Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate Synpcc7942_0513 Synpcc7942_0513 ATPase
Query= TCDB::Q8DQH7 (236 letters) >FitnessBrowser__SynE:Synpcc7942_0513 Length = 250 Score = 139 bits (351), Expect = 4e-38 Identities = 86/237 (36%), Positives = 135/237 (56%), Gaps = 7/237 (2%) Query: 4 LKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIEFL 63 +++EN+ YG V VS V +GEVV L+G NGAGKTT +GL RP G + Sbjct: 11 IRLENVRKSYGKRLIVNRVSLSVAQGEVVGLLGPNGAGKTTTFYMTTGLERPDEGHVWLD 70 Query: 64 GQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLK--KNREENQANLKKVFS 121 E+ ++P + G+ + + +F LTV+ENL + + RE+ Q ++++ S Sbjct: 71 ETELTRLPMTQRARLGIGYLAQEASIFRHLTVVENLLLVLQQTGIRGREQRQ-RVEELLS 129 Query: 122 RFPRLEERKNQDAATLSGGEQQMLAMGRALM---STPKLLLLDEPSMGLAPIFIQEIFDI 178 F RLE+ + +SGGE++ + RAL PK LLLDEP G+ PI + E+ +I Sbjct: 130 EF-RLEKVAHTQGIRVSGGERRRTEIARALAVGSQGPKFLLLDEPFAGIDPIAVAEVQEI 188 Query: 179 IQDIQKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASSEEVRKAYLG 235 I ++ Q +L+ + N + L I+DR Y+L G+I+ +G+ +ELAS+ VR+ YLG Sbjct: 189 IARLRAQQMGILITDHNVRETLKITDRAYILRDGEILAAGSAEELASNPLVRQYYLG 245 Lambda K H 0.315 0.134 0.358 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: 136 Number of extensions: 3 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 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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