Align Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale)
to candidate GFF2276 PGA1_c23080 ribose transport system permease protein RbsC
Query= uniprot:B2T9V8 (351 letters) >FitnessBrowser__Phaeo:GFF2276 Length = 324 Score = 131 bits (329), Expect = 3e-35 Identities = 96/310 (30%), Positives = 156/310 (50%), Gaps = 29/310 (9%) Query: 38 LRELALLPALALLIVIGAFISPSFLTKANLISVLGASAALALVVLAESLIVLTGKFDLSL 97 L + +L A AL I+ +P FLT N +V+ +SA L ++ L + +V++G DLS+ Sbjct: 13 LAKQGILIAFALFIIGFTIANPKFLTLDNFENVVRSSAILGVMALGVTFVVISGNLDLSV 72 Query: 98 ESTVGIAPAV--------GAMLVMPAASAGFGMQWPAAAGLLAIVVVGAVIGFINGFLVV 149 S + + V G L +PA A + +GA+IGF+ G+L Sbjct: 73 GSMMSFSTIVVLDLHDKLGPTLAIPAMFA-------------MTLCLGALIGFLVGYL-- 117 Query: 150 RLRLNAFIVTLAMLIVLRGMLVGATKGGTL--FDMPTSFFAL-ATTIVLGLPLSVWLAAA 206 +LN+ IVTL ML + G+ + + G + D ++FA+ +LG+ + + A Sbjct: 118 --KLNSLIVTLGMLSAIHGLTLTYSGGKNMDIADKEGTWFAIFGQGNILGIQTPILIFIA 175 Query: 207 AFAIAAFMLRYHRLGRALYAIGGNPEAARAAGIRVERITWGVFVLGSILASVGGLIVTGY 266 A+ +L GR +YA+GGN AA +GIR R+ + +++ ++ + GLI Sbjct: 176 LAALLGIILAKTPFGRKVYAVGGNGTAATFSGIRRARVVFLCYIMSALCVATAGLIQASR 235 Query: 267 VGAINANQGNGMIFTVFAAAVIGGISLDGGKGTMFGALTGVLLLGVVQNLLTLAQVPSFW 326 G G+ V AA ++GG SL GG GT+F + GVL+LG +QN L L + F Sbjct: 236 SMGSQNTVGQGLELEVLAAVILGGASLLGGSGTIFKTVIGVLILGFIQNGLLLVGL-DFS 294 Query: 327 IQAIYGAIIL 336 +Q + II+ Sbjct: 295 VQYVVTWIII 304 Score = 25.8 bits (55), Expect = 0.002 Identities = 28/84 (33%), Positives = 40/84 (47%), Gaps = 6/84 (7%) Query: 98 ESTVGIAPAVGAMLVMPAASAGFGMQWPAAAGLLAIVVVGAVI-GFI-NGFLVVRLRLNA 155 ++TVG G L + AA G +G + V+G +I GFI NG L+V L + Sbjct: 240 QNTVG----QGLELEVLAAVILGGASLLGGSGTIFKTVIGVLILGFIQNGLLLVGLDFSV 295 Query: 156 FIVTLAMLIVLRGMLVGATKGGTL 179 V ++I+L L A K G L Sbjct: 296 QYVVTWIIIILAVWLDIAAKRGKL 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: 290 Number of extensions: 19 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 351 Length of database: 324 Length adjustment: 28 Effective length of query: 323 Effective length of database: 296 Effective search space: 95608 Effective search space used: 95608 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