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 Ac3H11_2432 Nucleoside ABC transporter, permease protein 1
Query= TCDB::Q8DU38 (358 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2432 Length = 353 Score = 158 bits (399), Expect = 2e-43 Identities = 110/348 (31%), Positives = 177/348 (50%), Gaps = 22/348 (6%) Query: 8 LVVPLISVILGIILGAIIMMIFGYDPIWAYEGLFQKAFGSLKDIGEIFRAMSPLILIALG 67 ++ P+ +V+ +I+ A++++ G Y L Q AFGS+ + E +PLIL L Sbjct: 15 VLAPVGAVVFTLIVSALLVLWAGAPVGQTYALLLQGAFGSVFALTETLTRATPLILTGLA 74 Query: 68 FAVASRAGFFNIGLSGQAYAGWIAA--------GWFALANPSLPRPLMILMTVLIGAASG 119 AVA RA FNIG GQ YAG +AA G +P + PLM+L L GAA Sbjct: 75 AAVAFRARLFNIGAEGQLYAGALAAVAVGGMHGGTGLEWSPYVLFPLMMLAAALAGAAL- 133 Query: 120 GVVGAIPGFLRAYLGTSEVIVTIMMNYIVLYIGNAIIQDGFAKNIMRNSDSSIYVGHNAS 179 ++G P ++A LG EV+ T+++N+I+L + +A++ + S+ + + Sbjct: 134 -LLG--PALMKARLGVDEVVTTLLLNFIMLLLVSALLDGPMKDPLSMGWPQSVALQGDLE 190 Query: 180 YQTEWLRALTNNSRMNIGFFLAIIAIVVVWYLLNKTTLGFEIRSVGLNPHASEYAGMSAK 239 L L +R++ G A+ V++W LL +T GF+IR+ G N A+ +AG+ Sbjct: 191 -----LAKLVPQTRLHTGLLWAVSLAVMLWALLARTVPGFDIRAAGANARAAAFAGVPIT 245 Query: 240 RTIVLSMIISGALAGLGGVVEGLGTFGNVYVQTSSLAIGFDGMAVSLLASNSPIGIFLSA 299 RT+VL ++SG LAGL G +E G G V S G+ G+ +++LA P+G+ + Sbjct: 246 RTVVLVALLSGGLAGLAGAIEVAGRTGYV-TPDMSPGYGYSGIVIAMLAGLHPLGVIAAG 304 Query: 300 FLFGALSVGAPGMSISDATHVGTPPELIKVVTALIIFFVGAHYIIEHY 347 + VGA MS + VG P + V+ A + V ++ Y Sbjct: 305 TFVAGVLVGADSMSRA----VGVPTYIADVIVATSLIAVLVAGLLTQY 348 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: 252 Number of extensions: 11 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: 358 Length of database: 353 Length adjustment: 29 Effective length of query: 329 Effective length of database: 324 Effective search space: 106596 Effective search space used: 106596 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