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 3608553 Dshi_1947 ABC transporter related (RefSeq)
Query= TCDB::A2RKA7 (506 letters) >FitnessBrowser__Dino:3608553 Length = 514 Score = 380 bits (975), Expect = e-110 Identities = 205/502 (40%), Positives = 302/502 (60%), Gaps = 3/502 (0%) Query: 6 VIQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHV 65 V+++ +TKRFG AND ++ +L GE+ ALLGENGAGK+TLMNIL G EG V V Sbjct: 10 VLRLDQITKRFGALTANDAISFDLHAGEVVALLGENGAGKTTLMNILFGHYTADEGTVEV 69 Query: 66 KGKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAKKKILE 125 G+ P A G+GMVHQHF L D +V +N+ILG L A++K+ Sbjct: 70 FGQTLPPGVPRAALAAGVGMVHQHFTLADNLSVLDNVILGTVPLWRAGLGSGAARRKLRA 129 Query: 126 LSERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQIM 185 L+E +GL V+P+A + +SVG++QRVEILK LYR A ILI DEPTAVLTP E L + Sbjct: 130 LAEDFGLQVDPEARVGTLSVGERQRVEILKALYRDARILILDEPTAVLTPQEAEALFATL 189 Query: 186 KNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRSVSF 245 + + G S+I I+HKL E+ +VA R+ V+R G+ + V + LAE+MVG ++ Sbjct: 190 RRAVARGMSVIFISHKLHEVMSVAHRVVVLRHGRVVGRVATDETDRHALAEMMVGAEITA 249 Query: 246 ITEKAAAQPKDVVLEIKDLNIKESRGSLK-VKGLSLDVRAGEIVGVAGIDGNGQTELVKA 304 + A L D ++RG+ ++ +SL +RAG+I G+AG+ GNGQ L Sbjct: 250 PAPRPAT--PGAALMTLDRVCTDARGTATGLRDVSLTLRAGQITGLAGVSGNGQAALADL 307 Query: 305 ITGLTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQTYY 364 I GL +G+++L N ++ + PR Q +G +PEDRH+ G + + T+ EN L+ Y Sbjct: 308 IGGLIAPVAGALRLGNAEVADWSPRAALAQGIGRIPEDRHKTGTIADFTLTENAILEAYP 367 Query: 365 KPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRNPDL 424 K S+ G++ + S AR+++ +DVR G LSGGN QK I+ R ++ P + Sbjct: 368 KAQFSRSGWMRWGAAESFARDVIASYDVRCPGPETPIRLLSGGNMQKLILGRVLEDGPRI 427 Query: 425 LIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQIQGI 484 ++ +QP RGLD+GA+ Y+ ++LI ARD G AVL+IS +LDE+L +SD I V+ +G++ Sbjct: 428 VLANQPVRGLDIGAVTYVQEQLIAARDGGAAVLLISEDLDEVLALSDVIHVMSEGRLSPE 487 Query: 485 VSPETTTKQELGILMVGGNINE 506 + + T +LG+ M G E Sbjct: 488 FARGSMTPAQLGVWMAGDGFAE 509 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: 596 Number of extensions: 17 Number of successful extensions: 5 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: 514 Length adjustment: 34 Effective length of query: 472 Effective length of database: 480 Effective search space: 226560 Effective search space used: 226560 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