Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_029133955.1 A3GO_RS0114200 ABC transporter ATP-binding protein
Query= uniprot:Q1MCU3 (247 letters) >NCBI__GCF_000428045.1:WP_029133955.1 Length = 236 Score = 313 bits (801), Expect = 3e-90 Identities = 153/235 (65%), Positives = 196/235 (83%) Query: 11 LLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVF 70 +L+++GV T+YG+I AL GV++ V GEIV+LIGANGAGKSTL+MT CG+PQA GS+ + Sbjct: 1 MLEISGVHTFYGSIEALKGVNLTVKAGEIVTLIGANGAGKSTLLMTTCGTPQAAKGSIHY 60 Query: 71 EGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKHFAEDVEKIFTLF 130 G+DIT + THEI L +AQ+PEGRRIFPRM+V+ENL MGA + + K+F +D+E++ TLF Sbjct: 61 LGQDITHLSTHEIMHLGLAQAPEGRRIFPRMSVMENLLMGAIVSDEKYFDQDLERVTTLF 120 Query: 131 PRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIRKLN 190 P LK+R QRGGTLSGGEQQML+I RA+M+RPKLLLLDEPSLGLAPL+VK IF+ I ++N Sbjct: 121 PILKKRANQRGGTLSGGEQQMLAIARAMMSRPKLLLLDEPSLGLAPLVVKQIFKVIEEIN 180 Query: 191 EAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYLEGG 245 + +TV LVEQNA+ AL+L+HR YVMVNG++T+SG K+LL PEVRAAYLEGG Sbjct: 181 REDNVTVLLVEQNAYHALKLAHRGYVMVNGEITLSGESKDLLERPEVRAAYLEGG 235 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: 238 Number of extensions: 5 Number of successful extensions: 1 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: 236 Length adjustment: 23 Effective length of query: 224 Effective length of database: 213 Effective search space: 47712 Effective search space used: 47712 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 24 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