Align Inositol transport system permease protein (characterized)
to candidate SM_b20352 SM_b20352 sugar ABC transporter permease
Query= reanno::WCS417:GFF2333 (340 letters) >FitnessBrowser__Smeli:SM_b20352 Length = 354 Score = 201 bits (511), Expect = 2e-56 Identities = 124/343 (36%), Positives = 192/343 (55%), Gaps = 23/343 (6%) Query: 11 TVPTKSRRRLPTELSIFLVLIGIGLVFELFGWIVRDQSFLMN---SQRLVLMILQVSIIG 67 T T + T S+ L L+ + LF + F N + L+LM V++ Sbjct: 3 TATTTTNATDATSGSVLLTLMKLRTFIALFAVVAFFSIFAPNFLSTANLILMSKHVALNA 62 Query: 68 LLAIGVTQVIITTGIDLSSGSVLALSAMIAASLAQTS---DFSRAVFPSLTDLPVWIPVA 124 LA+G+T VIIT GIDLS GS++ L M+A L F V+ ++ ++ + Sbjct: 63 FLAMGMTFVIITGGIDLSVGSIVGLCGMVAGGLILNGIDLQFGYTVYFNVVEVCL----- 117 Query: 125 MGLGVGLLAGAINGSIIAVTGIPPFIATLGMMVSARGLARYYTEGQPVSML-------SD 177 + L VG++ GA+NG +I + PFIATLG + ARG A + GQ L + Sbjct: 118 ITLAVGIVIGAVNGLLITKLNVAPFIATLGTLYVARGFALLSSGGQTFPNLVGKPELATT 177 Query: 178 SYTAIGHG---AMPVIIFLVVAVIFHIAL--RYTKYGKYTYAIGGNMQAARTSGINVKRH 232 + +G G +PV I++++ V A RYT G++ +A+GGN +AAR SGI V R Sbjct: 178 GFAFLGSGRLLGLPVSIWVLIVVALAAAYVARYTPIGRHIFAVGGNERAARMSGIRVDRV 237 Query: 233 LIIVYSIAGLLAGLAGVVASARAATGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTV 292 + VY +G A + G+V S+ G S+EL+AIAAAV+GGTS++GG G I GT+ Sbjct: 238 KMFVYMFSGFCAAIVGLVISSELMASHPATGNSFELNAIAAAVLGGTSMSGGRGTIGGTI 297 Query: 293 IGALILGVMASGFTFVGVDAYIQDIIKGLIIVVAVVIDQYRNK 335 IGA ++G+++ G +G+ ++ Q +IKG++I+VAVV+DQ + + Sbjct: 298 IGAFVIGILSDGLVMMGISSFWQMVIKGIVIIVAVVVDQAQRR 340 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: 304 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: 340 Length of database: 354 Length adjustment: 29 Effective length of query: 311 Effective length of database: 325 Effective search space: 101075 Effective search space used: 101075 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