Align ATPase (characterized, see rationale)
to candidate WP_011612685.1 TERY_RS15440 ABC transporter ATP-binding protein
Query= uniprot:Q31RN8 (261 letters) >NCBI__GCF_000014265.1:WP_011612685.1 Length = 378 Score = 150 bits (379), Expect = 4e-41 Identities = 86/241 (35%), Positives = 136/241 (56%), Gaps = 2/241 (0%) Query: 21 MIYAEGVEKWYGNQFQ-ALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEI 79 ++Y E V K + A+ V+LT+ +G+++ ++GPSG GK+T LR + E Q G + Sbjct: 6 ILYLESVSKKFSRSTTTAVQNVNLTLYQGDILGLLGPSGCGKTTLLRIIAGFEEPQSGIV 65 Query: 80 WIEGHRLSHDRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAEATAR 139 I G ++ I ++ VGMVFQ + LFPHLTV +N+ + Q R Sbjct: 66 TINGRLVAGKHDWIVPEKRNVGMVFQDYALFPHLTVAKNIAFGLHNSGKKSSTQINHQVR 125 Query: 140 QLLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREVLDV 199 +LE V +++ ++YP +LSGGQQQRVA+ARALA P ++L DEP S LD ++ + Sbjct: 126 DVLELVGLSDLENRYPHELSGGQQQRVALARALAPNPALVLLDEPLSNLDVQVRIRLRQE 185 Query: 200 MRD-LASEGMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQSDRAKQFLA 258 +RD L + G + ++ TH+ A ++DRV +M G + + P +T P S +F+ Sbjct: 186 LRDILKNAGASGIIVTHDQEEAMAISDRVAVMRAGSVEQFGTPKDIYTEPASKFVAEFVT 245 Query: 259 Q 259 Q Sbjct: 246 Q 246 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: 234 Number of extensions: 11 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: 378 Length adjustment: 27 Effective length of query: 234 Effective length of database: 351 Effective search space: 82134 Effective search space used: 82134 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