Align Fructose import permease protein FrcC (characterized)
to candidate 3606962 Dshi_0389 Monosaccharide-transporting ATPase (RefSeq)
Query= SwissProt::Q9F9B1 (360 letters) >FitnessBrowser__Dino:3606962 Length = 357 Score = 493 bits (1269), Expect = e-144 Identities = 251/348 (72%), Positives = 287/348 (82%) Query: 12 QEFEKVLADSSTDVASFDAHDKTLLQKLQHFLHSSPAAVPLIVLVLSLIAFGVILGGKFF 71 Q++E L DS+ VA FD + +K QH LH +PA VPLIVLV ++ FG++LG KFF Sbjct: 9 QDYESALKDSAAAVAEFDHGPQGFTRKFQHALHQTPALVPLIVLVAAIAVFGLLLGSKFF 68 Query: 72 SAFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSVGAIMVLSSVIMGQFTFRYGFPPALS 131 S F +TLILQQV IVGIV AAQ+LVILTAGIDLSVGAIMV+SSV+MGQFTFRYG P ++ Sbjct: 69 SPFALTLILQQVQIVGIVAAAQSLVILTAGIDLSVGAIMVMSSVVMGQFTFRYGLPVEVA 128 Query: 132 VICGLGVGALCGYINGTLVARMKLPPFIVTLGMWQIVLASNFLYSANETIRAQDISANAS 191 V CGL G L G+ING LVA++KLPPFIVTLGMWQIVLA+NFLYS NETIR+QDI A Sbjct: 129 VACGLLCGTLLGFINGWLVAKVKLPPFIVTLGMWQIVLAANFLYSRNETIRSQDIRDQAP 188 Query: 192 ILQFFGQNFRIGNAVFTYGVVVMVLLVCLLWYVLNRTAWGRYVYAVGDDPEAAKLAGVNV 251 +LQFFG IG A TYGV+ MVLLV +L Y L TAWGR+VYAVGDDPEAA+L+GV V Sbjct: 189 LLQFFGTTLEIGGARLTYGVIFMVLLVIVLAYALRHTAWGRHVYAVGDDPEAAELSGVQV 248 Query: 252 TRMLISIYTLSGLICALAGWALIGRIGSVSPTAGQFANIESITAVVIGGISLFGGRGSIM 311 +R LIS+Y LSGLICA AGWALIGRIGSVSPT+GQ ANIESITAVVIGGISLFGGRGSI+ Sbjct: 249 SRTLISVYMLSGLICAFAGWALIGRIGSVSPTSGQLANIESITAVVIGGISLFGGRGSIL 308 Query: 312 GMLFGALIVGVFSLGLRLMGTDPQWTYLLIGLLIIIAVAIDQWIRKVA 359 G FGALIVGVF+LGLRL+G D QWT+LLIGLLII AVA+DQWIRKV+ Sbjct: 309 GAFFGALIVGVFTLGLRLLGADAQWTFLLIGLLIIAAVAVDQWIRKVS 356 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: 511 Number of extensions: 19 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: 357 Length adjustment: 29 Effective length of query: 331 Effective length of database: 328 Effective search space: 108568 Effective search space used: 108568 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