Align Phosphotransferase system transporter fructose-specific IIBC component, FruA, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized)
to candidate WP_007154191.1 MDG893_RS12700 PTS fructose-like transporter subunit IIB
Query= TCDB::Q9HY57 (585 letters) >NCBI__GCF_000170835.1:WP_007154191.1 Length = 579 Score = 626 bits (1615), Expect = 0.0 Identities = 340/571 (59%), Positives = 410/571 (71%), Gaps = 6/571 (1%) Query: 1 MKLAIVTACPGGQVTSVLAARLLRGAAERLGWETCVEANAGSRPEGELSAEQIAEADWVL 60 MKL IVTACP G TS LAAR L A+++ GWE + + +P L + IA AD V+ Sbjct: 1 MKLIIVTACPQGVATSFLAARALERASQQKGWEARTDIRSPQQPLSSLPVDVIASADLVV 60 Query: 61 LVGVEPLAAARFVGKPVYRARPAEALADPRAFLQRAAALASVEVAGDEAGLVAPEAG--A 118 P + GK +Y+ AL D A L +A A EA P A A Sbjct: 61 AATGTPTDLNAYAGKRLYQIPVTAALPDAAAVLDQAEKQAEPYQL-TEASQPEPAASGNA 119 Query: 119 APRIVAVTACPTGVAHTFMAAEALQLAAGQLGFALQVETQGSVGARNPLDPADIAAADVV 178 RIVAVTACPTGVAHTFMAAEAL AA G ++VETQGSVGA++PL +I AADVV Sbjct: 120 GQRIVAVTACPTGVAHTFMAAEALTAAATAAGHQIRVETQGSVGAQDPLTAEEIEAADVV 179 Query: 179 LLAADIDVDTARFAGKKIYRCGTGVALKQARATLERALAEGQVESAGAASAVVARDEKRG 238 +LA DI+VD +RFAGK+++R TG ALK+ T++ A+ VE + EKRG Sbjct: 180 ILACDIEVDPSRFAGKRLWRTSTGSALKKPGPTIDDAMTNASVEEGQKKATSGGGGEKRG 239 Query: 239 VYKHLLTGVSFMLPMVVAGGLLIALSLAFGIDAYKQPGSLAAVLRTVGD-TAFVLMVPML 297 YKHLLTGVSFMLPMVVAGGLLIALS FGIDA+++ G+LAA L +G AF LM+P+L Sbjct: 240 PYKHLLTGVSFMLPMVVAGGLLIALSFVFGIDAFEEEGTLAAALMQIGGGAAFQLMIPLL 299 Query: 298 AGYIAYSIADRPGLAPGMLGGLLAGTLGAGFIGGIVAGFIAGYAARAISHGLRLPASLEA 357 AGYIA+SIADRPGLAPGM+GG LA TLGAGF+GGI+AGF+AGY AR IS L +P S+E+ Sbjct: 300 AGYIAWSIADRPGLAPGMIGGYLASTLGAGFLGGIIAGFLAGYVARFISQKLPMPESVES 359 Query: 358 LKPILVIPLLASLVTGLLMLYVVGKPVAGMLAALTGFLDGMGTSNAILLGLLLGGMMCVD 417 LKPIL+IPLLASLVTGL M+YV+G+P A ++ LT FL+ MGT+NAILLG +LG MMC D Sbjct: 360 LKPILIIPLLASLVTGLAMIYVIGEPAATLMDGLTNFLESMGTTNAILLGGILGAMMCFD 419 Query: 418 LGGPVNKAAYAFSVGLLS--SHSYAPMAAVMAAGMVPPIGMGLATLLARRKFAESERQAG 475 LGGPVNKAAY F VGLLS S APMAA+MA+GMVP IGMG+A+ +A KFAE+ERQAG Sbjct: 420 LGGPVNKAAYTFGVGLLSEGSGGSAPMAAIMASGMVPAIGMGVASFIAHTKFAEAERQAG 479 Query: 476 KAASVLGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKLQAPHGGLFVMLV 535 +A+ VLGLCFISEGAIPF AKDPLRVIP + GGA+TGALSM F KL APHGGLFV+ + Sbjct: 480 RASFVLGLCFISEGAIPFMAKDPLRVIPVCMVGGAITGALSMLFTVKLMAPHGGLFVLAI 539 Query: 536 PNAINHALAYLLAIVAGSLLTGLLYAVLKRG 566 PNA++ L Y+ AI GSL+ G YA++K G Sbjct: 540 PNAVSAVLPYVAAIAIGSLVIGFGYAMIKTG 570 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: 894 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: 579 Length adjustment: 36 Effective length of query: 549 Effective length of database: 543 Effective search space: 298107 Effective search space used: 298107 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