Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate 7026050 Shewana3_3192 sulfate ABC transporter, ATPase subunit (RefSeq)
Query= reanno::Smeli:SM_b21106 (365 letters) >FitnessBrowser__ANA3:7026050 Length = 376 Score = 218 bits (556), Expect = 2e-61 Identities = 122/320 (38%), Positives = 190/320 (59%), Gaps = 19/320 (5%) Query: 4 VTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAIEIG 63 + L + K++G + + ++L++++ E I L+GPSG GK+T LR+IAGLE G I G Sbjct: 3 IRLTNISKKFGQFQALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGQIHFG 62 Query: 64 GRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAG---RPAE-EIKTRVAEAAA 119 R V + R R + VFQ+YAL+ HMTVA+N+ F L++ RP++ EI+ RV+ Sbjct: 63 NRDVTQVHVRDRRVGFVFQNYALFRHMTVADNVAFGLEVIPKKQRPSKAEIQKRVSHLLE 122 Query: 120 ILDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKL 179 ++ L HL +R P QLSGGQ+QR+A+ RA+ QP+V L DEP LDAK+R ++R ++ L Sbjct: 123 MVQLGHLAQRYPEQLSGGQKQRIALARALATQPEVLLLDEPFGALDAKVRKELRRWLRSL 182 Query: 180 HARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPM 239 H ++ T ++VTHDQ EA+ LSDR+V+M +G+IEQV TP +++ +P ++FV F+G+ + Sbjct: 183 HDELKFTSVFVTHDQDEALELSDRVVVMSNGNIEQVNTPIELYAQPNSRFVFDFLGN--V 240 Query: 240 NMEEAVLTDGKLAFASGATLPLPPRFRSLVREGQKVTFGLRPDDVYPSGHGLHAGD-ADA 298 N EA + + +G +PP L + G +Y H L D ++ Sbjct: 241 NRFEASWQQNR--WTNGDAFLVPPEQTPLQQNGA----------LYVRSHELALADKPNS 288 Query: 299 VHEIELPVTITEPLGNETLV 318 I + P+G E V Sbjct: 289 QAHIPFTIVAITPVGAEVRV 308 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: 343 Number of extensions: 14 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: 376 Length adjustment: 30 Effective length of query: 335 Effective length of database: 346 Effective search space: 115910 Effective search space used: 115910 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