Align glucose transporter, ATPase component (characterized)
to candidate 350090 BT0562 putative ABC transporter ATP-binding protein (NCBI ptt file)
Query= reanno::Phaeo:GFF3641 (260 letters) >FitnessBrowser__Btheta:350090 Length = 489 Score = 97.4 bits (241), Expect = 5e-25 Identities = 65/220 (29%), Positives = 118/220 (53%), Gaps = 8/220 (3%) Query: 12 ATPLVEMKDISISFGGIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGE 71 A P++E++ ++ SFG AVDH+S + GE+ G LG NGAGK+T +++L G + +G Sbjct: 244 AAPVIEVEQLTKSFGHFTAVDHISFQVQRGEIFGFLGANGAGKTTAMRMLCGLSRPTSGV 303 Query: 72 IRVNGDKVEITNPRDARSHNIETIYQTLALADNLDAASNLFLGRELVTPFGLVDDSAMEA 131 +V G +I + +I + Q +L ++L N+ R +G+ + +E Sbjct: 304 GKVAG--YDIFREAEQVKRHIGYMSQKFSLYEDLKVWENI---RLFAGIYGM-KEMEIEE 357 Query: 132 ECRKIMNRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALGPHETQM 191 + +++ RL ++ V L G +Q +A + +++ KI+ +DEPT + P + Sbjct: 358 KTDELLERLGFADER-DTLVKNLPLGWKQKLAFSVSIFHEPKIVFLDEPTGGVDPATRRQ 416 Query: 192 VAELIQQLKAQGIGIFLIDHDVNAVMELCDRASVMKNGQL 231 ELI Q +GI +F+ H ++ E C+R S+M +GQ+ Sbjct: 417 FWELIYQAADRGITVFVTTHYMDEA-EYCNRISIMVDGQI 455 Score = 95.9 bits (237), Expect = 1e-24 Identities = 69/225 (30%), Positives = 121/225 (53%), Gaps = 20/225 (8%) Query: 14 PLVEMKDISISFGGIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGEIR 73 P+V +K+IS S+G ++A+ VS + GEV GL+G +GAGKSTL ++L+ D G Sbjct: 6 PIVVVKEISKSYGKVEALKEVSFAVEQGEVFGLIGPDGAGKSTLFRILTTLLLADKGTAT 65 Query: 74 VNGDKVEITNPRDARSH-----NIETIYQTLALADNLDAASNLFLGRELVTPFGLVDDSA 128 VNG V +T+ + R+ ++YQ L++ +NL+ + +F + + L+ D Sbjct: 66 VNGLDV-VTDYKQIRTKVGYMPGRFSLYQDLSVEENLEFFATVF-HTLIQENYDLIKD-- 121 Query: 129 MEAECRKIMNRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALGPHE 188 I ++ P F+K ALSGG +Q +A++ ++ IL +DEPT + P Sbjct: 122 -------IYQQIEP-FKK--RRAGALSGGMKQKLALSCSLIHKPDILFLDEPTTGVDPVS 171 Query: 189 TQMVAELIQQLKAQGIGIFLIDHDVNAVMELCDRASVMKNGQLVG 233 + ++++ L+ QGI I ++ + CDR + + +GQ+ G Sbjct: 172 RKEFWQMLRNLRKQGITI-IVSTPIMDEARQCDRIAFINHGQVHG 215 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: 248 Number of extensions: 13 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: 260 Length of database: 489 Length adjustment: 29 Effective length of query: 231 Effective length of database: 460 Effective search space: 106260 Effective search space used: 106260 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