Align PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized)
to candidate BWI76_RS27885 BWI76_RS27885 PTS alpha-glucoside transporter subunit IICB
Query= CharProtDB::CH_001857 (699 letters) >FitnessBrowser__Koxy:BWI76_RS27885 Length = 540 Score = 258 bits (659), Expect = 5e-73 Identities = 182/538 (33%), Positives = 270/538 (50%), Gaps = 50/538 (9%) Query: 9 LQKIGRALMLPVAILPAAGILLAIGNAMQNKDMIQVLHFLSNDNVQLVAGVMESAGQIVF 68 +Q+ G A+ PV + P AGI++ I ++N + + + ++E G VF Sbjct: 5 IQRFGGAMFTPVLLFPFAGIVVGIAIMLRNPMFVGEALTAPDSLFAQIVHIIEEGGWTVF 64 Query: 69 DNLPLLFAVGVAIGLAN-GDGVAGIAAIIGYLVMNVSMSAVLLANGTI--PSDSVERAKF 125 N+PL+FAVG+ IGLA G A +A ++ +L N ++A+ + G SVE Sbjct: 65 RNMPLIFAVGLPIGLAKQAQGRACLAVLVSFLTWNYFINAMGMTWGHFFGVDFSVEPTA- 123 Query: 126 FTENHPAYVNMLGIPTLATGVFGGIIVGVLAALLFNRFYTIELPQYLGFFAGKRFVPIVT 185 M GI TL T + G I++ L L NR++ LP +LG F G FV IV Sbjct: 124 ----GSGLTMMAGIKTLDTSIIGAIVISGLVTALHNRYFDKPLPVFLGIFQGSSFVVIVA 179 Query: 186 SISALILGLIMLVIWPPIQHGLNAFSTGLVEANPTLAAFIFGVIERSLIPFGLHHIFYSP 245 ++ + + L+ WP +Q G+ + L A L +++ +ER LIP GLHH Y P Sbjct: 180 FLAMIPCAWLTLLGWPKVQMGIESLQAFLRSAG-ALGVWVYIFLERILIPTGLHHFVYGP 238 Query: 246 FWYEFFSYKSAAGEIIRGDQRIFMAQ----IKDGVQLTAGTFMTGKYPF----MMFGLPA 297 F + ++ G +++ AQ + F G + +FG Sbjct: 239 FIF--------GPAVVEGGIQVYWAQHLQAFSQSTEALKTLFPEGGFALHGNSKVFGSVG 290 Query: 298 AALAIYHEAKPQNKKLVAGIMGSAALTSFLTGITEPLEFSFLFVAPVLFAIHCLFAGLSF 357 ALA+Y A P+N+ VAG++ A LT+ L GITEPLEF+FLF++P+LFA+H + A Sbjct: 291 IALALYFTAAPENRVKVAGLLIPATLTAMLVGITEPLEFTFLFISPLLFAVHAVLAATMA 350 Query: 358 MVMQLLNVKIGMTFSGGLIDYFL----FGILPNRTAWWLV-IPVGLGLAVIYYFGFRFAI 412 VM + V +G F GGL+D FL + N + + I VG+ +Y+ FR I Sbjct: 351 TVMYICGV-VG-NFGGGLLDQFLPQNWIPMFHNHASMMFIQIGVGVCFTALYFVIFRTLI 408 Query: 413 RKFNLKTPGREDA-------AEETAAPGKTGEAGDLPYEI------LQAMGDQENIKHLD 459 + NLKTPGRE++ A+ AA GKT AG ++ LQA+G NI+ ++ Sbjct: 409 LRLNLKTPGREESEIKLYSKADYQAARGKTSAAGAADTKLGQAAGFLQALGGAGNIESIN 468 Query: 460 ACITRLRVTVNDQKKVDKDRL-KQLGASGVLEVGNNIQAIFGPR----SDGLKTQMQD 512 C TRLR+ + D K D + K LGA GV+ GN IQ I G D L+T M+D Sbjct: 469 NCATRLRIALVDMAKTQSDDVFKALGAHGVVRRGNGIQVIVGLHVPQVRDQLETLMKD 526 Lambda K H 0.323 0.141 0.412 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: 904 Number of extensions: 49 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 699 Length of database: 540 Length adjustment: 37 Effective length of query: 662 Effective length of database: 503 Effective search space: 332986 Effective search space used: 332986 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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