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_097028703.1 CRO07_RS00315 ABC transporter permease
Query= TCDB::A2RKA5 (317 letters) >NCBI__GCF_900207575.1:WP_097028703.1 Length = 322 Score = 207 bits (526), Expect = 4e-58 Identities = 120/330 (36%), Positives = 190/330 (57%), Gaps = 22/330 (6%) Query: 1 MNVVNTLQIIVANMLIYSTPLIFTSIGGVFSERGGIVNVGLEGIMTIGAFSSVVFNLTTA 60 M++ LQI+ +M+ TPL+ + G+FSER GI ++GLEG M AF S T Sbjct: 2 MDLPTALQIL-DSMIRLGTPLLLACLAGLFSERAGIFDIGLEGKMLSAAFLSAAVAFVTG 60 Query: 61 GMFGSMTPWLSILFGALIGALFSSLHAVATVNLRADHIVSGTVLNLMAPALGVFLLQVFY 120 + WL +L G + + S++H +A++ R + ++SG +N +A L V L Q ++ Sbjct: 61 SV------WLGVLAGLVAALMMSAIHGLASITFRGNQLISGVAINFLASGLTVLLGQYWF 114 Query: 121 QQGQININEQIGYWNVPL-------LSNIPVIGKIFFT----QTSLPGFLAIVVAILAWY 169 G + + P+ L +PV+G I+ T+L +LA + L+W+ Sbjct: 115 ALGGRTPSLEGAARFQPITLPFAQELREVPVLGLIYAELISGHTALV-YLAFALVPLSWW 173 Query: 170 VLFKTRFGLRLRSVGENPQAADTLGINVYAYRWAGVLLSGVLGGVGGAIYAQAISGNFSV 229 +L++TRFGLRLR+VGENP A DT G++V R+A V + G+L G+ GA A +S F Sbjct: 174 LLYRTRFGLRLRAVGENPAAVDTAGVSVVGIRYAAVAICGLLTGLAGAYLACGLSAGFVK 233 Query: 230 STIAGQGFISLAAMIFGKWNPIGAMLSSLLFGLFTSLA--VVGGQIPGIKEIPSSFLQMA 287 AG+G+I+LAA+IF KW P A+ +++LFGL ++A + G+ +P F+Q Sbjct: 234 EMTAGRGYIALAALIFAKWRPWQALAATMLFGLLEAVANRYQSLDLWGV-PLPVQFMQAL 292 Query: 288 PYVFTIIVLALFLGKAIAPKADGVNYIKSK 317 PY+ T+++LA F+GKAI P+A G Y+K + Sbjct: 293 PYILTVVILAGFVGKAIPPRAGGQPYVKER 322 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: 246 Number of extensions: 12 Number of successful extensions: 4 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: 322 Length adjustment: 28 Effective length of query: 289 Effective length of database: 294 Effective search space: 84966 Effective search space used: 84966 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