Align Inositol transport system ATP-binding protein (characterized)
to candidate CCNA_03235 CCNA_03235 spermidine/putrescine transport ATP-binding protein potA
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__Caulo:CCNA_03235 Length = 381 Score = 114 bits (286), Expect = 2e-30 Identities = 78/238 (32%), Positives = 124/238 (52%), Gaps = 16/238 (6%) Query: 1 MSMSQPLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPT 60 M+ +P+I + + K FG + A+ VS+ V GE LLG +G GK+T ++ ++G PT Sbjct: 8 MTTPKPIITFENVTKRFGKLAAVDNVSLTVNEGEFFALLGPSGCGKTTLLRMLAGFETPT 67 Query: 61 KGDILFEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFD 120 +G IL +GQ + P + V Q A+ P M+V+ N G K+ + + Sbjct: 68 EGRILIDGQDISNVPPN---KRPVNMVFQSYAVFPHMTVADNVAYG----LKVDNVPKAE 120 Query: 121 HDYANRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALG 180 + +E ++ G+ R PDQ LSGG+RQ VA+ARA+ +VL+LDEP SAL Sbjct: 121 REARVAEALELVQLGGLGGRKPDQ----LSGGQRQRVALARALVKRPRVLLLDEPLSALD 176 Query: 181 VR---QTANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDI 235 + Q L T+ + K G+ + +TH+ ALA+ R V+++G A D+ Sbjct: 177 AKLREQMRTELCTLQE--KVGITFIMVTHDQDEALALASRCAVMSKGLLQQVATPSDL 232 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: 230 Number of extensions: 10 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: 381 Length adjustment: 27 Effective length of query: 234 Effective length of database: 354 Effective search space: 82836 Effective search space used: 82836 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