Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate PP_0411 PP_0411 Polyamine ABC transporter, ATP-binding protein
Query= reanno::Smeli:SM_b21106 (365 letters) >FitnessBrowser__Putida:PP_0411 Length = 374 Score = 233 bits (595), Expect = 5e-66 Identities = 136/363 (37%), Positives = 205/363 (56%), Gaps = 19/363 (5%) Query: 4 VTLKKLVKRY-GALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAIEI 62 V+ + + K Y G +V ++L+++ EF+ L+GPSG GK+T+L M+AG E + G I++ Sbjct: 15 VSFRGVQKSYDGESLIVKDLNLDIRKGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEIQL 74 Query: 63 GGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAILD 122 GGR +N++PP R+I MVFQ+YAL+PHMTVAEN+ F L + +I RV ++ Sbjct: 75 GGRSINNVPPHKRDIGMVFQNYALFPHMTVAENLAFPLTVRNLSKTDISERVKRVLNMVQ 134 Query: 123 LAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLHAR 182 L +R P QLSGGQ+QRVA+ RA+V +P + L DEPL LD +LR ++ EIK +H R Sbjct: 135 LDAFAKRYPGQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREHMQMEIKHIHQR 194 Query: 183 MQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPMNME 242 + T++YVTHDQ EA+T+SDR+ + G I+Q+ P ++ P FVA FIG Sbjct: 195 LGVTVVYVTHDQGEALTMSDRVAVFHQGEIQQIADPRTLYEEPCNTFVANFIGENNRISG 254 Query: 243 EAVLTDGKLAFASGATLPLPPRFRSLV----REGQKVTFGLRPDDVYPSGHGLHAGDADA 298 + +DGK LP R +L + G+ VT +RP+ V +GH Sbjct: 255 TLLASDGK---RCQVQLPRGERVEALAVNVGQAGEPVTLSIRPERVRLNGH-----SESC 306 Query: 299 VHEIELPVTITEPLGNETLVFTQFNGR-DWVSRM----LNPRPLRPGEAVPMSFDLARAH 353 V+ V LG+ V + G+ D+ + L+P L G+ VP+ +++ A Sbjct: 307 VNRFSGRVAEFIYLGDHVRVRLEVCGKGDFFVKQPIAELDP-ALAVGDVVPLGWEVEHAR 365 Query: 354 LFD 356 D Sbjct: 366 ALD 368 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: 356 Number of extensions: 11 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: 374 Length adjustment: 30 Effective length of query: 335 Effective length of database: 344 Effective search space: 115240 Effective search space used: 115240 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