Align PTS system trehalose-specific EIIBC component; EIIBC-Tre; EII-Tre; EC 2.7.1.201 (characterized)
to candidate BWI76_RS07290 BWI76_RS07290 PTS beta-glucoside transporter subunit EIIBCA
Query= SwissProt::P39794 (470 letters) >FitnessBrowser__Koxy:BWI76_RS07290 Length = 626 Score = 201 bits (511), Expect = 6e-56 Identities = 139/467 (29%), Positives = 224/467 (47%), Gaps = 30/467 (6%) Query: 5 NKSARQIVEAVGGAENIAAATHCVTRLRFALIDESKVDQEMLDQIDVVKGSFSTNGQFQV 64 N++A +I+ AVGGAENI THC TRLR D +KV+ + + V GQFQ+ Sbjct: 4 NETADKILHAVGGAENIRMLTHCATRLRMEFNDRAKVNDAQIGTLPGVISVVEKGGQFQI 63 Query: 65 VIGQGTVNKVYAELVKETGIGESTKDEVKKASEKNMNP---LQRAVKTLADIFIPILPAI 121 VIG V +VY L K + + +KN P + R + ++ F P++PAI Sbjct: 64 VIGN-EVQQVYRRLNKAL-----PEKKGPAGGDKNAKPAGIVARIISVISTTFTPVIPAI 117 Query: 122 VTAGLLMGINNILTAEGIFFSTKSIVQVYPQWADLANMINLIAGTAFTFLPALIGWSAVK 181 AG++ + IL G+ T S Q ++N+IA AF FLP L+ + A Sbjct: 118 TGAGMIKALLAILKLTGVISETSSTYQ----------LLNIIADAAFFFLPVLLAYGASL 167 Query: 182 RFGGNPLLGIVLGVMLVHPDLLNAWGYGAAEQSGEIPVWNLFGLEVQKVGYQGQVLPILL 241 +F NP+L + L +L+HP + G A + G+ V Y G VLPI+L Sbjct: 168 KFECNPILAMTLAGVLLHPGIGQMLAAGKAV--------DFVGINVLLSDYAGSVLPIIL 219 Query: 242 ASYMLAKIEVFLTKRTPEGIQLLVVAPITLLLTGFASFIIIGPITFAIGNVLTSGLISVF 301 ++++ +E F K +P I+ V + LL+T + +++GP + +++ +G ++ Sbjct: 220 TVWLMSWVERFAEKVSPSIIKFFVKPMLILLITAPLALVVVGPAGILLNDLVAAGAGAID 279 Query: 302 GSFAALGGLLYGGFYSALVITGMHHTFLAVDLQLIGSKLGGTFLWPMLALSNIAQGSAAL 361 + L +L G L+ITG + + P + SN+A G+A L Sbjct: 280 RHASWLIPMLMGTLQPFLIITGTAWAMTPIATGQLSKSGYEMINGPGMLASNVAMGAATL 339 Query: 362 AMMFIVKDEKQKGLSLTSGISAYLGITEPAIFGVNLRYRFPFIIAMVSSGLAGMYISSQG 421 + K+ + L+ +SG +A LGITEPA++GV L++R I AM+ G AG+Y G Sbjct: 340 CVALKTKNSNLRQLASSSGFTALLGITEPALYGVLLKFRRVLIAAMIGGGCAGVYAGVSG 399 Query: 422 VLA---SSVGVGGVPGIFSIMSQYWGAFAIGMAIVLIVPFAGTYAYA 465 ++ S G+ +P + AI ++V F T+ A Sbjct: 400 LVRYAFVSPGLAALPAFIGENPMNIVHALVTCAISIVVTFTLTWFIA 446 Lambda K H 0.323 0.140 0.406 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: 680 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: 470 Length of database: 626 Length adjustment: 35 Effective length of query: 435 Effective length of database: 591 Effective search space: 257085 Effective search space used: 257085 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 (22.0 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