Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate 208681 DVU3161 ABC transporter, ATP-binding protein
Query= uniprot:Q6MNM2 (347 letters) >MicrobesOnline__882:208681 Length = 349 Score = 248 bits (632), Expect = 2e-70 Identities = 142/353 (40%), Positives = 204/353 (57%), Gaps = 21/353 (5%) Query: 1 MAKIQFSNIKKSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTI 60 M+ I + + +G + + ++ G+ LVL+GPSGCGKST LR +AGLES SG I Sbjct: 1 MSTIVLDKVSRHWGDVRAVDDVSFEVEQGDMLVLLGPSGCGKSTTLRLIAGLESVTSGRI 60 Query: 61 SIDGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISEL 120 I G+ + ++ P R +AMVFQSYAL+PH+TV +N+ FGL ++ + AAE KR++ E+ Sbjct: 61 LIGGRDVTNLPPAQRQLAMVFQSYALFPHLTVRDNILFGLVVRKVPAAERQKRLDRAVEI 120 Query: 121 LQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLH 180 L + LL+RKP ELSGGQ+QRVALGRAL + V L DEPLSNLDA LR +MR EI+ L Sbjct: 121 LGLGKLLERKPGELSGGQQQRVALGRALVAEAAVCLMDEPLSNLDAKLRQEMRREIRALQ 180 Query: 181 HNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMN 240 TM+YVTHDQ EA ++ DRI +++ G I Q TP+E+Y RP F +FIG+P MN Sbjct: 181 QTLGMTMVYVTHDQTEAMSMADRIILMQGGRIVQNATPTEMYSRPATAFAGSFIGTPPMN 240 Query: 241 FLE-----------GAVLEKIPWPEARKADQILGIRPDAFALNQGPLGTQEVALGDFQID 289 + G+ ++ AD +LGIRP+ + G + V ++ Sbjct: 241 LVRLQGNDDGIRVAGSRSGRVTCHAG--ADCMLGIRPEHIRIVDD--GWRAV------VE 290 Query: 290 ISENLGGQQMLHGTLAGNNVRILVDSMDNFSMKQTLPLKIDLTKAHLFDKKTG 342 E LG +L + + ++V + + + + L H+FD TG Sbjct: 291 SVEYLGSNSVLSCRVGSEELSVVVHGVTDTVVGAEIYLHCPEEHVHIFDAATG 343 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: 266 Number of extensions: 5 Number of successful extensions: 1 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: 349 Length adjustment: 29 Effective length of query: 318 Effective length of database: 320 Effective search space: 101760 Effective search space used: 101760 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