Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate WP_085638943.1 MGEO_RS13990 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::Smeli:SM_b21106 (365 letters) >NCBI__GCF_002115805.1:WP_085638943.1 Length = 350 Score = 329 bits (844), Expect = 6e-95 Identities = 185/362 (51%), Positives = 240/362 (66%), Gaps = 20/362 (5%) Query: 1 MAPVTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAI 60 M+ VTL+ ++KRYG +V+HG+DL+V+D EF VGPSGCGKST LRM+AGLEE + G I Sbjct: 1 MSGVTLESVIKRYGQTQVIHGVDLDVQDGEFCVFVGPSGCGKSTLLRMVAGLEETTEGTI 60 Query: 61 EIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAI 120 IGGR V L P R +SMVFQ+YALYPHMTV ENMGF LK+ G A++IK +VAEA+ I Sbjct: 61 RIGGRDVTRLDPSDRGVSMVFQTYALYPHMTVEENMGFGLKMTGHAAKDIKEKVAEASRI 120 Query: 121 LDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLH 180 L L L+R+P LSGGQRQRVA+GRAIVR P+VFLFDEPLSNLDA+LR ++R EI +LH Sbjct: 121 LKLDDYLKRKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVEMRVEIARLH 180 Query: 181 ARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPMN 240 + ATMIYVTHDQVEAMTL+D+IV++R G IEQVG P +++R P +FVAGFIGSP MN Sbjct: 181 KEIGATMIYVTHDQVEAMTLADKIVVLRAGRIEQVGAPMELYRDPDNRFVAGFIGSPSMN 240 Query: 241 MEEAVLTDGKLAFASGATLPLPPRFRSLVREGQKVTFGLRPDDVYPSGHGLHAGDADAVH 300 + G++ + G + + +EGQ+V GLRP+ + L G + H Sbjct: 241 FIRGRVQGGEVV-SDGLVHSVSK--TASAQEGQEVLIGLRPEHL-----ELRPGSS---H 289 Query: 301 EIELPVTITEPLGNETLVFTQFNGRDWVSRMLNPR---PLRPGEAVPMSFDLARAHLFDG 357 ++L TE LG + + G D ++ R G+ V + D LFD Sbjct: 290 RVDL----TESLGG--VSYAHLIGPDGEKIIVEERGDHRSSDGDMVDLVVDPDHMFLFDA 343 Query: 358 ET 359 +T Sbjct: 344 KT 345 Lambda K H 0.320 0.137 0.397 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: 371 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: 365 Length of database: 350 Length adjustment: 29 Effective length of query: 336 Effective length of database: 321 Effective search space: 107856 Effective search space used: 107856 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 24 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