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 WP_069332735.1 C8J29_RS16570 sugar ABC transporter ATP-binding protein
Query= TCDB::A2RKA7 (506 letters) >NCBI__GCF_003046325.1:WP_069332735.1 Length = 499 Score = 300 bits (769), Expect = 6e-86 Identities = 177/502 (35%), Positives = 285/502 (56%), Gaps = 13/502 (2%) Query: 4 ETVIQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEV 63 E V+ + V++ FG V+ +L+ GE+HAL+GENGAGKST M IL+G L PS GEV Sbjct: 3 EPVLAIRQVSRLFGPVQVLFDVDFDLRPGEVHALIGENGAGKSTTMKILAGYLAPSAGEV 62 Query: 64 HVKGKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAKKKI 123 + G+ + S +A G+ M+HQ F L TV ENI LG E+ +G LD + + + Sbjct: 63 LLDGRPVHFPSSREAEAAGVVMIHQEFNLATPLTVEENIFLGRELKRGPFLDHRAMQAES 122 Query: 124 LELSERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQ 183 L ER +V+P A + +SV +Q VEI K L A +LI DEPTAVLT E L++ Sbjct: 123 RRLLERLHCAVDPRARVSTLSVPNRQMVEIAKALGLKARVLIMDEPTAVLTHRETDTLLE 182 Query: 184 IMKNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRSV 243 + L G +I+ +HKLDE+ +ADR+TV+R G+ + T + +AE MVGR + Sbjct: 183 QVDRLRAAGTAILYTSHKLDEVARIADRVTVLRDGRRVMTAPAKGLSEDRMAETMVGREL 242 Query: 244 SFITEKAAAQPKDVVLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVK 303 S + ++ + VLE+ L + V+ S +R GE++G AG+ G+G+TEL++ Sbjct: 243 SGLFPPKSSPAPEPVLEVAGLTVPGF-----VRDASFTLRRGEVLGFAGLVGSGRTELME 297 Query: 304 AITGLTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQTY 363 I GL + +G +++ + + + ++ EDR GL+L + EN+ L Sbjct: 298 GIVGL-RPATGEVRMEGSPLPHASVSAARAAGLVYLTEDRKEKGLLLGKPLGENLTLLA- 355 Query: 364 YKPPMSKYG--FLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRN 421 + ++G +D + + +FD+R +SA SLSGGNQQK ++A+ + Sbjct: 356 ----LDRFGRVLIDKAAEERALTQAISDFDIRVGDRGISAGSLSGGNQQKLLLAKTMLAE 411 Query: 422 PDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQI 481 P ++I+ +PTRG+DVG + I+ + + EG++V+V+S EL E++ +++R+ V+ G+I Sbjct: 412 PRVVIIDEPTRGIDVGTKQQIYGFIARLAAEGRSVIVVSSELPEVIGLANRVVVMSAGRI 471 Query: 482 QGIVSPETTTKQELGILMVGGN 503 G V E T++ + L +G N Sbjct: 472 AGEVEGEAITEENIVRLAMGLN 493 Score = 74.3 bits (181), Expect = 9e-18 Identities = 55/228 (24%), Positives = 107/228 (46%), Gaps = 8/228 (3%) Query: 278 LSLDVRAGEIVGVAGIDGNGQTELVKAITGLTKVDSGSIKLHNKDITNQRPRKITEQSVG 337 + D+R GE+ + G +G G++ +K + G +G + L + + R+ V Sbjct: 24 VDFDLRPGEVHALIGENGAGKSTTMKILAGYLAPSAGEVLLDGRPVHFPSSREAEAAGVV 83 Query: 338 HVPEDRHRDGLVLEMTVAENIALQTYYKPPMSKYGFLDYNKINSHARELMEEFDVRGAGE 397 + ++ + L +TV ENI L K + FLD+ + + +R L+E Sbjct: 84 MIHQEFN---LATPLTVEENIFLGRELK----RGPFLDHRAMQAESRRLLERLHC-AVDP 135 Query: 398 WVSASSLSGGNQQKAIIAREIDRNPDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVL 457 S+LS N+Q IA+ + +LI+ +PT L + + +++ + R G A+L Sbjct: 136 RARVSTLSVPNRQMVEIAKALGLKARVLIMDEPTAVLTHRETDTLLEQVDRLRAAGTAIL 195 Query: 458 VISFELDEILNVSDRIAVIHDGQIQGIVSPETTTKQELGILMVGGNIN 505 S +LDE+ ++DR+ V+ DG+ + ++ + MVG ++ Sbjct: 196 YTSHKLDEVARIADRVTVLRDGRRVMTAPAKGLSEDRMAETMVGRELS 243 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: 595 Number of extensions: 41 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: 499 Length adjustment: 34 Effective length of query: 472 Effective length of database: 465 Effective search space: 219480 Effective search space used: 219480 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 24 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