Align Fructose import permease protein FrcC (characterized)
to candidate RR42_RS32890 RR42_RS32890 ABC transporter permease
Query= SwissProt::Q9F9B1 (360 letters) >FitnessBrowser__Cup4G11:RR42_RS32890 Length = 322 Score = 167 bits (422), Expect = 5e-46 Identities = 102/313 (32%), Positives = 169/313 (53%), Gaps = 23/313 (7%) Query: 49 AVPLIVLVLSLIAFGVILGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSVGA 108 A+ L+ L+L++ + + G + +L+Q +++ ++ + TLVILT G+DLSVGA Sbjct: 23 ALGLLCLLLAVASDAFLTLGNILN------VLRQASLLFLLASGVTLVILTGGLDLSVGA 76 Query: 109 IMVLSSVIMGQFTFRYGFPPALSVICGLGVGALCGYINGTLVARMKLPPFIVTLGMWQIV 168 + +S+ + G L V GLG GAL G NG LVA +++PPFI T GM ++ Sbjct: 77 NVAMSACVAATVMKATG-STMLGVGAGLGTGALIGLANGLLVAMLRIPPFIATYGMLWVL 135 Query: 169 LASNFLYSANETIRAQDISANASILQFFGQNFRIGNAVFTYGVVVMVLLVCLLWY----V 224 + + A ETI F FR + + +GV + V L+ + + Sbjct: 136 HGVTYWFMAGETIHG------------FPPAFRAIGSGYLWGVPIPVYLMLVFLVAGTAM 183 Query: 225 LNRTAWGRYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSVSPTA 284 +T +G+ +YA+G +P AA+L+GV V R L+ +Y +SG + +A + R+ S Sbjct: 184 SQKTTYGQEIYAIGANPVAARLSGVPVRRRLVLVYLVSGAMAGIASLVFLARLNSAEGDI 243 Query: 285 GQFANIESITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLLIGLL 344 G+ + +I AV+IGG SLFGG G + G L GA+I+ + G+ L+ W L+ G++ Sbjct: 244 GEALTLPAIAAVLIGGTSLFGGVGRVSGTLVGAIILTLVLNGMNLLTVSANWQPLVTGVI 303 Query: 345 IIIAVAIDQWIRK 357 +++AV +D RK Sbjct: 304 VVLAVFLDTLSRK 316 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: 317 Number of extensions: 22 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: 322 Length adjustment: 28 Effective length of query: 332 Effective length of database: 294 Effective search space: 97608 Effective search space used: 97608 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