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 BPHYT_RS11500 BPHYT_RS11500 ABC transporter permease
Query= TCDB::A2RKA5 (317 letters) >FitnessBrowser__BFirm:BPHYT_RS11500 Length = 309 Score = 158 bits (400), Expect = 1e-43 Identities = 91/289 (31%), Positives = 152/289 (52%), Gaps = 12/289 (4%) Query: 10 IVANMLIYSTPLIFTSIGGVFSERGGIVNVGLEGIMTIGAFSSVVFNLTTAGMFGSMTPW 69 + ++ + + PL+F G + +E+ G++N+G+EG+M +GA + T +PW Sbjct: 9 LTSSAVTAAIPLMFAGAGELVTEKSGVLNLGVEGMMLMGAVTGYAVTAITG------SPW 62 Query: 70 LSILFGALIGALFSSLHAVATVNLRADHIVSGTVLNLMAPALGVFLLQVFYQQGQININE 129 L +L G S L A T+ + A+ + +G L + L ++ + + + Sbjct: 63 LGVLAAIGAGLAMSLLFAFLTLTMLANQVATGLSLTIFGIGLSAYVGKPYTSAA---VRA 119 Query: 130 QIGYWNVPLLSNIPVIGKIFFTQTSLPGFLAIVVAILAWYVLFKTRFGLRLRSVGENPQA 189 I W +P LS IPV+G FF+ T L ++ A++ W+ L++TR GL LRSVGE+PQ Sbjct: 120 TIDTWTIPGLSKIPVLGPAFFSLTPLDYLAFLMFAVIGWF-LYRTRAGLVLRSVGESPQV 178 Query: 190 ADTLGINVYAYRWAGVLLSGVLGGVGGAIYAQAISGNFSVSTIAGQGFISLAAMIFGKWN 249 A ++G V R+ V G + G+ G Y+ + +G+G+I+LA ++F W Sbjct: 179 AHSVGFPVIGVRYGAVAFGGGMAGLAGGYYSIVNLHLWQEQLTSGRGWIALALVVFATWR 238 Query: 250 PIGAMLSSLLFGLFTSLAVVGGQIPGIKEIPSSFLQMAPYVFTIIVLAL 298 P ++ +LLFG T L Q G+ +P+ FL M PYV T++VL L Sbjct: 239 PGRLLIGALLFGAVTGLQFY-AQAIGV-PVPTQFLAMLPYVATVVVLVL 285 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: 271 Number of extensions: 17 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: 309 Length adjustment: 27 Effective length of query: 290 Effective length of database: 282 Effective search space: 81780 Effective search space used: 81780 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