Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate AZOBR_RS20990 AZOBR_RS20990 amino acid ABC transporter ATPase
Query= uniprot:Q1MCU3 (247 letters) >FitnessBrowser__azobra:AZOBR_RS20990 Length = 233 Score = 223 bits (568), Expect = 3e-63 Identities = 114/235 (48%), Positives = 165/235 (70%), Gaps = 3/235 (1%) Query: 11 LLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVF 70 +L V ++ +YG I+ L G+D+ V +GE+VS++GAN AGK+TL+ I G+ + R G V F Sbjct: 1 VLTVRKLDAFYGEIQTLHGIDLDVLEGEVVSVVGANAAGKTTLLNAISGTVE-RYGRVSF 59 Query: 71 EGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLK-HFAEDVEKIFTL 129 +DI +P H IAR + Q PEGRR+FP MTV ENL++GA + + H AE +EK+F L Sbjct: 60 FDQDIGTLPPHAIARHGLVQVPEGRRLFPFMTVRENLELGAFAPHARAHRAESLEKVFDL 119 Query: 130 FPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIRKL 189 PRL+ER Q G++SGGEQQM +IGRALMA+P+ ++ DEP+LGLAP++V +F+ +R + Sbjct: 120 MPRLRERSGQLAGSMSGGEQQMCAIGRALMAKPRAIMFDEPTLGLAPIMVDVVFKLVRSI 179 Query: 190 NEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYLEG 244 E G+T+ LVEQN +L +S R YV+ NG + +SG +LL +P ++ AYL G Sbjct: 180 KET-GITILLVEQNVKHSLAMSDRGYVLENGHIVLSGPAADLLTDPRLKEAYLGG 233 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: 190 Number of extensions: 12 Number of successful extensions: 4 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: 233 Length adjustment: 23 Effective length of query: 224 Effective length of database: 210 Effective search space: 47040 Effective search space used: 47040 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