Align PTS system trehalose-specific EIIBC component; EIIBC-Tre; EII-Tre; EC 2.7.1.201 (characterized)
to candidate BWI76_RS07315 BWI76_RS07315 PTS sugar transporter
Query= SwissProt::P39794 (470 letters) >FitnessBrowser__Koxy:BWI76_RS07315 Length = 456 Score = 358 bits (920), Expect = e-103 Identities = 187/461 (40%), Positives = 280/461 (60%), Gaps = 24/461 (5%) Query: 3 ELNKSARQIVEAVGGAENIAAATHCVTRLRFALIDESKVDQEMLDQIDVVKGSFSTNGQF 62 + + +R ++ +GG ENIA+A HC TRLR L+D+S DQ+ + +I+ VKG F GQ Sbjct: 2 DFEQISRSLLPLLGGKENIASAAHCATRLRLVLVDDSLADQQAIGKIEGVKGCFRNAGQM 61 Query: 63 QVVIGQGTVNKVYAELVKETGIGESTKDEVKKASEKNMNPLQRAVKTLADIFIPILPAIV 122 Q++ G G VNKVYA ++ GI ES+K E + K +NP QR + L++IF+PI+PAIV Sbjct: 62 QIIFGTGVVNKVYAAFIQAAGISESSKSEAADIAAKKLNPFQRIARLLSNIFVPIIPAIV 121 Query: 123 TAGLLMGINNILTAEGIFFSTKSIVQVYPQWADLAN----MINLIAGTAFTFLPALIGWS 178 +GLLMG+ ++ G W D +N M+++ + AF LP LIG++ Sbjct: 122 ASGLLMGLLGMVKTYG--------------WVDPSNALYIMLDMCSSAAFIILPILIGFT 167 Query: 179 AVKRFGGNPLLGIVLGVMLVHPDLLNAWGYGAAEQSGEIPVWNLFGLEVQKVGYQGQVLP 238 A + FGGNP LG LG +L HP L NAWG A N FGLE+ +GYQG V P Sbjct: 168 AAREFGGNPYLGATLGGILTHPALTNAWGVAAG-----FHTMNFFGLEIAMIGYQGTVFP 222 Query: 239 ILLASYMLAKIEVFLTKRTPEGIQLLVVAPITLLLTGFASFIIIGPITFAIGNVLTSGLI 298 +LLA + ++ +E L + P+ + L++ +T++++GF + +IIGP A+G+ ++ L Sbjct: 223 VLLAVWFMSIVEKQLRRAIPDALDLILTPFLTVIISGFIALLIIGPAGRALGDGISFVLS 282 Query: 299 SVFGSFAALGGLLYGGFYSALVITGMHHTFLAVDLQLIGS-KLGGTFLWPMLALSNIAQG 357 ++ L GLL+GG YS +VITG+HH+F A++ L+G+ +G FL P+ +++N+AQG Sbjct: 283 TLISHAGWLAGLLFGGLYSVIVITGIHHSFHAIEAGLLGNPSIGVNFLLPIWSMANVAQG 342 Query: 358 SAALAMMFIVKDEKQKGLSLTSGISAYLGITEPAIFGVNLRYRFPFIIAMVSSGLAGMYI 417 A LA+ F KD K K ++L S SA LGITE AIFG+NLR+ PFI A++ G ++ Sbjct: 343 GACLAVWFKTKDVKIKAIALPSAFSAMLGITEAAIFGINLRFMKPFIAALIGGAAGGAWV 402 Query: 418 SSQGVLASSVGVGGVPGIFSIMSQYWGAFAIGMAIVLIVPF 458 S V S+VG+ +PG+ + + + IGM I V F Sbjct: 403 VSVHVYMSAVGLTAIPGMAIVQASSLLNYIIGMVIAFGVAF 443 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: 570 Number of extensions: 27 Number of successful extensions: 4 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: 456 Length adjustment: 33 Effective length of query: 437 Effective length of database: 423 Effective search space: 184851 Effective search space used: 184851 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: 51 (24.3 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