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 Echvi_1282 Echvi_1282 ABC-type sugar transport system, ATPase component
Query= TCDB::A2RKA7 (506 letters) >FitnessBrowser__Cola:Echvi_1282 Length = 502 Score = 298 bits (763), Expect = 3e-85 Identities = 173/487 (35%), Positives = 278/487 (57%), Gaps = 5/487 (1%) Query: 11 DVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHVKGKLE 70 ++TK F A D V+LEL+ G + A+LGENGAGKSTLM ILSG+ +G ++ G Sbjct: 6 NITKEFVGVKALDDVSLELQAGRVTAILGENGAGKSTLMKILSGVYPDYKGTIYYNGDPV 65 Query: 71 NIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINL-DLKTAKKKILELSER 129 + A GI ++HQ L+ ++ ENI LG E + L D+ K+ +L R Sbjct: 66 KFQNTRDAQEKGINIIHQELNLIPYLSIRENIFLGREPETPMGLLDVAKMHKEAAQLLHR 125 Query: 130 YGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQIMKNLI 189 L+V+P+ + + VGQQQ VEI K L + ++I DEPT+ ++ E+ L I++ L Sbjct: 126 LKLNVDPETPVSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQEVEILFGIIRALR 185 Query: 190 KEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRSVSFITEK 249 EGK+I I+HKLDE+ A+ADR V+R GK I++ E+ T + L + MVGR + Sbjct: 186 AEGKAIAYISHKLDELFAIADRYVVLRDGKMIESGEMEGMTEEALIQKMVGREIVIERSC 245 Query: 250 AAAQPKDVVLEIKDLNIKESRGSLK--VKGLSLDVRAGEIVGVAGIDGNGQTELVKAITG 307 + Q + VL +K L +K + + K ++ ++ ++ GE++G+ G+ G G+TEL++A+ G Sbjct: 246 SGRQFDETVLSVKHLTVKHPKIADKFLLQDINFELGKGEVLGIFGLMGAGRTELMEALFG 305 Query: 308 LTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQTYYKPP 367 + I L K Q+P++ + + VPEDR +DGLVL M + N +L Sbjct: 306 VLPHQGAEITLAGKVHEFQKPQEAMDAGLALVPEDRKQDGLVLCMDLCTNSSLTVV--DS 363 Query: 368 MSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRNPDLLIV 427 + G LD K A++ M E ++ + LSGGNQQK ++A+ + P +L++ Sbjct: 364 ILSGGLLDDKKEKGLAQKYMGELKIKASSHRQLVEKLSGGNQQKVVLAKWLATRPKVLML 423 Query: 428 SQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQIQGIVSP 487 +PTRG+D+ A I+K + Q +EG ++V+S EL EIL VSDR+ V+ +G++ + Sbjct: 424 DEPTRGIDINAKNEIYKLIRQLANEGLGLIVVSSELPEILAVSDRVLVMAEGRLTANIPI 483 Query: 488 ETTTKQE 494 + T ++ Sbjct: 484 DAQTSED 490 Score = 93.2 bits (230), Expect = 2e-23 Identities = 67/247 (27%), Positives = 124/247 (50%), Gaps = 8/247 (3%) Query: 258 VLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKAITGLTKVDSGSIK 317 +L +K++ KE G + +SL+++AG + + G +G G++ L+K ++G+ G+I Sbjct: 1 MLTVKNIT-KEFVGVKALDDVSLELQAGRVTAILGENGAGKSTLMKILSGVYPDYKGTIY 59 Query: 318 LHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQTYYKPPMSKYGFLDYN 377 + + Q R E+ + + ++ + L+ +++ ENI L + PM G LD Sbjct: 60 YNGDPVKFQNTRDAQEKGINIIHQELN---LIPYLSIRENIFLGREPETPM---GLLDVA 113 Query: 378 KINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRNPDLLIVSQPTRGLDVG 437 K++ A +L+ + E S L G QQ IA+ + ++I+ +PT + Sbjct: 114 KMHKEAAQLLHRLKLNVDPE-TPVSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQ 172 Query: 438 AIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQIQGIVSPETTTKQELGI 497 +E + + R EGKA+ IS +LDE+ ++DR V+ DG++ E T++ L Sbjct: 173 EVEILFGIIRALRAEGKAIAYISHKLDELFAIADRYVVLRDGKMIESGEMEGMTEEALIQ 232 Query: 498 LMVGGNI 504 MVG I Sbjct: 233 KMVGREI 239 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: 646 Number of extensions: 27 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: 502 Length adjustment: 34 Effective length of query: 472 Effective length of database: 468 Effective search space: 220896 Effective search space used: 220896 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