Align ATPase (characterized, see rationale)
to candidate WP_090275879.1 BLU11_RS18455 methionine ABC transporter ATP-binding protein
Query= uniprot:Q31RN8 (261 letters) >NCBI__GCF_900105005.1:WP_090275879.1 Length = 334 Score = 160 bits (406), Expect = 2e-44 Identities = 98/242 (40%), Positives = 134/242 (55%), Gaps = 5/242 (2%) Query: 21 MIYAEGVEKWY---GNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRG 77 MI + V K Y G AL LT++ G+V ++G SG+GKST LR +N LE G Sbjct: 1 MIEFQQVNKAYRVGGRDIPALHATDLTIEAGQVYGIIGHSGAGKSTLLRLINRLEEPSNG 60 Query: 78 EIWIEGHRLSH-DRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAEA 136 I + G + + + RQ VGM+FQ FNL TV N+ L Q A Sbjct: 61 RIMVAGEDTTALNAEGLRRFRQRVGMIFQHFNLLSSATVADNVALPLRLAGSANRQQIAA 120 Query: 137 TARQLLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREV 196 LL+RV +++ A KYP QLSGGQ+QRV IARALA +P ILL DE TSALDP +V Sbjct: 121 RVASLLDRVGLSDHASKYPAQLSGGQKQRVGIARALATEPSILLCDEATSALDPHTTGQV 180 Query: 197 LDVMRDLASE-GMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQSDRAKQ 255 L ++ ++ E +T+++ THE+ R V D+V +M G+IVE+ F PQ + Sbjct: 181 LQLLSEINRELNLTIVLITHEMDVIRRVCDQVAVMDGGRIVEQGTVADVFLHPQHPTTRS 240 Query: 256 FL 257 F+ Sbjct: 241 FV 242 Lambda K H 0.321 0.134 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: 219 Number of extensions: 18 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: 261 Length of database: 334 Length adjustment: 26 Effective length of query: 235 Effective length of database: 308 Effective search space: 72380 Effective search space used: 72380 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 (21.9 bits) S2: 48 (23.1 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