Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate RR42_RS12955 RR42_RS12955 glycerol-3-phosphate ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__Cup4G11:RR42_RS12955 Length = 367 Score = 315 bits (808), Expect = 9e-91 Identities = 175/369 (47%), Positives = 238/369 (64%), Gaps = 16/369 (4%) Query: 1 MSALEIRNIRKRY-GEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGD 59 M+ L +RN++K Y G V+ + GID+ + GEF+V++G SGCGKSTLL ++AGL SGG+ Sbjct: 1 MAKLSLRNVQKTYAGNVKVVHGIDMEINDGEFIVIVGPSGCGKSTLLRMVAGLEAISGGE 60 Query: 60 ILIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTAR 119 + IG++ V + P +RDIAMVFQ+YALYP++SV N+ +GL++R + ++E ++ V+ A Sbjct: 61 VHIGDKVVNHLEPAERDIAMVFQNYALYPHMSVYDNMAYGLKIRGMDKSEIEQRVKHAAG 120 Query: 120 LLQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRL 179 +L++ LL+RKP LSGGQRQRVA+GRA+VR P VFLFDEPLSNLDAKLR++MR ELK L Sbjct: 121 ILELAPLLERKPRALSGGQRQRVAMGRAIVREPAVFLFDEPLSNLDAKLRVQMRLELKEL 180 Query: 180 HQMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPM 239 H+ LRTT +YVTHDQ+EAMTLA R+ V+ G +EQ+ P EVY RPA+ +VA F+GSPPM Sbjct: 181 HRRLRTTSMYVTHDQVEAMTLADRMMVLNGGSVEQIGTPLEVYARPASTFVASFIGSPPM 240 Query: 240 NILDAEMTANGLKIEGCEEVLPLPAAFNGAAWAG---------RRVKVGIRPEALRLAAG 290 N++ T NG + E V P A A G R +G+RPE + A Sbjct: 241 NLVPVTRT-NGGQGEAQMRVEQKPGAQGAPATLGHLPMGLHLPERALLGLRPEHIEPCAA 299 Query: 291 SEAQRLTASVEV--VELTGPELVTTATVGSQRITACLPPRTAVGMGSAHAFTFDGTALHL 348 EA A +EV VE G + T+G Q + L V G T LH Sbjct: 300 HEA---IAEIEVRLVEALGADSYAYGTLGGQPVVVRLDSNMPVSSGDRLPITAAAEHLHF 356 Query: 349 FDPESGRSL 357 FD +SG+ + Sbjct: 357 FDADSGKRI 365 Lambda K H 0.320 0.136 0.385 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: 393 Number of extensions: 24 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: 360 Length of database: 367 Length adjustment: 29 Effective length of query: 331 Effective length of database: 338 Effective search space: 111878 Effective search space used: 111878 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