Align Extracellular solute-binding protein family 1, component of Trehalose porter. Also binds sucrose (Boucher and Noll, 2011). Induced by glucose and trehalose. Directly regulated by trehalose-responsive regulator TreR (characterized)
to candidate Synpcc7942_0950 Synpcc7942_0950 putative multiple sugar transport system substrate-binding protein
Query= TCDB::G4FGN8 (411 letters) >FitnessBrowser__SynE:Synpcc7942_0950 Length = 438 Score = 238 bits (607), Expect = 3e-67 Identities = 141/382 (36%), Positives = 228/382 (59%), Gaps = 16/382 (4%) Query: 34 EVLKKQLEMFHQQYPDIEVEIIPMPDSSTERHDLYVTYFAAGETDPDVLMLDVIWPAEF- 92 E ++ + F ++P+I++E++ P+ ++ DLY T F G D++ LDV W +F Sbjct: 58 EAMQPAIARFTAEHPEIQLELVAGPNDTSLVSDLYTTAFLLGNAPYDLVFLDVTWLPKFV 117 Query: 93 -APFLEDLTADKDYFEL-GEFLPGTVMSVTVNGRIVAVPWFTDAGLLYYRKDLLEKYGYD 150 A +L DL+ D+ E+ EFLP + R+ +P GLLYYR+DL+ + Sbjct: 118 AAGWLLDLS-DRVLPEIQAEFLPAALNGSFYRDRLYRLPLNAAVGLLYYRQDLMPE---- 172 Query: 151 HAPRTWDELVEMAKKISQAEGI--HGFVWQGARYEGLVCDFLEYLWSFGGDVLD-ESGKV 207 P+T+ ELV+ ++++ QA+G+ G+VWQG +YEGLVC+FLE L FGG +D ++G+V Sbjct: 173 -PPQTFTELVQRSQQL-QAQGVVPWGYVWQGKQYEGLVCNFLEVLAGFGGYWIDPQTGEV 230 Query: 208 VIDSPEAVAALQFMVDLIYKHKVTPEGVTTYMEEDARRIFQNGEAVFMRNWPYAWSLVNS 267 +D PEA+AA ++ I +++P GV+T+ E +A ++F+ G++ FMRNWPYA L+ Sbjct: 231 GLDHPEAIAAADWLHSTI-TDQISPAGVSTFQENEALKLFETGQSAFMRNWPYAEMLLER 289 Query: 268 DESPIKGKVGVAPLPMGPGGRRAATLGGWVLGINKFSSPEEKEAAKKLIKFLTSYDQQLY 327 ES ++GKVG+AP+ PG AAT G W +GI + E EAA + LT + Q Sbjct: 290 PESAVRGKVGIAPMVHAPGQTSAATQGTWGVGIAQ--QTEHPEAALTALLALTDAESQRL 347 Query: 328 KAINAGQNPTRKAVYKDPKLKEAAPFMVELLGVFINALPRPRVANYTEVSDVIQRYVHAA 387 ++ + PTR A+Y+DP+L PF L + + + R + Y +SD++QR++ AA Sbjct: 348 ISLGSNYIPTRSALYQDPELLARYPFYATLPPILESTVLRSPLPAYDALSDILQRHLSAA 407 Query: 388 LTRQTTSEDAIKNIAKELKFLL 409 ++ QT A++ A+E + LL Sbjct: 408 ISGQTPVAIALQQAARESRQLL 429 Lambda K H 0.320 0.138 0.413 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: 456 Number of extensions: 28 Number of successful extensions: 6 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: 411 Length of database: 438 Length adjustment: 32 Effective length of query: 379 Effective length of database: 406 Effective search space: 153874 Effective search space used: 153874 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. 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