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_090274680.1 BLU11_RS14815 polyamine ABC transporter ATP-binding protein
Query= TCDB::Q8DQH8 (254 letters) >NCBI__GCF_900105005.1:WP_090274680.1 Length = 378 Score = 126 bits (317), Expect = 6e-34 Identities = 83/251 (33%), Positives = 131/251 (52%), Gaps = 29/251 (11%) Query: 4 LEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVTLD 63 +++++++K F AV DVTL +N GE+ L+G +G+GK+TL +L G PSEG V LD Sbjct: 21 VKIERVSKQFDDALAVDDVTLTINRGEIFALLGGSGSGKSTLLRILAGFETPSEGRVLLD 80 Query: 64 GHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPAFYK 123 G + P+K + FQ+ LF +TV N IAFG L Sbjct: 81 GQNITALPPHKRP---INMMFQSYALFPHMTVEQN--IAFG-------------LKQDKL 122 Query: 124 SEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPAAGMN 183 S E+ + E+LK+ + A+ LS GQ++R+ + R+LA PK+L LDEP ++ Sbjct: 123 SNTEISERVAEMLKLVHMAKYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALD 182 Query: 184 ----PQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEI 239 Q EL E+I R+ +T +++ HD M + +RI +++ G ++ GTP +I Sbjct: 183 KKLRSQMQLELVEIIERV----GVTCIMVTHDQEEAMTMAQRIAIMDQGWIVQVGTPMDI 238 Query: 240 ---KTNKRVIE 247 N+ V E Sbjct: 239 YESPVNRHVAE 249 Lambda K H 0.319 0.139 0.385 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: 192 Number of extensions: 13 Number of successful extensions: 2 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: 254 Length of database: 378 Length adjustment: 27 Effective length of query: 227 Effective length of database: 351 Effective search space: 79677 Effective search space used: 79677 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 (21.7 bits) S2: 48 (23.1 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