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 GFF782 PS417_03975 FruA
Query= TCDB::Q5V5X5 (383 letters) >FitnessBrowser__WCS417:GFF782 Length = 569 Score = 277 bits (709), Expect = 5e-79 Identities = 147/347 (42%), Positives = 216/347 (62%), Gaps = 23/347 (6%) Query: 20 TSVKEDLMTGVSFMIPFVTIGGIFLAVAYAIGDTQAVFENTGSAGWFLAQIGVAGLTIMV 79 T V + L+TGVSFM+P V GG+ +A+++ G T FE G+ L +G +MV Sbjct: 229 TGVYKHLLTGVSFMLPMVVAGGLLIALSFMFGIT--AFEEKGTLAAALKTVGDQAFMLMV 286 Query: 80 PILGGYIAYAIADRPGLAPGFLLAYILQQGNVVAEAATVIGISGGEAGAGYLGAIVAGLL 139 P+L GYIAY+IADRP LAPG + G ++A GAG++G I AG L Sbjct: 287 PLLAGYIAYSIADRPALAPGMI-------GGLLATTL----------GAGFIGGIFAGFL 329 Query: 140 AGYVARFF-KNLDVPEFIQPMMPVLLIPVATMAVLTPIMLFVLGVPVALANEGLTSFLQS 198 AGY + + + +P+ + + P+L+IP+ M++++G PVA GLT FL + Sbjct: 330 AGYCVKLITRAVQLPQSLDALKPILIIPLLASLFTGLAMIYLVGPPVARMLVGLTEFLNT 389 Query: 199 MQGGQAIVVGLILGGMMAFDMGGPVNKVAYVFATGLITEEIYAPMAAVMIGGMIPPIGLA 258 M A+++G++LGGMM D+GGP+NK AY F+ G++ AP+AA M GM+PPIG+ Sbjct: 390 MGTTNAVLLGILLGGMMCVDLGGPINKAAYAFSVGMLAAHSGAPIAATMAAGMVPPIGMG 449 Query: 259 LSNFIAPHKYAAEMYENGKSGVVLGLSFITEGAIPYAAADPLRVIPAIVAGSAVGGATSM 318 ++ F+A K+A E GK+ ++LG+ FI+EGAIP+AA DPLRVIPA +AG A+ GA SM Sbjct: 450 IATFLARRKFAQTEREAGKAAIILGMVFISEGAIPFAAKDPLRVIPASIAGGALAGALSM 509 Query: 319 ALGVTMPAPHGGIFVVLL---SNQPLAFLGSILLGSLVTAVVATVIK 362 G + APHGG+ V+++ N L +L +I+ GSL+T +V +IK Sbjct: 510 YFGCKLAAPHGGLAVLVIPNAMNHALLYLLAIVAGSLLTGLVYALIK 556 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: 751 Number of extensions: 48 Number of successful extensions: 4 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: 569 Length adjustment: 33 Effective length of query: 350 Effective length of database: 536 Effective search space: 187600 Effective search space used: 187600 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