Align Inositol transport system ATP-binding protein (characterized)
to candidate 5208462 Shew_0974 spermidine/putrescine ABC transporter ATPase subunit (RefSeq)
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__PV4:5208462 Length = 378 Score = 105 bits (263), Expect = 1e-27 Identities = 74/245 (30%), Positives = 124/245 (50%), Gaps = 12/245 (4%) Query: 2 SMSQPLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTK 61 + + L++++ + K F V A+ VS+++ GE LLG +G+GKST ++ ++G KPT+ Sbjct: 15 TQGEVLLKIERVSKLFDDVRAVDDVSLNINRGEIFALLGGSGSGKSTLLRMLAGFEKPTE 74 Query: 62 GDILFEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDH 121 G I +GQ + P + I + Q A+ P M+V++N G + + P + Sbjct: 75 GRIYLDGQDITDMPPYE---RPINMMFQSYALFPHMTVAQNIAFGLKQDKM--PKAEIEQ 129 Query: 122 DYANRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGV 181 + + M R P+Q LSGG+RQ VA+AR++ K+L+LDEP AL Sbjct: 130 RVKEMLKLVHMEPYA--KRKPNQ----LSGGQRQRVALARSLAKRPKLLLLDEPMGALDK 183 Query: 182 R-QTANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEEL 240 + +T L +D + GV V +TH+ A+ + +R ++N G T DI Sbjct: 184 KLRTQMQLEVVDILEAVGVTCVMVTHDQEEAMTMAERIAIMNDGWIAQTGSPMDIYESPA 243 Query: 241 QDMMA 245 M+A Sbjct: 244 NRMVA 248 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: 204 Number of extensions: 8 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: 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