Align protein-Npi-phosphohistidine-sucrose phosphotransferase (EC 2.7.1.211) (characterized)
to candidate BWI76_RS22290 BWI76_RS22290 PTS cellobiose/arbutin/salicin transporter subunit IIBC
Query= BRENDA::P51184 (480 letters) >FitnessBrowser__Koxy:BWI76_RS22290 Length = 480 Score = 181 bits (458), Expect = 6e-50 Identities = 140/480 (29%), Positives = 237/480 (49%), Gaps = 37/480 (7%) Query: 2 NYKKSAENILQALGGEDNVEAMTHCATRLRLVLKDEGLVDEKALGDMDVVKGTFSTGGQY 61 NY A+ ++ A+GG DNV A+THC TRLR V+KD VD L + V G + Q Sbjct: 4 NYAALAQQVVAAIGGADNVAAVTHCMTRLRFVVKDNERVDSATLKGLKGVLGVVRSDNQC 63 Query: 62 QVIIGSGTVNKVFSELEKITGKEASSVSEVKTQGTKNMNPFQRFVKMLSDIFV----PII 117 QVIIG+ TV++ + E+ + + V+ QG + +R + D + P+I Sbjct: 64 QVIIGN-TVSQAYREVVALL---PGDLRPVEPQGKPPIT-LKRIGAGILDALIGTMSPLI 118 Query: 118 PAIVAGGLLMGINNILTAPGIFYDNQSLIEVQNQFSGLAEMINIFANAPFTLLPILIGFS 177 PAI+ G ++ + IL G + + + + + F LP+++ S Sbjct: 119 PAIIGGSMVKLLAMILEMTGALPKGAPTLTI----------LTVIGDGAFFFLPLMVAAS 168 Query: 178 AAKRFGGNAYLGAALGMILVHPELMSAYDYPKALEAGKEIPHWNLFGLEINQVGYQGQVL 237 AA +F N L A+ +LVHP + + + + H + + V Y V+ Sbjct: 169 AAVKFKTNMSLAIAIAGVLVHPSFI------ELMAKAAQGEHVEFAFIPVTAVKYTYTVI 222 Query: 238 PMLVATYILATIEKGLRKVIPTVLDNLLTPLLAILSTGFITFSFVGPLTRTLGYWLSDGL 297 P LV T+ L+ IE+ + ++ P V N L P+L +L ++ +GPL +G +S + Sbjct: 223 PALVMTWCLSYIERWVDRITPAVTKNFLKPMLIVLIAAPLSILLIGPLGIWIGSAISALV 282 Query: 298 TWLYEFGGAIGGLIFGLLYAPIVITGMHHSFIAIETQLIADSSSTGGSFIFPIATMSNIA 357 ++ + G + I G L+ +V+TGMH F Q IA++ G + P +N++ Sbjct: 283 YTIHSYLGWLSVAIMGALWPLLVMTGMHRVFTPTIIQTIAETGKEG--MVMPSEIGANLS 340 Query: 358 QGAAALAAFFIIKENKKLKGVASAAGVSALL-GITEPAMFGVNLKLRYPFI-----GAIV 411 G ++LA + K N +L+ A AA SA+L GI+EPA++GV ++L+ P I G I Sbjct: 341 LGGSSLAVAWKTK-NPELRQTALAAAASAILAGISEPALYGVAVRLKRPLIASLISGFIC 399 Query: 412 GSGIGSAYIAFFKVKAIALGTAGIPGFISISGQNNGWLHYGIAMIIAFIVAFGVTYALSY 471 G+ G A +A + A L T+ + F + W+ +G+ M +A +++F +T L + Sbjct: 400 GAVAGIAGLASHSMAAPGLFTS-VQFFDPANPMTIVWV-FGV-MALAVVLSFVLTLMLGF 456 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: 513 Number of extensions: 21 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: 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