Align ATPase (characterized, see rationale)
to candidate GFF16 Psest_0016 ectoine/hydroxyectoine ABC transporter, ATP-binding protein
Query= uniprot:Q31RN8 (261 letters) >FitnessBrowser__psRCH2:GFF16 Length = 278 Score = 226 bits (576), Expect = 4e-64 Identities = 125/272 (45%), Positives = 171/272 (62%), Gaps = 20/272 (7%) Query: 1 MTPLGRQPEPVTAIASAPETMIYAEGVEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSG 60 + P +QPE + ++ GV K YG + L G+ L ++ GE V ++GPSGSG Sbjct: 11 LNPTPQQPEQA-------QPLVRFAGVTKRYG-ELTVLDGLDLQIEEGEKVAIIGPSGSG 62 Query: 61 KSTFLRTLNALESHQRGEIWIEGHRLSH-----------DRRDIATIRQEVGMVFQQFNL 109 KST LR L LE G I ++G L+H + R + +R +VGMVFQ FNL Sbjct: 63 KSTLLRVLMTLEGIDEGVIEVDGEPLTHMPDASGQLVPANARHLRRVRGKVGMVFQSFNL 122 Query: 110 FPHLTVLQNLMLAPVQVRRWPVAQAEATARQLLERVRIAEQADKYPGQLSGGQQQRVAIA 169 FPH+ LQN+M APVQV A+A A +LL V + ++ + +P QLSGGQQQRVAIA Sbjct: 123 FPHMNALQNVMEAPVQVLGLSKAEARGRAEELLAMVGLEDKLEHFPAQLSGGQQQRVAIA 182 Query: 170 RALAMQPRILLFDEPTSALDPEMVREVLDVMRDLA-SEGMTMLVATHEVGFAREVADRVV 228 RALAM+P+++LFDE TSALDPE+ EVL+V+R L + +TML+ TH++GFARE ADRV Sbjct: 183 RALAMRPKVMLFDEVTSALDPELCGEVLNVIRRLGEAHNLTMLMVTHQMGFAREFADRVC 242 Query: 229 LMADGQIVEEAPPDRFFTAPQSDRAKQFLAQI 260 G+I E+ PD F PQ +R ++FL+ + Sbjct: 243 FFHQGRIHEQGSPDELFNNPQEERTREFLSAV 274 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: 230 Number of extensions: 12 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: 278 Length adjustment: 25 Effective length of query: 236 Effective length of database: 253 Effective search space: 59708 Effective search space used: 59708 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 17 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