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 N515DRAFT_3232 N515DRAFT_3232 xylose ABC transporter ATP-binding protein
Query= TCDB::A2RKA7 (506 letters) >FitnessBrowser__Dyella79:N515DRAFT_3232 Length = 513 Score = 259 bits (662), Expect = 2e-73 Identities = 174/503 (34%), Positives = 274/503 (54%), Gaps = 10/503 (1%) Query: 1 MANETVI-QMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPS 59 MA E+ + +M + K FG A D ++L L+ GE L GENGAGKSTLM +LSG+ Sbjct: 1 MAGESCLFEMRGIAKSFGGVKALDGIDLRLRAGECLGLCGENGAGKSTLMKVLSGVYPHG 60 Query: 60 --EGEVHVKGKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTK-GINLDL 116 +GE+ +G+ S + GI ++HQ MLV +V ENI LG+E+T+ G +D Sbjct: 61 SWDGEILWQGQPLRARSVRDSERAGIVIIHQELMLVPQLSVAENIFLGHEITRPGGRMDY 120 Query: 117 KTAKKKILELSERYGLSVEPDAL-IRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTP 175 K L + GL AL G QQ EI K L + A +LI DEPT+ LT Sbjct: 121 DAMYAKADALLQELGLHDVNVALPAMHYGGGHQQLFEIAKALAKQAKLLILDEPTSSLTS 180 Query: 176 AEITELMQIMKNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELA 235 +E L+ I+++L + G + I I+HKLDE+ V D + VIR G+ I T + + L Sbjct: 181 SETEVLLGIVEDLKRRGVACIYISHKLDEVERVCDTVCVIRDGRHIATQPMHELDVDTLI 240 Query: 236 ELMVGRSVSFITEKAAAQPKDVVLEIKDLNIKE--SRGSLKVKGLSLDVRAGEIVGVAGI 293 LMVGR + + + +V+ E + + + +V +S +R GEI+G+AG+ Sbjct: 241 TLMVGRKLENLYPRIEHAIGEVIFEARHATCLDPVNPQRKRVDDVSFQLRRGEILGIAGL 300 Query: 294 DGNGQTELVKAITGL-TKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEM 352 G G+TELV AI G T S + L + + + P +G VPEDR R G+V + Sbjct: 301 VGAGRTELVSAIFGAYTGKSSVELFLEGRPLKIRSPADAIRAGLGMVPEDRKRHGIVPLL 360 Query: 353 TVAENIALQTYYKPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKA 412 V +NI L T + G +D + + E V+ A + + LSGGNQQKA Sbjct: 361 GVGDNITLATL--DHYAHAGHIDRQRELVAIEAQIAERRVKTASPALPIARLSGGNQQKA 418 Query: 413 IIAREIDRNPDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDR 472 ++A+ + P +LI+ +PTRG+DVGA I++ + + +G A++++S E+ E+L ++DR Sbjct: 419 VLAKMLLARPKVLILDEPTRGVDVGAKAEIYRLIFELAAQGVAIVLVSSEMPEVLGMADR 478 Query: 473 IAVIHDGQIQGIVSPETTTKQEL 495 + V+ +G+++G + T++++ Sbjct: 479 VLVMGEGRLRGDFPNQGLTQEQV 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: 613 Number of extensions: 35 Number of successful extensions: 10 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: 513 Length adjustment: 34 Effective length of query: 472 Effective length of database: 479 Effective search space: 226088 Effective search space used: 226088 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