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 WP_097031108.1 CRO07_RS12920 ABC transporter permease
Query= TCDB::A2RKA5 (317 letters) >NCBI__GCF_900207575.1:WP_097031108.1 Length = 315 Score = 172 bits (437), Expect = 7e-48 Identities = 107/292 (36%), Positives = 151/292 (51%), Gaps = 8/292 (2%) Query: 18 STPLIFTSIGGVFSERGGIVNVGLEGIMTIGAFSSVVFNLTTAGMFGSMTPWLSILFGAL 77 ++PLIF ++G + ER G++N+G+EGIM IGAFS + AG+ W + L Sbjct: 21 ASPLIFATMGELICERAGVLNLGIEGIMVIGAFSGWITVWAGAGL------WEGVAVAML 74 Query: 78 IGALFSSLHAVATVNLRADHIVSGTVLNLMAPALGVFLLQVFYQQGQININ-EQIGYWNV 136 G LF LHAV V V G + L+A + F ++ Q E W V Sbjct: 75 AGMLFGLLHAVLVVPFGLSQHVVGLGVTLLATSTSYFAYRLMLPQVTSPPKIEPFAVWEV 134 Query: 137 PLLSNIPVIGKIFFTQTSLPGFLAIVVAILAWYVLFKTRFGLRLRSVGENPQAADTLGIN 196 P+LS+IP+IG F QT L + A VA L VL++T GL +R+ GENP A D G++ Sbjct: 135 PVLSDIPLIGPALFAQTPLT-YAAFAVAALVALVLWRTPLGLAIRAAGENPSAVDAQGLS 193 Query: 197 VYAYRWAGVLLSGVLGGVGGAIYAQAISGNFSVSTIAGQGFISLAAMIFGKWNPIGAMLS 256 V R V++ L VGGA + +F + G+G+I +A ++FG W P A+L Sbjct: 194 VTGLRIGAVVVGSGLMAVGGAFLTLSAFSSFFFEMVNGRGWICIALVVFGAWRPGKAVLG 253 Query: 257 SLLFGLFTSLAVVGGQIPGIKEIPSSFLQMAPYVFTIIVLALFLGKAIAPKA 308 +LLF F +L V Q P + +P MAPYV +I L L +A P A Sbjct: 254 ALLFAAFDALQVRLQQTPLGQVVPYQLFLMAPYVLSIAALVLMSRRASVPAA 305 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: 277 Number of extensions: 21 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: 315 Length adjustment: 27 Effective length of query: 290 Effective length of database: 288 Effective search space: 83520 Effective search space used: 83520 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 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