Align Sugar phosphotransferase system IIC component, component of Fructose-specific Enzyme I-HPr-Enzyme IIABC complex, all encoded within a single operon with genes in the order: ptsC (IIC), ptsA (IIA), ptsH (HPr), ptsI (Enzyme I) and ptsB (IIB) (characterized)
to candidate GFF3289 Psest_3353 PTS system, fructose-specific, IIB component/PTS system, fructose subfamily, IIC component
Query= TCDB::Q5V5X5 (383 letters) >FitnessBrowser__psRCH2:GFF3289 Length = 579 Score = 296 bits (757), Expect = 1e-84 Identities = 160/357 (44%), Positives = 222/357 (62%), Gaps = 24/357 (6%) Query: 11 AESALRAHVTSVKEDLMTGVSFMIPFVTIGGIFLAVAYAIGDTQAVFENTGSAGWFLAQI 70 A + T V + ++TGVS+M+P V GG+ +A+++ G F+ G+ L +I Sbjct: 229 ASGEKKGEKTGVYKHMLTGVSYMLPMVVAGGLLIALSFVFGIE--AFKEEGTLAAALMKI 286 Query: 71 G-VAGLTIMVPILGGYIAYAIADRPGLAPGFLLAYILQQGNVVAEAATVIGISGGEAGAG 129 G +MVP+L GYIAY+IADRPGLAPG + G+ G GAG Sbjct: 287 GGETAFQLMVPLLAGYIAYSIADRPGLAPGM-----------------IGGLLAGTLGAG 329 Query: 130 YLGAIVAGLLAGYVARFFKN-LDVPEFIQPMMPVLLIPVATMAVLTPIMLFVLGVPVALA 188 ++G I+AG +AGY A+ + +P I+ + P+L+IP+ V +M++++G PVA Sbjct: 330 FIGGIIAGFVAGYAAKAVSRWIPLPASIESLKPILIIPLLASLVTGLVMIYIVGTPVAKL 389 Query: 189 NEGLTSFLQSMQGGQAIVVGLILGGMMAFDMGGPVNKVAYVFATGLITEEIYAPMAAVMI 248 GLT FL +M AI++GL+LG MM D+GGPVNK AY F+ GL+ + YAPMAA M Sbjct: 390 LAGLTEFLDTMGTSNAILLGLLLGTMMCVDLGGPVNKAAYAFSVGLLASQSYAPMAATMA 449 Query: 249 GGMIPPIGLALSNFIAPHKYAAEMYENGKSGVVLGLSFITEGAIPYAAADPLRVIPAIVA 308 GM+PPIG+ ++ IA K+A E GK+ +VLG FI+EGAIP+AA DPLRVIPA +A Sbjct: 450 AGMVPPIGMGIATLIARRKFAQTEREAGKAALVLGCCFISEGAIPFAAKDPLRVIPASIA 509 Query: 309 GSAVGGATSMALGVTMPAPHGGIFVVLLS---NQPLAFLGSILLGSLVTAVVATVIK 362 G A+ GA SMA G + APHGG+FV+L+ N L +L +IL GSLVT V+ VIK Sbjct: 510 GGALTGALSMAFGAKLLAPHGGLFVLLIPNAINHALLYLVAILAGSLVTGVIYAVIK 566 Lambda K H 0.322 0.139 0.399 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: 750 Number of extensions: 47 Number of successful extensions: 6 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: 383 Length of database: 579 Length adjustment: 33 Effective length of query: 350 Effective length of database: 546 Effective search space: 191100 Effective search space used: 191100 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: 51 (24.3 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