Align ATPase (characterized, see rationale)
to candidate Synpcc7942_1414 Synpcc7942_1414 ATPase
Query= uniprot:Q31RN8 (261 letters) >FitnessBrowser__SynE:Synpcc7942_1414 Length = 241 Score = 146 bits (368), Expect = 4e-40 Identities = 94/237 (39%), Positives = 138/237 (58%), Gaps = 13/237 (5%) Query: 14 IASAPETMIYAEGVEKWYGN---QFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNA 70 +A + +I E V K YG +AL V V+ GE +MG SGSGKST + + Sbjct: 1 MAESAPPVIQFEHVSKIYGEGETTVRALDHVDFQVRAGEYCAIMGASGSGKSTAMNLIGC 60 Query: 71 LESHQRGEIWIEGHRLSH-DRRDIATIR-QEVGMVFQQFNLFPHLTVLQNLMLAPVQVRR 128 L+ G +++G ++ D +A +R +++G VFQQF+L P L+ ++N+ML + Sbjct: 61 LDRPTAGRYYLDGTDVADLDDDALAAVRNRKIGFVFQQFHLLPQLSAVENVMLPMIYAG- 119 Query: 129 WPVAQAEATARQL--LERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTS 186 ++Q E R + L +V +A++ D P QLSGGQQQRVAIARA+ QP +LL DEPT Sbjct: 120 --ISQQERRDRAVAALTQVGLAQRLDNKPNQLSGGQQQRVAIARAIVNQPVLLLADEPTG 177 Query: 187 ALDPEMVREVLDVMRDLASEGMTMLVATHEVGFAREVADRVVLMADGQIVEEA--PP 241 ALD + EVL++ L G+T+++ THE A + A+RV+ DGQI E PP Sbjct: 178 ALDSQTTEEVLNIFDQLHQRGITIVIVTHEAEVA-DRAERVIWFRDGQIQRETQNPP 233 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: 179 Number of extensions: 11 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: 241 Length adjustment: 24 Effective length of query: 237 Effective length of database: 217 Effective search space: 51429 Effective search space used: 51429 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: 46 (22.3 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