Align protein-Npi-phosphohistidine-sucrose phosphotransferase (EC 2.7.1.211) (characterized)
to candidate 18265 b4240 fused trehalose(maltose)-specific PTS enzyme: IIB component/IIC component (NCBI)
Query= BRENDA::P51184 (480 letters) >FitnessBrowser__Keio:18265 Length = 473 Score = 278 bits (711), Expect = 3e-79 Identities = 158/471 (33%), Positives = 269/471 (57%), Gaps = 17/471 (3%) Query: 8 ENILQALGGEDNVEAMTHCATRLRLVLKDEGLVDEKALGDMDVVKGTFSTGGQYQVIIGS 67 + +++ +GG N+ ++HC TRLR VL K + + +VKG F+ GQ+QV+IG+ Sbjct: 11 DRLIELVGGRGNIATVSHCITRLRFVLNQPANARPKEIEQLPMVKGCFTNAGQFQVVIGT 70 Query: 68 GTVNKVFSELEKITGKEASSVSEVKTQGTKNMNPFQRFVKMLSDIFVPIIPAIVAGGLLM 127 V + L TG+ +VK NM ++ + + IF P++PA+++GGL++ Sbjct: 71 N-VGDYYQALIASTGQAQVDKEQVKKAARHNMKWHEQLISHFAVIFFPLLPALISGGLIL 129 Query: 128 GINNILTAPGIFYDNQSLIEVQNQFSGLAEMINIFANAPFTLLPILIGFSAAKRFGGNAY 187 G N++ + + Q+L ++ + + + + A F LP+ I +SA K+ GG Sbjct: 130 GFRNVIGDLPMS-NGQTLAQMYPSLQTIYDFLWLIGEAIFFYLPVGICWSAVKKMGGTPI 188 Query: 188 LGAALGMILVHPELMSAYDYPKALEAGKEIPH-WNLFGLEINQVGYQGQVLPMLVATYIL 246 LG LG+ LV P+LM+AY G+++P W+ I +VGYQ QV+P L+A L Sbjct: 189 LGIVLGVTLVSPQLMNAY------LLGQQLPEVWDFGMFSIAKVGYQAQVIPALLAGLAL 242 Query: 247 ATIEKGLRKVIPTVLDNLLTPLLAILSTGFITFSFVGPLTRTLGYWLSDGLTWLYEFGGA 306 IE L++++P L ++ P+ +++ F+ + +GP R +G ++ + L A Sbjct: 243 GVIETRLKRIVPDYLYLVVVPVCSLILAVFLAHALIGPFGRMIGDGVAFAVRHLMTGSFA 302 Query: 307 -IGGLIFGLLYAPIVITGMHHSFIAIETQLIADSSSTGGSFIFPIATMSNIAQGAAALAA 365 IG +FG LYAP+VITG+H + +AI+ Q+I S GG+ ++P+ +SNIAQG+A + Sbjct: 303 PIGAALFGFLYAPLVITGVHQTTLAIDLQMI---QSMGGTPVWPLIALSNIAQGSAVIGI 359 Query: 366 FFIIKENKKLKGVASAAGVSALLGITEPAMFGVNLKLRYPFIGAIVGSGIGSAYIAFFKV 425 +++ + + ++ A +SA LG+TEPAM+G+NLK R+P + A++GSG+ V Sbjct: 360 IISSRKHNE-REISVPAAISAWLGVTEPAMYGINLKYRFPMLCAMIGSGLAGLLCGLNGV 418 Query: 426 KAIALGTAGIPGFISISGQNNGWLHYGIAMIIAFIVAFGVTYALSYRKKYR 476 A +G G+PG +SI Q + W + +AM IA I+ +T + Y++KYR Sbjct: 419 MANGIGVGGLPGILSI--QPSYWQVFALAMAIAIIIPIVLT-SFIYQRKYR 466 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: 573 Number of extensions: 26 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: 480 Length of database: 473 Length adjustment: 33 Effective length of query: 447 Effective length of database: 440 Effective search space: 196680 Effective search space used: 196680 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