Align ATPase (characterized, see rationale)
to candidate Pf1N1B4_4804 ABC-type polar amino acid transport system protein, ATP-binding protein
Query= uniprot:Q31RN8 (261 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4804 Length = 254 Score = 244 bits (624), Expect = 1e-69 Identities = 125/251 (49%), Positives = 177/251 (70%), Gaps = 11/251 (4%) Query: 20 TMIYAEGVEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEI 79 +++ A + K+Y + F AL +++ V++GEV+ ++GPSGSGKST LR +N LE +G + Sbjct: 3 SIVKAVSLNKYY-DHFHALKDINIEVEQGEVLCIIGPSGSGKSTLLRCVNQLEKIDKGGL 61 Query: 80 WIEGHRLSH----------DRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRW 129 W++G + + + IA R GMVFQ+FNLFPH+TVLQN++ P QV + Sbjct: 62 WVDGELVGYRIVGNKLHELNESQIARQRLATGMVFQRFNLFPHMTVLQNIIEGPCQVLKR 121 Query: 130 PVAQAEATARQLLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALD 189 +A A +LL RV +A++ + YP +LSGGQQQRVAIARALAM+P+++LFDEPTSALD Sbjct: 122 SPKEAHEEALELLARVGLADKRNSYPIELSGGQQQRVAIARALAMRPKLMLFDEPTSALD 181 Query: 190 PEMVREVLDVMRDLASEGMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQ 249 PE+V EVL VMRDLA GMTM+V THE+GFAREV++R+V M +GQIVE P+ +PQ Sbjct: 182 PELVGEVLSVMRDLAQTGMTMIVVTHELGFAREVSNRMVFMDEGQIVEAGSPEEILISPQ 241 Query: 250 SDRAKQFLAQI 260 + R + F++ + Sbjct: 242 NPRTQSFISAV 252 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: 5 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: 254 Length adjustment: 24 Effective length of query: 237 Effective length of database: 230 Effective search space: 54510 Effective search space used: 54510 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