Align deoxynucleoside transporter, permease component 1 (characterized)
to candidate HSERO_RS05100 HSERO_RS05100 sugar ABC transporter permease
Query= reanno::Burk376:H281DRAFT_01115 (357 letters) >FitnessBrowser__HerbieS:HSERO_RS05100 Length = 337 Score = 373 bits (958), Expect = e-108 Identities = 190/312 (60%), Positives = 242/312 (77%), Gaps = 1/312 (0%) Query: 12 ADRQLNFLLIVNVLVVLVATWLSRGQFVDIDNLQSMGGQLPELGLLALGIMLSMVSGNGG 71 +D QL FLL++NV ++LVAT S G F+DI N QSM QLPELGLLA+G+ L+M+SGNGG Sbjct: 8 SDPQLLFLLVINVAILLVATVFSHGDFLDIYNFQSMASQLPELGLLAIGVALAMISGNGG 67 Query: 72 IDLSGVGLANLSGMVAAMLVPRLVNGDDS-PVLYTSLFCAIVLMMGLLGGLLNGVVIARL 130 IDLSG+GLANL+G+VAA +P LV D+ P YT F A+ L+ GLLGG LNG +I+R Sbjct: 68 IDLSGIGLANLAGVVAAAAMPLLVAAPDAAPWTYTLGFIAVALVTGLLGGALNGWLISRG 127 Query: 131 RLTPILCTLGTQLLFTGFAVVISNGASVHVDYVEPLSDIGNGTVLQVPIAFCIFLAAVIV 190 LTPILCTLGTQ++FTG AVV++NG+S+ + V+P+S IGN +VL VPI F IF+A +++ Sbjct: 128 NLTPILCTLGTQMIFTGLAVVLTNGSSLRISVVDPISAIGNESVLGVPIPFIIFVALLLL 187 Query: 191 LGWLLKRSPFGLRLYLMGTNPKAAFYAGIPRARMLITTYAMCGVLASLAGLISATHTSSA 250 +GWL++ S FG++LYL+GTN +AA YAGI + R+ TY + GVLAS+AG+I A T+S Sbjct: 188 VGWLMRYSLFGIKLYLLGTNARAARYAGISQNRLRFATYVISGVLASVAGIIIAARTASV 247 Query: 251 KWDYGNSYLLIAILIAVMGGVNPAGGHGRIICVFFAATVLQFLSSLFNLLGVSQFFGDCA 310 K DYGNSYLLIAILIAVM GV P GG+GR++C+FF+A LQ LSS FNLL +S FF DCA Sbjct: 248 KADYGNSYLLIAILIAVMAGVRPQGGYGRMVCLFFSALALQLLSSTFNLLEISNFFRDCA 307 Query: 311 WGFLLLLSLAFA 322 WG LLL LA A Sbjct: 308 WGLLLLCFLASA 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: 379 Number of extensions: 15 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: 357 Length of database: 337 Length adjustment: 29 Effective length of query: 328 Effective length of database: 308 Effective search space: 101024 Effective search space used: 101024 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