Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate 16257 b2148 beta-methylgalactoside transporter inner membrane component (NCBI)
Query= uniprot:D8IZC8 (344 letters) >FitnessBrowser__Keio:16257 Length = 336 Score = 192 bits (488), Expect = 1e-53 Identities = 114/316 (36%), Positives = 177/316 (56%), Gaps = 24/316 (7%) Query: 37 VLVVLYLLFYGLTLYLSGDGTSNFASAENTMNILRQVAINLVLAAGMTFVILTAGIDLSV 96 + VVL +L L + + D T F S N NIL Q ++ +++A G+ +I+T G DLS Sbjct: 18 IYVVLLVL---LAIIIFQDPT--FLSLLNLSNILTQSSVRIIIALGVAGLIVTQGTDLSA 72 Query: 97 GSVLAVSAVLGMQV------------SLGAAPGWAIPMFIFS-GLVMGMVNGAMVALLNI 143 G + ++AV+ + + P + + + + G V+G++NG ++A LN+ Sbjct: 73 GRQVGLAAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLINGLIIAYLNV 132 Query: 144 NAFVVTLGTMTAFRGAAYLLAD--GTTVLNNDIPSFEWIGNG----DFLHVPWLIWVAVA 197 F+ TLGTM G L D G + ++ F G + ++ + A+ Sbjct: 133 TPFITTLGTMIIVYGINSLYYDFVGASPISGFDSGFSTFAQGFVALGSFRLSYITFYALI 192 Query: 198 VVLLSWVILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLLFVYSISGLFSGLAGAMSASR 257 V WV+ KT G +I+AIGGN +AA+++G+ VGL LL +Y++SG+F G + A R Sbjct: 193 AVAFVWVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYAFGGMLEAGR 252 Query: 258 LYGANGNWGSGYELDAIAAVVLGGTSLMGGVGSIWGTVVGALIIGVMNNGLTILGLSSFW 317 + A N G YELDAIAA V+GG S GGVG++ G V G +I V+N GLT +G++ +W Sbjct: 253 IGSATNNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYGLTYIGVNPYW 312 Query: 318 QYVAKGAVIVLAVILD 333 QY+ KGA+I+ AV LD Sbjct: 313 QYIIKGAIIIFAVALD 328 Lambda K H 0.324 0.138 0.417 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: 329 Number of extensions: 17 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: 344 Length of database: 336 Length adjustment: 28 Effective length of query: 316 Effective length of database: 308 Effective search space: 97328 Effective search space used: 97328 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 (21.6 bits) S2: 49 (23.5 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