Align Inositol transport system ATP-binding protein (characterized)
to candidate 6937163 Sama_1333 lipoprotein releasing system ATP-binding protein LolD (RefSeq)
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__SB2B:6937163 Length = 229 Score = 84.7 bits (208), Expect = 2e-21 Identities = 76/239 (31%), Positives = 115/239 (48%), Gaps = 20/239 (8%) Query: 3 MSQPLIRMQGIEKHFGS----VIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHK 58 M L++++ + K + L GV + V+ GE ++G +G+GKST + M + K Sbjct: 1 MQDILLKVENVSKTYREGKLETQVLCGVDLSVYRGEQLAIVGGSGSGKSTLLHIMGSLDK 60 Query: 59 PTKGDILFEGQPLH---FADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGP 115 PT G +L EG+ L+ A A + ++Q ++P S N M P R G Sbjct: 61 PTSGKVLLEGEDLYSLSAARQAQIRNASLGFIYQFHHLLPEFSALENVAM---PARIAGV 117 Query: 116 LKLFDHDYANRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEP 175 K A + + ++G++ R A LSGGERQ VAIARA+ ++++ DEP Sbjct: 118 DKKTAFGRAEAL----LERVGLSHR-LSHAPSELSGGERQRVAIARALINQPRLVLADEP 172 Query: 176 TSALGVRQTANVLATIDKVRKQ-GVAVVFITHNVRHALAVG-DRFTVLNRGK-TLGTAQ 231 T L V A I ++ Q G A V +TH+ +ALA DR + GK T G Q Sbjct: 173 TGNLDAASGEAVYALIRELAAQLGTAFVVVTHD--NALAARMDRQLSMKSGKLTTGARQ 229 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: 136 Number of extensions: 9 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: 229 Length adjustment: 24 Effective length of query: 237 Effective length of database: 205 Effective search space: 48585 Effective search space used: 48585 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