Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate Synpcc7942_0815 Synpcc7942_0815 ATPase
Query= uniprot:G8ALJ1 (236 letters) >FitnessBrowser__SynE:Synpcc7942_0815 Length = 243 Score = 186 bits (473), Expect = 3e-52 Identities = 96/219 (43%), Positives = 146/219 (66%), Gaps = 1/219 (0%) Query: 14 IEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMGRITFEGQDITQMPTYEL 73 ++ ++GV++++ AGE+++L+G NGAGKSTL T+ G R G I F GQ+I+++ + + Sbjct: 20 LDIVQGVNLQVAAGELLTLLGPNGAGKSTLAKTLLGLVPVRSGSIRFRGQEISRLSSEAI 79 Query: 74 VRLGIAQSPEGRRIFPRMSVLENLQMGSITAKPGSFANELERVLTLFPRLKERISQRAGT 133 VRLGI P+ R +F ++V ENL+MG +P + R+ LFP L R SQRAGT Sbjct: 80 VRLGIGYVPQVRNVFASLTVAENLEMGLFQIRPQHRPAAIARIYDLFPTLATRRSQRAGT 139 Query: 134 MSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPLVVKQIFQAVKDINREQKMTVFMVEQN 193 +SGGE+Q+LA+GRAL ++P LL+LDEPS L+PL+V +F+ ++ IN T+ +VEQN Sbjct: 140 LSGGERQLLAMGRALAAEPTLLVLDEPSAALSPLMVATVFEQIRAIN-NSGTTIILVEQN 198 Query: 194 AFHALKLAHRGYVMVNGKVTMSGTGAELLANEEVRSAYL 232 AL+LA RG ++ +G+ +G AELL + + YL Sbjct: 199 TRRALQLADRGCILESGRDRQTGPAAELLDDPLLGELYL 237 Lambda K H 0.320 0.136 0.377 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: 158 Number of extensions: 8 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: 236 Length of database: 243 Length adjustment: 23 Effective length of query: 213 Effective length of database: 220 Effective search space: 46860 Effective search space used: 46860 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