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 3609044 Dshi_2433 ABC transporter related (RefSeq)
Query= TCDB::A2RKA7 (506 letters) >FitnessBrowser__Dino:3609044 Length = 510 Score = 290 bits (741), Expect = 1e-82 Identities = 165/501 (32%), Positives = 281/501 (56%), Gaps = 13/501 (2%) Query: 3 NETVIQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGE 62 ++ + + +TK F A V+L L G++ AL+GENGAGKST++ IL+G+ +P G Sbjct: 17 SQAALALAHITKTFPGVKALSDVSLSLYPGKVTALIGENGAGKSTVVKILTGIYQPDGGR 76 Query: 63 VHVKGKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINL-DLKTAKK 121 + V G+ +P AA+ G+ +HQ +L D +V ENI LG+ L D K + Sbjct: 77 ILVDGQPVPFSTPQAAADHGVTAIHQETVLFDELSVAENIFLGHAPRGAFGLIDWKKTTE 136 Query: 122 KILELSERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITEL 181 L G ++PD ++D+ + + V I + L A ++I DEPTA L+ EI EL Sbjct: 137 NARALLTSIGAELDPDHKLKDLGIANKHLVAIARALSIEARVVIMDEPTAALSHKEIEEL 196 Query: 182 MQIMKNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGR 241 +++++L +GK+I+ I+HK DEI +AD TV R G+ I + D T +L ++MVGR Sbjct: 197 YELVESLKAQGKAILFISHKFDEIFRIADNYTVFRDGQLIGDGAIADVTEADLVKMMVGR 256 Query: 242 SVSFITEKAAAQPKDVVLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTEL 301 VS I + A D VL ++ + +S +R GEI+G G+ G G++E Sbjct: 257 DVSQIFPQRAPNVGDTVLTVQGY-----AHPTEFDDISFTLREGEILGFYGLVGAGRSEF 311 Query: 302 VKAITGLTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQ 361 ++++ G+T+ +GS+++ P + + +VPEDR + G +L++ + +N+ L Sbjct: 312 MQSLFGITRPSAGSVEIGGARAEISSPADAVDHGIVYVPEDRGKQGAILDLPIFQNVTLP 371 Query: 362 TYYKPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRN 421 + + +S+ GFL + + ARE E D+R A +LSGGNQQK +IA+ + Sbjct: 372 SLGR--ISRKGFLRLAEEFALAREYTERLDLRAASLDTHVGNLSGGNQQKVVIAKWLATR 429 Query: 422 PDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQI 481 P ++I+ +PT+G+D+G+ +H + + +G AV+++S E+ E+L +SDR+ V+ +G+I Sbjct: 430 PRVIILDEPTKGVDIGSKAAVHDFMAELAAQGLAVIMVSSEIPEVLGMSDRVIVMREGRI 489 Query: 482 QGIVS-----PETTTKQELGI 497 ++ PET + GI Sbjct: 490 VAELAGDDLQPETLVRHAAGI 510 Score = 93.2 bits (230), Expect = 2e-23 Identities = 62/237 (26%), Positives = 118/237 (49%), Gaps = 9/237 (3%) Query: 271 GSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKAITGLTKVDSGSIKLHNKDITNQRPRK 330 G + +SL + G++ + G +G G++ +VK +TG+ + D G I + + + P+ Sbjct: 32 GVKALSDVSLSLYPGKVTALIGENGAGKSTVVKILTGIYQPDGGRILVDGQPVPFSTPQA 91 Query: 331 ITEQSVGHVPEDRHRDGLVL-EMTVAENIALQTYYKPPMSKYGFLDYNKINSHARELMEE 389 + V + H++ ++ E++VAENI L P +G +D+ K +AR L+ Sbjct: 92 AADHGVTAI----HQETVLFDELSVAENIFLG---HAPRGAFGLIDWKKTTENARALLTS 144 Query: 390 FDVRGAGEWVSASSLSGGNQQKAIIAREIDRNPDLLIVSQPTRGLDVGAIEYIHKRLIQA 449 + L N+ IAR + ++I+ +PT L IE +++ + Sbjct: 145 IGAELDPDH-KLKDLGIANKHLVAIARALSIEARVVIMDEPTAALSHKEIEELYELVESL 203 Query: 450 RDEGKAVLVISFELDEILNVSDRIAVIHDGQIQGIVSPETTTKQELGILMVGGNINE 506 + +GKA+L IS + DEI ++D V DGQ+ G + T+ +L +MVG ++++ Sbjct: 204 KAQGKAILFISHKFDEIFRIADNYTVFRDGQLIGDGAIADVTEADLVKMMVGRDVSQ 260 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: 2 Number of HSP's successfully gapped: 2 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