Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate SMc02031 SMc02031 permease
Query= uniprot:A0A0C4Y7K0 (337 letters) >FitnessBrowser__Smeli:SMc02031 Length = 349 Score = 236 bits (603), Expect = 5e-67 Identities = 144/347 (41%), Positives = 201/347 (57%), Gaps = 23/347 (6%) Query: 10 ASTGAPLPAGTLGRLTTQERLRAL----GMLPVLVLLCIGFSVLTENFAGWQNLSIIAQQ 65 A +PAG G T +L+A+ G L LVLL + T NF NLS +A+Q Sbjct: 5 AEKNPDIPAGGAGARKT--KLKAVVFQAGPLIALVLLMAYLAFATSNFLTLDNLSNVARQ 62 Query: 66 ASINMVLAAGMTFVILTGGIDLSVGSILSISAVVAMLVSLMP------QLGMLSVPAALL 119 ++ +LA G TFVILTGGIDLSV +I ++SA + ++ P G + P A+L Sbjct: 63 SAFVAILAVGQTFVILTGGIDLSVAAIAALSASITAVLLTQPLVLFGIDFGFVPPPVAIL 122 Query: 120 CGLLFGI----VNGALVAFMKLPPFIVTLGTLTAVRGLARLVGNDSTIYNPDIG------ 169 G+L G+ +NG L++ K+P FI TLGT+TA RG A LV + + + + G Sbjct: 123 IGILIGMAAGALNGWLISKFKIPDFIATLGTMTAFRGAALLVTDGLPVPSFNAGRQLPES 182 Query: 170 FAFIGNGEVLGVPWLVIIAFAVVAVSWFVLRRTVLGLQIYAVGGNAEAARLSGIKVWVVL 229 ++G G++ GVP +IA A W+VLR T LG IYAVGGN AA SGI + Sbjct: 183 LIWVGGGQLFGVPVSALIALLCAAAGWYVLRYTALGRAIYAVGGNRAAAHSSGISISRTK 242 Query: 230 LFVYAVSGLLAGLGGVMSSARLYAANGLQLGQSYELDAIAAVILGGTSFVGGTGSIVGTL 289 + YA+SGLLA + G++ RL +AN L + EL +IA+V++GGT+ GG G + G++ Sbjct: 243 IMTYAISGLLAAIAGIILVGRLNSANAL-MADGEELRSIASVVIGGTNLFGGEGGVWGSI 301 Query: 290 VGALIIAVLSNGLVLLGVSDIWQYIIKGLVIIGAVALDSYRRKGSAR 336 +GA II VL NGL LL VS WQ I +G+VI+ V D +RR+ R Sbjct: 302 IGAAIIGVLGNGLNLLDVSPFWQRIAQGVVIVVVVIFDQWRRRSMTR 348 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: 377 Number of extensions: 27 Number of successful extensions: 5 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: 349 Length adjustment: 29 Effective length of query: 308 Effective length of database: 320 Effective search space: 98560 Effective search space used: 98560 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