Align deoxynucleoside transporter, permease component 1 (characterized)
to candidate 15635 b1514 AI2 transporter (NCBI)
Query= reanno::Burk376:H281DRAFT_01115 (357 letters) >FitnessBrowser__Keio:15635 Length = 342 Score = 118 bits (295), Expect = 3e-31 Identities = 94/311 (30%), Positives = 152/311 (48%), Gaps = 13/311 (4%) Query: 13 DRQLNFLLIVNVLVVLVATWLSRGQFVDIDNLQSMGGQLPELGLLALGIMLSMVSGNGGI 72 +R++ LL V +L VL +L R Q++ + L + L LLA+G L M++ N I Sbjct: 8 NREITALLAVVLLFVLPG-FLDR-QYLSVQTLTMVYSSAQILILLAMGATLVMLTRN--I 63 Query: 73 DLSGVGLANLSGMVAAMLVPRLVNGDDSPVLYTSLFCAIVLMMGLLGGLLNGVVIARLRL 132 D+S + +++GM A +L L G PV C L++GLL G NGV++A L++ Sbjct: 64 DVS---VGSITGMCAVLLGMLLNAGYSLPVA-----CVATLLLGLLAGFFNGVLVAWLKI 115 Query: 133 TPILCTLGTQLLFTGFAVVISNGASVHVDYVEPLSDIGNGTVLQVPIAFCIFLAAVIVLG 192 I+ TLGT L+ G ++ + G + E L + +L V + + V + Sbjct: 116 PAIVATLGTLGLYRGIMLLWTGGKWIEGLPAE-LKQLSAPLLLGVSAIGWLTIILVAFMA 174 Query: 193 WLLKRSPFGLRLYLMGTNPKAAFYAGIPRARMLITTYAMCGVLASLAGLISATHTSSAKW 252 WLL ++ FG Y G N + A G+ + I +++ G +A+LAG++ A+ Sbjct: 175 WLLAKTAFGRSFYATGDNLQGARQLGVRTEAIRIVAFSLNGCMAALAGIVFASQIGFIPN 234 Query: 253 DYGNSYLLIAILIAVMGGVNPAGGHGRIICVFFAATVLQFLSSLFNLLGVSQFFGDCAWG 312 G + AI V+GG++ GG G II A L + S+ LL + ++ D G Sbjct: 235 QTGTGLEMKAIAACVLGGISLLGGSGAIIGAVLGAWFLTQIDSVLVLLRIPAWWNDFIAG 294 Query: 313 FLLLLSLAFAG 323 +LL L F G Sbjct: 295 LVLLAVLVFDG 305 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: 306 Number of extensions: 15 Number of successful extensions: 2 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: 342 Length adjustment: 29 Effective length of query: 328 Effective length of database: 313 Effective search space: 102664 Effective search space used: 102664 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