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 AZOBR_RS06960 AZOBR_RS06960 ABC transporter permease
Query= TCDB::A2RKA5 (317 letters) >FitnessBrowser__azobra:AZOBR_RS06960 Length = 310 Score = 149 bits (377), Expect = 6e-41 Identities = 102/289 (35%), Positives = 156/289 (53%), Gaps = 13/289 (4%) Query: 10 IVANMLIYSTPLIFTSIGGVFSERGGIVNVGLEGIMTIGAFSSVVFNLTTAGMFGSMTPW 69 I+A ML +TPL+F ++G + E+ G++N+G+EG+M +GA V A GS T Sbjct: 11 ILAAMLAAATPLLFAALGELVVEKSGVLNLGVEGMMLVGA----VCGFAVAVQTGSST-- 64 Query: 70 LSILFGALIGALFSSLHAVATVNLRADHIVSGTVLNLMAPALGVFLLQVFYQQGQININE 129 L + GA GA ++L V T+ L A+ + +G L L L + Q F ++ E Sbjct: 65 LGFVAGAAAGAGMAALFGVLTLLLLANQVATGLALTLFGVGLSALIGQGFVGIPIADVPE 124 Query: 130 QIGYWNVPLLSNIPVIGKIFFTQTSLPGFLAIVVAILAWYVLFKTRFGLRLRSVGENPQA 189 +P L+++PVIGK F Q +L V + W+ L+ TR GL LR+VGEN A Sbjct: 125 LY----IPGLTDLPVIGKALFGQDALVYLALAAVPAVHWF-LYATRKGLILRAVGENHAA 179 Query: 190 ADTLGINVYAYRWAGVLLSGVLGGVGGAIYAQAISGNFSVSTIAGQGFISLAAMIFGKWN 249 A LG V R+ VL G + G+ GA + + ++ +G+G+I+LA ++F W Sbjct: 180 AHALGYKVIRIRFLAVLFGGAMSGMAGAFLSLDYTPMWAEGISSGRGWIALALVVFATWK 239 Query: 250 PIGAMLSSLLFGLFTSLAVVGGQIPGIKEIPSSFLQMAPYVFTIIVLAL 298 P +L + LFG T +A + Q GI +IPS L M PY+ T++VL + Sbjct: 240 PGRVLLGAWLFGGVT-IAQLHVQGLGI-DIPSQLLSMLPYLATVVVLVV 286 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: 273 Number of extensions: 14 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: 310 Length adjustment: 27 Effective length of query: 290 Effective length of database: 283 Effective search space: 82070 Effective search space used: 82070 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