Align glucose transporter, ATPase component (characterized)
to candidate 5208462 Shew_0974 spermidine/putrescine ABC transporter ATPase subunit (RefSeq)
Query= reanno::Phaeo:GFF3641 (260 letters) >FitnessBrowser__PV4:5208462 Length = 378 Score = 109 bits (273), Expect = 7e-29 Identities = 74/239 (30%), Positives = 126/239 (52%), Gaps = 15/239 (6%) Query: 15 LVEMKDISISFGGIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGEIRV 74 L++++ +S F ++AVD VS+++ GE+ LLG +G+GKSTL+++L+G + G I + Sbjct: 20 LLKIERVSKLFDDVRAVDDVSLNINRGEIFALLGGSGSGKSTLLRMLAGFEKPTEGRIYL 79 Query: 75 NGDKVEITNPRDARSHNIETIYQTLALADNLDAASNLFLGRELVTPFGLVDDSAMEAECR 134 +G + P + I ++Q+ AL ++ A N+ FGL D +AE Sbjct: 80 DGQDITDMPPYE---RPINMMFQSYALFPHMTVAQNI--------AFGLKQDKMPKAEIE 128 Query: 135 ---KIMNRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALGPH-ETQ 190 K M +L + LSGGQRQ VA+AR++ K+L++DEP AL TQ Sbjct: 129 QRVKEMLKLVHMEPYAKRKPNQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQ 188 Query: 191 MVAELIQQLKAQGIGIFLIDHDVNAVMELCDRASVMKNGQLVGTVDIDDVTDDDLLSMI 249 M E++ L+A G+ ++ HD M + +R ++M +G + T D+ + M+ Sbjct: 189 MQLEVVDILEAVGVTCVMVTHDQEEAMTMAERIAIMNDGWIAQTGSPMDIYESPANRMV 247 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: 169 Number of extensions: 13 Number of successful extensions: 3 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: 260 Length of database: 378 Length adjustment: 27 Effective length of query: 233 Effective length of database: 351 Effective search space: 81783 Effective search space used: 81783 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: 48 (23.1 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