Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate Synpcc7942_0513 Synpcc7942_0513 ATPase
Query= uniprot:G8ALJ1 (236 letters) >FitnessBrowser__SynE:Synpcc7942_0513 Length = 250 Score = 114 bits (286), Expect = 1e-30 Identities = 72/238 (30%), Positives = 125/238 (52%), Gaps = 11/238 (4%) Query: 2 LKVSGVHTFYGAIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMGRITFE 61 +++ V YG + V + + GE+V L+G NGAGK+T G R G + + Sbjct: 11 IRLENVRKSYGKRLIVNRVSLSVAQGEVVGLLGPNGAGKTTTFYMTTGLERPDEGHVWLD 70 Query: 62 GQDITQMPTYELVRLGIAQSPEGRRIFPRMSVLENLQMGSITAKPGSFANE----LERVL 117 ++T++P + RLGI + IF ++V+ENL + + + G E +E +L Sbjct: 71 ETELTRLPMTQRARLGIGYLAQEASIFRHLTVVENLLL--VLQQTGIRGREQRQRVEELL 128 Query: 118 TLFPRLKERISQRAGTMSGGEQQMLAIGRAL---MSQPRLLLLDEPSLGLAPLVVKQIFQ 174 + F RL++ + +SGGE++ I RAL P+ LLLDEP G+ P+ V ++ + Sbjct: 129 SEF-RLEKVAHTQGIRVSGGERRRTEIARALAVGSQGPKFLLLDEPFAGIDPIAVAEVQE 187 Query: 175 AVKDINREQKMTVFMVEQNAFHALKLAHRGYVMVNGKVTMSGTGAELLANEEVRSAYL 232 + + R Q+M + + + N LK+ R Y++ +G++ +G+ EL +N VR YL Sbjct: 188 IIARL-RAQQMGILITDHNVRETLKITDRAYILRDGEILAAGSAEELASNPLVRQYYL 244 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: 130 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: 236 Length of database: 250 Length adjustment: 23 Effective length of query: 213 Effective length of database: 227 Effective search space: 48351 Effective search space used: 48351 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 Apr 09 2024. 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