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 PP_0795 PP_0795 fructose PTS permease - IIBC component
Query= TCDB::Q5V5X5 (383 letters) >FitnessBrowser__Putida:PP_0795 Length = 580 Score = 299 bits (765), Expect = 2e-85 Identities = 166/361 (45%), Positives = 225/361 (62%), Gaps = 24/361 (6%) Query: 7 DQNRAESALRAHVTSVKEDLMTGVSFMIPFVTIGGIFLAVAYAIGDTQAVFENTGSAGWF 66 D A + ++ T V + L+TGVSFM+P V GG+ +A+++ G ++ G+ Sbjct: 224 DAAAATTPTKSEKTGVYKHLLTGVSFMLPMVVAGGLLIALSFVFGIE--AYKEAGTLPAA 281 Query: 67 LAQIG-VAGLTIMVPILGGYIAYAIADRPGLAPGFLLAYILQQGNVVAEAATVIGISGGE 125 L QIG A +MVP+L GYIA++IADRPGLAPG + G+ Sbjct: 282 LMQIGGEAAFKLMVPLLAGYIAWSIADRPGLAPGM-----------------IGGLLAST 324 Query: 126 AGAGYLGAIVAGLLAGYVARFFKN-LDVPEFIQPMMPVLLIPVATMAVLTPIMLFVLGVP 184 GAG++G IVAG LAGY A+ +P ++ + P+L+IP+ +M++V+G P Sbjct: 325 LGAGFIGGIVAGFLAGYSAKAIARWARLPSSLEALKPILIIPLLASLFTGLVMIYVVGQP 384 Query: 185 VALANEGLTSFLQSMQGGQAIVVGLILGGMMAFDMGGPVNKVAYVFATGLITEEIYAPMA 244 VA EGLT FL SM AI++GL+LGGMM D+GGP+NK AY F+ GL+ YAPMA Sbjct: 385 VAAMLEGLTHFLDSMGTTNAILLGLLLGGMMCVDLGGPINKAAYAFSVGLLASSSYAPMA 444 Query: 245 AVMIGGMIPPIGLALSNFIAPHKYAAEMYENGKSGVVLGLSFITEGAIPYAAADPLRVIP 304 A M GM+PPIGL ++ F+A K+A E GK+ + LGL FI+EGAIP+AA DPLRVIP Sbjct: 445 ATMAAGMVPPIGLGIATFLARRKFAQSEREAGKAALALGLCFISEGAIPFAAKDPLRVIP 504 Query: 305 AIVAGSAVGGATSMALGVTMPAPHGGIFVVLLS---NQPLAFLGSILLGSLVTAVVATVI 361 A +AG A+ GA SM G + APHGG+FV+L+ N L +L +I+ GSLVTAVV VI Sbjct: 505 ASIAGGALTGALSMYFGCKLMAPHGGLFVLLIPNAINHALLYLLAIVAGSLVTAVVYAVI 564 Query: 362 K 362 K Sbjct: 565 K 565 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: 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: 383 Length of database: 580 Length adjustment: 33 Effective length of query: 350 Effective length of database: 547 Effective search space: 191450 Effective search space used: 191450 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