Align deoxynucleoside transporter, permease component 2 (characterized)
to candidate Echvi_1280 Echvi_1280 Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components
Query= reanno::Burk376:H281DRAFT_01112 (364 letters) >FitnessBrowser__Cola:Echvi_1280 Length = 318 Score = 132 bits (331), Expect = 2e-35 Identities = 93/322 (28%), Positives = 154/322 (47%), Gaps = 52/322 (16%) Query: 58 IVVTCLIVGAINPRFFQFATLFDLLHSATTMSLFALGTLVVLASGGIDVSFTAIAALTMY 117 +++ CL++ ++ RF A ++++ + ++G +V+ + GID+S +I AL Sbjct: 13 LIILCLVLSLLSDRFLTLANGWNVMRQVSVNICISVGMTLVILTAGIDLSVGSILALC-- 70 Query: 118 GITKAVFAWWPDAPFALILVTG--ALGGVVLGM--------VNGLLVHRLKAPSLIVTIG 167 G A A L L G LG V+LG+ NG + R K P + T+ Sbjct: 71 GAVTASLIKNGIAVEGLNLHIGFAPLGAVILGVGLGFGLGWFNGWTITRFKVPPFVATLA 130 Query: 168 TQYLYRGLLL---------------TFIGTTFFMNIPHSMDRFGRIPLFFYHTADGLRAV 212 + RGL + F+GT +F+ IP Sbjct: 131 MLTIARGLTMLWTGGFPINGLGEDFAFLGTGWFLGIP----------------------- 167 Query: 213 LPVSVLALVAAAVVTWWLLNRTMMGRAVYAMGGSLAIAERLGYNLRAIHLFVFGYTGMLA 272 +PV + A++ A V L +T GR VYA+GG+ A G N+ + + V+ G LA Sbjct: 168 MPVWITAVIVALAVL--LTKKTKFGRYVYAIGGNERAARLSGINISRVKMTVYAIAGGLA 225 Query: 273 GIAGILHVSNNRLANPFDLVGSELDVIAAVILGGARITGGTGTVVGTLLGVVLVTLIKSV 332 + G++ S A P + ELD IAAV++GG ++GG GT++G +LG +++ ++ + Sbjct: 226 AVGGMIVTSRLDSAQPNAGISYELDAIAAVVIGGTSLSGGKGTIMGAVLGGIIIGVLNNG 285 Query: 333 LILVGVPSTWQKVIIGAFILLA 354 L+L+ V WQ+V+ GA ILLA Sbjct: 286 LVLLNVSPFWQQVVKGAVILLA 307 Lambda K H 0.328 0.141 0.426 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: 271 Number of extensions: 14 Number of successful extensions: 3 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: 364 Length of database: 318 Length adjustment: 28 Effective length of query: 336 Effective length of database: 290 Effective search space: 97440 Effective search space used: 97440 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