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_RS26075 BPHYT_RS26075 ABC transporter permease
Query= TCDB::A2RKA6 (364 letters) >FitnessBrowser__BFirm:BPHYT_RS26075 Length = 363 Score = 122 bits (305), Expect = 2e-32 Identities = 101/328 (30%), Positives = 163/328 (49%), Gaps = 9/328 (2%) Query: 12 LIAIVFGFLLGAIIMLAFGYNPIWGYEDLFISALGSARSIGETLQTMGPLILTALSFAVA 71 L+AIV L AI+ + G + + + D A GS +IG ++ L F +A Sbjct: 30 LVAIVAAMALIAIVHVPLG-DAMAAFAD---GAWGSPYAIGASINRSLVFALVGSGFVLA 85 Query: 72 MKVGLFNIGMSGQALAGWISSMWFALSFPDIPRLLMIPLVV-IIGMVF-GAFMGFIPGIL 129 + L N+G GQ G I++ +L L +P VV ++G GA G IPG L Sbjct: 86 NRAQLTNVGGEGQIAMGGIAATAVSLYGHVAHLPLGLPFVVPMLGAALAGAAWGAIPGWL 145 Query: 130 RALLGTSEVITTIMLNYIMLFFSTFMIHSMFQKNILMDNTTDQTKLISANASFRTNWMSS 189 +A GT+EVI+T++L +I ++F + + S M N + + S R ++S Sbjct: 146 KARAGTNEVISTLLLTFIAVWFLYWCVQSEALLRQPMSNAATLPESLDIPDSTRLPLLAS 205 Query: 190 LTDNSTLNIGLIIAIIALVIMAIIFTKTTLGFEIKAVGLNPDASEYAGISAKRTLILSMV 249 + ++ L+IGL I ++ + +A++ + G ++AVGLN A+ AG+ T++ ++ Sbjct: 206 -SSSTGLHIGLPITVVLCIAVALVLVYSRFGMHLRAVGLNALAARRAGMPITSTIVGALA 264 Query: 250 VAGALAGLGGVVYGFGYMQNFVSQSASLDIGFYGMAVALLGGNSPIGILFAALLFSVLQT 309 +AGAL GL G + G Q + S GF G+ V LL S G+ AALLF L++ Sbjct: 265 LAGALGGLAGALMLQG-DQYSLKAGFSSGYGFDGLVVGLLARGSITGVCAAALLFGFLRS 323 Query: 310 GAPGMTN-DGIPPEIVKVVTAAIIFFIA 336 G M +P +V VV +I +A Sbjct: 324 GGINMEMVASVPSALVLVVQGIVIVALA 351 Lambda K H 0.327 0.141 0.404 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: 316 Number of extensions: 21 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: 364 Length of database: 363 Length adjustment: 29 Effective length of query: 335 Effective length of database: 334 Effective search space: 111890 Effective search space used: 111890 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 (21.7 bits) S2: 49 (23.5 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