Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate RR42_RS18590 RR42_RS18590 hypothetical protein
Query= uniprot:Q6MNM2 (347 letters) >FitnessBrowser__Cup4G11:RR42_RS18590 Length = 359 Score = 293 bits (749), Expect = 6e-84 Identities = 162/362 (44%), Positives = 214/362 (59%), Gaps = 26/362 (7%) Query: 1 MAKIQFSNIKKSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTI 60 MA +Q I+K FGS V++G+D+DIA G+F VLVGPSGCGKSTLLR +AGLE +G I Sbjct: 1 MASVQIRGIQKYFGSTQVIRGVDIDIADGQFTVLVGPSGCGKSTLLRMIAGLEEITTGEI 60 Query: 61 SIDGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISEL 120 +I + +N + P+ RDIAMVFQ+YALYPHMTV +NM F LKL EI ++V + S + Sbjct: 61 AIGNRVVNRLPPKERDIAMVFQNYALYPHMTVYDNMAFSLKLAKGDKEEIKRKVAKASAI 120 Query: 121 LQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRLH 180 L + LL+R P++LSGGQRQRVA+GRA+ R V LFDEPLSNLDA LR QMR EIK LH Sbjct: 121 LGLDSLLERYPRQLSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRAEIKELH 180 Query: 181 HNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEMN 240 ++T +YVTHDQ+EA T+ D+I V++DG +EQ G P +Y P N F+A FIGSP MN Sbjct: 181 QRLRTTSVYVTHDQIEAMTMADQIVVMRDGRVEQRGKPLALYDHPDNLFVAGFIGSPAMN 240 Query: 241 FLEGAVLE-------------KIPWPEARKADQ-------ILGIRPDAFALNQGPLGTQE 280 F+ G + ++P P A I G+RP+ L G Q Sbjct: 241 FVPGVLRRSGGDAAVEFPDGTRLPAPARFDATAGTDGQRVIYGVRPEHLTLGMPGQGLQT 300 Query: 281 VALGDFQIDISENLGGQQMLHGTLAGNNVRILVDSMDNFSMKQTLPLKIDLTKAHLFDKK 340 ++ + E G ++ + +F+ L L D HLFD Sbjct: 301 ------RVSVVEPTGANTEIYSRFCEAEFISIFRERHDFAAGDILNLVPDHQHTHLFDAD 354 Query: 341 TG 342 +G Sbjct: 355 SG 356 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: 332 Number of extensions: 17 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: 359 Length adjustment: 29 Effective length of query: 318 Effective length of database: 330 Effective search space: 104940 Effective search space used: 104940 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