Align ATPase (characterized, see rationale)
to candidate WP_010994303.1 AVA_RS07575 sulfate/molybdate ABC transporter ATP-binding protein
Query= uniprot:Q31RN8 (261 letters) >NCBI__GCF_000204075.1:WP_010994303.1 Length = 338 Score = 160 bits (406), Expect = 3e-44 Identities = 92/240 (38%), Positives = 143/240 (59%), Gaps = 7/240 (2%) Query: 22 IYAEGVEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIWI 81 I E V K +G+ F+A+ V+L +Q G++V ++GPSGSGKST LR + LE G I + Sbjct: 3 IVVENVSKQFGS-FRAVDQVNLEIQSGKLVALLGPSGSGKSTLLRLIAGLEKPDDGRIIL 61 Query: 82 EGHRLSHDRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAEATARQL 141 G D + + + +G VFQ + LF HLTV QN+ +++R+ P + + QL Sbjct: 62 TGK----DATNQSVQERNIGFVFQHYALFKHLTVRQNIAFG-LEIRKAPANKVKGRVEQL 116 Query: 142 LERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREVLDVMR 201 LE V+++ D+YP QLSGGQ+QRVA+ARALA++P +LL DEP ALD ++ +++ +R Sbjct: 117 LELVQLSGLGDRYPSQLSGGQRQRVALARALAVEPSVLLLDEPFGALDAKVRKDLRAWLR 176 Query: 202 DLASE-GMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQSDRAKQFLAQI 260 L E +T + TH+ A EV+D VV+M G++ + P + P + F+ + Sbjct: 177 RLHDEVHVTTVFVTHDQEEAMEVSDEVVVMNQGRVEQVGTPAEIYDNPATSFVMSFIGPV 236 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: 190 Number of extensions: 11 Number of successful extensions: 4 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: 338 Length adjustment: 26 Effective length of query: 235 Effective length of database: 312 Effective search space: 73320 Effective search space used: 73320 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