Align ABC-type transporter, integral membrane subunit, 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_0471 Synpcc7942_0471 ABC-type sugar transport system permease component-like
Query= TCDB::G4FGN6 (278 letters) >FitnessBrowser__SynE:Synpcc7942_0471 Length = 276 Score = 162 bits (411), Expect = 6e-45 Identities = 88/271 (32%), Positives = 153/271 (56%), Gaps = 5/271 (1%) Query: 9 ILLYIAVVLILIWCVFPLYWAFISSIKP-DRDLFEKNPSLFPKRITFENYVKVFKERPFH 67 +LLY+ + I + + PL W ++ K D+F+ P P + T +N+ +V+ E P Sbjct: 10 LLLYLLLGTIAVAMLIPLLWLVSTAFKSAGEDIFQFPPQFLPTQPTLDNFRRVWTENPLG 69 Query: 68 INIKNSIIVAGITTVLALVVGSLAGYAIARLKFRGKVIVMSLILAVSMFPQVSILGSLFL 127 NS VA +T L L+ SLA Y +ARL+F+G+ + LI+A + P ++ L++ Sbjct: 70 QYFLNSTWVALLTVGLNLLFCSLAAYPLARLEFKGRQTLFLLIVATILIPFQVVMIPLYV 129 Query: 128 ILRGLKLINTYTGLIIPYTAMNLPLTVWVLQSFFRELPKEVEESAFIDGASKLRTLWSIV 187 ++ L L NTY GL+ PY A +++L+ F+ +PK++EE+A IDG + L W+++ Sbjct: 130 LIINLGLRNTYLGLVFPYLAS--AFGIFLLRQAFQGIPKDLEEAARIDGCNDLGVWWNVM 187 Query: 188 LPMSAPGLVATGLLTFIAAWNEFLFALTFMQKPSLYTVPVAVALFKGASQYEIPWGQLMA 247 +P + P L+ + FI +W++FL+ L + +P YT+P+ +A AS + + W + A Sbjct: 188 IPSARPALITLAIFVFIGSWSDFLWPLIILDEPDRYTLPLGIATL--ASGFSLDWRLVAA 245 Query: 248 AAVIVTLPLVILVLVFQNRIIAGLSAGAVKG 278 +V+ LP+ + L Q I+ +A VKG Sbjct: 246 GSVLSILPVFGVFLALQRYIVPSAAASGVKG 276 Lambda K H 0.329 0.142 0.424 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: 219 Number of extensions: 13 Number of successful extensions: 3 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: 278 Length of database: 276 Length adjustment: 25 Effective length of query: 253 Effective length of database: 251 Effective search space: 63503 Effective search space used: 63503 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 47 (22.7 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