Align β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized)
to candidate BWI76_RS19555 BWI76_RS19555 PTS beta-glucoside transporter subunit EIIBCA
Query= TCDB::P08722 (625 letters) >FitnessBrowser__Koxy:BWI76_RS19555 Length = 619 Score = 710 bits (1833), Expect = 0.0 Identities = 348/622 (55%), Positives = 457/622 (73%), Gaps = 8/622 (1%) Query: 4 LARKIVAGVGGADNIVSLMHCATRLRFKLKDESKAQAEVLKKTPGIIMVVESGGQFQVVI 63 LA+ I+ VGG +NIVSL+HCATRLRFKLKD KA AE LK PG+IMVVESGGQFQVVI Sbjct: 6 LAQDILTRVGGRENIVSLVHCATRLRFKLKDSKKADAEGLKANPGVIMVVESGGQFQVVI 65 Query: 64 GNHVADVFLAVNSVAGLDEKAQQAPENDDKGNLLNRFVYVISGIFTPLIGLMAATGILKG 123 GNHV DV+LAV S AGL + ++ +K +L+ + + ++SGIFTP IG++AA+GILKG Sbjct: 66 GNHVHDVWLAVRSEAGLTDDSEPVAVKGEKVSLIGQLIDIVSGIFTPFIGVLAASGILKG 125 Query: 124 MLALALTFQWTTEQSGTYLILFSASDALFWFFPIILGYTAGKRFGGNPFTAMVIGGALVH 183 +LALA+ W T Q TY I F+ASDALF+FFP+ LGYTAGK+FGGNPF MVIGGAL H Sbjct: 126 LLALAVVCGWLTTQQATYKIWFAASDALFFFFPLFLGYTAGKKFGGNPFITMVIGGALTH 185 Query: 184 PLILTAFENGQKADALGLDFLGIPVTLLNYSSSVIPIIFSAWLCSILERRLNAWLPSAIK 243 PL++ AF+ A FLGIPVT +NYSSSVIPII ++W+ +E+R NA LPS++K Sbjct: 186 PLMIQAFDASMAPGAATEYFLGIPVTFINYSSSVIPIILASWVSCWIEKRSNAILPSSMK 245 Query: 244 NFFTPLLCLMVITPVTFLLVGPLSTWISELIAAGYLWLYQAVPAFAGAVMGGFWQIFVMF 303 NFFTP +CL V+ P+TFL++GP++TW+S+L+A GY +YQ P AGA MG WQ+ V+F Sbjct: 246 NFFTPAICLAVVVPLTFLIIGPVATWLSQLLANGYQLIYQVAPWLAGAAMGALWQVCVIF 305 Query: 304 GLHWGLVPLCINNFTVLGYDTMIPLLMPAIMAQVGAALGVFLCERDAQKKVVAGSAALTS 363 GLHWGL+PL INN VLG+D+M+P+L+PA+M QVGAALG+FL RDA++KV+AGSA Sbjct: 306 GLHWGLIPLMINNLAVLGHDSMMPMLLPAVMGQVGAALGIFLRTRDARQKVLAGSAVSAG 365 Query: 364 LFGITEPAVYGVNLPRKYPFVIACISGALGATIIGYAQTKVYSFGLPSIFTFMQTIPSTG 423 +FG+TEPA+YG+NLP + PF+ C++GA+G ++G++ + VYSFG +IFT Q IP G Sbjct: 366 IFGVTEPAIYGLNLPLRRPFIFGCVAGAIGGAMVGFSDSHVYSFGFGNIFTLAQMIPPEG 425 Query: 424 IDFTVWASVIGGVIAIGCAFVGTVMLHFITAKRQPAQGAPQEKTPEVITPPEQGGICSPM 483 ID TVW G ++ A V T++ P A E+ V+ P + I +PM Sbjct: 426 IDATVWGGAAGMFASLIIACVLTLVAGL------PRSSA--EQAAVVVAPASENDILAPM 477 Query: 484 TGEIVPLIHVADTTFASGLLGKGIAILPSVGEVRSPVAGRIASLFATLHAIGIESDDGVE 543 TG ++ L V D+TFASGLLG+G+AI+PSVG+V +P +G +AS+F T HAIG+ SD G+E Sbjct: 478 TGSVLALDQVPDSTFASGLLGQGVAIIPSVGKVIAPFSGEVASIFQTKHAIGLLSDSGIE 537 Query: 544 ILIHVGIDTVKLDGKFFSAHVNVGDKVNTGDRLISFDIPAIREAGFDLTTPVLISNSDDF 603 +LIHVGIDTVKLDG F+AHV GDK+ GD L+ FD AI +AG+DL TP++ISNSDDF Sbjct: 538 LLIHVGIDTVKLDGAPFTAHVKEGDKIKAGDLLLEFDRQAILDAGYDLATPIIISNSDDF 597 Query: 604 TDVLPHGTAQISAGEPLLSIIR 625 + + + AG+PLLS+ R Sbjct: 598 RTLDMVSASAVDAGQPLLSVSR 619 Lambda K H 0.324 0.141 0.427 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: 1322 Number of extensions: 76 Number of successful extensions: 2 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: 625 Length of database: 619 Length adjustment: 37 Effective length of query: 588 Effective length of database: 582 Effective search space: 342216 Effective search space used: 342216 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: 40 (21.5 bits) S2: 54 (25.4 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