Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_084935579.1 HA51_RS15825 ABC transporter ATP-binding protein
Query= uniprot:Q1MCU3 (247 letters) >NCBI__GCF_002095475.1:WP_084935579.1 Length = 249 Score = 258 bits (658), Expect = 1e-73 Identities = 137/236 (58%), Positives = 173/236 (73%), Gaps = 1/236 (0%) Query: 9 QPLLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSV 68 + +L V+ +YG ++AL V + VN+GE V+LIGANGAGKSTL+M+I G P+ +G + Sbjct: 3 ESMLSFEQVDVFYGPVQALKQVSLTVNQGETVALIGANGAGKSTLLMSIFGQPRIASGDI 62 Query: 69 VFEGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKHFAEDVEKIFT 128 G I TH IA IAQ+PEGRRIFP MTV ENL MG +H ED E+++ Sbjct: 63 RLRGESIGHRSTHFIAASGIAQAPEGRRIFPDMTVEENLLMGTIAVGERHVKEDKERMYQ 122 Query: 129 LFPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIRK 188 LFPRL ER QR TLSGGEQQML+I RALM+RPKLLLLDEPSLGLAP++VK IF +R+ Sbjct: 123 LFPRLLERRKQRAMTLSGGEQQMLAIARALMSRPKLLLLDEPSLGLAPIVVKQIFNILRE 182 Query: 189 LNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYLEG 244 L + +G+T+FLVEQNA AL+L+ R YVMVNG++ +SG G+ELL N EVR+AYL G Sbjct: 183 LTQ-QGMTLFLVEQNARHALQLADRGYVMVNGEIKLSGRGEELLNNDEVRSAYLGG 237 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: 215 Number of extensions: 8 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: 249 Length adjustment: 24 Effective length of query: 223 Effective length of database: 225 Effective search space: 50175 Effective search space used: 50175 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