Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate 8500851 DvMF_1589 ABC transporter related (RefSeq)
Query= reanno::Smeli:SMc03065 (362 letters) >FitnessBrowser__Miya:8500851 Length = 354 Score = 212 bits (540), Expect = 1e-59 Identities = 129/309 (41%), Positives = 183/309 (59%), Gaps = 22/309 (7%) Query: 1 MTGLLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDM 60 M+ + L ++ K +G V + ++L+I GE +GPSGCGK+T LRM+AG E++ G++ Sbjct: 1 MSYVRLVNVTKRFGGVTAVDSLNLEIGRGECFSMLGPSGCGKTTTLRMVAGFEDLDDGEI 60 Query: 61 FIDGERVND-------VPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRR 113 + G+R+ +PP KR MVFQ++A++PH++VY+N+AF +RI R S EIDRR Sbjct: 61 HV-GDRLLSARRNNYYLPPEKRDFGMVFQAFAVWPHLSVYENVAFPLRIRRLSAAEIDRR 119 Query: 114 VRGAADMLQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATR 173 R A L + P LSGG +QRVA+ RA+ NP V L DEPLS+LD LR R Sbjct: 120 TREALHHTSLADVAQKSPDDLSGGGKQRVALARALAINPDVMLLDEPLSSLDPHLREEMR 179 Query: 174 IEIAKLSERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVAR 233 EI L +R +++YVTHDQ EAM L+DRI+V+ G ++QVG PL++Y PAN FV Sbjct: 180 FEIKDL-QRTFGFSILYVTHDQSEAMALSDRIMVMRNGVVQQVGTPLDVYTNPANSFVFG 238 Query: 234 FIGSPAMNVIPATITATGQQTAVSLAGGKS-VTLDVPTNAS-ENGKTASFGVRPEDLRVT 291 FIG N + +T G V + GG + VT P +A + A+ RP ++ Sbjct: 239 FIG--LSNFLDVNLTPEG---LVRVNGGDARVTPATPPSARLVSAGRAALASRPSEI--- 290 Query: 292 EADDFLFEG 300 DF EG Sbjct: 291 ---DFTAEG 296 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: 321 Number of extensions: 11 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: 354 Length adjustment: 29 Effective length of query: 333 Effective length of database: 325 Effective search space: 108225 Effective search space used: 108225 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