Align glucose transporter, ATPase component (characterized)
to candidate 350819 BT1291 spermidine/putrescine transport ATP-binding protein (NCBI ptt file)
Query= reanno::Phaeo:GFF3641 (260 letters) >FitnessBrowser__Btheta:350819 Length = 463 Score = 106 bits (265), Expect = 8e-28 Identities = 75/228 (32%), Positives = 122/228 (53%), Gaps = 14/228 (6%) Query: 15 LVEMKDISISFGGIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGEIRV 74 ++E+ +S FG A+D V++++ GE V +LG +G GK+TL+++++G GEIR+ Sbjct: 9 IIEVSHVSKFFGDKTALDDVTLNVKKGEFVTILGPSGCGKTTLLRLIAGFQTASEGEIRI 68 Query: 75 NGDKVEITNPRDARSHNIETIYQTLALADNLDAASNLFLGREL-VTPFGLVDDSAMEAEC 133 +G ++ T P + T++Q AL +L+ N+ G +L TP + A Sbjct: 69 SGKEITQTPP---HKRPVNTVFQKYALFPHLNVYDNIAFGLKLKKTPKQTIGKKVKAA-- 123 Query: 134 RKIMNRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALG-PHETQMV 192 K++ + ++ V +LSGGQ+Q VAIARA+ ++L++DEP AAL M Sbjct: 124 LKMVGMTDYEYR----DVDSLSGGQQQRVAIARAIVNEPEVLLLDEPLAALDLKMRKDMQ 179 Query: 193 AELIQQLKAQGIGIFLIDHDVNAVMELCDRASVMKNG--QLVGT-VDI 237 EL + K+ GI + HD + L D VM G Q +GT +DI Sbjct: 180 MELKEMHKSLGITFVYVTHDQEEALTLSDTIVVMSEGKIQQIGTPIDI 227 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: 231 Number of extensions: 12 Number of successful extensions: 3 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: 260 Length of database: 463 Length adjustment: 29 Effective length of query: 231 Effective length of database: 434 Effective search space: 100254 Effective search space used: 100254 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: 49 (23.5 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