Align ATPase (characterized, see rationale)
to candidate WP_011319604.1 AVA_RS14435 ABC transporter ATP-binding protein
Query= uniprot:Q31RN8 (261 letters) >NCBI__GCF_000204075.1:WP_011319604.1 Length = 252 Score = 152 bits (384), Expect = 7e-42 Identities = 93/226 (41%), Positives = 140/226 (61%), Gaps = 8/226 (3%) Query: 17 APET-MIYAEGVEKWYG---NQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALE 72 AP++ +I E + K YG + +AL V+L + GE +MGPSGSGKST + + L+ Sbjct: 16 APQSAIIRLENIFKVYGIGETEVKALNDVNLVINEGEYCSIMGPSGSGKSTAMNIIGCLD 75 Query: 73 SHQRGEIWIEGHRLSH-DRRDIATIR-QEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWP 130 G +++G ++ + +D+A IR +++G VFQQF+L P L+ L+N+ML V P Sbjct: 76 RPTEGHYYLDGLDVAQMNDKDLAHIRNRKLGFVFQQFHLLPQLSALENVMLPMVYADVTP 135 Query: 131 VAQAEATARQLLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDP 190 + + L+ RV + ++ + P QLSGGQQQRVAIARA+ +P +LL DEPT ALD Sbjct: 136 NERRDRATEALI-RVGLEKRLNNKPTQLSGGQQQRVAIARAIVNRPVVLLADEPTGALDS 194 Query: 191 EMVREVLDVMRDLASEGMTMLVATHEVGFAREVADRVVLMADGQIV 236 +EVLD+ +L S G+T+++ THE AR+ R+V DGQ+V Sbjct: 195 RTTQEVLDIFTELNSGGITVVMVTHEPEVARQ-TKRIVWFKDGQVV 239 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: 176 Number of extensions: 9 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: 252 Length adjustment: 24 Effective length of query: 237 Effective length of database: 228 Effective search space: 54036 Effective search space used: 54036 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