Align Fructose import permease protein FrcC (characterized)
to candidate H281DRAFT_02703 H281DRAFT_02703 monosaccharide ABC transporter membrane protein, CUT2 family
Query= SwissProt::Q9F9B1 (360 letters) >FitnessBrowser__Burk376:H281DRAFT_02703 Length = 333 Score = 179 bits (453), Expect = 1e-49 Identities = 117/351 (33%), Positives = 187/351 (53%), Gaps = 42/351 (11%) Query: 18 LADSSTDVASFDAHDKTLLQKLQHFLHSSPAAVPLIVLVLSLIAFGVILGGKFFSAFTMT 77 + ++ + A +A + ++++L+ + AA+ +I + LS I +F + T+T Sbjct: 1 MTSTAANRADTEALSRRVIRQLRSGIGPLFAALVIICIALS------IASPEFLTTSTLT 54 Query: 78 LILQQVAIVGIVGAAQTLVILTAGIDLSVGAIMVLSSVIMGQFTFRYGFPPA-----LSV 132 I+ QV++VGI T VI+T+GIDLSVG+++ L+ ++ T G P ++ Sbjct: 55 NIMVQVSVVGIAAVGGTFVIITSGIDLSVGSLVALTGMVAA--TVMAGSSPGAIGLGIAG 112 Query: 133 ICG-LGVGALCGYINGTLVARMKLPPFIVTLGMWQIVLASNFLYSANETIRAQDISANAS 191 +C L VGA G +NG VA ++L PFIVTL M + S T Sbjct: 113 LCAALAVGAAAGALNGLAVAWLRLVPFIVTLAMMAMARGLTLAISDGRT----------- 161 Query: 192 ILQFFGQNFRIGNAVFTYG----------VVVMVLLVCLLWYVLNRTAWGRYVYAVGDDP 241 F NA +G ++VM+++ + +L +T +G V+AVG + Sbjct: 162 -------KFDFPNAFTAFGAKTVAGLPMPMIVMLVIFVIGHVLLRKTTFGHQVFAVGGNQ 214 Query: 242 EAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSVSPTAGQFANIESITAVVIGGI 301 EAA+LAG+ V R++ Y L+G+ A+AG L GR+ S P+A ++ I AVVIGG Sbjct: 215 EAARLAGIPVHRVVFLTYMLAGVTAAIAGIVLAGRLNSALPSAANGLELQVIAAVVIGGT 274 Query: 302 SLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLLIGLLIIIAVAID 352 SL GGRGSI+G G +++GV ++GL L+G +P WT + G +I AV +D Sbjct: 275 SLAGGRGSIVGTFIGVVLIGVINVGLSLLGVNPFWTQFIQGGVIFAAVLLD 325 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: 362 Number of extensions: 16 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: 360 Length of database: 333 Length adjustment: 29 Effective length of query: 331 Effective length of database: 304 Effective search space: 100624 Effective search space used: 100624 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