Align Purine/cytidine ABC transporter permease protein, component of General nucleoside uptake porter, NupABC/BmpA (transports all common nucleosides as well as 5-fluorocytidine, inosine, deoxyuridine and xanthosine) (Martinussen et al., 2010) (Most similar to 3.A.1.2.12). NupA is 506aas with two ABC (C) domains. NupB has 8 predicted TMSs, NupC has 9 or 10 predicted TMSs in a 4 + 1 (or 2) + 4 arrangement (characterized)
to candidate HSERO_RS21320 HSERO_RS21320 ABC transporter permease
Query= TCDB::A2RKA5 (317 letters) >FitnessBrowser__HerbieS:HSERO_RS21320 Length = 306 Score = 151 bits (381), Expect = 2e-41 Identities = 94/289 (32%), Positives = 156/289 (53%), Gaps = 14/289 (4%) Query: 10 IVANMLIYSTPLIFTSIGGVFSERGGIVNVGLEGIMTIGAFSSVVFNLTTAGMFGSMTPW 69 ++A + TPL+ +IG + +ER G++N+G EG+M + A + TT +P Sbjct: 7 LIAASINAGTPLLLAAIGLLINERSGVLNLGAEGMMLVAAIAGFAVGYTTK------SPL 60 Query: 70 LSILFGALIGALFSSLHAVATVNLRADHIVSGTVLNLMAPALGVFLLQVFYQQGQININE 129 L + GA+ G L ++L A + L + + +G L++ L F+ Q F + + Sbjct: 61 LGFMAGAVCGMLMATLFAWLALRLATNQVATGLALSIFGAGLSAFVGQRF-----VGLAL 115 Query: 130 QIGYWNVPLLSNIPVIGKIFFTQTSLPGFLAIVVAILAWYVLFKTRFGLRLRSVGENPQA 189 +VPLL ++P +G+ F Q + ++A + + + + L++TR GL LR+VGE+P++ Sbjct: 116 PAQSTSVPLLGDLPFLGQALFHQHWM-SYVAFALCLASIWFLYRTRAGLVLRAVGESPES 174 Query: 190 ADTLGINVYAYRWAGVLLSGVLGGVGGAIYAQAISGNFSVSTIAGQGFISLAAMIFGKWN 249 A LG +V R+ +L G G+ GA + + + +AG+G+I+LA F W Sbjct: 175 AHALGYSVRGIRYLALLFGGACCGLAGAYMSLVYTPMWVEGLVAGRGWIALALTAFATWR 234 Query: 250 PIGAMLSSLLFGLFTSLAVVGGQIPGIKEIPSSFLQMAPYVFTIIVLAL 298 P +L SLLFG T +A Q G+ +PS L MAPY+ TI+VLAL Sbjct: 235 PARVLLGSLLFGGVT-IAQFYLQGMGV-TVPSQILSMAPYLATIVVLAL 281 Lambda K H 0.326 0.142 0.419 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: 251 Number of extensions: 13 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: 317 Length of database: 306 Length adjustment: 27 Effective length of query: 290 Effective length of database: 279 Effective search space: 80910 Effective search space used: 80910 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 (21.6 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