Align ATPase (characterized, see rationale)
to candidate WP_013645374.1 METBO_RS08905 ABC transporter ATP-binding protein
Query= uniprot:Q31RN8 (261 letters) >NCBI__GCF_000191585.1:WP_013645374.1 Length = 223 Score = 142 bits (357), Expect = 8e-39 Identities = 89/219 (40%), Positives = 133/219 (60%), Gaps = 6/219 (2%) Query: 20 TMIYAEGVEKWYGN-QFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGE 78 T+I + ++K Y + AL V L ++RGE V ++GPSGSGKST L + L+ G+ Sbjct: 5 TIIKIKNLKKEYEDGSIIALNNVDLEIERGESVSIIGPSGSGKSTLLNMIGGLDKANEGQ 64 Query: 79 IWIEGHRLSHDRRDIATIRQ-EVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAEAT 137 I + G L D D++ R E+G VFQ NL P+LTVL+N+ + P+ + E Sbjct: 65 ISVAGVNLM-DNSDLSNFRSNEIGFVFQLHNLIPNLTVLENVQI-PLLGTDIDDKKMEER 122 Query: 138 ARQLLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREVL 197 A +LL+ V + + D+ P +LSGG++QRVAIARAL P I+L DEPT ALD E +L Sbjct: 123 ALKLLKSVNLENKVDQKPTKLSGGERQRVAIARALVNHPSIILADEPTGALDSETQEVIL 182 Query: 198 DVMRDL-ASEGMTMLVATHEVGFAREVADRVVLMADGQI 235 ++ D+ E +T+++ THE A++ ADR + + DG+I Sbjct: 183 KLLLDIHKKENVTLIMVTHEPYVAKQ-ADRSIYVLDGKI 220 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: 112 Number of extensions: 6 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: 261 Length of database: 223 Length adjustment: 23 Effective length of query: 238 Effective length of database: 200 Effective search space: 47600 Effective search space used: 47600 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: 46 (22.3 bits)
This GapMind analysis is from Apr 09 2024. 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