Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate SMc02474 SMc02474 ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b21106 (365 letters) >FitnessBrowser__Smeli:SMc02474 Length = 356 Score = 368 bits (945), Expect = e-106 Identities = 201/367 (54%), Positives = 249/367 (67%), Gaps = 15/367 (4%) Query: 1 MAPVTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAI 60 MA V L+ + K Y ALEVVHG+ L + + EFIALVGPSGCGKST LRMIAGLEE+S G + Sbjct: 1 MASVELRDIRKSYAALEVVHGVSLSIAEGEFIALVGPSGCGKSTLLRMIAGLEEISDGEV 60 Query: 61 EIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAI 120 IGG+ VN L PR RNI+MVFQSYALYPHM+VAENMGF+LK++G EI +V EAA + Sbjct: 61 LIGGKVVNPLTPRERNIAMVFQSYALYPHMSVAENMGFNLKLSGLSRPEIDKKVGEAARM 120 Query: 121 LDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLH 180 L L LL+R+PSQLSGGQRQR AMGRAIVR P VFLFDEPLSNLDAKLR Q+RTEIK LH Sbjct: 121 LALTELLDRKPSQLSGGQRQRAAMGRAIVRDPAVFLFDEPLSNLDAKLRVQMRTEIKALH 180 Query: 181 ARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPMN 240 ++ T IYVTHDQ+EAMTL+DRIV++ G IEQVGTP +++R PA FVAGFIGSP MN Sbjct: 181 QKVATTSIYVTHDQIEAMTLADRIVVLNGGRIEQVGTPLELYRTPANLFVAGFIGSPAMN 240 Query: 241 MEEAVL--TDGKLA--FASGATLPLPPRFRSLVREGQKVTFGLRPDDVYPSGHGLHAGDA 296 + + + DG+ A G+ + + P + VR GQ V GLRP+ G G Sbjct: 241 VLDGTVDADDGEPAVRLGDGSAIRIAPERK--VRPGQAVRIGLRPEHFVAGGEG------ 292 Query: 297 DAVHEIELPVTITEPLGNETLVFTQFNGRDWVSRMLNPRPLRPGEAVPMSFDLARAHLFD 356 + I + EP G +T V +F G + + P R G + D ++ ++FD Sbjct: 293 ---NAIAGQTLLVEPTGAQTHVLFEFAGEQITAVVDGDHPARHGSLFRAAMDRSQVYVFD 349 Query: 357 GETGRAL 363 +TG AL Sbjct: 350 RQTGAAL 356 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: 428 Number of extensions: 13 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: 365 Length of database: 356 Length adjustment: 29 Effective length of query: 336 Effective length of database: 327 Effective search space: 109872 Effective search space used: 109872 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