Align Inositol transport system permease protein (characterized)
to candidate BWI76_RS14865 BWI76_RS14865 ribose ABC transporter permease
Query= reanno::WCS417:GFF2333 (340 letters) >FitnessBrowser__Koxy:BWI76_RS14865 Length = 339 Score = 235 bits (600), Expect = 1e-66 Identities = 140/342 (40%), Positives = 210/342 (61%), Gaps = 27/342 (7%) Query: 6 DNKPAT-VPTKSRRRLPTELSIFLVLIGIGLVFELFGWIVRDQSFLMNSQR---LVLMIL 61 +NKP T +P K+ P + + + +GI +V L ++ +F N R L+ + Sbjct: 3 NNKPVTELPVKA----PFDFAKWWDRVGILIV--LLVLLILMSTFAPNFNRVDNLLNIAR 56 Query: 62 QVSIIGLLAIGVTQVIITTGIDLSSGSVLALSAMIAASLAQTSDFSRAVFPSLTDLPVWI 121 +S+ +LA G+T VI+T+GIDLS GS++A+S +++ V ++ +P + Sbjct: 57 SISVNAILAAGMTFVILTSGIDLSVGSIVAVSGVVS------------VVAAMAGIPAPL 104 Query: 122 PVAMGLGVGLLAGAINGSIIAVTGIPPFIATLGMMVSARGLARYYTEGQPVSMLSDSYTA 181 + G+GVG L G +NG + A + PFI TLG M RG+A TEGQP+ S S+ Sbjct: 105 AILAGVGVGALCGLLNGVLTAYLALAPFIVTLGTMTFLRGMAYTITEGQPIVSSSLSFRE 164 Query: 182 IGHGAM-----PVIIFLVVAVIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLIIV 236 +G+G + PVII LVV ++ L T++G++ YA+GGN QAAR +G+ VKR L V Sbjct: 165 LGNGYLIGIPIPVIIMLVVYLLAWFILERTRFGRHIYAVGGNAQAARLAGVRVKRVLAAV 224 Query: 237 YSIAGLLAGLAGVVASARAATGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGAL 296 Y IAG+ AGLAG++ +AR + Q G YELDAIAA V+GGTSLAGG GRI GT+IG++ Sbjct: 225 YMIAGVCAGLAGIIFAARVISAQPTAGTGYELDAIAAVVLGGTSLAGGRGRIIGTLIGSI 284 Query: 297 ILGVMASGFTFVGVDAYIQDIIKGLIIVVAVVIDQYRNKRKL 338 ILGV+++G + V + Q +IKG++I++AV ID + +L Sbjct: 285 ILGVLSTGLILLSVPFFTQLLIKGIVIILAVAIDGLKQHPEL 326 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: 282 Number of extensions: 12 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: 340 Length of database: 339 Length adjustment: 28 Effective length of query: 312 Effective length of database: 311 Effective search space: 97032 Effective search space used: 97032 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 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