Align High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)
to candidate N515DRAFT_3494 N515DRAFT_3494 sodium transport system ATP-binding protein
Query= uniprot:A0A159ZWS6 (255 letters) >FitnessBrowser__Dyella79:N515DRAFT_3494 Length = 244 Score = 110 bits (274), Expect = 4e-29 Identities = 78/239 (32%), Positives = 122/239 (51%), Gaps = 18/239 (7%) Query: 5 ILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGGTILL 64 +++V++L FG + AV+GV + ++ Q+ L+GPNGAGKTT L +P G IL+ Sbjct: 1 MIEVKDLHKAFGAIKAVDGVGFSARDGQITGLLGPNGAGKTTTLRMLYTLMKPDRGQILV 60 Query: 65 DGEPIQGLPGHHIARKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFFAGLFKTPAFR 124 DG P + GV+ + L+K +TA EN+ ++FA L P Sbjct: 61 DGIDAAADPLAVRRQLGVLPDARG--LYKRLTARENI----------DYFARLHGLP--- 105 Query: 125 KSEREAMEYAEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGL 184 E E E + + + E A+R + GQ+ + IAR ++ PR ++LDEP GL Sbjct: 106 --ENELASRREALVKALEMEEIADRRTEGFSQGQRVKTAIARALIHDPRNVILDEPTNGL 163 Query: 185 NPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLADGTPEQIRD 243 + T L+ + L+ E VL H M+ V ++ D IVVI G +AD TP+ +R+ Sbjct: 164 DVMATRALRQFMLKLKAEGR-CVLFSSHIMQEVAALCDRIVVIAHGRVVADETPQALRE 221 Lambda K H 0.321 0.138 0.398 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: 149 Number of extensions: 8 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: 255 Length of database: 244 Length adjustment: 24 Effective length of query: 231 Effective length of database: 220 Effective search space: 50820 Effective search space used: 50820 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: 46 (22.3 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