Align ATPase (characterized, see rationale)
to candidate WP_076482473.1 BW971_RS17350 amino acid ABC transporter ATP-binding protein
Query= uniprot:Q31RN8 (261 letters) >NCBI__GCF_900156495.1:WP_076482473.1 Length = 250 Score = 247 bits (631), Expect = 1e-70 Identities = 129/251 (51%), Positives = 178/251 (70%), Gaps = 11/251 (4%) Query: 21 MIYAEGVEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIW 80 M+ A+ V K +G Q L G+SL V+RGEV ++GPSGSGKSTFLR +N LES G ++ Sbjct: 1 MVLADRVCKSFG-ALQVLKGISLEVERGEVTCLIGPSGSGKSTFLRCVNHLESVTAGRLY 59 Query: 81 IEGHRLSH----------DRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWP 130 ++ + + +D A R+++GMVFQ FNLFPH T L N++ AP+QV+ Sbjct: 60 VDDDLIGYREKGGKLYELSAKDAAAQRRDIGMVFQHFNLFPHRTALDNIIEAPIQVKGVV 119 Query: 131 VAQAEATARQLLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDP 190 A+A + LL++V +A++A YP QLSGGQQQRVAIARALAM P+++LFDEPTSALDP Sbjct: 120 RARAVERGKDLLDQVGLADKASAYPAQLSGGQQQRVAIARALAMDPKLMLFDEPTSALDP 179 Query: 191 EMVREVLDVMRDLASEGMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQS 250 E+V +VL VMR+LA +GMTM+V THE+GFAREVAD++V M G++VE+ P +PQ Sbjct: 180 ELVGDVLAVMRNLAKDGMTMVVVTHEMGFAREVADQLVFMDAGKVVEKGDPREVLNSPQH 239 Query: 251 DRAKQFLAQIL 261 +R + FL+++L Sbjct: 240 ERTQSFLSKLL 250 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: 216 Number of extensions: 9 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: 261 Length of database: 250 Length adjustment: 24 Effective length of query: 237 Effective length of database: 226 Effective search space: 53562 Effective search space used: 53562 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: 47 (22.7 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