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 SM_b20126 SM_b20126 sugar ABC transporter permease
Query= TCDB::A2RKA6 (364 letters) >FitnessBrowser__Smeli:SM_b20126 Length = 365 Score = 185 bits (469), Expect = 2e-51 Identities = 108/337 (32%), Positives = 181/337 (53%), Gaps = 11/337 (3%) Query: 6 RKVLVPLIAIVFGFLLGAIIMLAFGYNPIWGYEDLFISALGSARSIGETLQTMGPLILTA 65 R ++ P A+V GA ++ GY + + + RSI E L PLIL Sbjct: 29 RTIIQPAAAVVLALACGAALLAFNGYEARAVIDVMVLGVFQDTRSIAEILLKATPLILIG 88 Query: 66 LSFAVAMKVGLFNIGMSGQALAGWISSMWFALSFPDIPRLLMIPLVVIIGMVFGAFMGFI 125 + VA + ++NIG GQ AG I++ +SF + + +PLV+I G + GA I Sbjct: 89 VGLCVAFRCSIWNIGAEGQFYAGAIAATAAGVSFDGLTAWIYVPLVMIAGALAGAAWAAI 148 Query: 126 PGILRALLGTSEVITTIMLNYIMLFFSTFMIHSMFQKNILMDNTTDQTKLISANASF-RT 184 G+L+ SE++TTIMLNYI + +++++ + D +A + Sbjct: 149 AGLLKVYFRASEIVTTIMLNYIAIIMTSYLVTGPLR---------DAAAAYPQSARLVQE 199 Query: 185 NWMSSLTDNSTLNIGLIIAIIALVIMAIIFTKTTLGFEIKAVGLNPDASEYAGISAKRTL 244 WM + + L+IG+++A+ V+M I ++T G+ ++ VG++PDA+ YAGIS R + Sbjct: 200 AWMPRILPPTRLHIGILVALALAVVMYIFLFRSTRGYALRVVGISPDAARYAGISVPRNI 259 Query: 245 ILSMVVAGALAGLGGVVYGFGYMQNFVSQSASLDIGFYGMAVALLGGNSPIGILFAALLF 304 +LS+ ++G++AGL G G + + QS S GF G+AVALL N+PIG +F+ LLF Sbjct: 260 MLSICLSGSMAGLAGAFEIAGVTRR-LFQSISPGYGFEGIAVALLANNNPIGAVFSGLLF 318 Query: 305 SVLQTGAPGMTNDGIPPEIVKVVTAAIIFFIAVKFII 341 ++L++G+ M P+++ +V I+ V F + Sbjct: 319 AILRSGSELMQITAQVPQVLVLVIQGIVILSVVGFAV 355 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: 324 Number of extensions: 15 Number of successful extensions: 3 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: 365 Length adjustment: 29 Effective length of query: 335 Effective length of database: 336 Effective search space: 112560 Effective search space used: 112560 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