Align High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)
to candidate WP_042441261.1 TX73_RS20605 ABC transporter ATP-binding protein
Query= uniprot:A0A159ZWS6 (255 letters) >NCBI__GCF_000195775.1:WP_042441261.1 Length = 275 Score = 209 bits (532), Expect = 5e-59 Identities = 105/249 (42%), Positives = 160/249 (64%) Query: 6 LKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGGTILLD 65 L+V N+S+RFGG+ A++ V+ V ++ ++IGPNGAGKT+V NC++G YQP+ G + Sbjct: 5 LEVRNVSLRFGGVRALSEVSFAVNHGELFSIIGPNGAGKTSVVNCISGRYQPSEGQLFYH 64 Query: 66 GEPIQGLPGHHIARKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFFAGLFKTPAFRK 125 G I GL + A G+ RTFQN+ LF M+ ++N+++ +H L NFF G R+ Sbjct: 65 GRDITGLKPNARASLGIGRTFQNLALFHHMSVLDNIMVGRHHLLKNNFFTGALYWFGARR 124 Query: 126 SEREAMEYAEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGLN 185 E E E +D ++L AGTL+YG ++R+E+AR M P +++LDEP AG+N Sbjct: 125 EELAHREKVEEIIDFLDLQSVRKATAGTLSYGLRKRVELARAMALEPTLILLDEPMAGMN 184 Query: 186 PKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLADGTPEQIRDNP 245 +E ED+ I L EE +TV++IEHDM +VM IS+ +VV++ G +A+G P ++ +P Sbjct: 185 FEEKEDMARYIVDLNEEFGMTVVMIEHDMGVVMDISNRVVVLDFGRKIAEGEPAEVLADP 244 Query: 246 EVIKAYLGE 254 V +AYLGE Sbjct: 245 HVRRAYLGE 253 Lambda K H 0.321 0.138 0.398 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: 196 Number of extensions: 8 Number of successful extensions: 1 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: 255 Length of database: 275 Length adjustment: 25 Effective length of query: 230 Effective length of database: 250 Effective search space: 57500 Effective search space used: 57500 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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