Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate 8499890 DvMF_0655 ABC transporter related (RefSeq)
Query= uniprot:Q6MNM2 (347 letters) >FitnessBrowser__Miya:8499890 Length = 350 Score = 259 bits (661), Expect = 9e-74 Identities = 149/351 (42%), Positives = 203/351 (57%), Gaps = 17/351 (4%) Query: 1 MAKIQFSNIKKSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTI 60 M+ IQ N+ + +G + + ++ G LVL+GPSGCGKST LR +AGLES SG I Sbjct: 1 MSAIQLLNVSRHWGDVRAVDDVSFEVEQGTMLVLLGPSGCGKSTTLRLIAGLESVTSGRI 60 Query: 61 SIDGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISEL 120 I + + + P R +AMVFQSYAL+PH+TV EN+ FGL ++ + AE KR+ ++ Sbjct: 61 MIGERDVTHLPPAQRQLAMVFQSYALFPHLTVRENILFGLTVRKVPEAEREKRLTRAVDI 120 Query: 121 LQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLH 180 L + LL RKP ELSGGQ+QRVALGRAL + V L DEPLSNLDA LR +MR EI+ L Sbjct: 121 LGLSALLQRKPGELSGGQQQRVALGRALVAEAAVCLMDEPLSNLDAKLRHEMRREIRALQ 180 Query: 181 HNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMN 240 TM+YVTHDQ EA ++ DRI +++ G I Q TPSE+Y RP TF FIG+P MN Sbjct: 181 QTLGMTMVYVTHDQTEAMSMADRIILMQGGRIVQNATPSELYSRPATTFAGNFIGTPPMN 240 Query: 241 FL-----EGAVL----EKIPWPEARKADQILGIRPDAFALNQGPLGTQEVALGDFQIDIS 291 + G+V AD +LGIRP+ + P G + V ++ Sbjct: 241 LVRLDDARGSVCVAGSRSGTVSVVDSADYVLGIRPEHIRI--VPEGWRAV------VESV 292 Query: 292 ENLGGQQMLHGTLAGNNVRILVDSMDNFSMKQTLPLKIDLTKAHLFDKKTG 342 E LG +L + G + ++VD + ++ + L H+FD KTG Sbjct: 293 EYLGSGSVLGCRVGGEELSVVVDGVPTIAVGAEIYLHCPDEHIHIFDAKTG 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: 289 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: 350 Length adjustment: 29 Effective length of query: 318 Effective length of database: 321 Effective search space: 102078 Effective search space used: 102078 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