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 H281DRAFT_02963 H281DRAFT_02963 nucleoside ABC transporter membrane protein
Query= TCDB::Q8DU39 (318 letters) >FitnessBrowser__Burk376:H281DRAFT_02963 Length = 305 Score = 140 bits (354), Expect = 3e-38 Identities = 99/311 (31%), Positives = 158/311 (50%), Gaps = 15/311 (4%) Query: 1 MSLENMLALLISSMLVYATPLIFTSIGGVFSERSGVVNVGLEGIMVMGAFAGVVFNIEFA 60 M+LE +LA+ + + A P++ S G + SER+GV+N+ +EG+M+ GAF G F Sbjct: 1 MNLE-LLAVFAGASIRLAAPMMLASTGELVSERAGVLNMSVEGMMLTGAFLGATF----- 54 Query: 61 HSFGKATPWIAALVGGLVGLLFSLLHALATINFRADHIVSGTVLNLLAPSLAVFFVKALY 120 S+ P I L G L + +LL A ++ RA+ IV+G +N+LA + ++ Sbjct: 55 -SWLTGNPVIGLLCGMLGVIPLALLQAFLSVTMRANQIVTGIGINILALGGTTLAYRKIF 113 Query: 121 NKGQTDNISQSFGKFDFPILSHIPFLG-PIFFQGTSLVAYLAVLFSVFAWFILTKTKFGL 179 + ++ + + P+L IP LG P+F Q L A LAVL ++ +T G+ Sbjct: 114 GE-RSSAVIPGLAHWSPPVLGKIPVLGEPVFGQVWLLYAGLAVLIGTSV--VMRRTALGV 170 Query: 180 RLRSVGEHPQAADTLGINVYLMRYLGVMISGLLGGIGGAIYAQSISVNFAGTTILGPGFI 239 L + G P+A D G+ V +RY V+ SG++ G + F G G++ Sbjct: 171 ALHATGVAPRAVDQSGLGVARLRYGAVVFSGVMSAAAGCFLSIGDIHTFTEGMTNGAGYL 230 Query: 240 ALAAMIFGKWNPIGAMLSSLFFGLSQSLAVIGGQLP-FLSKIPTVYLQIAPYALTILVLA 298 A+AA+IFG W L+ L FG + ++ QLP F +PT L + PY L ++ +A Sbjct: 231 AIAAIIFGNWKVGRTALACLLFGAATAMQF---QLPMFGLHVPTALLIMLPYLLALVAVA 287 Query: 299 VFFGQAVAPKA 309 G+ AP A Sbjct: 288 GLIGRQSAPPA 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: 267 Number of extensions: 13 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