Align ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized)
to candidate RR42_RS12955 RR42_RS12955 glycerol-3-phosphate ABC transporter ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3039 (367 letters) >FitnessBrowser__Cup4G11:RR42_RS12955 Length = 367 Score = 356 bits (913), Expect = e-103 Identities = 181/366 (49%), Positives = 253/366 (69%), Gaps = 17/366 (4%) Query: 1 MANLKIKNLQKGFEG-FSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGGT 59 MA L ++N+QK + G ++ GID+E+ND EF+V VGPSGCGKSTLLR++AGLE +SGG Sbjct: 1 MAKLSLRNVQKTYAGNVKVVHGIDMEINDGEFIVIVGPSGCGKSTLLRMVAGLEAISGGE 60 Query: 60 IELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVSEAAR 119 + + + + + PA+RD+AMVFQ YALYPHMSV NM++ L + G+ K+E+E++V AA Sbjct: 61 VHIGDKVVNHLEPAERDIAMVFQNYALYPHMSVYDNMAYGLKIRGMDKSEIEQRVKHAAG 120 Query: 120 ILELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLRL 179 ILEL P+LERKP+ LSGGQRQRVA+GRAIVR P +FLFDEPLSNLDA LRVQMRLEL L Sbjct: 121 ILELAPLLERKPRALSGGQRQRVAMGRAIVREPAVFLFDEPLSNLDAKLRVQMRLELKEL 180 Query: 180 HKELQATMIYVTHDQVEAMTMADKVVVLNGGKIEQVGSPLDLYHQPANLFVAGFLGTPKM 239 H+ L+ T +YVTHDQVEAMT+AD+++VLNGG +EQ+G+PL++Y +PA+ FVA F+G+P M Sbjct: 181 HRRLRTTSMYVTHDQVEAMTLADRMMVLNGGSVEQIGTPLEVYARPASTFVASFIGSPPM 240 Query: 240 GFLKGKITRVDSQGCEVQLDA----------GTRVSLPLGGRHLSVGSAVTLGIRPEHLE 289 + +TR + E Q+ T LP+G L + LG+RPEH+E Sbjct: 241 NLV--PVTRTNGGQGEAQMRVEQKPGAQGAPATLGHLPMG---LHLPERALLGLRPEHIE 295 Query: 290 LAKPGDCALQVTADVSERLGSDTFCHVRTASGEALTMRVRGDLASRYGETLSLHLDAQHC 349 + ++ + E LG+D++ + T G+ + +R+ ++ G+ L + A+H Sbjct: 296 PCAAHEAIAEIEVRLVEALGADSYAY-GTLGGQPVVVRLDSNMPVSSGDRLPITAAAEHL 354 Query: 350 HLFDAD 355 H FDAD Sbjct: 355 HFFDAD 360 Lambda K H 0.320 0.137 0.389 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: 433 Number of extensions: 15 Number of successful extensions: 3 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: 367 Length of database: 367 Length adjustment: 30 Effective length of query: 337 Effective length of database: 337 Effective search space: 113569 Effective search space used: 113569 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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