Align glucose transporter, ATPase component (characterized)
to candidate WP_170920503.1 B9A12_RS09210 energy-coupling factor transporter ATPase
Query= reanno::Phaeo:GFF3641 (260 letters) >NCBI__GCF_900176285.1:WP_170920503.1 Length = 571 Score = 89.0 bits (219), Expect = 2e-22 Identities = 73/221 (33%), Positives = 117/221 (52%), Gaps = 16/221 (7%) Query: 16 VEMKDISISFG-GIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGEIRV 74 +EM S ++G G A+++VS + GE + L+G NGAGKSTL L+G + G+ + Sbjct: 312 LEMLGFSYAYGDGTVALENVSFQVGRGERLALVGPNGAGKSTLAACLAGI-RWGTGQYLL 370 Query: 75 NGDKVEITNPRDARSHNIETIYQTLALADNLDAASNLFLGRELVTPFGLVDDSAMEAECR 134 +G KVE R+ H + ++Q D+ D G E+ FGL + E+ R Sbjct: 371 DGRKVEGAFRRNLWRH-VGLVFQ-----DSADQMVCSRCGDEVA--FGLRNLGWPESRIR 422 Query: 135 KIMNRLN--PNFQKFSEPVSA-LSGGQRQSVAIARAVYFNAKILIMDEPTAALGPHETQM 191 K + + + F + V LSGG+R+ +A+A + ++LI+DEPTA L P Q Sbjct: 423 KKVQAMLHWAGLEGFEDRVPQHLSGGERKRLALAAVLAMEPEVLILDEPTAGLDPQTEQK 482 Query: 192 VAELIQQLKAQGIGIFLIDHDVNAVMELCDRASVMKNGQLV 232 + +L+ +++A + LI HDV V L DR +M G++V Sbjct: 483 LLQLLDEVEAT---LVLISHDVCFVSMLTDRTLLMHRGRIV 520 Score = 79.3 bits (194), Expect = 2e-19 Identities = 60/208 (28%), Positives = 97/208 (46%), Gaps = 18/208 (8%) Query: 27 GIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGEIRVNGDKVEITNPRD 86 G +A+ H+ + ++ GE + +LGHNG+GK+TL +VLSG G + GD + D Sbjct: 31 GRQALRHIDLSIHEGERIAVLGHNGSGKTTLARVLSGLAPPTQGRVLFQGDPLSRERLED 90 Query: 87 ARSHNIETIYQTLALADNLDAASNLFLGREL-VTPFGL----VDDSAMEAECRKIMNRLN 141 R + ++Q D LF L FGL V E RK + + Sbjct: 91 LR-QRVGFLFQ--------DPDDQLFCPTVLDDVLFGLLNFQVPPKEAEERARKALAAMG 141 Query: 142 PNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALGPHETQMVAELIQQLKA 201 + P LS GQR+ A+A + +LI+DEPTA + P +++++++ Sbjct: 142 LEAEAHRAP-HHLSYGQRKRAALAAILALEPDVLILDEPTANMDPTSEALLSKVLKDYPG 200 Query: 202 QGIGIFLIDHDVNAVMELCDRASVMKNG 229 + I HD+ + LC RA V++ G Sbjct: 201 T---LICISHDILFLYGLCTRAVVLQAG 225 Lambda K H 0.317 0.135 0.373 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: 288 Number of extensions: 19 Number of successful extensions: 6 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: 260 Length of database: 571 Length adjustment: 30 Effective length of query: 230 Effective length of database: 541 Effective search space: 124430 Effective search space used: 124430 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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