Align Inositol transport system permease protein (characterized)
to candidate RR42_RS32895 RR42_RS32895 ABC transporter permease
Query= reanno::WCS417:GFF2333 (340 letters) >FitnessBrowser__Cup4G11:RR42_RS32895 Length = 318 Score = 178 bits (451), Expect = 2e-49 Identities = 103/302 (34%), Positives = 177/302 (58%), Gaps = 22/302 (7%) Query: 41 GWIVRDQSFLMNSQRLVLMILQVSIIGLLAIGVTQVIITTGIDLSSGSVLALSAMIAASL 100 G+ V FL + + L+ + Q +I+ L+A+ +T +I+T G+DLS G+VL L ++ A + Sbjct: 31 GFSVTGPGFL-SVENLLNIGAQSTILLLIALPMTLIIMTEGLDLSMGAVLTLCGVVLAMV 89 Query: 101 AQTSDFSRAVFPSLTDLPVWIPVAMGLGV--GLLAGAINGSIIAVTGIPPFIATLGMMVS 158 ++ +P+A+G + GL G +NG++++ IPPF+ATLG + Sbjct: 90 MVATES--------------LPLALGAALLTGLAFGLLNGALVSWLEIPPFVATLGTLGV 135 Query: 159 ARGLARYYTEGQPVSMLSDSYTAIGHGAM-----PVIIFLVVAVIFHIALRYTKYGKYTY 213 A+GLA T+GQ V+ + ++ I G + P+ I V +FH L +T++G Y + Sbjct: 136 AQGLALVATDGQSVTGIGEAIPLIYAGQLLGVPLPIWIAAVFYGLFHWLLYHTRFGAYVF 195 Query: 214 AIGGNMQAARTSGINVKRHLIIVYSIAGLLAGLAGVVASARAATGQAGMGMSYELDAIAA 273 A+GGN +A + SG+ + +LI VY++ GL+AG+A ++ +AR G + E DAIAA Sbjct: 196 ALGGNREALKFSGVRINVYLIAVYALGGLMAGVAALLLTARMNAGHPTAAIGLEFDAIAA 255 Query: 274 AVIGGTSLAGGVGRITGTVIGALILGVMASGFTFVGVDAYIQDIIKGLIIVVAVVIDQYR 333 +GGT+ G G + GTV+G L +GV+ +G VGV + +Q GL+++V ++I+ ++ Sbjct: 256 VAVGGTTFDRGNGWLPGTVLGVLAVGVLRNGLNLVGVPSSVQVAAIGLLVLVVLLIESFK 315 Query: 334 NK 335 K Sbjct: 316 GK 317 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: 238 Number of extensions: 8 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: 318 Length adjustment: 28 Effective length of query: 312 Effective length of database: 290 Effective search space: 90480 Effective search space used: 90480 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