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_084931811.1 HA51_RS03115 sugar ABC transporter ATP-binding protein
Query= TCDB::A2RKA7 (506 letters) >NCBI__GCF_002095475.1:WP_084931811.1 Length = 504 Score = 318 bits (816), Expect = 2e-91 Identities = 179/493 (36%), Positives = 288/493 (58%), Gaps = 10/493 (2%) Query: 4 ETVIQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEV 63 + +I++ D+ K FG A L+++ GE+HALLGENGAGKSTLM +L G P G V Sbjct: 3 QPLIELRDIVKTFGGIHALKGAQLQIRAGEVHALLGENGAGKSTLMRVLGGEHTPDSGTV 62 Query: 64 HVKGKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAKKKI 123 + KG+ I P A GI ++HQ L TV ENI L + T + + K Sbjct: 63 YDKGEAVQIKGPKAAMARGITLIHQEMALAQELTVAENIFLHDLPTF---IAWPKLRAKA 119 Query: 124 LELSERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQ 183 + R G ++P A + D+SV QQ VEI + L + A +++FDEPTAVL+ + L++ Sbjct: 120 ANILRRLGFEIDPAATVGDLSVAHQQIVEIARALSQDARVIVFDEPTAVLSTQDANRLLE 179 Query: 184 IMKNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRSV 243 I+ +L G +I+ I+H+LDE+ +ADR+T+++ G+ I T T QE+ LMVGR V Sbjct: 180 IISDLRSVGVAIVYISHRLDEVFRIADRMTIMKDGQWIATESPQQTTLQEVIRLMVGRPV 239 Query: 244 -SFITEKAAAQPKDVVLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELV 302 +++A + VL ++ LN + KV+ +S VRAGE+VG+ G+ G+G+TE+ Sbjct: 240 DQLFSDRATYGMGEEVLRVEKLNARR-----KVRDVSFSVRAGEVVGLGGLVGSGRTEVA 294 Query: 303 KAITGLTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQT 362 + I G + DSG I LH K ++ + P++ + + VPEDR R G+VL+M + N+ + Sbjct: 295 RLIFGADRCDSGDIYLHGKKVSLRSPQQAVKAGIALVPEDRKRQGVVLDMPIRANVTMAN 354 Query: 363 YYKPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRNP 422 K M+ GF+ ++ +L ++ ++ AG SSLSGGNQQK ++A+ + Sbjct: 355 -DKAVMAPLGFIHSSRETQVVSKLAQQMRLKCAGLHAPVSSLSGGNQQKVVLAKWFNLGG 413 Query: 423 DLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQIQ 482 ++I+ +PTRG+DVGA I++ + + +G AV+VIS E E+ + +R+ V+ +G I Sbjct: 414 QVIILDEPTRGVDVGAKREIYQLIAELAQQGMAVVVISSEHIELFGLCNRVLVMSEGAIC 473 Query: 483 GIVSPETTTKQEL 495 G + P+ +++ L Sbjct: 474 GELQPDDYSEENL 486 Score = 95.1 bits (235), Expect = 5e-24 Identities = 67/251 (26%), Positives = 128/251 (50%), Gaps = 16/251 (6%) Query: 258 VLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKAITGLTKVDSGSIK 317 ++E++D+ +K G +KG L +RAGE+ + G +G G++ L++ + G DSG++ Sbjct: 5 LIELRDI-VKTFGGIHALKGAQLQIRAGEVHALLGENGAGKSTLMRVLGGEHTPDSGTVY 63 Query: 318 LHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQTYYKPPMSKYGFLDYN 377 + + + P+ + + + ++ L E+TVAENI L F+ + Sbjct: 64 DKGEAVQIKGPKAAMARGITLIHQEM---ALAQELTVAENIFLHDLPT-------FIAWP 113 Query: 378 KINSHARELMEE--FDVRGAGEWVSASSLSGGNQQKAIIAREIDRNPDLLIVSQPTRGLD 435 K+ + A ++ F++ A + LS +QQ IAR + ++ +++ +PT L Sbjct: 114 KLRAKAANILRRLGFEIDPAA---TVGDLSVAHQQIVEIARALSQDARVIVFDEPTAVLS 170 Query: 436 VGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQIQGIVSPETTTKQEL 495 + + + R G A++ IS LDE+ ++DR+ ++ DGQ SP+ TT QE+ Sbjct: 171 TQDANRLLEIISDLRSVGVAIVYISHRLDEVFRIADRMTIMKDGQWIATESPQQTTLQEV 230 Query: 496 GILMVGGNINE 506 LMVG +++ Sbjct: 231 IRLMVGRPVDQ 241 Score = 68.9 bits (167), Expect = 4e-16 Identities = 47/220 (21%), Positives = 107/220 (48%), Gaps = 7/220 (3%) Query: 25 VNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHVKGKLENIDSPSKAANLGIG 84 V+ ++ GE+ L G G+G++ + ++ G G++++ GK ++ SP +A GI Sbjct: 270 VSFSVRAGEVVGLGGLVGSGRTEVARLIFGADRCDSGDIYLHGKKVSLRSPQQAVKAGIA 329 Query: 85 MVHQHFM---LVDAFTVTENIILGNEVTKGINLDLKTAKKK---ILELSERYGLSVEP-D 137 +V + +V + N+ + N+ L + ++ + +L+++ L Sbjct: 330 LVPEDRKRQGVVLDMPIRANVTMANDKAVMAPLGFIHSSRETQVVSKLAQQMRLKCAGLH 389 Query: 138 ALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQIMKNLIKEGKSIIL 197 A + +S G QQ+V + K G ++I DEPT + E+ Q++ L ++G ++++ Sbjct: 390 APVSSLSGGNQQKVVLAKWFNLGGQVIILDEPTRGVDVGAKREIYQLIAELAQQGMAVVV 449 Query: 198 ITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAEL 237 I+ + E+ + +R+ V+ G ++ D + + L + Sbjct: 450 ISSEHIELFGLCNRVLVMSEGAICGELQPDDYSEENLLSM 489 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: 588 Number of extensions: 31 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 506 Length of database: 504 Length adjustment: 34 Effective length of query: 472 Effective length of database: 470 Effective search space: 221840 Effective search space used: 221840 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