Align protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized)
to candidate BWI76_RS27885 BWI76_RS27885 PTS alpha-glucoside transporter subunit IICB
Query= BRENDA::P09323 (648 letters) >FitnessBrowser__Koxy:BWI76_RS27885 Length = 540 Score = 218 bits (554), Expect = 7e-61 Identities = 176/537 (32%), Positives = 259/537 (48%), Gaps = 86/537 (16%) Query: 3 ILGFFQRLGRALQLPIAVLPVA------ALLLR--------FGQPDLLN---VAFIAQAG 45 +L QR G A+ P+ + P A A++LR PD L V I + G Sbjct: 1 MLSQIQRFGGAMFTPVLLFPFAGIVVGIAIMLRNPMFVGEALTAPDSLFAQIVHIIEEGG 60 Query: 46 GAIFDNLALIFAIGVASSWSKDSAGAAALAGAVG-----YFVLTKAMV---------TIN 91 +F N+ LIFA+G+ +K + G A LA V YF+ M ++ Sbjct: 61 WTVFRNMPLIFAVGLPIGLAKQAQGRACLAVLVSFLTWNYFINAMGMTWGHFFGVDFSVE 120 Query: 92 PEINMGV--LAGI------------ITGLVGGAAYNRWSDIKLPDFLSFFGGKRFVPIAT 137 P G+ +AGI I+GLV A +NR+ D LP FL F G FV I Sbjct: 121 PTAGSGLTMMAGIKTLDTSIIGAIVISGLVT-ALHNRYFDKPLPVFLGIFQGSSFVVIVA 179 Query: 138 GFFCLVLAAIFGYVWPPVQHAIHAGGEWIVSAGALGSGIFGFINRLLIPTGLHQVLNTIA 197 + A + WP VQ I + ++ SAGALG ++ F+ R+LIPTGLH Sbjct: 180 FLAMIPCAWLTLLGWPKVQMGIESLQAFLRSAGALGVWVYIFLERILIPTGLHH------ 233 Query: 198 WFQIGEFTNAAGTVFHGDINRFYAG---------DGTAGMFMSGFFPI----MMFGLPGA 244 F G F V G I ++A + +F G F + +FG G Sbjct: 234 -FVYGPFIFGPAVV-EGGIQVYWAQHLQAFSQSTEALKTLFPEGGFALHGNSKVFGSVGI 291 Query: 245 ALAMYFAAPKERRPMVGGMLLSVAVTAFLTGVTEPLEFLFMFLAPLLYLLHALLTGISLF 304 ALA+YF A E R V G+L+ +TA L G+TEPLEF F+F++PLL+ +HA+L Sbjct: 292 ALALYFTAAPENRVKVAGLLIPATLTAMLVGITEPLEFTFLFISPLLFAVHAVLAATMAT 351 Query: 305 VATLLGIHAGFSFSAGAIDYALMYN-LPAASQNVWMLLV---MGVIFFAIYFVVFSLVIR 360 V + G+ +F G +D L N +P + M+ + +GV F A+YFV+F +I Sbjct: 352 VMYICGVVG--NFGGGLLDQFLPQNWIPMFHNHASMMFIQIGVGVCFTALYFVIFRTLIL 409 Query: 361 MFNLKTPGREDKEDEIVTEEANSNTEEGLTQL----------ATNYIAAVGGTDNLKAID 410 NLKTPGRE+ E ++ + +A+ G T A ++ A+GG N+++I+ Sbjct: 410 RLNLKTPGREESEIKLYS-KADYQAARGKTSAAGAADTKLGQAAGFLQALGGAGNIESIN 468 Query: 411 ACITRLRLTVADSARV-NDTMCKRLGASGVVKLNKQTIQVIVGAKAESIGDAMKKVV 466 C TRLR+ + D A+ +D + K LGA GVV+ IQVIVG + D ++ ++ Sbjct: 469 NCATRLRIALVDMAKTQSDDVFKALGAHGVVR-RGNGIQVIVGLHVPQVRDQLETLM 524 Lambda K H 0.324 0.139 0.408 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: 809 Number of extensions: 45 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: 648 Length of database: 540 Length adjustment: 37 Effective length of query: 611 Effective length of database: 503 Effective search space: 307333 Effective search space used: 307333 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 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