Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate GFF262 PGA1_c02740 sn-glycerol-3-phosphate import ATP-binding protein UgbC
Query= uniprot:Q6MNM2 (347 letters) >FitnessBrowser__Phaeo:GFF262 Length = 348 Score = 295 bits (754), Expect = 2e-84 Identities = 161/348 (46%), Positives = 220/348 (63%), Gaps = 9/348 (2%) Query: 1 MAKIQFSNIKKSF-GSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGT 59 MA++ ++++K + + + I GEF+VLVGPSGCGKSTLLR +AGLE GT Sbjct: 1 MAQVTLNSVRKVYPNGVEAVTSSSFKIEDGEFVVLVGPSGCGKSTLLRMIAGLEDITEGT 60 Query: 60 ISIDGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISE 119 + I + +N+++P +RDIAMVFQ+YALYPHMTV +N+ +GLK + AEI ++V E ++ Sbjct: 61 LEIGDRVVNNVDPADRDIAMVFQNYALYPHMTVRKNIAYGLKNRKTPEAEIKQKVAEAAK 120 Query: 120 LLQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRL 179 +L ++ LDRKP +LSGGQRQRVA+GRA+ R + LFDEPLSNLDA LR+QMR+EIK L Sbjct: 121 MLNLEEYLDRKPSQLSGGQRQRVAMGRAIVRDPALFLFDEPLSNLDAKLRNQMRIEIKAL 180 Query: 180 HHNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEM 239 T IYVTHDQ+EA T+ DRI VL G IEQIGTPSEIYH P + F+A+F+G+P M Sbjct: 181 QRRLGVTSIYVTHDQVEAMTMADRIIVLNGGRIEQIGTPSEIYHNPASVFVASFMGAPPM 240 Query: 240 NFLEGAVLE-KIPWPEARKADQILGIRPDAFALNQGPLGTQEVALGDFQIDIS--ENLGG 296 N L+ + ++ P+ + A L P Q VA G ID+ E LG Sbjct: 241 NLLDATIANGQVTLPDGVSMGALDTSAQGAVKLGIRPEDVQLVAEGGLAIDVELIEELGA 300 Query: 297 QQMLHGTLAGN--NVRILVDSMDNFSMKQTLPLKIDLTKAHLFDKKTG 342 ++LHG L G + +L D + Q + +D LFD ++G Sbjct: 301 HRLLHGKLGGQPFTIHVLKDIPVDPGTHQ---ISVDPAAICLFDAESG 345 Lambda K H 0.318 0.136 0.383 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: 304 Number of extensions: 7 Number of successful extensions: 1 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: 347 Length of database: 348 Length adjustment: 29 Effective length of query: 318 Effective length of database: 319 Effective search space: 101442 Effective search space used: 101442 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 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