Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate GFF4127 HP15_4067 spermidine/putrescine ABC transporter ATPase subunit
Query= reanno::Smeli:SM_b21106 (365 letters) >FitnessBrowser__Marino:GFF4127 Length = 362 Score = 226 bits (576), Expect = 7e-64 Identities = 117/301 (38%), Positives = 175/301 (58%), Gaps = 28/301 (9%) Query: 9 LVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAIEIGGRKVN 68 LV+R+G+ V + L+V F +++GPSGCGK+T LR++AG ++ G I I G ++N Sbjct: 10 LVRRFGSNAAVDHVSLDVPAGTFFSILGPSGCGKTTLLRLLAGFDKPDQGDIHIRGERMN 69 Query: 69 DLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAILDLAHLLE 128 D+PP R ++MVFQ AL+P MTV +N+ + LK P E + R+A + L L Sbjct: 70 DVPPNRRPVNMVFQHLALFPTMTVGDNIAYGLKRRKMPLVERRKRIARVLEQVGLPDLEH 129 Query: 129 RRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLHARMQATMI 188 R P +LSGGQRQRVA+ R +V +P + L DEPL LD KLR Q++ E+K L + T + Sbjct: 130 RNPQELSGGQRQRVALARCLVLEPTLLLLDEPLGALDLKLREQMKVELKHLQKQFGTTFV 189 Query: 189 YVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGS------------ 236 Y+THDQ EAM +SD++ +MRDG +QV PE+++R PAT FVAGF+G Sbjct: 190 YITHDQSEAMVMSDQVAVMRDGRFDQVAPPEELYREPATPFVAGFVGDNNRLSGELVSVR 249 Query: 237 ---PPMNMEEAVLTDGKLAFASGATLPLPPRFRSLVREGQKVTFGLRPDDVYPSGHGLHA 293 + +++ VL G++A + ++ G + +RP+ + SG L Sbjct: 250 DSLAELRLDDGVLVQGRVASDN-------------LQAGHRAELYIRPESLVLSGDALSP 296 Query: 294 G 294 G Sbjct: 297 G 297 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: 349 Number of extensions: 18 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: 362 Length adjustment: 29 Effective length of query: 336 Effective length of database: 333 Effective search space: 111888 Effective search space used: 111888 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