Align deoxynucleoside transporter, permease component 1 (characterized)
to candidate Echvi_1280 Echvi_1280 Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components
Query= reanno::Burk376:H281DRAFT_01115 (357 letters) >FitnessBrowser__Cola:Echvi_1280 Length = 318 Score = 108 bits (270), Expect = 2e-28 Identities = 90/304 (29%), Positives = 158/304 (51%), Gaps = 9/304 (2%) Query: 20 LIVNVLVVLVATWLSRGQFVDIDNLQSMGGQLPELGLLALGIMLSMVSGNGGIDLSGVGL 79 LI +++ LV + LS +F+ + N ++ Q+ +++G+ L +++ GIDLS + Sbjct: 10 LIALIILCLVLSLLS-DRFLTLANGWNVMRQVSVNICISVGMTLVILTA--GIDLSVGSI 66 Query: 80 ANLSGMVAAMLVPR--LVNGDDSPVLYTSLFCAIVLMMGLLGGL--LNGVVIARLRLTPI 135 L G V A L+ V G + + + L A++L +GL GL NG I R ++ P Sbjct: 67 LALCGAVTASLIKNGIAVEGLNLHIGFAPLG-AVILGVGLGFGLGWFNGWTITRFKVPPF 125 Query: 136 LCTLGTQLLFTGFAVVISNGASVHVDYVEPLSDIGNGTVLQVPIAFCIFLAAVIVLGWLL 195 + TL + G ++ + G ++ E + +G G L +P+ I V + L Sbjct: 126 VATLAMLTIARGLTMLWTGGFPIN-GLGEDFAFLGTGWFLGIPMPVWITAVIVALAVLLT 184 Query: 196 KRSPFGLRLYLMGTNPKAAFYAGIPRARMLITTYAMCGVLASLAGLISATHTSSAKWDYG 255 K++ FG +Y +G N +AA +GI +R+ +T YA+ G LA++ G+I + SA+ + G Sbjct: 185 KKTKFGRYVYAIGGNERAARLSGINISRVKMTVYAIAGGLAAVGGMIVTSRLDSAQPNAG 244 Query: 256 NSYLLIAILIAVMGGVNPAGGHGRIICVFFAATVLQFLSSLFNLLGVSQFFGDCAWGFLL 315 SY L AI V+GG + +GG G I+ ++ L++ LL VS F+ G ++ Sbjct: 245 ISYELDAIAAVVIGGTSLSGGKGTIMGAVLGGIIIGVLNNGLVLLNVSPFWQQVVKGAVI 304 Query: 316 LLSL 319 LL++ Sbjct: 305 LLAV 308 Lambda K H 0.327 0.143 0.429 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: 307 Number of extensions: 16 Number of successful extensions: 1 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: 357 Length of database: 318 Length adjustment: 28 Effective length of query: 329 Effective length of database: 290 Effective search space: 95410 Effective search space used: 95410 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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