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_017557172.1 C892_RS0110655 ABC transporter ATP-binding protein
Query= TCDB::Q8DQH7 (236 letters) >NCBI__GCF_000341205.1:WP_017557172.1 Length = 281 Score = 130 bits (327), Expect = 3e-35 Identities = 84/250 (33%), Positives = 137/250 (54%), Gaps = 20/250 (8%) Query: 3 VLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIEF 62 VL VE L+V +G + A+ V+F+V VV LIG NGAGKTT+ +SG+VRP SG + Sbjct: 7 VLAVEQLTVAFGGLTALDRVTFDVPHRSVVGLIGPNGAGKTTVFNAVSGVVRPRSGTLTR 66 Query: 63 LGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLKKNREENQANLKKVFSR 122 G+ +++ + G+S++ +G +F G+TV+EN+ +GA + R Sbjct: 67 HGRPLRRHRPHHLPRLGISRMLQGLGLFSGMTVLENVMVGA--DPLATGRLPGMLTGLGR 124 Query: 123 FPRLEERKNQDA-----------------ATLSGGEQQMLAMGRALMSTPKLLLLDEPSM 165 PR E R + A TL G Q+ +A+ RA + P+LLLLDEP+ Sbjct: 125 APRDERRVRERAESALREFGVAHAAHALPGTLPYGVQKRVALARACVCGPELLLLDEPAS 184 Query: 166 GLAPIFIQEIFDIIQDIQKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELAS 225 GL+ + E+ + ++ ++ G +VLL+E + + + + DR VL+ G+++ GT E+ + Sbjct: 185 GLSADEMSELAERVRAMRAYG-SVLLVEHHMDLVMRVCDRVVVLDFGRVIADGTPDEVRA 243 Query: 226 SEEVRKAYLG 235 V +AYLG Sbjct: 244 DPAVERAYLG 253 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: 170 Number of extensions: 11 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: 281 Length adjustment: 24 Effective length of query: 212 Effective length of database: 257 Effective search space: 54484 Effective search space used: 54484 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: 47 (22.7 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