Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate 207079 DVU1627 ABC transporter, ATP-binding protein
Query= TCDB::Q8DQH7 (236 letters) >MicrobesOnline__882:207079 Length = 241 Score = 152 bits (384), Expect = 6e-42 Identities = 85/238 (35%), Positives = 135/238 (56%), Gaps = 6/238 (2%) Query: 1 MSVLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKI 60 M+VL+ E+L +G + VR VS V +GE+V L+G NGAGKTT L+G+++P++G + Sbjct: 2 MAVLQGEDLRKRFGQREVVRGVSVSVQQGEIVGLLGPNGAGKTTTFYMLTGIIKPTAGIV 61 Query: 61 EFLGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEM---GAFLKKNREENQANLK 117 GQ+I P + GLS +P+ VF LTV ENLE+ L R++ +A Sbjct: 62 RLDGQDIADWPLHERARVGLSYLPQESSVFKRLTVRENLEIILEHTGLPAARQKERAEAL 121 Query: 118 KVFSRFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFD 177 L + A LSGGE++ L + R ++ PK +LLDEP G+ P+ + +I Sbjct: 122 MADFGIAHLASSR---AMHLSGGERRRLEIARCMIREPKFVLLDEPFAGIDPLAVGDIQG 178 Query: 178 IIQDIQKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASSEEVRKAYLG 235 +I+ ++ +G VL+ + N + L I DR Y++ G+++L GT + + E+ R YLG Sbjct: 179 LIRKLRDRGIGVLISDHNVRETLTICDRAYLVHQGQVILDGTPEHIVGDEQARLVYLG 236 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: 135 Number of extensions: 6 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: 241 Length adjustment: 23 Effective length of query: 213 Effective length of database: 218 Effective search space: 46434 Effective search space used: 46434 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