Align β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized)
to candidate BWI76_RS07290 BWI76_RS07290 PTS beta-glucoside transporter subunit EIIBCA
Query= TCDB::P08722 (625 letters) >FitnessBrowser__Koxy:BWI76_RS07290 Length = 626 Score = 375 bits (963), Expect = e-108 Identities = 221/627 (35%), Positives = 338/627 (53%), Gaps = 22/627 (3%) Query: 3 ELARKIVAGVGGADNIVSLMHCATRLRFKLKDESKAQAEVLKKTPGIIMVVESGGQFQVV 62 E A KI+ VGGA+NI L HCATRLR + D +K + PG+I VVE GGQFQ+V Sbjct: 5 ETADKILHAVGGAENIRMLTHCATRLRMEFNDRAKVNDAQIGTLPGVISVVEKGGQFQIV 64 Query: 63 IGNHVADVFLAVNSVAGLDEKAQQAPENDDKGNLLNRFVYVISGIFTPLIGLMAATGILK 122 IGN V V+ +N + +N ++ R + VIS FTP+I + G++K Sbjct: 65 IGNEVQQVYRRLNKALPEKKGPAGGDKNAKPAGIVARIISVISTTFTPVIPAITGAGMIK 124 Query: 123 GMLALALTFQWTTEQSGTYLILFSASDALFWFFPIILGYTAGKRFGGNPFTAMVIGGALV 182 +LA+ +E S TY +L +DA F+F P++L Y A +F NP AM + G L+ Sbjct: 125 ALLAILKLTGVISETSSTYQLLNIIADAAFFFLPVLLAYGASLKFECNPILAMTLAGVLL 184 Query: 183 HPLILTAFENGQKADALGLDFLGIPVTLLNYSSSVIPIIFSAWLCSILERRLNAWLPSAI 242 HP I G+ +DF+GI V L +Y+ SV+PII + WL S +ER PS I Sbjct: 185 HPGIGQMLAAGK-----AVDFVGINVLLSDYAGSVLPIILTVWLMSWVERFAEKVSPSII 239 Query: 243 KNFFTPLLCLMVITPVTFLLVGPLSTWISELIAAGYLWLYQAVPAFAGAVMGGFWQIFVM 302 K F P+L L++ P+ ++VGP +++L+AAG + + +MG ++ Sbjct: 240 KFFVKPMLILLITAPLALVVVGPAGILLNDLVAAGAGAIDRHASWLIPMLMGTLQPFLII 299 Query: 303 FGLHWGLVPLCINNFTVLGYDTMI-PLLMPAIMAQVGAALGVFLCERDAQKKVVAGSAAL 361 G W + P+ + GY+ + P ++ + +A A L V L +++ + +A S+ Sbjct: 300 TGTAWAMTPIATGQLSKSGYEMINGPGMLASNVAMGAATLCVALKTKNSNLRQLASSSGF 359 Query: 362 TSLFGITEPAVYGVNLPRKYPFVIACISGALGATIIGYAQTKVYSF---GLPSIFTFMQT 418 T+L GITEPA+YGV L + + A I G G + Y+F GL ++ F+ Sbjct: 360 TALLGITEPALYGVLLKFRRVLIAAMIGGGCAGVYAGVSGLVRYAFVSPGLAALPAFIGE 419 Query: 419 IPSTGIDFTVWASVIGGVIAIGCAFVGTVML-HFITAKRQPAQGAPQEKTPEVITPPEQG 477 P +++ ++ + V T L FI K P + + P+ P+ Sbjct: 420 NP---------MNIVHALVTCAISIVVTFTLTWFIAFKDVPEEQEEVGEAPQPAVSPKNE 470 Query: 478 G---ICSPMTGEIVPLIHVADTTFASGLLGKGIAILPSVGEVRSPVAGRIASLFATLHAI 534 G + SP+ G++V L V D F+ GLLG+G+AI P G +R+P +G + + HA+ Sbjct: 471 GETEVFSPLRGQVVALSEVNDDVFSGGLLGEGLAIRPEEGVLRAPFSGTVMMFLPSCHAV 530 Query: 535 GIESDDGVEILIHVGIDTVKLDGKFFSAHVNVGDKVNTGDRLISFDIPAIREAGFDLTTP 594 G++SD G+E+LIH+GIDTV L+G+ FS+ + VGD+V G LI FDIPAI +AG+DL TP Sbjct: 531 GLQSDSGLELLIHIGIDTVNLNGQHFSSTLKVGDRVEAGQELIRFDIPAIEQAGYDLITP 590 Query: 595 VLISNSDDFTDVLPHGTAQISAGEPLL 621 V++ N D+ + AQ+ GE L+ Sbjct: 591 VIVVNGDEQHSLRLTAAAQVDYGEQLM 617 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: 1121 Number of extensions: 68 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: 626 Length adjustment: 38 Effective length of query: 587 Effective length of database: 588 Effective search space: 345156 Effective search space used: 345156 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