVVAGGLLIALSLAFGIDAYKQPGSLAAVLRTVGD-TAF 290 EK+G YKHLLTGVSFMLPMVVAGGLLIALS FGI+A+++ G+LAA L +G TAF Sbjct: 241 GSGEKKGPYKHLLTGVSFMLPMVVAGGLLIALSFVFGIEAFQEEGTLAAALMQIGGGTAF 300 Query: 291 VLMVPMLAGYIAYSIADRPGLAPGMLGGLLAGTLGAGFIGGIVAGFIAGYAARAISHGLR 350 LM+P+LAGYIA+SIADRPGLAPGM+GG LAG LGAGF+GGIVAGF+AGY AR IS L Sbjct: 301 KLMIPLLAGYIAWSIADRPGLAPGMIGGFLAGELGAGFLGGIVAGFLAGYVARFISQKLP 360 Query: 351 LPASLEALKPILVIPLLASLVTGLLMLYVVGKPVAGMLAALTGFLDGMGTSNAILLGLLL 410 +P S+E+LKPIL+IPLLASLVTGL M+YV+G+P+A ++ ALTGFL+GMGT+NAILLG +L Sbjct: 361 MPESIESLKPILIIPLLASLVTGLGMIYVIGEPMAAIMGALTGFLEGMGTTNAILLGGIL 420 Query: 411 GGMMCVDLGGPVNKAAYAFSVGLLS--SHSYAPMAAVMAAGMVPPIGMGLATLLARRKFA 468 G MMC DLGGPVNKAAY F VGLLS S APMAA+MAAGMVP IGMG+A+ +ARRKFA Sbjct: 421 GAMMCFDLGGPVNKAAYTFGVGLLSEGSGGSAPMAAIMAAGMVPAIGMGVASFIARRKFA 480 Query: 469 ESERQAGKAASVLGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKLQAPHG 528 E+ERQAG+A+ VLGLCFISEGAIPF AKDPLRVIP + GGA+TGALSM F KL APHG Sbjct: 481 EAERQAGRASFVLGLCFISEGAIPFMAKDPLRVIPVCMIGGAITGALSMLFTVKLMAPHG 540 Query: 529 GLFVMLVPNAINHALAYLLAIVAGSLLTGLLYAVLKRG 566 GLFV+ +PNA++ L YL+AI GSL+ G YA+LK G Sbjct: 541 GLFVLAIPNAVSAVLPYLIAIAVGSLVIGFGYALLKTG 578 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: 923 Number of extensions: 44 Number of successful extensions: 9 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: 585 Length of database: 587 Length adjustment: 37 Effective length of query: 548 Effective length of database: 550 Effective search space: 301400 Effective search space used: 301400 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