Align Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale)
to candidate AO356_20255 AO356_20255 arabinose ABC transporter permease
Query= uniprot:B2T9V8 (351 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_20255 Length = 322 Score = 152 bits (383), Expect = 2e-41 Identities = 95/307 (30%), Positives = 160/307 (52%), Gaps = 19/307 (6%) Query: 43 LLPALALLIV----IGAFISPSFLTKANL-ISVLGASAALALVVLAESLIVLTGKFDLSL 97 LL A+ + ++ I F+SP + L IS G +A L LA +G FDLS+ Sbjct: 27 LLAAIGIFVLCTLMIDNFLSPLNMRGLGLAISTTGIAACTMLYCLA------SGHFDLSV 80 Query: 98 ESTVGIAPAVGAMLVMPAASAGFGMQWPAAAGLLAIVVVGAVIGFINGFLVVRLRLNAFI 157 S + A V A+++ S G+ A + +G ++G ING ++ +LR+NA I Sbjct: 81 GSVIACAGVVAAVVMRDTNSVFLGVS--------AALAMGLIVGLINGIVIAKLRVNALI 132 Query: 158 VTLAMLIVLRGMLVGATKGGTLFDMPTSFFALATTIVLGLPLSVWLAAAAFAIAAFMLRY 217 TLA + ++RG+ G + SFF + G+P+ + + A F ++L Y Sbjct: 133 TTLATMQIVRGLAYIFANGKAVGVSQESFFVFGNGQLFGVPVPILITIACFLFFGWLLNY 192 Query: 218 HRLGRALYAIGGNPEAARAAGIRVERITWGVFVLGSILASVGGLIVTGYVGAINANQGNG 277 GR AIGGN EAA AG+ V+R +F + ++ ++ G+I+ + + G G Sbjct: 193 TTYGRNTMAIGGNQEAALLAGVNVDRTKIIIFAVHGLIGALAGVILASRMTSGQPMIGQG 252 Query: 278 MIFTVFAAAVIGGISLDGGKGTMFGALTGVLLLGVVQNLLTLAQVPSFWIQAIYGAIILG 337 TV +A V+GG+SL GG G + + GVL+L +++N + L + +F+ I G+I+L Sbjct: 253 FELTVISACVLGGVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDTFYQYVIRGSILLL 312 Query: 338 SLMVARL 344 ++++ RL Sbjct: 313 AVVIDRL 319 Lambda K H 0.326 0.140 0.397 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: 243 Number of extensions: 7 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 351 Length of database: 322 Length adjustment: 28 Effective length of query: 323 Effective length of database: 294 Effective search space: 94962 Effective search space used: 94962 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: 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