Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate 7023651 Shewana3_0880 ABC transporter related (RefSeq)
Query= TCDB::Q8DQH7 (236 letters) >FitnessBrowser__ANA3:7023651 Length = 241 Score = 115 bits (288), Expect = 8e-31 Identities = 69/228 (30%), Positives = 127/228 (55%), Gaps = 12/228 (5%) Query: 3 VLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIEF 62 ++ + NL YG ++ ++ + +GEVVS+IG +G+GK+T LR ++ L +P+ G IE Sbjct: 1 MINITNLHKSYGDNAVLKGINEHIRQGEVVSVIGPSGSGKSTFLRCINLLEKPTQGDIEI 60 Query: 63 LGQEIQKMPA------QKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLKKNREENQANL 116 GQ I A QK+ V + ++FP TV++N+ + K + +A+ Sbjct: 61 EGQSITAKDACVDKLRQKV-----GMVFQNFNLFPHKTVLQNITLAPVSLKLMTQAEADN 115 Query: 117 KKV-FSRFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEI 175 K + L+++ N ++LSGG++Q +A+ RAL P L+L DEP+ L P + ++ Sbjct: 116 KALALLTQVGLQDKANAYPSSLSGGQKQRVAIARALAMEPDLMLFDEPTSALDPEMVGDV 175 Query: 176 FDIIQDIQKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKEL 223 D+++D+ ++G T++++ A +SDR ++ G +V S +EL Sbjct: 176 LDVMKDLAQKGMTMVIVTHEMGFARDVSDRVIFMDGGYVVESNIPEEL 223 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: 102 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