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_067649690.1 I596_RS14985 ABC transporter ATP-binding protein
Query= TCDB::A2RKA7 (506 letters) >NCBI__GCF_001632775.1:WP_067649690.1 Length = 298 Score = 101 bits (252), Expect = 3e-26 Identities = 81/258 (31%), Positives = 130/258 (50%), Gaps = 15/258 (5%) Query: 2 ANETVIQMID-VTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSE 60 + ET+ +D V+KR+G VA D V ++++ GE+ ALLG NGAGK+T + +L GL +P Sbjct: 3 STETIPARLDRVSKRYGGAVALDGVAVDIRAGELLALLGPNGAGKTTAIGLLLGLHQPDA 62 Query: 61 GEVHVKGKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAK 120 G V + G+ + AA +G++ Q + D V E + E+T+ + Sbjct: 63 GGVELFGQAPQ----TLAARREVGVMLQSAGIPDTLKVRELL----ELTRSYYAE----P 110 Query: 121 KKILELSERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITE 180 + I + GL + L +S GQQ+RV+ L +L DEPT L Sbjct: 111 RSIADCVALAGLDGLLERLYGRLSGGQQRRVQFALALCGRPRLLFLDEPTTGLDIEARMG 170 Query: 181 LMQIMKNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVG 240 L + ++ L+ +G +++L TH L+E A+ADR+ V+ RG+ + + Q L+ Sbjct: 171 LWKAIRELVGQGCAVLLTTHYLEEAEALADRVVVLNRGRIVAEGSVAQIRAQVDRRLI-- 228 Query: 241 RSVSFITEKAAAQPKDVV 258 R VS +T A A VV Sbjct: 229 RCVSRLTAAAVAAWPGVV 246 Score = 73.2 bits (178), Expect = 1e-17 Identities = 59/218 (27%), Positives = 110/218 (50%), Gaps = 26/218 (11%) Query: 267 KESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKAITGLTKVDSGSIKLHNK---DI 323 K G++ + G+++D+RAGE++ + G +G G+T + + GL + D+G ++L + + Sbjct: 16 KRYGGAVALDGVAVDIRAGELLALLGPNGAGKTTAIGLLLGLHQPDAGGVELFGQAPQTL 75 Query: 324 TNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQTYYKPPMSKYGFLDYNKINSHA 383 +R + QS G + R+ +LE+T ++YY P S + ++ Sbjct: 76 AARREVGVMLQSAGIPDTLKVRE--LLELT-------RSYYAEPRSIADCVALAGLDG-- 124 Query: 384 RELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRNPDLLIVSQPTRGLDVGAIEYIH 443 L+E R LSGG Q++ A + P LL + +PT GLD+ A + Sbjct: 125 --LLERLYGR----------LSGGQQRRVQFALALCGRPRLLFLDEPTTGLDIEARMGLW 172 Query: 444 KRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQI 481 K + + +G AVL+ + L+E ++DR+ V++ G+I Sbjct: 173 KAIRELVGQGCAVLLTTHYLEEAEALADRVVVLNRGRI 210 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: 332 Number of extensions: 25 Number of successful extensions: 4 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: 298 Length adjustment: 30 Effective length of query: 476 Effective length of database: 268 Effective search space: 127568 Effective search space used: 127568 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: 50 (23.9 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