Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate GFF729 PGA1_c07440 ABC transporter, ATP binding protein
Query= reanno::Smeli:SMc03065 (362 letters) >FitnessBrowser__Phaeo:GFF729 Length = 353 Score = 327 bits (839), Expect = 2e-94 Identities = 188/354 (53%), Positives = 230/354 (64%), Gaps = 9/354 (2%) Query: 1 MTGLLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDM 60 MTG+ L K YG V VIH +DL I +GEF VFVGPSGCGKSTLLRMIAGLEE + G++ Sbjct: 1 MTGVTLAKAVKKYGDVQVIHDVDLSIDDGEFCVFVGPSGCGKSTLLRMIAGLEETSSGNI 60 Query: 61 FIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADM 120 I V + + RG+AMVFQSYALYPHMTV DNM FG+++ KE+I +V A+ + Sbjct: 61 HIGDRDVTRLDAADRGVAMVFQSYALYPHMTVEDNMGFGLKMNGHPKEKIREKVAEASRI 120 Query: 121 LQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLS 180 L+L YL R PKALSGGQRQRVAIGRAI R P+VFLFDEPLSNLDA LRV R+EIA+L Sbjct: 121 LKLDDYLKRKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVDMRVEIARLH 180 Query: 181 ERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAM 240 + + TMIYVTHDQVEAMTLAD+IVVL AG +EQVG+P+ELY P N FVA FIGSP+M Sbjct: 181 KEIG-ATMIYVTHDQVEAMTLADKIVVLRAGRVEQVGSPMELYANPDNRFVAGFIGSPSM 239 Query: 241 NVIPATITATGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTEADDFLFEG 300 N + T+ G V + V V A +G G+RP+ L VT AD L Sbjct: 240 NFLEGTVQGDG--VVVPALENRRVATSVALPA--DGSKVLLGLRPQHLSVTAADSSL--- 292 Query: 301 TVSIVEALGEVTLLYIEGLVENEPIIAKMPGIARVGRGDKVRFTADKAKLHLFD 354 + + E LG V+ Y+ E +I + G + G V D A ++FD Sbjct: 293 VLDLRERLGGVSYDYL-STPTGEKLIVETRGDEALPEGTAVALGFDDADAYIFD 345 Lambda K H 0.320 0.137 0.387 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: 373 Number of extensions: 14 Number of successful extensions: 2 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: 362 Length of database: 353 Length adjustment: 29 Effective length of query: 333 Effective length of database: 324 Effective search space: 107892 Effective search space used: 107892 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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