Align Fructose import permease protein FrcC (characterized)
to candidate BWI76_RS00280 BWI76_RS00280 ribose ABC transporter permease
Query= SwissProt::Q9F9B1 (360 letters) >FitnessBrowser__Koxy:BWI76_RS00280 Length = 321 Score = 179 bits (454), Expect = 9e-50 Identities = 100/300 (33%), Positives = 170/300 (56%), Gaps = 5/300 (1%) Query: 53 IVLVLSLIAFGVILGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSVGAIMVL 112 ++ +L LIA + FF+ + ILQQ ++ I+ TLVILT+GIDLSVG+++ L Sbjct: 23 LIALLVLIAIVSTMSPNFFTVNNLFNILQQTSVNAIMAVGMTLVILTSGIDLSVGSLLAL 82 Query: 113 SSVIMGQFTFRYGFPPALSVICGLGVGALCGYINGTLVARMKLPPFIVTLGMWQIVLASN 172 + + ++V L +GA G + G +VA+ ++ FI TL M ++ Sbjct: 83 TGAVAASIV-GIEVNALVAVAAALALGAAIGAVTGVIVAKGRVQAFIATLVMMLLLRGVT 141 Query: 173 FLYSANETIRAQDISANASILQFFGQNFRIGNAVFTYGVVVMVLLVCLLWYVLNRTAWGR 232 +Y+ + + NA + +FG +G V +M ++ WY+L+ T GR Sbjct: 142 MVYTNGSPVNT-GFTDNADLFGWFGIGRPLG---IPTPVWIMAIVFLAAWYMLHHTRLGR 197 Query: 233 YVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSVSPTAGQFANIES 292 Y+YA+G + A +L+G++V ++ I +Y+L G++ +LAG + R+ S PTAG +++ Sbjct: 198 YIYALGGNEAATRLSGISVNKVKIIVYSLCGMLASLAGIIEVARLSSAQPTAGTGYELDA 257 Query: 293 ITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLLIGLLIIIAVAID 352 I AVV+GG SL GG+G I+G L GALI+G + GL L+G + ++ ++I++AV +D Sbjct: 258 IAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQMIVKAVVILLAVLVD 317 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: 343 Number of extensions: 23 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: 321 Length adjustment: 28 Effective length of query: 332 Effective length of database: 293 Effective search space: 97276 Effective search space used: 97276 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 Apr 09 2024. 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