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 GFF2652 PGA1_c26920 ABC transporter, permease protein
Query= TCDB::Q8DU38 (358 letters) >FitnessBrowser__Phaeo:GFF2652 Length = 349 Score = 151 bits (382), Expect = 2e-41 Identities = 98/327 (29%), Positives = 166/327 (50%), Gaps = 10/327 (3%) Query: 6 QKLVVPLISVILGIILGAIIMMIFGYDPIWAYEGLFQKAFGSLKDIGEIFRAMSPLILIA 65 ++L+ P ++++ L A++ I G +P+ + + AFGS + E +PLI Sbjct: 13 RRLMPPALALLATFALAALLAQIAGGEPLSIFGLILTGAFGSKFALLETLNRATPLIFTG 72 Query: 66 LGFAVASRAGFFNIGLSGQAYAGWIAAGWFALANPSLPRPLMILMTVLIGAASGGVVGAI 125 L AVA RA +NIG Q YAG + +LP PL++ + +G V+ Sbjct: 73 LAIAVAFRAKLWNIGAEAQLYAGAVITVVLGTGALNLPAPLLLPLLGAAALIAGAVLLLG 132 Query: 126 PGFLRAYLGTSEVIVTIMMNYIVLYIGNAIIQDGFAKNIMRNSDSSIYVGHNASYQTEWL 185 P L+ LG EV+ T++ N+I L + +++ + S + +A L Sbjct: 133 PALLKTRLGVDEVVTTLLFNFIFLLFVSYLLEGPLKDPMGMGWPKSPRLSADAR-----L 187 Query: 186 RALTNNSRMNIGFFLAIIAIVVVWYLLNKTTLGFEIRSVGLNPHASEYAGMSAKRTIVLS 245 + + R++ GF LA+I+ +V+W + +TTLG+E+R+VG N A+ +AG+ + I+ + Sbjct: 188 PRVVDGLRLHWGFALALISALVIWVINTRTTLGYEMRAVGQNAEAARFAGIPVTKVILKT 247 Query: 246 MIISGALAGLGGVVEGLGTFGNVYVQTSSLAIGFDGMAVSLLASNSPIGIFLSAFLFGAL 305 ++SG LAGL G E G G + + S G+ G+ V++LA PIG+ +A A+ Sbjct: 248 ALLSGGLAGLAGYSEVSGLKGALTLDLSP-GFGYTGIVVAMLALLHPIGVVFAALFVAAI 306 Query: 306 SVGAPGMSISDATHVGTPPELIKVVTA 332 VGA MS + G P L ++ A Sbjct: 307 FVGADSMSRA----AGVPSYLADIMLA 329 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: 275 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: 358 Length of database: 349 Length adjustment: 29 Effective length of query: 329 Effective length of database: 320 Effective search space: 105280 Effective search space used: 105280 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