Align Inositol transport system ATP-binding protein (characterized)
to candidate Synpcc7942_2492 Synpcc7942_2492 ATPase
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__SynE:Synpcc7942_2492 Length = 237 Score = 111 bits (278), Expect = 1e-29 Identities = 71/234 (30%), Positives = 123/234 (52%), Gaps = 10/234 (4%) Query: 3 MSQPLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKG 62 MS+PL+++ I ++G+V+AL +++++FPGE L+G NGAGKST ++ +S + +G Sbjct: 1 MSEPLLQLSQIAVNYGAVVALTDLTLEIFPGEIVALIGANGAGKSTTLRAISRLVPLQQG 60 Query: 63 DILFEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIR-KIGPLKLFDH 121 I ++ Q L + G+A + ++ SV N +G R +IG + Sbjct: 61 RIYYDQQDLGLIPAPQLVGRGLAHCPEGRRVLARQSVRINLELGAYCRRDRIGIQTDLEL 120 Query: 122 DYANRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGV 181 + + E + +Q GTLSGGE+Q +AIARA+ ++L+LDEP+ L Sbjct: 121 QFDRFPRLRERQ---------NQPAGTLSGGEQQMLAIARALMSRPRLLLLDEPSLGLAP 171 Query: 182 RQTANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDI 235 + + + I +R+QG+ ++ + N AL DR VL G+ L + D+ Sbjct: 172 QIVQEIFSVIRSLREQGMTILLVEQNATLALQTADRGYVLEAGQLLFSGPAADL 225 Lambda K H 0.321 0.137 0.395 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: 149 Number of extensions: 6 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: 237 Length adjustment: 24 Effective length of query: 237 Effective length of database: 213 Effective search space: 50481 Effective search space used: 50481 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