Align High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)
to candidate AZOBR_RS22350 AZOBR_RS22350 ABC transporter
Query= uniprot:A0A159ZWS6 (255 letters) >FitnessBrowser__azobra:AZOBR_RS22350 Length = 268 Score = 211 bits (536), Expect = 2e-59 Identities = 102/251 (40%), Positives = 162/251 (64%), Gaps = 1/251 (0%) Query: 5 ILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGGTILL 64 I + +S+RFGG+ A+ V ++++ ++ ++IGPNGAGKT++ NC++G Y+PT G + Sbjct: 1 IFEARGVSLRFGGVQALTDVGFSIRKGELFSIIGPNGAGKTSMVNCISGRYRPTDGKVYF 60 Query: 65 DGEPIQGLPGHHIARKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFFAG-LFKTPAF 123 G+ I G+ +H A G+ RTFQN+ LF MT ++N+++ +H L NFF G L+ Sbjct: 61 KGQDITGMTPNHRASLGIGRTFQNLALFGHMTVLDNIMVGRHHLLKNNFFTGSLYWLTGA 120 Query: 124 RKSEREAMEYAEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAG 183 RK E E +D + + AGTL+YG ++R+E+AR + +P +++LDEP AG Sbjct: 121 RKEELAHRREVEEIIDFLEIQHVRKATAGTLSYGLRKRVELARAIALKPDLILLDEPMAG 180 Query: 184 LNPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLADGTPEQIRD 243 +N +E ED+ I L EE +TV++IEHDM +VM IS ++V+ G +A+GTPE++ Sbjct: 181 MNLEEKEDMARYIVDLNEEFGMTVVMIEHDMGVVMDISHRVIVLEFGKKIAEGTPEEVLA 240 Query: 244 NPEVIKAYLGE 254 +P V +AYLGE Sbjct: 241 DPRVKRAYLGE 251 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: 193 Number of extensions: 10 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: 255 Length of database: 268 Length adjustment: 25 Effective length of query: 230 Effective length of database: 243 Effective search space: 55890 Effective search space used: 55890 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 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