Align Phosphotransferase system transporter fructose-specific IIBC component, FruA, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized)
to candidate GFF782 PS417_03975 FruA
Query= TCDB::Q9HY57 (585 letters) >FitnessBrowser__WCS417:GFF782 Length = 569 Score = 781 bits (2017), Expect = 0.0 Identities = 411/565 (72%), Positives = 469/565 (83%), Gaps = 8/565 (1%) Query: 1 MKLAIVTACPGGQVTSVLAARLLRGAAERLGWETCVEANAGSRPEGELSAEQIAEADWVL 60 MKLAIVTACP G VTSVL ARLL AA+R GW T VE RPE +LS I +A+WVL Sbjct: 1 MKLAIVTACPNGMVTSVLCARLLDAAAQRQGWSTSVEVVDVQRPERQLSQATIDDAEWVL 60 Query: 61 LVGVEPLAAARFVGKPVYRARPAEALADPRAFLQRAAALASVEVAGDEAGLVAPEAGAAP 120 LV P+ RFVGK V+++ PA+ALAD A L+R A A V VA +A A AP Sbjct: 61 LVSSTPVDMQRFVGKRVFQSTPAQALADVDAVLRRGAEEAQVYVATQQA------AENAP 114 Query: 121 RIVAVTACPTGVAHTFMAAEALQLAAGQLGFALQVETQGSVGARNPLDPADIAAADVVLL 180 RIVA+TACPTGVAHTFMAAEALQ A +LG+ LQVETQGSVGAR PL P IA ADVVLL Sbjct: 115 RIVAITACPTGVAHTFMAAEALQQTAKRLGYDLQVETQGSVGARTPLSPQAIAEADVVLL 174 Query: 181 AADIDVDTARFAGKKIYRCGTGVALKQARATLERALAEGQVESAGAASAVVARDEKRGVY 240 AADI+V T RFAGKKIYRCGTG+ALKQ+ ATL +ALAEG VESA AS VA+ EK GVY Sbjct: 175 AADIEVATERFAGKKIYRCGTGIALKQSEATLNKALAEGAVESA--ASGAVAKKEKTGVY 232 Query: 241 KHLLTGVSFMLPMVVAGGLLIALSLAFGIDAYKQPGSLAAVLRTVGDTAFVLMVPMLAGY 300 KHLLTGVSFMLPMVVAGGLLIALS FGI A+++ G+LAA L+TVGD AF+LMVP+LAGY Sbjct: 233 KHLLTGVSFMLPMVVAGGLLIALSFMFGITAFEEKGTLAAALKTVGDQAFMLMVPLLAGY 292 Query: 301 IAYSIADRPGLAPGMLGGLLAGTLGAGFIGGIVAGFIAGYAARAISHGLRLPASLEALKP 360 IAYSIADRP LAPGM+GGLLA TLGAGFIGGI AGF+AGY + I+ ++LP SL+ALKP Sbjct: 293 IAYSIADRPALAPGMIGGLLATTLGAGFIGGIFAGFLAGYCVKLITRAVQLPQSLDALKP 352 Query: 361 ILVIPLLASLVTGLLMLYVVGKPVAGMLAALTGFLDGMGTSNAILLGLLLGGMMCVDLGG 420 IL+IPLLASL TGL M+Y+VG PVA ML LT FL+ MGT+NA+LLG+LLGGMMCVDLGG Sbjct: 353 ILIIPLLASLFTGLAMIYLVGPPVARMLVGLTEFLNTMGTTNAVLLGILLGGMMCVDLGG 412 Query: 421 PVNKAAYAFSVGLLSSHSYAPMAAVMAAGMVPPIGMGLATLLARRKFAESERQAGKAASV 480 P+NKAAYAFSVG+L++HS AP+AA MAAGMVPPIGMG+AT LARRKFA++ER+AGKAA + Sbjct: 413 PINKAAYAFSVGMLAAHSGAPIAATMAAGMVPPIGMGIATFLARRKFAQTEREAGKAAII 472 Query: 481 LGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKLQAPHGGLFVMLVPNAIN 540 LG+ FISEGAIPFAAKDPLRVIPASIAGGAL GALSMYFGCKL APHGGL V+++PNA+N Sbjct: 473 LGMVFISEGAIPFAAKDPLRVIPASIAGGALAGALSMYFGCKLAAPHGGLAVLVIPNAMN 532 Query: 541 HALAYLLAIVAGSLLTGLLYAVLKR 565 HAL YLLAIVAGSLLTGL+YA++KR Sbjct: 533 HALLYLLAIVAGSLLTGLVYALIKR 557 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: 925 Number of extensions: 39 Number of successful extensions: 5 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: 569 Length adjustment: 36 Effective length of query: 549 Effective length of database: 533 Effective search space: 292617 Effective search space used: 292617 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