Align Purine/cytidine ABC transporter ATP-binding 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 18115 b4087 fused D-allose transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= TCDB::A2RKA7 (506 letters) >FitnessBrowser__Keio:18115 Length = 510 Score = 310 bits (793), Expect = 1e-88 Identities = 183/501 (36%), Positives = 292/501 (58%), Gaps = 19/501 (3%) Query: 7 IQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHVK 66 I M + K FG A VNL + GEIHALLGENGAGKSTLM +LSG+ EP++G + + Sbjct: 6 ISMAGIGKSFGPVHALKSVNLTVYPGEIHALLGENGAGKSTLMKVLSGIHEPTKGTITIN 65 Query: 67 GKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTK---GINL-DLKTAKKK 122 N AA LGIG+++Q ++D TV EN+ +G +TK G+N+ D + + + Sbjct: 66 NISYNKLDHKLAAQLGIGIIYQELSVIDELTVLENLYIGRHLTKKICGVNIIDWREMRVR 125 Query: 123 ILELSERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELM 182 + R GL V+ D + ++S+ +Q +EI KTL A ++I DEPT+ LT E+ L Sbjct: 126 AAMMLLRVGLKVDLDEKVANLSISHKQMLEIAKTLMLDAKVIIMDEPTSSLTNKEVDYLF 185 Query: 183 QIMKNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRS 242 IM L KEG +I+ I+HKL EIR + DR TV++ G S+ + + D +N ++ LMVGR Sbjct: 186 LIMNQLRKEGTAIVYISHKLAEIRRICDRYTVMKDGSSVCSGIVSDVSNDDIVRLMVGRE 245 Query: 243 V----SFITEKAAAQPKDVVLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQ 298 + + + E + + V E++++ SR KV+ +S V GEI+G AG+ G+G+ Sbjct: 246 LQNRFNAMKENVSNLAHETVFEVRNVT---SRDRKKVRDISFSVCRGEILGFAGLVGSGR 302 Query: 299 TELVKAITGLTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENI 358 TEL+ + G+ K G I+L+ KDI+ + P ++ + ++ E R +G ++A+N+ Sbjct: 303 TELMNCLFGVDKRAGGEIRLNGKDISPRSPLDAVKKGMAYITESRRDNGFFPNFSIAQNM 362 Query: 359 ALQTY-----YKPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAI 413 A+ YK M + +D + + REL+ ++ + + LSGGNQQK + Sbjct: 363 AISRSLKDGGYKGAMGLFHEVDEQRTAENQRELLA---LKCHSVNQNITELSGGNQQKVL 419 Query: 414 IAREIDRNPDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRI 473 I++ + P+++I +PTRG+DVGA I+K + Q D+GK +L++S EL EI+ V DRI Sbjct: 420 ISKWLCCCPEVIIFDEPTRGIDVGAKAEIYKVMRQLADDGKVILMVSSELPEIITVCDRI 479 Query: 474 AVIHDGQIQGIVSPETTTKQE 494 AV +G++ I++ +E Sbjct: 480 AVFCEGRLTQILTNRDDMSEE 500 Lambda K H 0.315 0.135 0.365 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: 642 Number of extensions: 30 Number of successful extensions: 8 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: 506 Length of database: 510 Length adjustment: 34 Effective length of query: 472 Effective length of database: 476 Effective search space: 224672 Effective search space used: 224672 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 52 (24.6 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