Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_003939931.1 C1M55_RS22595 ABC transporter ATP-binding protein
Query= TCDB::Q8DQH7 (236 letters) >NCBI__GCF_002893965.1:WP_003939931.1 Length = 237 Score = 196 bits (499), Expect = 3e-55 Identities = 109/236 (46%), Positives = 156/236 (66%), Gaps = 3/236 (1%) Query: 1 MSVLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKI 60 MS+L V++L YG + VS +V G V ++GANGAGKTT++R L+GL+ P G I Sbjct: 1 MSLLSVDDLHAGYGRGNVLHGVSLDVEPGGVAVVLGANGAGKTTMMRALAGLI-PHQGTI 59 Query: 61 EFLGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLKKNREENQANLKKVF 120 F G + P ++ VA G+S VP+GR L+V +NL +GA L+ ++ E +A++++ Sbjct: 60 TFNGSPLGSKP-ERAVAAGVSLVPQGRGTLGQLSVRDNLLVGAALRNDKAEIEADIERWC 118 Query: 121 SRFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFDIIQ 180 FP L R Q A +LSGGEQQMLA+ RALMS P LLL DEPS+GLAPI I E+FD + Sbjct: 119 ETFPVLARRSTQLAGSLSGGEQQMLAVARALMSRPTLLLCDEPSLGLAPIVIAELFDTLG 178 Query: 181 DIQK-QGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASSEEVRKAYLG 235 I + GT +L++EQNA+ A+ ++ + ++L+ G IV +GT +E S + VR AYLG Sbjct: 179 AINRSDGTALLIVEQNADLAMKLASKVFLLDVGTIVAAGTPEEFRSDDVVRSAYLG 234 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: 4 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: 237 Length adjustment: 23 Effective length of query: 213 Effective length of database: 214 Effective search space: 45582 Effective search space used: 45582 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 24 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