Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate 17272 b3201 predicted transporter subunit: ATP-binding component of ABC superfamily (NCBI)
Query= TCDB::Q8DQH7 (236 letters) >FitnessBrowser__Keio:17272 Length = 241 Score = 140 bits (352), Expect = 3e-38 Identities = 80/239 (33%), Positives = 132/239 (55%), Gaps = 7/239 (2%) Query: 1 MSVLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKI 60 M+ L +NL+ Y + V DVS VN GE+V L+G NGAGKTT + G+V +G I Sbjct: 1 MATLTAKNLAKAYKGRRVVEDVSLTVNSGEIVGLLGPNGAGKTTTFYMVVGIVPRDAGNI 60 Query: 61 EFLGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENL----EMGAFLKKNREENQANL 116 +I +P G+ +P+ +F L+V +NL ++ L + E++AN Sbjct: 61 IIDDDDISLLPLHARARRGIGYLPQEASIFRRLSVYDNLMAVLQIRDDLSAEQREDRAN- 119 Query: 117 KKVFSRFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIF 176 ++ F +E ++ +LSGGE++ + + RAL + PK +LLDEP G+ PI + +I Sbjct: 120 -ELMEEF-HIEHLRDSMGQSLSGGERRRVEIARALAANPKFILLDEPFAGVDPISVIDIK 177 Query: 177 DIIQDIQKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASSEEVRKAYLG 235 II+ ++ G VL+ + N + LA+ +R Y++ G ++ GT E+ E V++ YLG Sbjct: 178 RIIEHLRDSGLGVLITDHNVRETLAVCERAYIVSQGHLIAHGTPTEILQDEHVKRVYLG 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: 123 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