Align Inner-membrane translocator (characterized, see rationale)
to candidate Echvi_1280 Echvi_1280 Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components
Query= uniprot:A0KWY6 (405 letters) >FitnessBrowser__Cola:Echvi_1280 Length = 318 Score = 172 bits (437), Expect = 9e-48 Identities = 109/315 (34%), Positives = 176/315 (55%), Gaps = 23/315 (7%) Query: 66 LLALSILLLANLFIDSSFFNISYQDDRLYGSLIDILNRSAPVALLSIGMSLVIATGGIDL 125 L+AL IL L + F ++ + +++ + + +S+GM+LVI T GIDL Sbjct: 10 LIALIILCLVLSLLSDRFLTLA--------NGWNVMRQVSVNICISVGMTLVILTAGIDL 61 Query: 126 SVGAVMAIAGAVCANLL----LVPDISL--------VTVIAAGLIVGLLAGCINGGLVSF 173 SVG+++A+ GAV A+L+ V ++L ++ GL GL G NG ++ Sbjct: 62 SVGSILALCGAVTASLIKNGIAVEGLNLHIGFAPLGAVILGVGLGFGL--GWFNGWTITR 119 Query: 174 LGIQPIVATLLLMVAGRGVAQLINQGQIITFQHPGFAAIGVGQFLGLPMPVWIVIGMLTF 233 + P VATL ++ RG+ L G I FA +G G FLG+PMPVWI ++ Sbjct: 120 FKVPPFVATLAMLTIARGLTMLWTGGFPINGLGEDFAFLGTGWFLGIPMPVWITAVIVAL 179 Query: 234 SQLLLRKTALGLFIEAVGCNAKASRYLGINDKSIKLFAYGIAGLCAALAGMISTADIQGS 293 + LL +KT G ++ A+G N +A+R GIN +K+ Y IAG AA+ GMI T+ + + Sbjct: 180 AVLLTKKTKFGRYVYAIGGNERAARLSGINISRVKMTVYAIAGGLAAVGGMIVTSRLDSA 239 Query: 294 DANNAGLWLELDAVLAVVIGGAALTGGRFSLILSVVGALIIQTLATTIIVSGLPAKFNLL 353 NAG+ ELDA+ AVVIGG +L+GG+ +++ +V+G +II L +++ + + + Sbjct: 240 QP-NAGISYELDAIAAVVIGGTSLSGGKGTIMGAVLGGIIIGVLNNGLVLLNVSPFWQQV 298 Query: 354 IKAIVILTVLLLQSA 368 +K VIL +++ A Sbjct: 299 VKGAVILLAVVIDKA 313 Lambda K H 0.323 0.136 0.379 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: 317 Number of extensions: 19 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 405 Length of database: 318 Length adjustment: 29 Effective length of query: 376 Effective length of database: 289 Effective search space: 108664 Effective search space used: 108664 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 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