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 RR42_RS03360 RR42_RS03360 sugar ABC transporter ATP-binding protein
Query= TCDB::A2RKA7 (506 letters) >FitnessBrowser__Cup4G11:RR42_RS03360 Length = 537 Score = 274 bits (701), Expect = 5e-78 Identities = 166/492 (33%), Positives = 269/492 (54%), Gaps = 16/492 (3%) Query: 6 VIQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEG-EVH 64 ++ + ++ K F A KV L GE+HAL+GENGAGKSTLM ILSG G E H Sbjct: 10 LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECH 69 Query: 65 VKGKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAKKKIL 124 + G+ ID P A +LG+ +++Q L +V ENI LG + + + + Sbjct: 70 IDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRACA 129 Query: 125 ELSERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQI 184 R G P A + +S+ Q+Q VEI + ++ A IL+ DEPT L+ E L + Sbjct: 130 PTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFAL 189 Query: 185 MKNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRSVS 244 ++ L EG +I+ I+H++ EI +ADR+TV+R G + T++ + L ++MVGR +S Sbjct: 190 IRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDLS 249 Query: 245 FITEKAAAQ--PKDVVLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELV 302 K Q ++V+L ++D + + R +VKG S D+RAGE++G+AG+ G G+TEL Sbjct: 250 GFYTKTHGQAVEREVMLSVRD--VADGR---RVKGCSFDLRAGEVLGLAGLVGAGRTELA 304 Query: 303 KAITGLTKVDSGSIKLHNK-------DITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVA 355 + + G G +++ N + PR+ + + ++ EDR GL L+ +V Sbjct: 305 RLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVH 364 Query: 356 ENIALQTYYKPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIA 415 ENI L + + G L+ E ++ +R A V+ +LSGGNQQK +++ Sbjct: 365 ENINLIVAARDALG-LGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLS 423 Query: 416 REIDRNPDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAV 475 R ++ P +LI+ +PTRG+D+GA I++ + G A+L+IS EL E++ + DR+ V Sbjct: 424 RLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLV 483 Query: 476 IHDGQIQGIVSP 487 + +G + G V P Sbjct: 484 MREGTLAGEVRP 495 Score = 62.8 bits (151), Expect = 3e-14 Identities = 54/236 (22%), Positives = 105/236 (44%), Gaps = 9/236 (3%) Query: 271 GSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKAITGLTKVD-SGSIKLHNKDITNQRPR 329 G ++ + L AGE+ + G +G G++ L+K ++G D G + + + P+ Sbjct: 22 GVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHIDGQRVQIDGPQ 81 Query: 330 KITEQSVGHVPEDRHRDGLVLEMTVAENIALQTYYKPPMSKYGFLDYNKINSHARELMEE 389 + V + ++ L ++VAENI Y + + G + + + Sbjct: 82 SARDLGVAVIYQEL---SLAPNLSVAENI----YLGRALQRRGLVARGDMVRACAPTLAR 134 Query: 390 FDVRGAGEWVSASSLSGGNQQKAIIAREIDRNPDLLIVSQPTRGLDVGAIEYIHKRLIQA 449 + + +SLS +Q IAR + +L++ +PT L + + + Q Sbjct: 135 LGADFSPA-ANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQL 193 Query: 450 RDEGKAVLVISFELDEILNVSDRIAVIHDGQIQGIVSPETTTKQELGILMVGGNIN 505 R EG A+L IS + EI ++DR+ V+ DG G + ++ L +MVG +++ Sbjct: 194 RGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDLS 249 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: 620 Number of extensions: 39 Number of successful extensions: 10 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: 537 Length adjustment: 35 Effective length of query: 471 Effective length of database: 502 Effective search space: 236442 Effective search space used: 236442 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