Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate RR42_RS12955 RR42_RS12955 glycerol-3-phosphate ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc03065 (362 letters) >FitnessBrowser__Cup4G11:RR42_RS12955 Length = 367 Score = 350 bits (898), Expect = e-101 Identities = 189/363 (52%), Positives = 250/363 (68%), Gaps = 10/363 (2%) Query: 1 MTGLLLKDIRKSY-GAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGD 59 M L L++++K+Y G V V+HGID++I +GEF+V VGPSGCGKSTLLRM+AGLE I+GG+ Sbjct: 1 MAKLSLRNVQKTYAGNVKVVHGIDMEINDGEFIVIVGPSGCGKSTLLRMVAGLEAISGGE 60 Query: 60 MFIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAAD 119 + I + VN + P++R IAMVFQ+YALYPHM+VYDNMA+G++I K EI++RV+ AA Sbjct: 61 VHIGDKVVNHLEPAERDIAMVFQNYALYPHMSVYDNMAYGLKIRGMDKSEIEQRVKHAAG 120 Query: 120 MLQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKL 179 +L+L P L+R P+ALSGGQRQRVA+GRAI R P VFLFDEPLSNLDA LRV R+E+ +L Sbjct: 121 ILELAPLLERKPRALSGGQRQRVAMGRAIVREPAVFLFDEPLSNLDAKLRVQMRLELKEL 180 Query: 180 SERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPA 239 R+ TT +YVTHDQVEAMTLADR++VL+ G +EQ+G PLE+Y RPA+ FVA FIGSP Sbjct: 181 HRRLR-TTSMYVTHDQVEAMTLADRMMVLNGGSVEQIGTPLEVYARPASTFVASFIGSPP 239 Query: 240 MNVIPATITATGQQTAVSL------AGGKSVTLDVPTNASENGKTASFGVRPEDLRVTEA 293 MN++P T T GQ A A G TL + A G+RPE + A Sbjct: 240 MNLVPVTRTNGGQGEAQMRVEQKPGAQGAPATLGHLPMGLHLPERALLGLRPEHIEPCAA 299 Query: 294 DDFLFEGTVSIVEALGEVTLLYIEGLVENEPIIAKMPGIARVGRGDKVRFTADKAKLHLF 353 + + E V +VEALG + Y G + +P++ ++ V GD++ TA LH F Sbjct: 300 HEAIAEIEVRLVEALGADSYAY--GTLGGQPVVVRLDSNMPVSSGDRLPITAAAEHLHFF 357 Query: 354 DTN 356 D + Sbjct: 358 DAD 360 Lambda K H 0.320 0.137 0.387 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: 402 Number of extensions: 16 Number of successful extensions: 4 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: 362 Length of database: 367 Length adjustment: 29 Effective length of query: 333 Effective length of database: 338 Effective search space: 112554 Effective search space used: 112554 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