Align ATPase (characterized, see rationale)
to candidate Synpcc7942_1680 Synpcc7942_1680 Sulphate transport system permease protein 1
Query= uniprot:Q31RN8 (261 letters) >FitnessBrowser__SynE:Synpcc7942_1680 Length = 338 Score = 160 bits (405), Expect = 3e-44 Identities = 93/241 (38%), Positives = 145/241 (60%), Gaps = 9/241 (3%) Query: 22 IYAEGVEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIWI 81 I V K +G+ FQA+ V LTV+ G +V ++GPSGSGKST LR + LE G I++ Sbjct: 3 IQVSQVSKQFGS-FQAVKDVDLTVETGSLVALLGPSGSGKSTLLRLIAGLEQPDSGRIFL 61 Query: 82 EGHRLSHDR-RDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAEATARQ 140 G +++ RD +++G VFQ + LF HLTV +N+ +++R+ + A + Sbjct: 62 TGRDATNESVRD-----RQIGFVFQHYALFKHLTVRKNIAFG-LELRKHTKEKVRARVEE 115 Query: 141 LLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREVLDVM 200 LLE V++ D+YP QLSGGQ+QRVA+ARALA+QP++LL DEP ALD ++ +++ + Sbjct: 116 LLELVQLTGLGDRYPSQLSGGQRQRVALARALAVQPQVLLLDEPFGALDAKVRKDLRSWL 175 Query: 201 RDLASE-GMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQSDRAKQFLAQ 259 R L E +T + TH+ A EVAD++V+M G++ + P + P + F+ Sbjct: 176 RKLHDEVHVTTVFVTHDQEEAMEVADQIVVMNHGKVEQIGSPAEIYDNPATPFVMSFIGP 235 Query: 260 I 260 + Sbjct: 236 V 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: 234 Number of extensions: 12 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 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