Align protein-Npi-phosphohistidine-sucrose phosphotransferase (EC 2.7.1.211) (characterized)
to candidate BWI76_RS02965 BWI76_RS02965 PTS trehalose transporter subunit IIBC
Query= BRENDA::P51184 (480 letters) >FitnessBrowser__Koxy:BWI76_RS02965 Length = 472 Score = 293 bits (749), Expect = 1e-83 Identities = 164/479 (34%), Positives = 275/479 (57%), Gaps = 25/479 (5%) Query: 4 KKSAENILQALGGEDNVEAMTHCATRLRLVLKDEGLVDEKALGDMDVVKGTFSTGGQYQV 63 ++ + +++ +GG DN+ ++HC TRLR VL + + K + + +VKG F+ GQ+QV Sbjct: 6 QQDIDKLIELVGGRDNIATVSHCITRLRFVLNNPAIAKPKDIEQLRMVKGCFTNAGQFQV 65 Query: 64 IIGSGTVNKVFSELEKITGKEASSVSEVKTQGTKNMNPFQRFVKMLSDIFVPIIPAIVAG 123 +IG+ V + L TG+ ++ + K +NM ++ + ++IF P++PA+++G Sbjct: 66 VIGT-EVGDYYKALLATTGQASADKEQAKKAARQNMKWHEQLISHFAEIFFPLLPALISG 124 Query: 124 GLLMGINNILTAPGIFYDNQSLIEVQNQFSGLAEMINIFANAPFTLLPILIGFSAAKRFG 183 GL++G N++ + + Q+L ++ + + + + A F LP+ I +SA K+ G Sbjct: 125 GLILGFRNVIGDLPMS-NGQTLAQMHPSLKTIYDFLWLIGEAIFFYLPVGICWSAVKKMG 183 Query: 184 GNAYLGAALGMILVHPELMSAYDYPKALEAGKEIPH-WNLFGLEINQVGYQGQVLPMLVA 242 G LG LG+ LV P+LM+AY G+++P WN I +VGYQ QV+P L+A Sbjct: 184 GTPILGIVLGVTLVSPQLMNAY------LLGQQVPEVWNFGLFTIEKVGYQAQVIPALLA 237 Query: 243 TYILATIEKGLRKVIPTVLDNLLTPLLAILSTGFITFSFVGPLTRTLGYWLSDGLTW--- 299 L IE L++++P L ++ P+ +++ F+ +F+GP R +G DG+ W Sbjct: 238 GLALGFIETRLKRIVPDYLYLVIVPVCSLILAVFLAHAFIGPFGRMIG----DGVAWAVR 293 Query: 300 --LYEFGGAIGGLIFGLLYAPIVITGMHHSFIAIETQLIADSSSTGGSFIFPIATMSNIA 357 L IG +FG LYAP+VITG+H + +AI+ Q+I S GG+ ++P+ +SNIA Sbjct: 294 HLLTGSFAPIGAALFGFLYAPLVITGVHQTTLAIDMQMI---QSMGGTPVWPLIALSNIA 350 Query: 358 QGAAALAAFFIIKENKKLKGVASAAGVSALLGITEPAMFGVNLKLRYPFIGAIVGSGIGS 417 Q A+A+ I + + ++ A +SA LG+TEPAM+G+NLK R+P + A+VGSG+ Sbjct: 351 Q-ASAVVGIIIASRKQNEREISVPAAISAYLGVTEPAMYGINLKYRFPMLCAMVGSGLAG 409 Query: 418 AYIAFFKVKAIALGTAGIPGFISISGQNNGWLHYGIAMIIAFIVAFGVTYALSYRKKYR 476 V A +G G+PG +SI Q W Y +AM IA +V +T + Y++K+R Sbjct: 410 LLCGLNGVMANGIGVGGLPGILSI--QPTYWQVYALAMAIAVVVPIVLT-TVVYQRKFR 465 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: 572 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: 472 Length adjustment: 33 Effective length of query: 447 Effective length of database: 439 Effective search space: 196233 Effective search space used: 196233 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