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 AZOBR_RS31245 AZOBR_RS31245 ABC transporter ATP-binding protein
Query= TCDB::A2RKA7 (506 letters) >FitnessBrowser__azobra:AZOBR_RS31245 Length = 518 Score = 284 bits (727), Expect = 5e-81 Identities = 175/506 (34%), Positives = 285/506 (56%), Gaps = 11/506 (2%) Query: 6 VIQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPS--EGEV 63 +++M +TK F A D VNL +++GEIHAL+GENGAGKSTLM +LSG+ +GE+ Sbjct: 5 ILEMKGITKTFPGVKALDDVNLSVREGEIHALIGENGAGKSTLMKVLSGVYPQGSFDGEI 64 Query: 64 HVKGKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAKKKI 123 +G+ + + + LGI ++HQ LV ++TEN+ LGNE +D A + Sbjct: 65 RFRGQPQAFRGIADSERLGIIIIHQELALVPLLSITENLFLGNEQASRGVIDWDAATLRA 124 Query: 124 LELSERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQ 183 EL GL P+ LI DI VG+QQ VEI K L + +LI DEPTA L ++ L++ Sbjct: 125 RELLRLVGLHDPPETLITDIGVGKQQLVEIAKALSKEVKLLILDEPTASLNESDSDALLE 184 Query: 184 IMKNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDK--TNQELAELMVGR 241 ++ G + ILI+HKL+EI VADR+T++R G +++T++ + + + MVGR Sbjct: 185 LLLQFKARGIASILISHKLNEIAKVADRVTILRDGTTVETLDCREAVVSQDRIIRGMVGR 244 Query: 242 SVSFITEKAAAQPKDVVLEIKDLNIKESR--GSLKVKGLSLDVRAGEIVGVAGIDGNGQT 299 ++S + P DV+ E+K + G V+ ++L VR GE+VG+AG+ G G+T Sbjct: 245 ALSDRYPRRTTVPGDVLFEVKGWSADHPAHPGRRVVRDVNLTVRRGEVVGIAGLMGAGRT 304 Query: 300 ELVKAITGLT--KVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAEN 357 E ++ G + + G L ++I + + + EDR GLVL+ + N Sbjct: 305 EFAMSLFGRSYGRNIRGQAFLDGREIDVSTISRAMANGLAYATEDRKHLGLVLDNDIRHN 364 Query: 358 IALQTYYKPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIARE 417 + L ++K +D+ + A E +R A + +LSGGNQQK ++++ Sbjct: 365 VTLANL--RGVAKRWVIDHEREVQVAEEFRRRLRIRCADVFQETVNLSGGNQQKVVLSKW 422 Query: 418 IDRNPDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIH 477 + +P +LI+ +PTRG+DVGA I+ + Q EG+ V++IS E+ E+L V+DRI V++ Sbjct: 423 LFADPQVLILDEPTRGIDVGAKYEIYTIINQLVAEGRGVVLISSEMPELLGVADRIYVMN 482 Query: 478 DGQ-IQGIVSPETTTKQELGILMVGG 502 G+ + + + E + ++ +G +M G Sbjct: 483 AGEMVAEMPAAEASQEKIMGAIMRSG 508 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: 657 Number of extensions: 36 Number of successful extensions: 9 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: 518 Length adjustment: 35 Effective length of query: 471 Effective length of database: 483 Effective search space: 227493 Effective search space used: 227493 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