Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate SM_b20784 SM_b20784 branched-chain amino acid ABC transporter ATP-binding protein
Query= uniprot:Q1MCU3 (247 letters) >FitnessBrowser__Smeli:SM_b20784 Length = 238 Score = 141 bits (355), Expect = 1e-38 Identities = 80/221 (36%), Positives = 127/221 (57%), Gaps = 6/221 (2%) Query: 12 LQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVFE 71 L+V+ + YG R L G+ V G ++++G NG GK+TL+ T+ G + G + Sbjct: 6 LEVDNLSAGYGPTRVLEGISFSVPAGARLAVLGRNGMGKTTLLATLAGQTRRYEGRIRIG 65 Query: 72 GRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKHFAED-VEKIFTLF 130 ++T +P+ A + P+ R +FP +TV ENL +G LK + + + + +F Sbjct: 66 DANVTALPSASRALKGLGFVPQARCVFPSLTVEENLFVG-----LKGRPKTALSEAYEMF 120 Query: 131 PRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIRKLN 190 PRL ER G LSGGEQQMLS R+++ RP +LLLDEP GLAP+I + + +A +L Sbjct: 121 PRLYERRRNLGSQLSGGEQQMLSTARSILGRPSVLLLDEPLEGLAPVICEELMKAFAELA 180 Query: 191 EAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKEL 231 + G+T+ LVEQ +AL + R ++ G++ SG+ + L Sbjct: 181 KTGGMTILLVEQRIQSALDFADRVIILERGRLAWSGTPEAL 221 Lambda K H 0.320 0.137 0.387 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: 181 Number of extensions: 9 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: 247 Length of database: 238 Length adjustment: 23 Effective length of query: 224 Effective length of database: 215 Effective search space: 48160 Effective search space used: 48160 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: 46 (22.3 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