Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate GFF1057 Psest_1090 ABC-type branched-chain amino acid transport systems, ATPase component
Query= uniprot:Q1MCU3 (247 letters) >FitnessBrowser__psRCH2:GFF1057 Length = 238 Score = 156 bits (395), Expect = 3e-43 Identities = 89/211 (42%), Positives = 129/211 (61%), Gaps = 4/211 (1%) Query: 12 LQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVFE 71 L+V+ + +YG L GVD+ V +GE+V+L+G NGAG+ST + I RTGS+V Sbjct: 10 LRVSDLHAFYGESHILHGVDLVVGRGELVTLLGRNGAGRSTTLRAIMNMVGRRTGSIVVN 69 Query: 72 GRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKHFAEDVEKIFTLFP 131 G + MP H+I RL + PE R IF ++V ENL + ++ +++++ +FP Sbjct: 70 GNETIGMPAHQIPRLGVGYCPEERGIFASLSVEENLLLP---PTVRSGGMSLDELYEMFP 126 Query: 132 RLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIRKLNE 191 L ER +G LSGGEQQML++ R L LLLLDE + GLAP+IV+ + E + KL + Sbjct: 127 NLYERRFSQGTRLSGGEQQMLAMARILRTGANLLLLDEITEGLAPVIVQKLGEVLIKLKQ 186 Query: 192 AEGLTVFLVEQNAFAALRLSHRAYVMVNGKV 222 GLT+ LVEQN A L+ R YVM +G++ Sbjct: 187 -RGLTIVLVEQNFRFAAPLADRHYVMEHGRI 216 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: 182 Number of extensions: 12 Number of successful extensions: 3 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