Align deoxynucleoside transporter, permease component 1 (characterized)
to candidate RR42_RS03365 RR42_RS03365 ribose ABC transporter permease
Query= reanno::Burk376:H281DRAFT_01115 (357 letters) >FitnessBrowser__Cup4G11:RR42_RS03365 Length = 333 Score = 128 bits (322), Expect = 2e-34 Identities = 100/317 (31%), Positives = 166/317 (52%), Gaps = 17/317 (5%) Query: 8 GKLFADRQLNFLLIVNVLVVL-VATWLSRGQFVDIDNLQSMGGQLPELGLLALGIMLSMV 66 G+L +L L ++ VLV+L + + F NL + Q +LA G+ ++ Sbjct: 18 GRLTTQERLRALGMLPVLVLLCIGFSVLTENFAGWQNLSIIAQQASINMVLAAGMTFVIL 77 Query: 67 SGNGGIDLSGVGLANLSGMVAAM--LVPRLVNGDDSPVLYTSLFCAIVLMMGLLGGLLNG 124 +G GIDLS + ++S +VA + L+P+L L L+ GLL G++NG Sbjct: 78 TG--GIDLSVGSILSISAVVAMLVSLMPQL----------GMLSVPAALLCGLLFGIVNG 125 Query: 125 VVIARLRLTPILCTLGTQLLFTGFAVVISNGASVHVDYVEPLSDIGNGTVLQVPIAFCIF 184 ++A ++L P + TLGT G A ++ N ++++ + + IGNG VL VP I Sbjct: 126 ALVAFMKLPPFIVTLGTLTAVRGLARLVGNDSTIYNPDIG-FAFIGNGEVLGVPWLVIIA 184 Query: 185 LAAVIVLGWLLKRSPFGLRLYLMGTNPKAAFYAGIPRARMLITTYAMCGVLASLAGLISA 244 A V V ++L+R+ GL++Y +G N +AA +GI +L+ YA+ G+LA L G++S+ Sbjct: 185 FAVVAVSWFVLRRTVLGLQIYAVGGNAEAARLSGIKVWVVLLFVYAVSGLLAGLGGVMSS 244 Query: 245 THTSSAK-WDYGNSYLLIAILIAVMGGVNPAGGHGRIICVFFAATVLQFLSSLFNLLGVS 303 +A G SY L AI ++GG + GG G I+ A ++ LS+ LLGVS Sbjct: 245 ARLYAANGLQLGQSYELDAIAAVILGGTSFVGGTGSIVGTLVGALIIAVLSNGLVLLGVS 304 Query: 304 QFFGDCAWGFLLLLSLA 320 + G +++ ++A Sbjct: 305 DIWQYIIKGLVIIGAVA 321 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: 374 Number of extensions: 27 Number of successful extensions: 4 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: 333 Length adjustment: 29 Effective length of query: 328 Effective length of database: 304 Effective search space: 99712 Effective search space used: 99712 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