Align Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale)
to candidate 16645 b2546 predicted sugar transporter subunit: membrane component of ABC superfamily (NCBI)
Query= uniprot:B2T9V8 (351 letters) >FitnessBrowser__Keio:16645 Length = 332 Score = 164 bits (414), Expect = 4e-45 Identities = 100/325 (30%), Positives = 178/325 (54%), Gaps = 13/325 (4%) Query: 19 SQLALPASRGKRARSELAR-LRELALLPALALLIVIGAFISPSFLTKANLISVLGASAAL 77 S L LP + + ++R + E+ LL +A+L ++ + +P F++ N ++VL +A + Sbjct: 4 SSLPLPQGKSVSLKQFVSRHINEIGLLVVIAILYLVFSLNAPGFISLNNQMNVLRDAATI 63 Query: 78 ALVVLAESLIVLTGKFDLSLESTVGIAPAVGAMLVMPAASAGFGMQW--PAAAGLLAIVV 135 + A +LI+++G+ D+S VG M+ + F +Q+ P A L +++ Sbjct: 64 GIAAWAMTLIIISGEIDVS----------VGPMVAFVSVCLAFLLQFEVPLAVACLLVLL 113 Query: 136 VGAVIGFINGFLVVRLRLNAFIVTLAMLIVLRGMLVGATKGGTLFDMPTSFFALATTIVL 195 +GA++G + G L + +F+ TL + LRGM + T + L Sbjct: 114 LGALMGTLAGVLRGVFNVPSFVATLGLWSALRGMGLFMTNALPVPIDENEVLDWLGGQFL 173 Query: 196 GLPLSVWLAAAAFAIAAFMLRYHRLGRALYAIGGNPEAARAAGIRVERITWGVFVLGSIL 255 G+P+S + FA+ F+ R GR+++A+GGN AA+ GI V R+ +F L +L Sbjct: 174 GVPVSALIMIVLFALFVFISRKTAFGRSVFAVGGNATAAQLCGINVRRVRILIFTLSGLL 233 Query: 256 ASVGGLIVTGYVGAINANQGNGMIFTVFAAAVIGGISLDGGKGTMFGALTGVLLLGVVQN 315 A+V G+++ +G+ NA NG+ F V AA V+GG +L GG+G++FG L GVL++ ++ N Sbjct: 234 AAVTGILLAARLGSGNAGAANGLEFDVIAAVVVGGTALSGGRGSLFGTLLGVLVITLIGN 293 Query: 316 LLTLAQVPSFWIQAIYGAIILGSLM 340 L L + SF+ Q + G II+ +++ Sbjct: 294 GLVLLGINSFFQQVVRGVIIVVAVL 318 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: 265 Number of extensions: 14 Number of successful extensions: 2 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: 351 Length of database: 332 Length adjustment: 29 Effective length of query: 322 Effective length of database: 303 Effective search space: 97566 Effective search space used: 97566 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