Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate Synpcc7942_0960 Synpcc7942_0960 ATPase
Query= reanno::Smeli:SM_b21106 (365 letters) >FitnessBrowser__SynE:Synpcc7942_0960 Length = 417 Score = 286 bits (733), Expect = 5e-82 Identities = 168/400 (42%), Positives = 241/400 (60%), Gaps = 45/400 (11%) Query: 1 MAPVTLKKLVKRY---------GALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAG 51 +A V +++ KR+ G + V++GI+LE+ D EF+ +VGPSGCGKST LR++AG Sbjct: 23 VAGVVFEEIEKRFPEQARSPQKGEVVVLNGINLEIADGEFMVVVGPSGCGKSTLLRLLAG 82 Query: 52 LEEVSGGAIEIGGRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAG------- 104 LE S G I++G R+V+ LP +AR+I+MVFQSYALYPH++V +N+ F L+ G Sbjct: 83 LETPSRGLIKVGDRRVDRLPAKARDIAMVFQSYALYPHLSVYDNLAFGLRRQGDRPWWQQ 142 Query: 105 ---------------RPAEE--IKTRVAEAAAILDLAHLLERRPSQLSGGQRQRVAMGRA 147 P +E IK RV E A +L L LL+R+P QLSGGQ+QRVA+GRA Sbjct: 143 QLALATRSLPKSLQYEPEQEARIKRRVREVATMLQLDTLLDRQPKQLSGGQKQRVALGRA 202 Query: 148 IVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLHARMQATMIYVTHDQVEAMTLSDRIVIM 207 I R P VFL DEPLSNLDAKLR + R +I L ++ T +YVTHDQ EAMT+ DRI ++ Sbjct: 203 IARNPQVFLMDEPLSNLDAKLRAETRAQIVSLQRQLGVTTLYVTHDQTEAMTMGDRIAVL 262 Query: 208 RDGHIEQVGTPEDVFRRPATKFVAGFIGSPPMNMEEAVLTDGKLAFASGATLPLPPRFRS 267 GH++QV +P +++ RPA +FVA FIGSPPMN+ + LP + Sbjct: 263 NRGHLQQVASPLEIYDRPANRFVAQFIGSPPMNLIPVTVRAPLQLTTENFRCTLPEAWEP 322 Query: 268 LVR--EGQKVTFGLRPDDVYPSGHGLHAGDADAVHEIELPVTITEPLGNETLVFTQF--N 323 ++R +GQ V G+RP+ L G A A + + VT E LG++T + + + Sbjct: 323 VLRLYDGQTVELGIRPEH-------LEVG-AAASKNLLITVTGVEALGSDTFIAGELKES 374 Query: 324 GRDWVSRMLNPRPLRPGEAVPMSFDLARAHLFDGETGRAL 363 G +R+ + + G+ + ++F + HLFD ETG+A+ Sbjct: 375 GIAVQARLAPQQCWQMGDRLWLTFKPDQIHLFDLETGKAI 414 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: 409 Number of extensions: 16 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: 417 Length adjustment: 31 Effective length of query: 334 Effective length of database: 386 Effective search space: 128924 Effective search space used: 128924 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