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 SMa2365 SMa2365 ABC transporter ATP-binding protein
Query= TCDB::A2RKA7 (506 letters) >FitnessBrowser__Smeli:SMa2365 Length = 508 Score = 390 bits (1001), Expect = e-113 Identities = 210/500 (42%), Positives = 316/500 (63%), Gaps = 6/500 (1%) Query: 3 NETVIQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGE 62 +E ++ + V+KRFGD +AND ++L L KGEI ALLGENGAGK+TLM+IL G P G+ Sbjct: 2 SEAILNICSVSKRFGDNLANDDISLSLGKGEIVALLGENGAGKTTLMSILFGHYVPDSGK 61 Query: 63 VHVKGKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAKKK 122 V V+G+ P A GIGMVHQHF L TV EN++ G E + A++K Sbjct: 62 VLVEGRELPPGKPRAAIRAGIGMVHQHFSLAPNLTVLENVMAGTERLWHLRSGTSAARRK 121 Query: 123 ILELSERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELM 182 + + +R+GL+VEPDA + D+SVG+QQRVEILK LY A IL+ DEPTAVLT E L Sbjct: 122 LHRICQRFGLTVEPDARVGDLSVGEQQRVEILKALYNDAHILVLDEPTAVLTNLEAERLF 181 Query: 183 QIMKNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQ-ELAELMVGR 241 +K++ +EG S+I I+HKLDE+ A A+RI V+R G+ + L +TN+ ELAELMVGR Sbjct: 182 STLKDMAREGLSLIFISHKLDEVMAAANRIVVLRGGRKV-AERLAKETNKAELAELMVGR 240 Query: 242 SVSFITEKAAAQPKDVVLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTEL 301 V+ + + P +VVL++ D+++ G ++K + +RAGE++G+ G+ GNGQT L Sbjct: 241 RVARPVREPST-PGEVVLKVADVSVSID-GVERLKSIDFSLRAGEVLGIIGVSGNGQTTL 298 Query: 302 VKAITGLTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQ 361 ++G + D G + L + I + +G +PEDR+++G + EM + EN L+ Sbjct: 299 AHLLSGTLRRDKGDLLLFGEPIGDLTVDDAVRAGIGRIPEDRNKEGAIGEMAIWENAVLE 358 Query: 362 TYYKPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRN 421 P S+YG +D + A ++++ FDVRG LSGGN QK I+ R + Sbjct: 359 RL--PRFSRYGLVDRPSGQAFAGQIIDAFDVRGGRPTTRTRLLSGGNMQKLILGRNLMDR 416 Query: 422 PDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQI 481 P +L+ +QP RGLD GA+ +H+RL++AR G AVL+IS +L+E++ ++DRI I +G++ Sbjct: 417 PRILLAAQPARGLDEGAVAAVHERLLEARRAGTAVLLISEDLEEVMALADRIQAIVNGRL 476 Query: 482 QGIVSPETTTKQELGILMVG 501 ++ ++ + +LG++M G Sbjct: 477 SPPIAADSASATKLGLMMAG 496 Score = 73.2 bits (178), Expect = 2e-17 Identities = 61/229 (26%), Positives = 103/229 (44%), Gaps = 12/229 (5%) Query: 278 LSLDVRAGEIVGVAGIDGNGQTELVKAITGLTKVDSGSIKLHNKDITNQRPRKITEQSVG 337 +SL + GEIV + G +G G+T L+ + G DSG + + +++ +PR +G Sbjct: 24 ISLSLGKGEIVALLGENGAGKTTLMSILFGHYVPDSGKVLVEGRELPPGKPRAAIRAGIG 83 Query: 338 HVPEDRHRDGLVLEMTVAENIALQTYYKPPMSKYGFLDYNKINSHARE--LMEEFDVRGA 395 V + L +TV EN+ T + K++ + L E D R Sbjct: 84 MVHQ---HFSLAPNLTVLENVMAGTERLWHLRSGTSAARRKLHRICQRFGLTVEPDAR-- 138 Query: 396 GEWVSASSLSGGNQQKAIIAREIDRNPDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKA 455 LS G QQ+ I + + + +L++ +PT L E + L EG + Sbjct: 139 -----VGDLSVGEQQRVEILKALYNDAHILVLDEPTAVLTNLEAERLFSTLKDMAREGLS 193 Query: 456 VLVISFELDEILNVSDRIAVIHDGQIQGIVSPETTTKQELGILMVGGNI 504 ++ IS +LDE++ ++RI V+ G+ + T K EL LMVG + Sbjct: 194 LIFISHKLDEVMAAANRIVVLRGGRKVAERLAKETNKAELAELMVGRRV 242 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: 663 Number of extensions: 41 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: 508 Length adjustment: 34 Effective length of query: 472 Effective length of database: 474 Effective search space: 223728 Effective search space used: 223728 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