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 H281DRAFT_02965 H281DRAFT_02965 nucleoside ABC transporter ATP-binding protein
Query= TCDB::A2RKA7 (506 letters) >FitnessBrowser__Burk376:H281DRAFT_02965 Length = 526 Score = 359 bits (922), Expect = e-103 Identities = 201/515 (39%), Positives = 311/515 (60%), Gaps = 22/515 (4%) Query: 4 ETVIQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEV 63 E ++ + D+ K FG F A + V+L+L G++H LLGENGAGKSTL N++ G+ +P G + Sbjct: 12 EPILSLTDIGKHFGSFTALEGVSLDLMPGDVHCLLGENGAGKSTLCNVIFGVHQPDAGAM 71 Query: 64 HVKGKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAKKKI 123 HV G +P +A GI MVHQHF LVD +V +N++LG + +N + A ++ Sbjct: 72 HVNGTPYRPKNPREALAHGIAMVHQHFSLVDDASVLDNLLLG-QARGWLNRQREAA--RL 128 Query: 124 LELSERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQ 183 E+ E GL+++ DA + D+SVG++QR+EI+K L R +L+ DEPTAVL PAEI L+ Sbjct: 129 REVLESVGLTLQLDAKVADLSVGERQRIEIVKCLMREPRLLLLDEPTAVLLPAEIDALLD 188 Query: 184 IMKNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGR-- 241 + + K G +++L+THKL EI +A TV++ G+ + L M+ R Sbjct: 189 TCERVAKRGCAVVLVTHKLKEICRIATHATVLQSGRVVARSAAPSAEIDRLVHAMIHRPD 248 Query: 242 ---------SVSFITEKAAAQP-----KDVVLEIKDLNIKESRGSLKVKGLSLDVRAGEI 287 S ++ + P + VL+I L+ +++ G +++ +L V GEI Sbjct: 249 HERGETDDDMASRLSLAESRSPYSRPLTEEVLQIDGLSARDAEGVTRLEHCTLVVNRGEI 308 Query: 288 VGVAGIDGNGQTELVKAITGLTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDG 347 VG+AG++GNGQ+EL + G+ +G + +D+T+ PR++T+ VG VPEDRH G Sbjct: 309 VGIAGVEGNGQSELGAVLAGMASASAGRFFVAGRDMTHASPRELTQAGVGIVPEDRHAVG 368 Query: 348 LVLEMTVAENIALQTYYKPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGG 407 V M+VA+N+ L + ++ GFL + + A +LM+ FDVR +G LSGG Sbjct: 369 CVTGMSVADNLLLN--HLDRYTRAGFLRRRAMRAAALDLMQRFDVRASGPDALFGGLSGG 426 Query: 408 NQQKAIIAREIDRNPDL-LIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEI 466 NQQKA++ARE+ +P L L+ +QPTRGLDVGA+ ++ + ARD G VL+IS ELDE+ Sbjct: 427 NQQKAVLARELTLDPLLFLLAAQPTRGLDVGAVAAVYSHIRAARDRGVGVLLISSELDEL 486 Query: 467 LNVSDRIAVIHDGQIQGIVSPETTTKQELGILMVG 501 ++V+DRI V++ G+I G +PE + + +G M G Sbjct: 487 MSVADRIVVLYRGRIMGTCTPEASNRGRIGAWMAG 521 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: 635 Number of extensions: 34 Number of successful extensions: 11 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: 526 Length adjustment: 35 Effective length of query: 471 Effective length of database: 491 Effective search space: 231261 Effective search space used: 231261 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