Align ATPase (characterized, see rationale)
to candidate WP_011974043.1 MAEO_RS06850 ABC transporter ATP-binding protein
Query= uniprot:Q31RN8 (261 letters) >NCBI__GCF_000017185.1:WP_011974043.1 Length = 238 Score = 155 bits (391), Expect = 1e-42 Identities = 92/223 (41%), Positives = 140/223 (62%), Gaps = 8/223 (3%) Query: 21 MIYAEGVEKWYGN---QFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRG 77 +I A+ + K YG + L G++L ++ GE V +MGPSG GKST L L L+ +G Sbjct: 17 LIEAKNIWKIYGGGEAKTVVLRGINLKIKEGEFVAIMGPSGCGKSTLLNILGLLDVPNKG 76 Query: 78 EIWIEGHRLS-HDRRDIATIRQEV-GMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAE 135 ++I+G + + D A R+++ G +FQQFNL LT L+N+ L P+ + Sbjct: 77 MVYIKGKKTTMFSENDRAVFRRKISGFIFQQFNLINTLTALENVEL-PLVLDEKNKNYRI 135 Query: 136 ATARQLLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVRE 195 A++LL+ + + + + YP QLSGGQQQRVAIARAL+ P+I+ DEPT LD + RE Sbjct: 136 KKAKKLLKIINLGHRENYYPNQLSGGQQQRVAIARALSNNPKIIFADEPTGNLDSKNSRE 195 Query: 196 VLDVMRDL-ASEGMTMLVATHEVGFAREVADRVVLMADGQIVE 237 V+D++++L EG+T+++ THE FA+ A R++ M DG+IVE Sbjct: 196 VMDILKELNEKEGITVIMVTHEPEFAK-YASRIINMKDGEIVE 237 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: 151 Number of extensions: 8 Number of successful extensions: 5 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: 238 Length adjustment: 24 Effective length of query: 237 Effective length of database: 214 Effective search space: 50718 Effective search space used: 50718 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