Align High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)
to candidate WP_018372124.1 BN415_RS07505 ABC transporter ATP-binding protein
Query= uniprot:A0A159ZWS6 (255 letters) >NCBI__GCF_000341525.1:WP_018372124.1 Length = 559 Score = 103 bits (258), Expect = 6e-27 Identities = 77/252 (30%), Positives = 130/252 (51%), Gaps = 20/252 (7%) Query: 5 ILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGGTILL 64 +L V++L + +G + G+ +T+ +KQ +A++G NGAGK+T+ L F PT G++ Sbjct: 296 LLVVKDLRVSYGSQEVLKGIDVTIPKKQRIAIVGKNGAGKSTLAKALCQFV-PTTGSLTW 354 Query: 65 DGEPIQGLPGHHIARKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFFAGLFKTPAFR 124 GE I G A + + QN N +I++ T F + K R Sbjct: 355 QGEDIAGDSIKERAER-IGYVLQN----------PNQMISE-----TMIFDEVAKGLRLR 398 Query: 125 K-SEREAMEYAEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAG 183 SE E E L L + P L++GQ++R+ IA ++ RP IL+LDEP AG Sbjct: 399 GVSESEIEARVEEVLKTCGLHAYRKWPISALSFGQKKRVTIASILVLRPEILLLDEPTAG 458 Query: 184 LNPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLADGTPEQIRD 243 + + ++ + L + + T+++I HDM+L++ SD +V+ G +AD +P ++ Sbjct: 459 QDQRNYTEIMNFLDDLHAKGH-TIIMITHDMQLMLDYSDRALVLVDGQIIADQSPLEVLT 517 Query: 244 NPEVI-KAYLGE 254 NP ++ KA L E Sbjct: 518 NPALLAKANLKE 529 Score = 82.4 bits (202), Expect = 2e-20 Identities = 64/250 (25%), Positives = 116/250 (46%), Gaps = 25/250 (10%) Query: 1 MSREILKVENLSMRFGGLL--AVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPT 58 M + +++ +N S ++ + + LT+ E + V +IGP+G+GK+T+ CL G Sbjct: 1 MKQAMIECKNFSFQYQAQTEPTLKNLDLTIYEGEKVLIIGPSGSGKSTLGQCLNGIIPSI 60 Query: 59 -----GGTILLDGEPIQGLPGHHIARKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNF 113 G++ + G+ L + + F +T E++ A + Sbjct: 61 YPGKQSGSLTIAGQEAFELSIYDKSNLVSTVLQDTDGQFIGLTVAEDVAFALENDVE--- 117 Query: 114 FAGLFKTPAFRKSEREAM-EYAEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTRP 172 E M E W +K++L L+ GQ++R+ +A ++ Sbjct: 118 -------------ELTTMREKVALWAEKLDLGYLLQHRPQDLSGGQKQRVSLAGVLIDES 164 Query: 173 RILMLDEPAAGLNPKETEDLKALIGVLREEHNVTVLLIEHDMKLVM-SISDHIVVINQGT 231 IL+ DEP A L+PK +D+ ALI L +E T ++IEH ++ V+ D I++IN+G Sbjct: 165 PILLFDEPLANLDPKSGQDIIALIDQLHKEAGTTTIIIEHRLEDVLYRPVDRIILINEGQ 224 Query: 232 PLADGTPEQI 241 L +GTP+ + Sbjct: 225 ILFNGTPDAL 234 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: 360 Number of extensions: 21 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 255 Length of database: 559 Length adjustment: 30 Effective length of query: 225 Effective length of database: 529 Effective search space: 119025 Effective search space used: 119025 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: 50 (23.9 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