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_011385946.1 AMB_RS18160 ABC transporter ATP-binding protein
Query= TCDB::Q8DQH8 (254 letters) >NCBI__GCF_000009985.1:WP_011385946.1 Length = 265 Score = 211 bits (536), Expect = 2e-59 Identities = 107/252 (42%), Positives = 169/252 (67%), Gaps = 5/252 (1%) Query: 3 LLEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVTL 62 +LEV+ ++ FGG+ A+ +V+ ++N+GEL +IGPNGAGKT++ N ++G Y+P+ G V + Sbjct: 8 VLEVRDVSLAFGGVRALTEVSFQVNKGELFSIIGPNGAGKTSMLNCVSGRYKPTSGRVFM 67 Query: 63 DGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHK--QHVFTSFLR-LP 119 DG + G SP A+LGLGRTFQN+ LF ++VLDN+++ G HH + T L L Sbjct: 68 DGRDVTGLSPNVRATLGLGRTFQNLALFGHMSVLDNIMV--GRHHLLGNNAATGALYWLS 125 Query: 120 AFYKSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPA 179 K E + K +++ ++ + +A L YG ++R+E+ RA+A EPK++ LDEP Sbjct: 126 GARKEELAHRRKVEDIIDFLEIAHIRKAVAGTLPYGLRKRVELARAMAVEPKVILLDEPM 185 Query: 180 AGMNPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEI 239 AGMN +E ++ I + +E+ +T+++IEHDM +VM+++ R+ VLE+GR IA+G PDE+ Sbjct: 186 AGMNLEEKEDMARYIVDLNEEWGMTVIMIEHDMGVVMDISHRVMVLEFGRKIAEGLPDEV 245 Query: 240 KTNKRVIEAYLG 251 N+RV AYLG Sbjct: 246 MNNERVKVAYLG 257 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: 191 Number of extensions: 8 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: 265 Length adjustment: 24 Effective length of query: 230 Effective length of database: 241 Effective search space: 55430 Effective search space used: 55430 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: 47 (22.7 bits)
This GapMind analysis is from Sep 17 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