Align protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191) (characterized)
to candidate BWI76_RS19725 BWI76_RS19725 PTS fructose transporter subunit EIIBC
Query= BRENDA::O31645 (650 letters) >FitnessBrowser__Koxy:BWI76_RS19725 Length = 558 Score = 370 bits (951), Expect = e-107 Identities = 199/461 (43%), Positives = 301/461 (65%), Gaps = 16/461 (3%) Query: 2 KLLAITSCPNGIAHTYMAAENLQKAADRLGVSIKVETQGGIGVENKLTEEEIREADAIII 61 +++A+T+CP G+AHT+MAAE ++ A + G +KVET+G +G N +T EE+ +AD +++ Sbjct: 105 RIVAVTACPTGVAHTFMAAEAIETEAKKRGWWVKVETRGSVGAGNAITPEEVEQADLVVV 164 Query: 62 AADRSVNKDRFIGKKLLSVGVQDGIRKPEELIQKALNGDIPVYRSATKSESGNHQEKKQN 121 AAD V+ +F GK + ++K + + KA+ P Y+ A KS++ +K+ Sbjct: 165 AADIEVDLAKFAGKPMYRTTTGLALKKTAQELDKAVVEAKP-YQPAGKSQAAAEGKKESA 223 Query: 122 PIYRHLMNGVSFMVPFIVVGGLLIAVALTLGGEKTPKGLVIPDDSFWKTIEQIGSASFSF 181 YRHL+ GVS+M+P +V GGL IA++ G K + D ++ G ++F+ Sbjct: 224 GAYRHLLTGVSYMLPMVVAGGLCIALSFAFG----IKAFEVKDTLAAALMQIGGGSAFAL 279 Query: 182 MIPILAGYIAYSIADKPGLVPGMIGGYIAATGSFYDSASGAGFLGGIIAGFLAGYAALWI 241 M+P+LAG+IA+SIAD+PGL PG+IGG +A + +G+GF+GGIIAGFLAGY A I Sbjct: 280 MVPVLAGFIAFSIADRPGLTPGLIGGMLAVS-------TGSGFIGGIIAGFLAGYVAKAI 332 Query: 242 K-KLKVPKAIQPIMPIIIIPVFASLIVGLAFVFLIGAPVAQIFASLTVWLAGMKGSSSIL 300 KLK+P++++ + PI+IIP+ +SLIVGLA ++LIG PVA I LT WL M ++++L Sbjct: 333 STKLKLPQSMEALKPILIIPLVSSLIVGLAMIYLIGKPVAGILEGLTHWLQTMGTANAVL 392 Query: 301 LALILGAMISFDMGGPVNKVAFLFGSAMIGEGNYEIMGPIAVAICIPPIGLGIATFLGKR 360 L ILG M+ DMGGPVNK A+ FG ++ Y M I A +PP+ LG+AT + ++ Sbjct: 393 LGAILGGMMCTDMGGPVNKAAYAFGVGLLSTQTYAPMAAIMAAGMVPPLALGLATLIARK 452 Query: 361 KFEASQREMGKAAFTMGLFGITEGAIPFAAQDPLRVIP-SIMAGSMTGSVIAMIGNVGDR 419 KF+ +Q+E GKAA +GL ITEGAIPFAA+DP+RV+P I+ G++TG++ +G Sbjct: 453 KFDKAQQEGGKAALVLGLCFITEGAIPFAARDPMRVLPCCIVGGAVTGAMSMWVG-AKLM 511 Query: 420 VAHGGPIVAVL-GAVDHVLMFFIAVIAGSLVTALFVNVLKK 459 HGG V ++ GA+ VL + +A++ G+LV L VLK+ Sbjct: 512 APHGGLFVLLIPGAITPVLGYLMAIVVGTLVAGLSYAVLKR 552 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: 834 Number of extensions: 52 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: 650 Length of database: 558 Length adjustment: 37 Effective length of query: 613 Effective length of database: 521 Effective search space: 319373 Effective search space used: 319373 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