Align deoxynucleoside transporter, permease component 1 (characterized)
to candidate BWI76_RS14865 BWI76_RS14865 ribose ABC transporter permease
Query= reanno::Burk376:H281DRAFT_01115 (357 letters) >FitnessBrowser__Koxy:BWI76_RS14865 Length = 339 Score = 142 bits (358), Expect = 1e-38 Identities = 100/309 (32%), Positives = 163/309 (52%), Gaps = 13/309 (4%) Query: 15 QLNFLLIVNVLVVLVATWLSRGQFVDIDNLQSMGGQLPELGLLALGIMLSMVSGNGGIDL 74 ++ L+++ VL++L++T+ F +DNL ++ + +LA G+ +++ GIDL Sbjct: 24 RVGILIVLLVLLILMSTFAPN--FNRVDNLLNIARSISVNAILAAGMTFVILTS--GIDL 79 Query: 75 SGVGLANLSGMVAAMLVPRLVNGDDSPVLYTSLFCAIVLMMGLLGGLLNGVVIARLRLTP 134 S + +SG+V+ + + G +P+ + + +G L GLLNGV+ A L L P Sbjct: 80 SVGSIVAVSGVVSVVAA---MAGIPAPLAILA-----GVGVGALCGLLNGVLTAYLALAP 131 Query: 135 ILCTLGTQLLFTGFAVVISNGASVHVDYVEPLSDIGNGTVLQVPIAFCIFLAAVIVLGWL 194 + TLGT G A I+ G + V ++GNG ++ +PI I L ++ ++ Sbjct: 132 FIVTLGTMTFLRGMAYTITEGQPI-VSSSLSFRELGNGYLIGIPIPVIIMLVVYLLAWFI 190 Query: 195 LKRSPFGLRLYLMGTNPKAAFYAGIPRARMLITTYAMCGVLASLAGLISATHTSSAKWDY 254 L+R+ FG +Y +G N +AA AG+ R+L Y + GV A LAG+I A SA+ Sbjct: 191 LERTRFGRHIYAVGGNAQAARLAGVRVKRVLAAVYMIAGVCAGLAGIIFAARVISAQPTA 250 Query: 255 GNSYLLIAILIAVMGGVNPAGGHGRIICVFFAATVLQFLSSLFNLLGVSQFFGDCAWGFL 314 G Y L AI V+GG + AGG GRII + +L LS+ LL V F G + Sbjct: 251 GTGYELDAIAAVVLGGTSLAGGRGRIIGTLIGSIILGVLSTGLILLSVPFFTQLLIKGIV 310 Query: 315 LLLSLAFAG 323 ++L++A G Sbjct: 311 IILAVAIDG 319 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: 334 Number of extensions: 21 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: 339 Length adjustment: 29 Effective length of query: 328 Effective length of database: 310 Effective search space: 101680 Effective search space used: 101680 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 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