Align β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized)
to candidate BWI76_RS07315 BWI76_RS07315 PTS sugar transporter
Query= TCDB::P08722 (625 letters) >FitnessBrowser__Koxy:BWI76_RS07315 Length = 456 Score = 240 bits (613), Expect = 8e-68 Identities = 139/456 (30%), Positives = 241/456 (52%), Gaps = 12/456 (2%) Query: 3 ELARKIVAGVGGADNIVSLMHCATRLRFKLKDESKAQAEVLKKTPGIIMVVESGGQFQVV 62 +++R ++ +GG +NI S HCATRLR L D+S A + + K G+ + GQ Q++ Sbjct: 5 QISRSLLPLLGGKENIASAAHCATRLRLVLVDDSLADQQAIGKIEGVKGCFRNAGQMQII 64 Query: 63 IGNHVAD-VFLAVNSVAGLDE--KAQQAPENDDKGNLLNRFVYVISGIFTPLIGLMAATG 119 G V + V+ A AG+ E K++ A K N R ++S IF P+I + A+G Sbjct: 65 FGTGVVNKVYAAFIQAAGISESSKSEAADIAAKKLNPFQRIARLLSNIFVPIIPAIVASG 124 Query: 120 ILKGMLALALTFQWTTEQSGTYLILFSASDALFWFFPIILGYTAGKRFGGNPFTAMVIGG 179 +L G+L + T+ W + Y++L S A F PI++G+TA + FGGNP+ +GG Sbjct: 125 LLMGLLGMVKTYGWVDPSNALYIMLDMCSSAAFIILPILIGFTAAREFGGNPYLGATLGG 184 Query: 180 ALVHPLILTAFENGQKADALGLDFLGIPVTLLNYSSSVIPIIFSAWLCSILERRLNAWLP 239 L HP + A+ G A ++F G+ + ++ Y +V P++ + W SI+E++L +P Sbjct: 185 ILTHPALTNAW--GVAAGFHTMNFFGLEIAMIGYQGTVFPVLLAVWFMSIVEKQLRRAIP 242 Query: 240 SAIKNFFTPLLCLMVITPVTFLLVGPLSTWISELIAAGYLWLYQAVPAFAGAVMGGFWQI 299 A+ TP L +++ + L++GP + + I+ L AG + GG + + Sbjct: 243 DALDLILTPFLTVIISGFIALLIIGPAGRALGDGISFVLSTLISHAGWLAGLLFGGLYSV 302 Query: 300 FVMFGLH--WGLVPLCINNFTVLGYDTMIPLLMPAIMAQVGAALGVFLCERDAQKKVVAG 357 V+ G+H + + + +G + ++P+ A +AQ GA L V+ +D + K +A Sbjct: 303 IVITGIHHSFHAIEAGLLGNPSIGVNFLLPIWSMANVAQGGACLAVWFKTKDVKIKAIAL 362 Query: 358 SAALTSLFGITEPAVYGVNLPRKYPFVIACISGALGATIIGYAQTKVYSFGLPSIFTFMQ 417 +A +++ GITE A++G+NL PF+ A I GA G + + + GL +I Sbjct: 363 PSAFSAMLGITEAAIFGINLRFMKPFIAALIGGAAGGAWVVSVHVYMSAVGLTAIPGMAI 422 Query: 418 TIPSTGIDFTVWASVIGGVIAIGCAFVGTVMLHFIT 453 S+ +++ +IG VIA G AFV +++L + T Sbjct: 423 VQASSLLNY-----IIGMVIAFGVAFVVSLLLKYKT 453 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: 855 Number of extensions: 55 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: 625 Length of database: 456 Length adjustment: 35 Effective length of query: 590 Effective length of database: 421 Effective search space: 248390 Effective search space used: 248390 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: 52 (24.6 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