Align Purine/cytidine ABC transporter permease 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 GFF383 PGA1_c03940 putative permease protein
Query= TCDB::A2RKA5 (317 letters) >FitnessBrowser__Phaeo:GFF383 Length = 278 Score = 181 bits (460), Expect = 1e-50 Identities = 106/284 (37%), Positives = 158/284 (55%), Gaps = 17/284 (5%) Query: 45 MTIGAFSSVVFNLTTAGMFGSMTPWLSILFGALIGALFSSLHAVATVNLRADHIVSGTVL 104 M + AF S TT + WL +L G + S LH +A++ R + ++SG + Sbjct: 1 MLMAAFFSAAVAATTGNV------WLGLLAGIASSLVLSGLHGLASITFRGNQLISGVAI 54 Query: 105 NLMAPALGVFLLQVFYQQGQININ-------EQIGYWNVPLLSNIPVIGKIF---FTQTS 154 N +A + V + Q ++QQG + E I L+N+PV+G I+ + S Sbjct: 55 NFLAAGMTVLIAQDWFQQGGRTPSLFSGGRFEPINLPFADALANVPVLGPIYSELLSGHS 114 Query: 155 LPGFLAIVVAILAWYVLFKTRFGLRLRSVGENPQAADTLGINVYAYRWAGVLLSGVLGGV 214 + +LA + +VLF TRFGLRLR+VGENP A DT G++V R+A V++ G+L G+ Sbjct: 115 VLVYLAFLAVPATAWVLFGTRFGLRLRAVGENPAAVDTAGVSVVGLRYAAVMICGLLCGI 174 Query: 215 GGAIYAQAISGNFSVSTIAGQGFISLAAMIFGKWNPIGAMLSSLLFGLFTSLAVVGGQIP 274 GA A A+ F AG+GFI+LAA+IF KW P A+ + LLFGL ++A+ I Sbjct: 175 AGAYLATALQAGFVKDMTAGRGFIALAALIFAKWRPWHALGACLLFGLLQAVALRFQNIE 234 Query: 275 -GIKEIPSSFLQMAPYVFTIIVLALFLGKAIAPKADGVNYIKSK 317 G IP + PY+ T+++LA F+GKA+ PKA G Y+K + Sbjct: 235 IGTFVIPVQMMDALPYILTVVILAGFVGKAVPPKAGGEPYVKER 278 Lambda K H 0.326 0.142 0.419 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: 229 Number of extensions: 12 Number of successful extensions: 3 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: 317 Length of database: 278 Length adjustment: 26 Effective length of query: 291 Effective length of database: 252 Effective search space: 73332 Effective search space used: 73332 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 48 (23.1 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