Align RnsD, 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 BPHYT_RS26070 BPHYT_RS26070 ABC transporter permease
Query= TCDB::Q8DU39 (318 letters) >FitnessBrowser__BFirm:BPHYT_RS26070 Length = 305 Score = 142 bits (357), Expect = 1e-38 Identities = 94/306 (30%), Positives = 163/306 (53%), Gaps = 16/306 (5%) Query: 7 LALLISSMLVYATPLIFTSIGGVFSERSGVVNVGLEGIMVMGAFAGVVFNIEFAHSFGKA 66 +A+ + S + +A PL+ S G + SER+GV+N+ +EG+M+ GAF G A + G A Sbjct: 6 VAVFVGSSIRFAAPLMLASTGELISERAGVLNMSVEGMMLSGAFLGAAG----AWATGNA 61 Query: 67 TPWIAALVGGLVGLL-FSLLHALATINFRADHIVSGTVLNLLAPSLAVFFVKALYNKGQT 125 T +A G++G+L +LL A ++ RA+ IV+G +N+LA + L+ + ++ Sbjct: 62 TLGLAI---GMLGVLPIALLQAFLSVTLRANQIVTGIGINILALGATTLAYRELFGE-RS 117 Query: 126 DNISQSFGKFDFPILSHIPFLG-PIFFQGTSLVAYLAVLFSVFAWFILTKTKFGLRLRSV 184 + ++ P L +P +G P+F Q + LA+L + ++ +T G+ L +V Sbjct: 118 SAVIPGLARWSPPGLGALPVIGEPVFHQVWLVYLGLAILLATS--LVMRRTALGVALHAV 175 Query: 185 GEHPQAADTLGINVYLMRYLGVMISGLLGGIGGAIYAQSISVNFAGTTILGPGFIALAAM 244 G P++ D G++V +RY V+ SG++ G G + F G G++A+AA+ Sbjct: 176 GAAPRSVDQSGLSVTRLRYGAVLFSGVMSGAAGCFISIGDIHTFTEGMTSGAGYLAIAAI 235 Query: 245 IFGKWNPIGAMLSSLFFGLSQSLAVIGGQLPFLS-KIPTVYLQIAPYALTILVLAVFFGQ 303 IFG W + + L FG + +L QLP + ++PT L + PY L ++ +A G+ Sbjct: 236 IFGNWKIGRTVGACLLFGAASALQF---QLPLIGVQVPTALLVMLPYLLALIAVAGLIGR 292 Query: 304 AVAPKA 309 AP A Sbjct: 293 QTAPLA 298 Lambda K H 0.328 0.143 0.422 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: 15 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: 318 Length of database: 305 Length adjustment: 27 Effective length of query: 291 Effective length of database: 278 Effective search space: 80898 Effective search space used: 80898 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: 48 (23.1 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