Align Phosphotransferase system transporter fructose-specific IIBC component, FruA, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized)
to candidate WP_086509379.1 BZY95_RS07790 PTS system fructose-like transporter subunit IIB
Query= TCDB::Q9HY57 (585 letters) >NCBI__GCF_002151265.1:WP_086509379.1 Length = 580 Score = 684 bits (1765), Expect = 0.0 Identities = 362/581 (62%), Positives = 445/581 (76%), Gaps = 5/581 (0%) Query: 1 MKLAIVTACPGGQVTSVLAARLLRGAAERLGWETCVEANAGSRPEGELSAEQIAEADWVL 60 M + IVTACP G T+ LAAR L AA RLGW+ +E ++ +SA+ IA A+ ++ Sbjct: 1 MNVIIVTACPSGMATTFLAARRLEQAARRLGWQASIEMHSQLEAVEPVSADAIAAAELIV 60 Query: 61 LVGVEPLAAARFVGKPVYRARPAEALADPRAFLQRAAALA-SVEVAGDEAGLVAPEAGAA 119 + + AA RF GK ++RA EAL DP AFLQRA A S A +A Sbjct: 61 VAADQIPAAERFAGKQLFRAAIGEALPDPEAFLQRAQREAESFTPPAQSAAANQHKAPGG 120 Query: 120 PRIVAVTACPTGVAHTFMAAEALQLAAGQLGFALQVETQGSVGARNPLDPADIAAADVVL 179 +IVAVTACPTGVAHTFMAAEAL A LG ++VETQGSVGA+N L +IAAADVV+ Sbjct: 121 SKIVAVTACPTGVAHTFMAAEALSEAGKSLGHEIRVETQGSVGAQNKLTDEEIAAADVVI 180 Query: 180 LAADIDVDTARFAGKKIYRCGTGVALKQARATLERALAEGQVESAGAA--SAVVARDEKR 237 LA DI+VD RFAGK+IYR TG ALK+ R T+E AL + +VE +G A S +++ Sbjct: 181 LACDIEVDPTRFAGKRIYRTSTGNALKKPRPTIEAALDQAEVEDSGTARRSDASRSIKEK 240 Query: 238 GVYKHLLTGVSFMLPMVVAGGLLIALSLAFGIDAYKQPGSLAAVLRTVGD-TAFVLMVPM 296 GVYKHLLTGVSFMLPMVVAGGLLIALS FGI+A+++ G+LAA L +G TAF LM+P+ Sbjct: 241 GVYKHLLTGVSFMLPMVVAGGLLIALSFVFGIEAFQEEGTLAAALMQIGGGTAFALMIPV 300 Query: 297 LAGYIAYSIADRPGLAPGMLGGLLAGTLGAGFIGGIVAGFIAGYAARAISHGLRLPASLE 356 LAGYIAYSIADRPG+APGM+GG+LA + AGFIGGI+AGF+AGY A A++ ++LPAS+E Sbjct: 301 LAGYIAYSIADRPGIAPGMIGGMLAANIEAGFIGGIIAGFLAGYVALAVTRHVKLPASVE 360 Query: 357 ALKPILVIPLLASLVTGLLMLYVVGKPVAGMLAALTGFLDGMGTSNAILLGLLLGGMMCV 416 +LKPIL+IPL++SLVTGL M+Y++G+PVA +LA LTGFL GM +NA+LLG+LLG MMC Sbjct: 361 SLKPILIIPLVSSLVTGLTMIYIIGEPVAAILAGLTGFLAGMDATNAVLLGILLGAMMCF 420 Query: 417 DLGGPVNKAAYAFSVGLLSSHSYAPMAAVMAAGMVPPIGMGLATLLARRKFAESERQAGK 476 DLGGPVNKAAY F VGLL+S +YAPMAA+MAAGMVP IGMG+A+ +AR KF+E ER+AGK Sbjct: 421 DLGGPVNKAAYTFGVGLLASQTYAPMAAIMAAGMVPAIGMGIASFVARHKFSEPEREAGK 480 Query: 477 AASVLGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKLQAPHGGLFVMLVP 536 A+ VLGLCFISEGAIPFAAKDPLRVIPA IAGGA+TGALSM G +L APHGG+FV+L+P Sbjct: 481 ASFVLGLCFISEGAIPFAAKDPLRVIPACIAGGAVTGALSMLVGAQLMAPHGGIFVLLIP 540 Query: 537 NAINHALAYLLAIVAGSLLTGLLYAVLKRGAEPGLALGTSS 577 NAI L YL AIV GSL+TGL YA +KRGA P +A+G ++ Sbjct: 541 NAITPVLLYLGAIVIGSLVTGLGYAAIKRGAAP-VAVGATA 580 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: 939 Number of extensions: 44 Number of successful extensions: 7 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: 580 Length adjustment: 36 Effective length of query: 549 Effective length of database: 544 Effective search space: 298656 Effective search space used: 298656 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 24 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