Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate SM_b20661 SM_b20661 sugar uptake ABC transporter ATP-binding protein
Query= uniprot:Q6MNM2 (347 letters) >FitnessBrowser__Smeli:SM_b20661 Length = 355 Score = 318 bits (814), Expect = 2e-91 Identities = 174/358 (48%), Positives = 227/358 (63%), Gaps = 24/358 (6%) Query: 1 MAKIQFSNIKKSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTI 60 MA + F +++KSFG+ V+KG++++I GEF++LVGPSGCGKSTLLR LAGLE+ +G I Sbjct: 1 MAGVDFVDVRKSFGAFPVIKGVNIEIEDGEFVILVGPSGCGKSTLLRMLAGLENITAGEI 60 Query: 61 SIDGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISEL 120 I + +N + P++RDIAMVFQ+YALYPHMTVA+NM F L L +EI KRV +E+ Sbjct: 61 RIGNQVVNRLPPKDRDIAMVFQNYALYPHMTVADNMAFSLMLAARPKSEIDKRVGVAAEI 120 Query: 121 LQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLH 180 L + LLDR P++LSGGQRQRVA+GRA+ R V LFDEPLSNLDA LR MR EIK LH Sbjct: 121 LGLSKLLDRYPRQLSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVAMRAEIKELH 180 Query: 181 HNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMN 240 K+T +YVTHDQ+EA T+ D+I V+ DG++EQIG P E+Y P N F+A FIGSP MN Sbjct: 181 QRLKTTTVYVTHDQIEAMTMADKIVVMHDGIVEQIGAPLELYDNPANLFVAGFIGSPAMN 240 Query: 241 FLEGAVLEKIP----------WPEARKA------DQILGIRPDAFALNQGPLGTQEVALG 284 L+G + P P AR A D + G+RP+ AL+ L Sbjct: 241 MLKGRLDPADPSVFLTADGTALPVARPAAAAQGRDLVYGLRPEYMALDPNGLPA------ 294 Query: 285 DFQIDISENLGGQQMLHGTLAGNNVRILVDSMDNFSMKQTLPLKIDLTKAHLFDKKTG 342 +I + E G + L L G++V + N +T+ L ID HLFD TG Sbjct: 295 --EIAVIEPTGYETQLIARLGGHDVTCVFRERVNAKPGETIHLAIDAAHVHLFDAGTG 350 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: 343 Number of extensions: 13 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: 347 Length of database: 355 Length adjustment: 29 Effective length of query: 318 Effective length of database: 326 Effective search space: 103668 Effective search space used: 103668 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