Align Inositol transport system permease protein (characterized)
to candidate 1936623 b4460 fused L-arabinose transporter subunits of ABC superfamily: membrane components (RefSeq)
Query= reanno::WCS417:GFF2333 (340 letters) >FitnessBrowser__Keio:1936623 Length = 328 Score = 179 bits (455), Expect = 7e-50 Identities = 103/282 (36%), Positives = 169/282 (59%), Gaps = 17/282 (6%) Query: 61 LQVSIIGLLAIGVTQVIITTGIDLSSGSVLALSAMIAASLAQTSDFSRAVFPSLTDLPVW 120 L +S+ G++A G+ + + DLS SV+A + + + AV +LT+ +W Sbjct: 56 LAISMSGMVACGMLFCLASGDFDLSVASVIACAGV-----------TTAVVINLTE-SLW 103 Query: 121 IPVAMGLGVGLLAGAINGSIIAVTGIPPFIATLGMMVSARGLARYYTEGQPVSMLSDSYT 180 I VA GL +G+L G +NG +IA I I TL M RGLA ++G+ V + +S+ Sbjct: 104 IGVAAGLLLGVLCGLVNGFVIAKLKINALITTLATMQIVRGLAYIISDGKAVGIEDESFF 163 Query: 181 AIGHG---AMPVIIFLVVA--VIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLII 235 A+G+ +P I+L VA +IF + L T +G+ T AIGGN +AAR +G+ V R II Sbjct: 164 ALGYANWFGLPAPIWLTVACLIIFGLLLNKTTFGRNTLAIGGNEEAARLAGVPVVRTKII 223 Query: 236 VYSIAGLLAGLAGVVASARAATGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGA 295 ++ ++GL++ +AG++ ++R +GQ + YEL I+A V+GG SL GG+G+I+ V G Sbjct: 224 IFVLSGLVSAIAGIILASRMTSGQPMTSIGYELIVISACVLGGVSLKGGIGKISYVVAGI 283 Query: 296 LILGVMASGFTFVGVDAYIQDIIKGLIIVVAVVIDQYRNKRK 337 LILG + + + + + Q +++GLI++ AV+ D+Y+ K K Sbjct: 284 LILGTVENAMNLLNISPFAQYVVRGLILLAAVIFDRYKQKAK 325 Lambda K H 0.325 0.140 0.394 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: 278 Number of extensions: 14 Number of successful extensions: 2 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: 340 Length of database: 328 Length adjustment: 28 Effective length of query: 312 Effective length of database: 300 Effective search space: 93600 Effective search space used: 93600 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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