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 SMc04126 SMc04126 ABC transporter permease
Query= TCDB::A2RKA6 (364 letters) >FitnessBrowser__Smeli:SMc04126 Length = 377 Score = 160 bits (404), Expect = 7e-44 Identities = 108/341 (31%), Positives = 179/341 (52%), Gaps = 26/341 (7%) Query: 9 LVPLIAIVFGFLLGAIIMLAFGYNPIWGYEDLFISALGSARSIGETLQTMGPLILTALSF 68 L+PLI + FL+ +++L G NP+ L A G IG TL I T L+ Sbjct: 16 LIPLINLAVAFLVAGLVVLLVGENPLEAAYHLINGAFGRGEYIGFTLYYATTFIFTGLAV 75 Query: 69 AVAMKVGLFNIGMSGQALAGWI----SSMWFALSFPDIPRLLMIPLVVIIGMVFGAFMGF 124 AVA GLFNIG GQA G I + +W + +P ++ PL ++ FGA F Sbjct: 76 AVAFHAGLFNIGGEGQAYVGGIGVALACLWLDQT---MPWYVVFPLAIVGSAFFGALWAF 132 Query: 125 IPGILRALLGTSEVITTIMLNYIMLFFSTFMIHSMFQKNILMDNTTDQTKLISANASF-R 183 +PG L+A G+ VITTIM N+I S+ M++ + + + + QT+ + + Sbjct: 133 LPGWLQAKRGSHIVITTIMFNFIA---SSLMVYLLTRVLKPLGSMAPQTRTFAEGGQLPK 189 Query: 184 TNWMSSL----TDNSTLNIGLIIAIIALVIMAIIFTKTTLGFEIKAVGLNPDASEYAGIS 239 +W+ S+ + NI ++A+ A + ++ +T LG+E++ +G +P A+ YAGIS Sbjct: 190 LDWLLSIFGLNIGTAPFNISFLLALAAAFAVWVLIWRTRLGYEMRTMGHSPSAARYAGIS 249 Query: 240 AKRTLILSMVVAGALAGLGGV--VYG--FGYMQNFVSQSASLDIGFYGMAVALLGGNSPI 295 R +++M+++G LAG+ + + G F +FV + GF G+AVAL+G + P Sbjct: 250 ESRITVVAMMISGGLAGMMALNPIMGEQFRMQLDFVQGA-----GFVGIAVALMGRSHPG 304 Query: 296 GILFAALLFSVLQTGAPGMTND--GIPPEIVKVVTAAIIFF 334 GI+ AA+LF VL G + + I +++ ++ +I F Sbjct: 305 GIIPAAILFGVLYQGGAEIAFEMPSISRDMIVIIQGLVILF 345 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: 346 Number of extensions: 22 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: 377 Length adjustment: 30 Effective length of query: 334 Effective length of database: 347 Effective search space: 115898 Effective search space used: 115898 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