Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate Synpcc7942_2574 Synpcc7942_2574 ATPase
Query= uniprot:G8ALJ0 (294 letters) >FitnessBrowser__SynE:Synpcc7942_2574 Length = 251 Score = 87.4 bits (215), Expect = 3e-22 Identities = 80/271 (29%), Positives = 120/271 (44%), Gaps = 37/271 (13%) Query: 1 MTTQSMTTTPLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGF 60 M+ S P L HL+ + + DV+ G++ I+GPNGAGK+T + G Sbjct: 1 MSQASAPNPPTLQAHHLSASYRDREVLQDVNLQLRAGQVVGIVGPNGAGKSTFLKALLGL 60 Query: 61 YTPTVGRLTLRHADGKEFLLERMPGYR-ISQKASV----ARTFQNIRLFGGMSVLENLIV 115 P G + R L R+P + Q+A V T ++ L G V Sbjct: 61 -VPHQGEVFWRGLP----LASRLPHVAYVPQRAQVDFDYPATVWDVVLMGR--------V 107 Query: 116 AQHNKLIRASGFSIAGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQR 175 AQ L R S S ++AV A LDRV L + G L G Q+ Sbjct: 108 AQTGWLRRFSAAS--------------QQAVKAA---LDRVELWDLRSRPIGELSGGQQQ 150 Query: 176 RLEIARAMCTEPVMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTI 235 R+ IAR++ E + LDEP AG++ R G L ++L + + GV+++ HD+ + Sbjct: 151 RVFIARSLAQEAELFLLDEPFAGIDRRSEGLLYEILRDLAQQGH-GVVVVHHDLGQAIQQ 209 Query: 236 SDHVVVLDYGRKISDGDPAFVKNDPAVIRAY 266 D +V+L+ R I+ G P V + RAY Sbjct: 210 FDELVLLNQ-RVIAQGHPRLVLQPDHLARAY 239 Lambda K H 0.319 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: 149 Number of extensions: 9 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: 294 Length of database: 251 Length adjustment: 25 Effective length of query: 269 Effective length of database: 226 Effective search space: 60794 Effective search space used: 60794 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: 47 (22.7 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