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 Ac3H11_1109 ABC transporter ATP-binding protein
Query= TCDB::A2RKA7 (506 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1109 Length = 513 Score = 337 bits (864), Expect = 6e-97 Identities = 196/494 (39%), Positives = 288/494 (58%), Gaps = 9/494 (1%) Query: 10 IDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHVKGKL 69 + +TKR+ VAN V+L + GEIHA+LGENGAGKSTLM I+ G ++P EG V G+ Sbjct: 1 VGITKRYPAVVANSGVSLTVLPGEIHAVLGENGAGKSTLMKIIYGSVKPDEGSVFFNGQA 60 Query: 70 ENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAKKKILELSER 129 + +P +A LGI MV QHF L D TV EN+ LG + + L L ++I + Sbjct: 61 VQVRNPQEARALGIAMVFQHFSLFDTLTVAENVWLGLDKS----LTLAEVTQRISAKAAE 116 Query: 130 YGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQIMKNLI 189 YGL ++P + +SVG+ QRVEI++ L +LI DEPT+VLTP + +L +++ L Sbjct: 117 YGLDIDPLRPVHTLSVGEMQRVEIIRALLTNPKVLILDEPTSVLTPQAVEKLFVVLRKLA 176 Query: 190 KEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRSVSFITEK 249 EG SI+ I+HKL EIRA+ TV+R GK ++TN L+ LM+G + E Sbjct: 177 SEGCSILYISHKLHEIRALCTACTVLRGGKVTGVCNPSEETNASLSRLMIGAEPPAL-EH 235 Query: 250 AAAQPKDVVLEIKDLNI-KESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKAITGL 308 A Q VL +K L++ + + + + L +V+AGE+VG+AG+ GNGQ EL+ A++G Sbjct: 236 RAVQTGATVLRVKGLSLPRADQFGVDLIDLQFEVKAGEVVGIAGVSGNGQKELLYALSGE 295 Query: 309 T-KVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQTYYKPP 367 + + SI++ ++ P + + VPE+R G V M +A N+ L K Sbjct: 296 DQRAEPASIQVTGQNAGRMGPGQRRALGLHFVPEERLGRGAVPTMGLAHNLLLTR--KNA 353 Query: 368 MSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRNPDLLIV 427 + G++ + HA ++++ F+V+ G +A SLSGGN QK I+ REID NP LLIV Sbjct: 354 VGGSGWIKVGALQKHAEDIIQRFNVKAGGPHSAAKSLSGGNLQKFIVGREIDANPKLLIV 413 Query: 428 SQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQIQGIVSP 487 SQPT G+DVGA I ++ RD G AVLV+S ELDE+ + DR+ V+ G++ V Sbjct: 414 SQPTWGVDVGAAAQIRGSILALRDAGCAVLVVSEELDELFEICDRLHVVAKGRLSPSVQR 473 Query: 488 ETTTKQELGILMVG 501 T + +G M G Sbjct: 474 AEATVERIGEWMSG 487 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: 614 Number of extensions: 31 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: 513 Length adjustment: 34 Effective length of query: 472 Effective length of database: 479 Effective search space: 226088 Effective search space used: 226088 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