Align Inositol transport system ATP-binding protein (characterized)
to candidate 6938538 Sama_2641 polyamine ABC transporter, ATP-binding protein (RefSeq)
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__SB2B:6938538 Length = 378 Score = 101 bits (251), Expect = 3e-26 Identities = 67/224 (29%), Positives = 119/224 (53%), Gaps = 12/224 (5%) Query: 2 SMSQPLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTK 61 + + L++++ + K F V A+ VS+ + GE LLG +G+GKST ++ ++G +PT+ Sbjct: 15 TQDEVLLKIERVSKLFDDVRAVDDVSLTINKGEIFALLGGSGSGKSTLLRMLAGFERPTE 74 Query: 62 GDILFEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDH 121 G I +GQ + P + I + Q A+ P M+V +N G + K+ Sbjct: 75 GRIYLDGQDITDLPPYE---RPINMMFQSYALFPHMTVEQNIAFG------LKQDKMSKA 125 Query: 122 DYANRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGV 181 D + R+ +EM K+ + + LSGG+RQ VA+AR++ K+L+LDEP AL Sbjct: 126 DISQRV--QEMLKLVHMEQYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDK 183 Query: 182 R-QTANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRG 224 + +T L ++ + + GV V +TH+ A+ + R +++ G Sbjct: 184 KLRTQMQLEVVEILERVGVTCVMVTHDQEEAMTMAGRIAIMSDG 227 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: 213 Number of extensions: 10 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: 378 Length adjustment: 27 Effective length of query: 234 Effective length of database: 351 Effective search space: 82134 Effective search space used: 82134 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