Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate AZOBR_RS25335 AZOBR_RS25335 putative ABC transporter (ATP-binding protein)
Query= reanno::Smeli:SM_b21106 (365 letters) >FitnessBrowser__azobra:AZOBR_RS25335 Length = 365 Score = 261 bits (668), Expect = 2e-74 Identities = 154/363 (42%), Positives = 209/363 (57%), Gaps = 22/363 (6%) Query: 1 MAPVTLKKLVKRYG-ALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGA 59 + P+ L +L KRYG A + + LEV E + LVGPSGCGK+T LR+IAGL SGG Sbjct: 7 LVPLALDRLAKRYGTAPPALAALSLEVAGGELLGLVGPSGCGKTTALRLIAGLTPASGGR 66 Query: 60 IEIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAA 119 + +GGR + LP AR I +VFQ+YAL+PHMT A+N+ F L++ G PA E R AEA A Sbjct: 67 VLVGGRDITALPAHARGIGLVFQNYALFPHMTAADNVAFGLRMRGLPAAERHARTAEALA 126 Query: 120 ILDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKL 179 ++ L+HL R+P LSGGQ+QRVA+ RA+ +P++ L DEPLSNLDA LR ++ EI+ L Sbjct: 127 MVRLSHLGGRKPRALSGGQQQRVALARALAIRPNLLLLDEPLSNLDAGLRAELLAEIRTL 186 Query: 180 HARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPM 239 R+ T ++VTHDQ EA+ + DRI ++RDG +EQVGTP +V RPA+ FVAGF+G Sbjct: 187 QRRLGITALFVTHDQGEALAVCDRIAVLRDGRLEQVGTPREVHDRPASGFVAGFVGR--T 244 Query: 240 NMEEAVLTDGKLAFASGATLPLPPRFRSLVREGQKVTFGLRPDDVYPSGHGLHAGDADAV 299 N A G G LP + +G P D++ H + G A Sbjct: 245 NRIPAERLAGGALRVGGTLLP-------ALADGP-----AGPVDLFVRPHRIRVGAAGGA 292 Query: 300 HEIELPVTITEPLGNETLVFTQFNGR----DWVSRMLNPRP---LRPGEAVPMSFDLARA 352 + + T LG+ + + G DW P P L PGE V +S+D A Sbjct: 293 GGLPAVLRGTAFLGDRIALSLEAGGAPVTVDWPVEAAPPAPGPALTPGETVALSWDPADM 352 Query: 353 HLF 355 +F Sbjct: 353 AVF 355 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: 425 Number of extensions: 23 Number of successful extensions: 1 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: 365 Length adjustment: 30 Effective length of query: 335 Effective length of database: 335 Effective search space: 112225 Effective search space used: 112225 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