Align protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191) (characterized)
to candidate 16276 b2167 fused fructose-specific PTS enzymes: IIBcomponent/IIC components (NCBI)
Query= BRENDA::O31645 (650 letters) >FitnessBrowser__Keio:16276 Length = 563 Score = 370 bits (950), Expect = e-107 Identities = 205/465 (44%), Positives = 302/465 (64%), Gaps = 23/465 (4%) Query: 2 KLLAITSCPNGIAHTYMAAENLQKAADRLGVSIKVETQGGIGVENKLTEEEIREADAIII 61 +++A+T+CP G+AHT+MAAE ++ A + G +KVET+G +G N +T EE+ AD +I+ Sbjct: 105 RVVAVTACPTGVAHTFMAAEAIETEAKKRGWWVKVETRGSVGAGNAITPEEVAAADLVIV 164 Query: 62 AADRSVNKDRFIGKKLLSVGVQDGIRKPEELIQKALNGDIPVYRSATKSESGNHQEKKQN 121 AAD V+ +F GK + ++K + + KA+ P Y A K+++ + KK++ Sbjct: 165 AADIEVDLAKFAGKPMYRTSTGLALKKTAQELDKAVAEATP-YEPAGKAQTATTESKKES 223 Query: 122 P-IYRHLMNGVSFMVPFIVVGGLLIAVALTLGGE--KTPKGLVIPDDSFWKTIEQIGSAS 178 YRHL+ GVS+M+P +V GGL IA++ G E K P L + QIG S Sbjct: 224 AGAYRHLLTGVSYMLPMVVAGGLCIALSFAFGIEAFKEPGTLAA-------ALMQIGGGS 276 Query: 179 -FSFMIPILAGYIAYSIADKPGLVPGMIGGYIAATGSFYDSASGAGFLGGIIAGFLAGYA 237 F+ M+P+LAGYIA+SIAD+PGL PG+IGG +A + +G+GF+GGIIAGFLAGY Sbjct: 277 AFALMVPVLAGYIAFSIADRPGLTPGLIGGMLAVS-------TGSGFIGGIIAGFLAGYI 329 Query: 238 ALWIK-KLKVPKAIQPIMPIIIIPVFASLIVGLAFVFLIGAPVAQIFASLTVWLAGMKGS 296 A I +LK+P++++ + PI+IIP+ +SL+VGLA ++LIG PVA I LT WL M + Sbjct: 330 AKLISTQLKLPQSMEALKPILIIPLISSLVVGLAMIYLIGKPVAGILEGLTHWLQTMGTA 389 Query: 297 SSILLALILGAMISFDMGGPVNKVAFLFGSAMIGEGNYEIMGPIAVAICIPPIGLGIATF 356 +++LL ILG M+ DMGGPVNK A+ FG ++ Y M I A +PP+ +G+AT Sbjct: 390 NAVLLGAILGGMMCTDMGGPVNKAAYAFGVGLLSTQTYGPMAAIMAAGMVPPLAMGLATM 449 Query: 357 LGKRKFEASQREMGKAAFTMGLFGITEGAIPFAAQDPLRVIP-SIMAGSMTGSVIAMIGN 415 + +RKF+ +Q+E GKAA +GL I+EGAIPFAA+DP+RV+P I+ G++TG++ IG Sbjct: 450 VARRKFDKAQQEGGKAALVLGLCFISEGAIPFAARDPMRVLPCCIVGGALTGAISMAIG- 508 Query: 416 VGDRVAHGGPIVAVL-GAVDHVLMFFIAVIAGSLVTALFVNVLKK 459 HGG V ++ GA+ VL + +A+IAG+LV L LK+ Sbjct: 509 AKLMAPHGGLFVLLIPGAITPVLGYLVAIIAGTLVAGLAYAFLKR 553 Lambda K H 0.319 0.137 0.386 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: 850 Number of extensions: 50 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: 650 Length of database: 563 Length adjustment: 37 Effective length of query: 613 Effective length of database: 526 Effective search space: 322438 Effective search space used: 322438 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 (21.7 bits) S2: 53 (25.0 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