Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate PP_5179 PP_5179 spermidine/putrescine ABC transporter - ATP binding subunit
Query= reanno::Smeli:SM_b21106 (365 letters) >FitnessBrowser__Putida:PP_5179 Length = 380 Score = 217 bits (552), Expect = 5e-61 Identities = 116/284 (40%), Positives = 175/284 (61%), Gaps = 7/284 (2%) Query: 4 VTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAIEIG 63 V + ++ K++ V + LE++ E AL+G SG GKST LRM+AG E S G I + Sbjct: 23 VKIDRVTKKFDETVAVDDVSLEIRKGEIFALLGGSGSGKSTLLRMLAGFERPSEGRIFLD 82 Query: 64 GRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAILDL 123 G + D+PP R I+M+FQSYAL+PHMTVA+N+ F L+ P EI RVAE ++ + Sbjct: 83 GVDITDMPPYERPINMMFQSYALFPHMTVAQNIAFGLQQDKMPKAEIDARVAEMLKLVHM 142 Query: 124 AHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLHARM 183 +R+P QLSGGQRQRVA+ R++ ++P + L DEP+ LD KLR+Q++ E+ ++ R+ Sbjct: 143 TQYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRSQMQLELVEIIERV 202 Query: 184 QATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPMNMEE 243 T + VTHDQ EAMT++ RI IM G I Q+G+P D++ P ++ V FIG+ +N+ E Sbjct: 203 GVTCVMVTHDQEEAMTMAQRIAIMHLGWIAQIGSPVDIYETPTSRLVCEFIGN--VNLFE 260 Query: 244 AVLTDGKLAFASGATLPLPPRFR-----SLVREGQKVTFGLRPD 282 + D +A A+ L + + E + +T+ LRP+ Sbjct: 261 GDVVDDAEGYAIIASPELERKIYVGHGITTSVEDKHITYALRPE 304 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: 352 Number of extensions: 11 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: 380 Length adjustment: 30 Effective length of query: 335 Effective length of database: 350 Effective search space: 117250 Effective search space used: 117250 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: 50 (23.9 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