Align Fructose import permease protein FrcC (characterized)
to candidate GFF2762 PGA1_c28050 putative sugar transport system, permease protein
Query= SwissProt::Q9F9B1 (360 letters) >FitnessBrowser__Phaeo:GFF2762 Length = 353 Score = 514 bits (1323), Expect = e-150 Identities = 258/348 (74%), Positives = 295/348 (84%) Query: 12 QEFEKVLADSSTDVASFDAHDKTLLQKLQHFLHSSPAAVPLIVLVLSLIAFGVILGGKFF 71 Q +E + S VA FD + + + + QH LH +P+ VPLIVLVLS+I FG++LG KFF Sbjct: 5 QSYEAAASGSPEAVADFDQGETSFISRFQHMLHVTPSLVPLIVLVLSVIVFGLLLGSKFF 64 Query: 72 SAFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSVGAIMVLSSVIMGQFTFRYGFPPALS 131 S F +TLILQQV IVGIV AQ+LVILTAGIDLSVGAIMVLSSV+MGQFTFRYG PP ++ Sbjct: 65 SPFALTLILQQVGIVGIVACAQSLVILTAGIDLSVGAIMVLSSVVMGQFTFRYGLPPEVA 124 Query: 132 VICGLGVGALCGYINGTLVARMKLPPFIVTLGMWQIVLASNFLYSANETIRAQDISANAS 191 V CGL G +CG+ING LVARMKLPPFIVTLGMWQIVLASNFLYSANETIR+Q I+A A Sbjct: 125 VACGLICGTICGFINGWLVARMKLPPFIVTLGMWQIVLASNFLYSANETIRSQTIAAEAP 184 Query: 192 ILQFFGQNFRIGNAVFTYGVVVMVLLVCLLWYVLNRTAWGRYVYAVGDDPEAAKLAGVNV 251 +LQ FG+ +IG AVFTYGV+ MV+LV LL YVL TAWGR+VYAVGDDPEAA+L+GV V Sbjct: 185 LLQLFGEKIKIGGAVFTYGVIFMVILVVLLAYVLRHTAWGRHVYAVGDDPEAAELSGVKV 244 Query: 252 TRMLISIYTLSGLICALAGWALIGRIGSVSPTAGQFANIESITAVVIGGISLFGGRGSIM 311 TR+LIS+Y LSGLICA AGWA+IGRIGSVSPT+GQ ANIESITAVVIGGISLFGGRGSI+ Sbjct: 245 TRVLISVYMLSGLICAFAGWAMIGRIGSVSPTSGQLANIESITAVVIGGISLFGGRGSIL 304 Query: 312 GMLFGALIVGVFSLGLRLMGTDPQWTYLLIGLLIIIAVAIDQWIRKVA 359 G FGALIVGVF+LGLRL+G D QWTYLLIGLLII AVA+DQWIRKV+ Sbjct: 305 GTFFGALIVGVFTLGLRLLGADAQWTYLLIGLLIIAAVAVDQWIRKVS 352 Lambda K H 0.327 0.141 0.420 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: 540 Number of extensions: 17 Number of successful extensions: 1 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: 360 Length of database: 353 Length adjustment: 29 Effective length of query: 331 Effective length of database: 324 Effective search space: 107244 Effective search space used: 107244 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 (21.7 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