Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate SM_b20352 SM_b20352 sugar ABC transporter permease
Query= uniprot:A0A0C4Y7K0 (337 letters) >FitnessBrowser__Smeli:SM_b20352 Length = 354 Score = 229 bits (583), Expect = 1e-64 Identities = 132/304 (43%), Positives = 188/304 (61%), Gaps = 18/304 (5%) Query: 46 FSVLTENFAGWQNLSIIAQQASINMVLAAGMTFVILTGGIDLSVGSILSISAVVA---ML 102 FS+ NF NL ++++ ++N LA GMTFVI+TGGIDLSVGSI+ + +VA +L Sbjct: 38 FSIFAPNFLSTANLILMSKHVALNAFLAMGMTFVIITGGIDLSVGSIVGLCGMVAGGLIL 97 Query: 103 VSLMPQLGMLSV-------PAALLCGLLFGIVNGALVAFMKLPPFIVTLGTLTAVRGLAR 155 + Q G L G++ G VNG L+ + + PFI TLGTL RG A Sbjct: 98 NGIDLQFGYTVYFNVVEVCLITLAVGIVIGAVNGLLITKLNVAPFIATLGTLYVARGFAL 157 Query: 156 LVGNDSTIYN----PDI---GFAFIGNGEVLGVPWLVIIAFAVVAVSWFVLRRTVLGLQI 208 L T N P++ GFAF+G+G +LG+P + + V + +V R T +G I Sbjct: 158 LSSGGQTFPNLVGKPELATTGFAFLGSGRLLGLPVSIWVLIVVALAAAYVARYTPIGRHI 217 Query: 209 YAVGGNAEAARLSGIKVWVVLLFVYAVSGLLAGLGGVMSSARLYAANGLQLGQSYELDAI 268 +AVGGN AAR+SGI+V V +FVY SG A + G++ S+ L A++ G S+EL+AI Sbjct: 218 FAVGGNERAARMSGIRVDRVKMFVYMFSGFCAAIVGLVISSELMASHPAT-GNSFELNAI 276 Query: 269 AAVILGGTSFVGGTGSIVGTLVGALIIAVLSNGLVLLGVSDIWQYIIKGLVIIGAVALDS 328 AA +LGGTS GG G+I GT++GA +I +LS+GLV++G+S WQ +IKG+VII AV +D Sbjct: 277 AAAVLGGTSMSGGRGTIGGTIIGAFVIGILSDGLVMMGISSFWQMVIKGIVIIVAVVVDQ 336 Query: 329 YRRK 332 +R+ Sbjct: 337 AQRR 340 Score = 26.6 bits (57), Expect = 0.001 Identities = 21/102 (20%), Positives = 45/102 (44%), Gaps = 2/102 (1%) Query: 214 NAEAARLSGIKVWVVLLFVYAVSGLLAGLGGVMSSARLYAANGLQLGQSYELDAIAAVIL 273 NA A + + ++ L + + + + L AN + + + L+A A+ + Sbjct: 9 NATDATSGSVLLTLMKLRTFIALFAVVAFFSIFAPNFLSTANLILMSKHVALNAFLAMGM 68 Query: 274 GGTSFVGGTGSIVGTLVGALIIAVLSNGLVLLGVSDIWQYII 315 GG VG++VG + +++ GL+L G+ + Y + Sbjct: 69 TFVIITGGIDLSVGSIVG--LCGMVAGGLILNGIDLQFGYTV 108 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: 390 Number of extensions: 20 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 337 Length of database: 354 Length adjustment: 29 Effective length of query: 308 Effective length of database: 325 Effective search space: 100100 Effective search space used: 100100 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