Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate 3607992 Dshi_1400 ABC transporter related (RefSeq)
Query= TCDB::Q8DQH7 (236 letters) >FitnessBrowser__Dino:3607992 Length = 251 Score = 185 bits (469), Expect = 8e-52 Identities = 100/233 (42%), Positives = 146/233 (62%), Gaps = 6/233 (2%) Query: 4 LKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPS--SGKIE 61 L V +L +YG V+ +SF V+EGE+++L+G NGAGKTT LR ++ L P G+I Sbjct: 21 LSVWDLHAYYGESYIVQGISFNVHEGEILALLGRNGAGKTTTLRAIARLGDPQVRHGEIW 80 Query: 62 FLGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLKKNREENQANLKKVFS 121 + +M + + GL VPE R + PGLTV ENL++ + E +L +++ Sbjct: 81 LDHARLHEMESHEAAVAGLGLVPEDRRIIPGLTVEENLQLAQIV----EPKGWSLDRLYD 136 Query: 122 RFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFDIIQD 181 FPRL ER+ Q+ TLSGGEQQML++ RAL K+LLLDEP GLAP+ + EI ++ Sbjct: 137 LFPRLGERRKQEGVTLSGGEQQMLSIARALARDLKVLLLDEPYEGLAPVIVDEIEKTLRV 196 Query: 182 IQKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASSEEVRKAYL 234 I++QG T +++EQNA +AL ++DR +L+TG IV G E+ + E+R YL Sbjct: 197 IKEQGMTTVIVEQNAVRALELADRAVILDTGSIVFDGAAAEVLENAELRAEYL 249 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: 155 Number of extensions: 9 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: 251 Length adjustment: 23 Effective length of query: 213 Effective length of database: 228 Effective search space: 48564 Effective search space used: 48564 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