Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate RR42_RS22875 RR42_RS22875 ABC transporter
Query= uniprot:Q6MNM2 (347 letters) >FitnessBrowser__Cup4G11:RR42_RS22875 Length = 351 Score = 258 bits (659), Expect = 2e-73 Identities = 139/306 (45%), Positives = 198/306 (64%), Gaps = 17/306 (5%) Query: 1 MAKIQFSNIKKSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTI 60 MA ++ ++ K F + + GIDL + EFLVL+GPSG GK+TLLR +AGLE+ SG I Sbjct: 1 MATVETRSLTKRFDGTNAVDGIDLAVHEAEFLVLLGPSGSGKTTLLRLIAGLEAPTSGDI 60 Query: 61 SIDGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISEL 120 + G+ + + P+ ++AMVFQSYALYPH++VA N+ F L+ + + I ++V+ + L Sbjct: 61 LVGGRVVTGLPPRAHNMAMVFQSYALYPHLSVAGNIAFPLEAQRMPREAIARKVSWAAAL 120 Query: 121 LQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLH 180 I HLL RKP++LSGG+RQRVAL RA+ R+ L DEPLSNLDA LR+ R E+++L Sbjct: 121 FGIGHLLSRKPRQLSGGERQRVALARAVVREPVAFLLDEPLSNLDAKLRTSAREELQQLQ 180 Query: 181 HNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMN 240 +T IYVTHDQ+EA LGDR+A+L G + Q+GTP ++Y +P +TF+ATFIGSP MN Sbjct: 181 RRLATTTIYVTHDQIEALALGDRVAILDHGRVHQLGTPQQVYEQPADTFVATFIGSPPMN 240 Query: 241 FLEGAVLEKIPWPEARKADQILGIRPDAFALNQGPLGTQEVALGDFQIDIS--ENLGGQQ 298 ++ L + G RP+ F L + G+ E AL F I+ ENLG + Sbjct: 241 LVDTDAL-------------VTGFRPEHF-LPREVYGSDE-ALEPFPFHITRIENLGSDR 285 Query: 299 MLHGTL 304 +++G L Sbjct: 286 LVYGLL 291 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: 288 Number of extensions: 9 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: 351 Length adjustment: 29 Effective length of query: 318 Effective length of database: 322 Effective search space: 102396 Effective search space used: 102396 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