Align Fructose import permease protein FrcC (characterized)
to candidate BWI76_RS14865 BWI76_RS14865 ribose ABC transporter permease
Query= SwissProt::Q9F9B1 (360 letters) >FitnessBrowser__Koxy:BWI76_RS14865 Length = 339 Score = 206 bits (524), Expect = 7e-58 Identities = 119/304 (39%), Positives = 184/304 (60%), Gaps = 11/304 (3%) Query: 50 VPLIVLVLSLIAFGVILGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSVGAI 109 V +++++L L+ F + I + +++ I+ A T VILT+GIDLSVG+I Sbjct: 25 VGILIVLLVLLILMSTFAPNFNRVDNLLNIARSISVNAILAAGMTFVILTSGIDLSVGSI 84 Query: 110 MVLSSVIMGQFTFRYGFPPALSVICGLGVGALCGYINGTLVARMKLPPFIVTLGMWQIVL 169 + +S V+ G P L+++ G+GVGALCG +NG L A + L PFIVTLG + Sbjct: 85 VAVSGVV-SVVAAMAGIPAPLAILAGVGVGALCGLLNGVLTAYLALAPFIVTLGTMTFLR 143 Query: 170 ASNFLYSANETIRAQDISANASILQFFGQNFRIGNAVFTYGVVVMVLLVCLLWYVLNRTA 229 + + + I + +S + G + IG + V++M+++ L W++L RT Sbjct: 144 GMAYTITEGQPIVSSSLS-----FRELGNGYLIGIPI---PVIIMLVVYLLAWFILERTR 195 Query: 230 WGRYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSVSPTAGQFAN 289 +GR++YAVG + +AA+LAGV V R+L ++Y ++G+ LAG R+ S PTAG Sbjct: 196 FGRHIYAVGGNAQAARLAGVRVKRVLAAVYMIAGVCAGLAGIIFAARVISAQPTAGTGYE 255 Query: 290 IESITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLLI-GLLIIIA 348 +++I AVV+GG SL GGRG I+G L G++I+GV S GL L+ P +T LLI G++II+A Sbjct: 256 LDAIAAVVLGGTSLAGGRGRIIGTLIGSIILGVLSTGLILLSV-PFFTQLLIKGIVIILA 314 Query: 349 VAID 352 VAID Sbjct: 315 VAID 318 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: 354 Number of extensions: 18 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: 339 Length adjustment: 29 Effective length of query: 331 Effective length of database: 310 Effective search space: 102610 Effective search space used: 102610 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