Align Ribose ABC transport system, permease protein RbsC (characterized, see rationale)
to candidate N515DRAFT_2415 N515DRAFT_2415 simple sugar transport system permease protein
Query= uniprot:A0A0C4Y7K0 (337 letters) >FitnessBrowser__Dyella79:N515DRAFT_2415 Length = 337 Score = 150 bits (380), Expect = 3e-41 Identities = 117/337 (34%), Positives = 175/337 (51%), Gaps = 24/337 (7%) Query: 14 APLPAGTLGRLTTQERLRALGMLPVLVLLCIGFS------VLTENFAGWQNLSIIAQQAS 67 A PA T + R +P+LV L + + VL F Q + + Sbjct: 3 AVAPAATSAAAGRRPWWRRRAQVPLLVTLVLFVAMAGAGGVLYHGFLTPQVFLNLLIDNA 62 Query: 68 INMVLAAGMTFVILTGGIDLSVGSILSISAVVAMLVSLMPQLG---MLSVPAALLCGLLF 124 ++A GMTFVIL GGIDLSVG++++ S V +L L+ + G + ++ L G F Sbjct: 63 FLCIVAVGMTFVILAGGIDLSVGAVVAFSTV--LLAELVQRHGWPPLAAIALVLAVGTGF 120 Query: 125 GIVNGALVAFMKLPPFIVTLGTLTAVRGLARLVGNDST-IYNPDIGFAF-----IGNGEV 178 G G L+ +L PF+VTL + RG+A L+ DS I P + +G G + Sbjct: 121 GAGMGVLIQRFRLQPFVVTLAGMFLARGVATLISVDSIDIDQPWLASVANLRLPLGGGSM 180 Query: 179 LGVPWLVIIAFAVVAVSWFVLRRTVLGLQIYAVGGNAEAARLSGIKVWVVLLFVYAVSGL 238 L V LV A AVVA + + G +YA+GG+ +ARL G+ V ++ VYA+SG Sbjct: 181 LSVGALV--ALAVVAAGALLAGASSFGRTVYAIGGSESSARLMGLPVDATVVRVYALSGF 238 Query: 239 LAGLGGVMSSARLYAANGL-QLGQSYELDAIAAVILGGTSFVGGTGSIVGTLVGALIIAV 297 A L GV+ + LY +G Q ELDAIAAV++GGT GG+G ++GTL+G L++ + Sbjct: 239 CAALAGVVYT--LYMLSGYSQHALGLELDAIAAVVIGGTVLAGGSGYVLGTLLGVLVLGL 296 Query: 298 LSNGLVLLG-VSDIWQYIIKGLVIIGAVALDS-YRRK 332 + +V G +S W I+ G +++ L +RRK Sbjct: 297 IQTLIVFDGELSSWWTRIVIGALLLAFCLLQRLFRRK 333 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: 371 Number of extensions: 21 Number of successful extensions: 6 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: 337 Length adjustment: 28 Effective length of query: 309 Effective length of database: 309 Effective search space: 95481 Effective search space used: 95481 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 Apr 09 2024. 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