Align RnsC, component of The (deoxy)ribonucleoside permease; probably takes up all deoxy- and ribonucleosides (cytidine, uridine, adenosine and toxic analogues, fluorocytidine and fluorouridine tested), but not ribose or nucleobases (characterized)
to candidate SMa2125 SMa2125 ABC transporter permease
Query= TCDB::Q8DU38 (358 letters) >FitnessBrowser__Smeli:SMa2125 Length = 359 Score = 176 bits (446), Expect = 9e-49 Identities = 111/329 (33%), Positives = 174/329 (52%), Gaps = 16/329 (4%) Query: 14 SVILGIILGAIIMMIFGYDPIWAYEGLFQKAFGSLKDIGEIFRAMSPLILIALGFAVASR 73 +++ ++ A ++ + G D A+ L AFGS K + +PL+L+ LG +A R Sbjct: 22 AMLCALVSAAALLHLSGGDVAKAFSSLIVGAFGSQKALLGSLAKATPLLLVGLGTVIAFR 81 Query: 74 AGFFNIGLSGQAYAGWIAAGWFALANPSLPRPLMILMTVLIGAASGGVVGAIPGFLRAYL 133 A +NIG GQ AG + A W +L LP + + VL G A GG +G + G L+ Sbjct: 82 AKIWNIGQEGQVLAGAMCAYWASLWIGPLPYWIAFTVLVLAGLAGGGALGVLAGVLKTRF 141 Query: 134 GTSEVIVTIMMNYIVLYIGNAIIQDGFAKNIMRNSDSSIYVGHNAS----YQTEWLRALT 189 GTSE+I T+M+NYIV+++ ++ G ++ + V ++ S EW L Sbjct: 142 GTSEIISTVMLNYIVIFLLAYLLDGG------PWMETGVTVAYHQSPPVNAMLEWPTLLG 195 Query: 190 NNS-RMNIGFFLAIIAIVVVWYLLNKTTLGFEIRSVGLNPHASEYAGMSAKRTIVLSMII 248 + +++ GF LA++A V+ LL +T LG+EIR+ G NP A + G R +++ M++ Sbjct: 196 QGAHKLHFGFLLALVATVLCAVLLERTPLGYEIRAFGSNPTALRFRGTDISRLLLVVMLV 255 Query: 249 SGALAGLGGVVEGLGTFGNVYVQTSSLAIGFDGMAVSLLASNSPIGIFLSAFLFGALSVG 308 SGALAGL G E GT + +T L IG G+ V+++ P G L+A FGAL G Sbjct: 256 SGALAGLAGAGELFGTSHRLRAET-LLGIGSSGIVVAMVGGLRPSGAMLAALFFGALKSG 314 Query: 309 APGMSISDATHVGTPPELIKVVTALIIFF 337 A M + GTP L+ + L++ F Sbjct: 315 AIYMRLQS----GTPAGLVSAMEGLVLLF 339 Lambda K H 0.325 0.141 0.416 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: 257 Number of extensions: 11 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: 358 Length of database: 359 Length adjustment: 29 Effective length of query: 329 Effective length of database: 330 Effective search space: 108570 Effective search space used: 108570 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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