Align ATPase (characterized, see rationale)
to candidate Synpcc7942_1406 Synpcc7942_1406 ATPase
Query= uniprot:Q31RN8 (261 letters) >FitnessBrowser__SynE:Synpcc7942_1406 Length = 368 Score = 149 bits (375), Expect = 1e-40 Identities = 90/245 (36%), Positives = 138/245 (56%), Gaps = 6/245 (2%) Query: 16 SAPETMIYAEGVEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQ 75 S E + +++ G+ A+ VS ++ GE++ ++GPSG GK+T LR + ES Q Sbjct: 2 SQSEVLCLDRVCKQFSGSSLAAVDQVSFELEAGEILGLVGPSGCGKTTLLRMIAGFESLQ 61 Query: 76 RGEIWIEGHRLSHDRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAE 135 G I + G ++ +R + + VGMVFQ + LFPHLTVL N+ ++ R+ + Sbjct: 62 SGSIQLAGETVATAQRSLPPETRSVGMVFQDYALFPHLTVLDNVCFG-LRDRK----GSA 116 Query: 136 ATARQLLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVRE 195 A ARQ L V + +YP +LSGGQQQRVA+ARALA QP ++L DEP S LD ++ Sbjct: 117 AVARQALALVGLEGLERRYPHELSGGQQQRVALARALAPQPPLILLDEPLSNLDVQVRLR 176 Query: 196 VLDVMRDLASEGM-TMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQSDRAK 254 + +RD+ + T ++ TH+ A + DRV +M G+ + P+ F P S Sbjct: 177 LRQELRDILRQAQATAILVTHDQEEALSICDRVAVMRLGRFEQIGQPEELFQHPASRFVA 236 Query: 255 QFLAQ 259 +FL+Q Sbjct: 237 EFLSQ 241 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: 264 Number of extensions: 15 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: 368 Length adjustment: 27 Effective length of query: 234 Effective length of database: 341 Effective search space: 79794 Effective search space used: 79794 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 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