Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate Dsui_0258 Dsui_0258 sulfate ABC transporter, ATP-binding protein
Query= reanno::Smeli:SMc03065 (362 letters) >FitnessBrowser__PS:Dsui_0258 Length = 360 Score = 203 bits (517), Expect = 5e-57 Identities = 124/326 (38%), Positives = 183/326 (56%), Gaps = 25/326 (7%) Query: 6 LKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDMFIDGE 65 +++I K +G + + L I GE V +GPSGCGK+TLLR+IAG+E G + +G Sbjct: 5 IRNIAKRFGNFVALDDVSLSIPTGELVALLGPSGCGKTTLLRIIAGMETADEGQVMFEGS 64 Query: 66 RVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRI----ARESKEEIDRRVRGAADML 121 + +R + VFQ YAL+ HM V++N+AFG+R+ R + EI +RV ++ Sbjct: 65 EATHLHARERQVGFVFQHYALFRHMNVFENVAFGLRVKPRKERPCESEIRKRVMDLLSLV 124 Query: 122 QLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLSE 181 QL DR P LSGGQRQR+A+ RA+ PKV L DEP LD +R R + +L + Sbjct: 125 QLDWLADRYPTQLSGGQRQRIALARALAVEPKVLLLDEPFGALDTKVRKELRRWLRRLHD 184 Query: 182 RMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAMN 241 M + ++VTHDQ EA+ +ADR+VV++ G IEQVG+P E+Y PA+ FV +F+G+ +N Sbjct: 185 EM-HISSVFVTHDQEEALEVADRVVVMNKGRIEQVGSPDEVYSNPASPFVYQFLGN--VN 241 Query: 242 VIPATITATGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRV-TEADDFLFEG 300 V + + + A DVP G+ A +RP D+ + T A E Sbjct: 242 VFHSRVHGAWAEVARD---------DVPA-----GQEAVAFIRPHDIDIDTVATPESLEA 287 Query: 301 TVSIVEALG---EVTLLYIEGLVENE 323 VS V+ +G V +++ LVE E Sbjct: 288 KVSYVQTIGPLVRVEVIHQGELVEVE 313 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: 328 Number of extensions: 12 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 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