Align protein-Npi-phosphohistidine-sucrose phosphotransferase (EC 2.7.1.211) (characterized)
to candidate GFF4503 PS417_23050 trehalose permease IIC protein
Query= BRENDA::P51184 (480 letters) >FitnessBrowser__WCS417:GFF4503 Length = 480 Score = 458 bits (1179), Expect = e-133 Identities = 226/474 (47%), Positives = 334/474 (70%), Gaps = 9/474 (1%) Query: 2 NYKKSAENILQALGGEDNVEAMTHCATRLRLVLKDEGLVDEKALGDMDVVKGTFSTGGQY 61 +Y A IL+ LGG DN+E HC TRLRL LKD LV+ AL +D+VKG+F TGG + Sbjct: 4 DYSTIAREILENLGGSDNLEQAAHCVTRLRLALKDPSLVNSSALNQVDLVKGSFFTGGLF 63 Query: 62 QVIIGSGTVNKVFSELEKITGKEASSVSEVKTQGTKNMNPFQRFVKMLSDIFVPIIPAIV 121 QV+IG G V KV++ L + TG A+++++VK +G N QR V++ SD+F+PI+PA++ Sbjct: 64 QVVIGPGEVEKVYAALREQTGLAAATIADVKKKGADKTNAMQRLVRVFSDVFMPILPALI 123 Query: 122 AGGLLMGINNILTAPGIFYDNQSLIEVQNQFSGLAEMINIFANAPFTLLPILIGFSAAKR 181 GLLMG+NN++ A G+F + ++L+E GL +IN+ AN F LP L+G+SAAKR Sbjct: 124 IAGLLMGVNNLMGAQGMFIEGKTLLEAYPNLDGLWSLINLMANTSFVFLPALVGWSAAKR 183 Query: 182 FGGNAYLGAALGMILVHPELMSAYDYPKALEA--GKEIPHWNLFG-LEINQVGYQGQVLP 238 FGG+ LG LG++LVHP+L++A++Y KA+ G+ +P++++FG +I +VGYQGQ+LP Sbjct: 184 FGGSEILGIVLGLMLVHPDLLNAWNYGKAVAGLDGQSLPYFDIFGWFKIEKVGYQGQILP 243 Query: 239 MLVATYILATIEKGLRKVIPTVLDNLLTPLLAILSTGFITFSFVGPLTRTLGYWLSDGLT 298 +L+A Y+++ IEKGLR +P + L+ P+ I+ TG + + +GP+TR LG +++G+ Sbjct: 244 ILMAAYVMSVIEKGLRARVPNAIQLLVVPITTIVVTGVLALAIIGPVTRHLGILITEGVV 303 Query: 299 WLYEFGGAIGGLIFGLLYAPIVITGMHHSFIAIETQLIADSSSTGGSFIFPIATMSNIAQ 358 L++ +GG IFGLLYAP+VITGMHH F+A++ QLI S+ GG+FI+P+ MSN+AQ Sbjct: 304 TLFDLAPMVGGAIFGLLYAPLVITGMHHMFLAVDLQLI---STQGGTFIWPMIVMSNLAQ 360 Query: 359 GAAALAAFFIIKENKKLKGVASAAGVSALLGITEPAMFGVNLKLRYPFIGAIVGSGIGSA 418 G+AALA F+ + N + K +AS + +SA GITEPAMFGVNL+ ++PF A+VGS +GS Sbjct: 361 GSAALAVFYTTR-NARDKSMASTSAISAYFGITEPAMFGVNLRFKFPFYAALVGSALGSI 419 Query: 419 YIAFFKVKAIALGTAGIPGFISISGQNNGWLHYGIAMIIAFIVAFGVTYALSYR 472 ++A KV+A A+G G+PGFISI Q+ + I M+IA +V F +T LS + Sbjct: 420 FLALNKVQASAIGVGGLPGFISIVPQSIA--VFVIGMVIAMVVPFVLTCGLSMK 471 Lambda K H 0.322 0.140 0.406 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: 589 Number of extensions: 18 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: 480 Length of database: 480 Length adjustment: 34 Effective length of query: 446 Effective length of database: 446 Effective search space: 198916 Effective search space used: 198916 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