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 Ac3H11_1111 Putative deoxyribose-specific ABC transporter, permease protein
Query= TCDB::A2RKA5 (317 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1111 Length = 306 Score = 137 bits (346), Expect = 3e-37 Identities = 93/293 (31%), Positives = 150/293 (51%), Gaps = 19/293 (6%) Query: 9 IIVANMLIYSTPLIFTSIGGVFSERGGIVNVGLEGIM---TIGAFSSVVFNLTTAGMFGS 65 +++ L T L ++G + +E+ GIVN+G EG+M I F++VV T Sbjct: 6 LLIGATLSAGTVLAIAALGLLINEKAGIVNLGAEGMMLCAAIAGFATVVHTGNT------ 59 Query: 66 MTPWLSILFGALIGALFSSLHAVATVNLRADHIVSGTVLNLMAPALGVFLLQVFYQQGQI 125 WL G GA+ +++ V + L + +G L+L F + Y Q ++ Sbjct: 60 ---WLGFAAGMAAGAVLAAIFGVLVIWLNTNQYATGLALSLFGVGFSAFA-GISYVQAKL 115 Query: 126 NINEQIGYWNVPLLSNIPVIGKIFFTQTSLPGFLAIVVAILAWYVLFKTRFGLRLRSVGE 185 ++ + +P+L ++P++G F Q L ++VA L W+ L+++R GL LRSVGE Sbjct: 116 ---PELPKYAIPVLGDVPLLGPALFQQHPLVYLTMLLVAGLIWF-LYRSRAGLVLRSVGE 171 Query: 186 NPQAADTLGINVYAYRWAGVLLSGVLGGVGGAIYAQAISGNFSVSTIAGQGFISLAAMIF 245 +P++A LG V R V++ G L G+ GA + + + +AG+G+I+LA F Sbjct: 172 SPESAHALGYPVRRIRLLAVVVGGALCGLAGAYISTVYTPLWVEGMVAGRGWIALALTTF 231 Query: 246 GKWNPIGAMLSSLLFGLFTSLAVVGGQIPGIKEIPSSFLQMAPYVFTIIVLAL 298 W P +L + LFG T L Q G+ ++ S L M PYV TI+VLAL Sbjct: 232 ATWRPARVLLGAYLFGGVTMLQ-FHLQATGV-QVASQLLSMLPYVATIVVLAL 282 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: 252 Number of extensions: 18 Number of successful extensions: 5 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: 306 Length adjustment: 27 Effective length of query: 290 Effective length of database: 279 Effective search space: 80910 Effective search space used: 80910 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