Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate RR42_RS12955 RR42_RS12955 glycerol-3-phosphate ABC transporter ATP-binding protein
Query= uniprot:Q6MNM2 (347 letters) >FitnessBrowser__Cup4G11:RR42_RS12955 Length = 367 Score = 310 bits (793), Expect = 5e-89 Identities = 168/367 (45%), Positives = 228/367 (62%), Gaps = 30/367 (8%) Query: 1 MAKIQFSNIKKSF-GSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGT 59 MAK+ N++K++ G+ V+ GID++I GEF+V+VGPSGCGKSTLLR +AGLE+ G Sbjct: 1 MAKLSLRNVQKTYAGNVKVVHGIDMEINDGEFIVIVGPSGCGKSTLLRMVAGLEAISGGE 60 Query: 60 ISIDGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEISE 119 + I K +N +EP RDIAMVFQ+YALYPHM+V +NM +GLK++ + +EI +RV + Sbjct: 61 VHIGDKVVNHLEPAERDIAMVFQNYALYPHMSVYDNMAYGLKIRGMDKSEIEQRVKHAAG 120 Query: 120 LLQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRL 179 +L++ LL+RKP+ LSGGQRQRVA+GRA+ R+ V LFDEPLSNLDA LR QMRLE+K L Sbjct: 121 ILELAPLLERKPRALSGGQRQRVAMGRAIVREPAVFLFDEPLSNLDAKLRVQMRLELKEL 180 Query: 180 HHNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEM 239 H ++T +YVTHDQ+EA TL DR+ VL G +EQIGTP E+Y RP +TF+A+FIGSP M Sbjct: 181 HRRLRTTSMYVTHDQVEAMTLADRMMVLNGGSVEQIGTPLEVYARPASTFVASFIGSPPM 240 Query: 240 NFL------------------------EGAVLEKIPWPEARKADQILGIRPDAFALNQGP 275 N + A L +P +LG+RP+ P Sbjct: 241 NLVPVTRTNGGQGEAQMRVEQKPGAQGAPATLGHLPMGLHLPERALLGLRPEHIE----P 296 Query: 276 LGTQEVALGDFQIDISENLGGQQMLHGTLAGNNVRILVDSMDNFSMKQTLPLKIDLTKAH 335 E A+ + ++ + E LG +GTL G V + +DS S LP+ H Sbjct: 297 CAAHE-AIAEIEVRLVEALGADSYAYGTLGGQPVVVRLDSNMPVSSGDRLPITAAAEHLH 355 Query: 336 LFDKKTG 342 FD +G Sbjct: 356 FFDADSG 362 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: 356 Number of extensions: 14 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: 367 Length adjustment: 29 Effective length of query: 318 Effective length of database: 338 Effective search space: 107484 Effective search space used: 107484 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