Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate GFF2333 PS417_11895 ABC transporter
Query= uniprot:A0A0C4Y7K0 (337 letters) >FitnessBrowser__WCS417:GFF2333 Length = 340 Score = 211 bits (537), Expect = 2e-59 Identities = 141/331 (42%), Positives = 195/331 (58%), Gaps = 33/331 (9%) Query: 26 TQERLRALGMLPVLVLLCIGFSVLTENFAGW-----------QNLSIIAQQASINMVLAA 74 T+ R R L + ++L IG ++ E F GW Q L ++ Q SI +LA Sbjct: 14 TKSRRRLPTELSIFLVL-IGIGLVFELF-GWIVRDQSFLMNSQRLVLMILQVSIIGLLAI 71 Query: 75 GMTFVILTGGIDLSVGSILSISAVVAMLVS--------LMPQLGMLSV--PAA--LLCGL 122 G+T VI+T GIDLS GS+L++SA++A ++ + P L L V P A L GL Sbjct: 72 GVTQVIITTGIDLSSGSVLALSAMIAASLAQTSDFSRAVFPSLTDLPVWIPVAMGLGVGL 131 Query: 123 LFGIVNGALVAFMKLPPFIVTLGTLTAVRGLARLVGNDSTIYNPDIGFAFIGNGEVLGVP 182 L G +NG+++A +PPFI TLG + + RGLAR + + IG+G Sbjct: 132 LAGAINGSIIAVTGIPPFIATLGMMVSARGLARYYTEGQPVSMLSDSYTAIGHGA----- 186 Query: 183 WLVIIAFAVVAVSWFV-LRRTVLGLQIYAVGGNAEAARLSGIKVWVVLLFVYAVSGLLAG 241 + +I F VVAV + + LR T G YA+GGN +AAR SGI V L+ VY+++GLLAG Sbjct: 187 -MPVIIFLVVAVIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLIIVYSIAGLLAG 245 Query: 242 LGGVMSSARLYAANGLQLGQSYELDAIAAVILGGTSFVGGTGSIVGTLVGALIIAVLSNG 301 L GV++SAR A +G SYELDAIAA ++GGTS GG G I GT++GALI+ V+++G Sbjct: 246 LAGVVASARA-ATGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGALILGVMASG 304 Query: 302 LVLLGVSDIWQYIIKGLVIIGAVALDSYRRK 332 +GV Q IIKGL+I+ AV +D YR K Sbjct: 305 FTFVGVDAYIQDIIKGLIIVVAVVIDQYRNK 335 Lambda K H 0.325 0.141 0.409 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: 352 Number of extensions: 21 Number of successful extensions: 4 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: 337 Length of database: 340 Length adjustment: 28 Effective length of query: 309 Effective length of database: 312 Effective search space: 96408 Effective search space used: 96408 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