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 BPHYT_RS11510 BPHYT_RS11510 ABC transporter
Query= TCDB::A2RKA7 (506 letters) >FitnessBrowser__BFirm:BPHYT_RS11510 Length = 533 Score = 338 bits (866), Expect = 4e-97 Identities = 198/497 (39%), Positives = 298/497 (59%), Gaps = 8/497 (1%) Query: 7 IQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHVK 66 + + +TK++ AND V L + GEIHA+LGENGAGKSTLM I+ G + P GE+ + Sbjct: 25 LMLQSITKQYPAVRANDDVTLIVAPGEIHAVLGENGAGKSTLMKIIYGAVRPDAGEIRWE 84 Query: 67 GKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAKKKILEL 126 G+ I +P+ A LGIGMV QHF L + TV ENI L + DLKT ++I E+ Sbjct: 85 GQTVEIANPAAARKLGIGMVFQHFSLFETLTVGENIALALDEP----FDLKTLSRRIREV 140 Query: 127 SERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQIMK 186 S YGL ++P + ++VG++QRVEI++ L + +LI DEPT+VLTP + +L + ++ Sbjct: 141 SADYGLDIDPQRHVHSLTVGERQRVEIVRCLLQNPRLLIMDEPTSVLTPQAVRKLFETLR 200 Query: 187 NLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRSVSFI 246 L EG SI+ I+HKLDEI+ + D TV+R G+ V+ +T+ LA+LMVG S+ Sbjct: 201 RLAAEGCSILYISHKLDEIQELCDTATVMRGGRVTGHVKPKGETHASLAQLMVGHSLPDY 260 Query: 247 TEKAAAQPKDVVLEIKDLNIK-ESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKAI 305 T + P V+L++K L+++ + + +S V AGEI G+AG+ GNGQ EL+ A+ Sbjct: 261 TRR-EHNPGAVLLDVKRLSVESDDPFGTSLHDVSFGVHAGEIFGIAGVSGNGQAELLSAL 319 Query: 306 TGLTK-VDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQTYY 364 +G + V + ++ + K G VPE+R G V MT++EN AL T + Sbjct: 320 SGEKRGVRADAVTICGKAAGRLGAGGRRALGFGFVPEERLGRGAVPAMTLSEN-ALLTAH 378 Query: 365 KPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRNPDL 424 + M G++ + + A+ ++ FDVR G A SLSGGN QK I+ REI + P + Sbjct: 379 RQQMVNSGWIKAGAMRAFAKRCIDAFDVRCGGSEALAQSLSGGNLQKYIMGREILQAPKV 438 Query: 425 LIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQIQGI 484 L+V+QPT G+DVGA +I ++L+ G A+LVIS EL+E+ ++ DRIAV+ G++ + Sbjct: 439 LVVAQPTWGVDVGAAAFIRQQLLDLSARGVAILVISEELEELFDICDRIAVLAGGRLSPV 498 Query: 485 VSPETTTKQELGILMVG 501 T +E+G M G Sbjct: 499 RGTGATNAEEIGRWMAG 515 Score = 87.4 bits (215), Expect = 1e-21 Identities = 77/268 (28%), Positives = 128/268 (47%), Gaps = 17/268 (6%) Query: 242 SVSFITEKAAAQPKD----VVLEIKDLNIKESRGSLKVKG-LSLDVRAGEIVGVAGIDGN 296 S S ++ AAAQP D + +I + +++ ++L V GEI V G +G Sbjct: 2 SDSSYSDGAAAQPADRPEQAAPRLMLQSITKQYPAVRANDDVTLIVAPGEIHAVLGENGA 61 Query: 297 GQTELVKAITGLTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAE 356 G++ L+K I G + D+G I+ + + P + +G V + L +TV E Sbjct: 62 GKSTLMKIIYGAVRPDAGEIRWEGQTVEIANPAAARKLGIGMVFQ---HFSLFETLTVGE 118 Query: 357 NIALQTYYKPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAR 416 NIAL +P D ++ RE+ ++ + SL+ G +Q+ I R Sbjct: 119 NIAL-ALDEP-------FDLKTLSRRIREVSADYGL-DIDPQRHVHSLTVGERQRVEIVR 169 Query: 417 EIDRNPDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVI 476 + +NP LLI+ +PT L A+ + + L + EG ++L IS +LDEI + D V+ Sbjct: 170 CLLQNPRLLIMDEPTSVLTPQAVRKLFETLRRLAAEGCSILYISHKLDEIQELCDTATVM 229 Query: 477 HDGQIQGIVSPETTTKQELGILMVGGNI 504 G++ G V P+ T L LMVG ++ Sbjct: 230 RGGRVTGHVKPKGETHASLAQLMVGHSL 257 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: 654 Number of extensions: 29 Number of successful extensions: 9 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: 533 Length adjustment: 35 Effective length of query: 471 Effective length of database: 498 Effective search space: 234558 Effective search space used: 234558 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