Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate SMc04140 SMc04140 ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc03065 (362 letters) >FitnessBrowser__Smeli:SMc04140 Length = 360 Score = 382 bits (981), Expect = e-111 Identities = 203/362 (56%), Positives = 260/362 (71%), Gaps = 6/362 (1%) Query: 2 TGLLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDMF 61 T ++L+ + K YGA+DVIHGIDL I GEF VFVGPSGCGKSTLLRMIAGLEEI+GG + Sbjct: 3 TSVVLQKVEKRYGALDVIHGIDLTIDPGEFAVFVGPSGCGKSTLLRMIAGLEEISGGTLM 62 Query: 62 IDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADML 121 +D +R+N+V P++RGIAMVFQSYALYPHM+VY N+AFG+ A K EI+ +VR AA++L Sbjct: 63 LDSDRMNEVAPARRGIAMVFQSYALYPHMSVYKNLAFGLETAGFKKAEIEPKVRRAAEIL 122 Query: 122 QLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLSE 181 Q+ LDR PKALSGGQRQRVAIGRAI R P++FLFDEPLSNLDA LRV R+EI++L Sbjct: 123 QIEKLLDRKPKALSGGQRQRVAIGRAIVREPRIFLFDEPLSNLDAELRVQMRVEISRLHR 182 Query: 182 RMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAMN 241 + + TMIYVTHDQVEAMT+AD+IVVL++G IEQVGAPL+LY P N FVA FIGSP MN Sbjct: 183 DLGN-TMIYVTHDQVEAMTMADKIVVLNSGRIEQVGAPLDLYNNPVNRFVAGFIGSPKMN 241 Query: 242 VIPATIT-ATGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTEADDFLFEG 300 + A I TG +TA+ + GG ++ L N + G+ +FG+RPE L E L Sbjct: 242 FLKARIADVTGSETAIEVCGG-TIRLPRRLNGATQGQDVTFGIRPEHLSAREGGIELATV 300 Query: 301 TVSIVEALGEVTLLYIEGLV-ENEPIIAKMPGIARVGRGDKVRFTADKAKLHLFDTNGQS 359 V IVE LG T+LY G+ + + + + G +V RG + D ++ H+F +G++ Sbjct: 301 NVEIVENLGGETMLY--GITPDRQQLTVALEGQQKVERGSNLAVHFDPSRCHVFGADGRA 358 Query: 360 YR 361 R Sbjct: 359 MR 360 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: 392 Number of extensions: 9 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: 362 Length of database: 360 Length adjustment: 29 Effective length of query: 333 Effective length of database: 331 Effective search space: 110223 Effective search space used: 110223 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