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 16258 b2149 fused methyl-galactoside transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= TCDB::A2RKA7 (506 letters) >FitnessBrowser__Keio:16258 Length = 506 Score = 302 bits (773), Expect = 2e-86 Identities = 169/494 (34%), Positives = 283/494 (57%), Gaps = 4/494 (0%) Query: 2 ANETVIQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEG 61 + E +++M + K F A D VNL+++ IHAL+GENGAGKSTL+ L G+ + G Sbjct: 9 SGEYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSG 68 Query: 62 EVHVKGKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAKK 121 + +GK + S +A GI MVHQ LV +V +N+ LG TKG+ +D + Sbjct: 69 TILFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYR 128 Query: 122 KILELSERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITEL 181 + + + + ++P A + +SV Q Q +EI K A I+I DEPT+ LT E+ L Sbjct: 129 ETKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHL 188 Query: 182 MQIMKNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGR 241 I++ L + G I+ I+HK++EI + D +TV+R G+ I T L T ++ +MVGR Sbjct: 189 FTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGR 248 Query: 242 SVSFITEKAAAQPKDVVLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTEL 301 S++ +P +V+LE+++L S ++ +S D+ GEI+G+AG+ G +T++ Sbjct: 249 SLNQRFPDKENKPGEVILEVRNLT---SLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDI 305 Query: 302 VKAITGLTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQ 361 V+ + G+ + +G+I LH K I N + V E+R G+ + + N +L Sbjct: 306 VETLFGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFN-SLI 364 Query: 362 TYYKPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRN 421 + + +K G LD +++ S + +++ V+ G SLSGGNQQK II R + Sbjct: 365 SNIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQ 424 Query: 422 PDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQI 481 P++L++ +PTRG+DVGA I++ + + +GK +++IS E+ E+L ++DRI V+ +G + Sbjct: 425 PEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLV 484 Query: 482 QGIVSPETTTKQEL 495 GIV +TTT+ E+ Sbjct: 485 SGIVDTKTTTQNEI 498 Score = 73.9 bits (180), Expect = 1e-17 Identities = 60/225 (26%), Positives = 107/225 (47%), Gaps = 17/225 (7%) Query: 25 VNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHVKGKLENIDSPSKAANLGIG 84 V+ +L KGEI + G GA ++ ++ L G+ E S G + + GK N + ++A N G Sbjct: 282 VSFDLHKGEILGIAGLVGAKRTDIVETLFGIREKSAGTITLHGKQINNHNANEAINHGFA 341 Query: 85 MVHQHFMLVDAFTVTE---NIILGN------EVTKGINLDLKTAKKKILELSERYGLSVE 135 +V + + + N ++ N +V N +K+ + +++ + V+ Sbjct: 342 LVTEERRSTGIYAYLDIGFNSLISNIRNYKNKVGLLDNSRMKSDTQWVID-----SMRVK 396 Query: 136 PDA---LIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQIMKNLIKEG 192 I +S G QQ+V I + L +IL+ DEPT + E+ Q++ L K+G Sbjct: 397 TPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKG 456 Query: 193 KSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAEL 237 K II+I+ ++ E+ + DRI V+ G V+ T E+ L Sbjct: 457 KGIIIISSEMPELLGITDRILVMSNGLVSGIVDTKTTTQNEILRL 501 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: 631 Number of extensions: 32 Number of successful extensions: 7 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: 506 Length adjustment: 34 Effective length of query: 472 Effective length of database: 472 Effective search space: 222784 Effective search space used: 222784 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