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_2413 N515DRAFT_2413 simple sugar transport system ATP-binding protein
Query= TCDB::A2RKA7 (506 letters) >FitnessBrowser__Dyella79:N515DRAFT_2413 Length = 505 Score = 255 bits (651), Expect = 3e-72 Identities = 165/503 (32%), Positives = 267/503 (53%), Gaps = 14/503 (2%) Query: 2 ANETVIQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEG 61 A V+Q + KRFG +A D V+L L+ GE+HAL+G+NGAGKSTL+ +L+G+ P G Sbjct: 8 ARPVVLQARGLGKRFGATLALDGVDLALRAGEVHALMGQNGAGKSTLIKLLTGVERPDRG 67 Query: 62 EVHVKGKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKG--INLDLKTA 119 V + G++ +P +A GIG V+Q L +V EN+ G + +D + Sbjct: 68 SVELDGRVIAPSTPMEAQRDGIGTVYQEVNLCPNLSVAENLYAGRYPRRRRLRMIDWRQV 127 Query: 120 KKKILELSERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEIT 179 + L + L ++ DA + V +Q V I + L A +LI DEPT+ L E+ Sbjct: 128 RDGARSLLRQLHLELDVDAPLGSYPVAIRQMVAIARALGVSARVLILDEPTSSLDEGEVR 187 Query: 180 ELMQIMKNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMV 239 EL +++ L + G +I+ +TH LD++ AV+DRITV+R G + + D L MV Sbjct: 188 ELFRVIAQLRERGMAILFVTHFLDQVYAVSDRITVLRDGCRVGEYAVADLPPAALVNAMV 247 Query: 240 GRSVSFI--TEKAAAQPKDVVLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNG 297 GR + + + A P D I D RG K+ + L VR GE++G+ G+ G+G Sbjct: 248 GRDLPTVAGADAERAPPPDAPPAI-DAQGLGCRG--KLHPVDLQVRRGEMLGLGGLLGSG 304 Query: 298 QTELVKAITGLTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAEN 357 +TEL + + GL + + G +++ + + + P + + PE+R DG+V E++V EN Sbjct: 305 RTELARLLFGLDRAERGELRIGGERVELKHPADAVVRGLALCPEERKTDGIVAELSVREN 364 Query: 358 IALQTYYKPPMSKYGFLDYNKINSH--ARELMEEFDVRGAGEWVSASSLSGGNQQKAIIA 415 I L ++ G+ ++ AR+L++ ++ A LSGGNQQK ++A Sbjct: 365 IVLAL-----QARQGWRGMSRARQDELARQLVQALGIKAADIETPVGLLSGGNQQKVMLA 419 Query: 416 REIDRNPDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAV 475 R + P LLI+ +PTRG+DV A + + + + G AVL IS E E+ DRIAV Sbjct: 420 RWLVTEPRLLILDEPTRGIDVAAKQELMAEVTRRAHAGMAVLFISAETGELTRWCDRIAV 479 Query: 476 IHDGQIQGIVSPETTTKQELGIL 498 + + + G + +T + L ++ Sbjct: 480 MRERRKAGELPGGSTEARVLAMI 502 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: 623 Number of extensions: 38 Number of successful extensions: 8 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: 505 Length adjustment: 34 Effective length of query: 472 Effective length of database: 471 Effective search space: 222312 Effective search space used: 222312 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 Apr 09 2024. 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