Align Inositol transport system ATP-binding protein (characterized)
to candidate WP_043743905.1 AMB_RS08470 ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF717 (261 letters) >NCBI__GCF_000009985.1:WP_043743905.1 Length = 234 Score = 117 bits (293), Expect = 2e-31 Identities = 79/225 (35%), Positives = 114/225 (50%), Gaps = 9/225 (4%) Query: 7 LIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILF 66 L+ + G+ H+G + AL G+ V V GE L+G NGAGK+T ++ +SGV T G I F Sbjct: 2 LLEISGLTSHYGRIQALKGIDVQVAEGELVALVGANGAGKTTLLRCISGVQGVTGGSIKF 61 Query: 67 EGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANR 126 GQ + P + GI+ + + MSV N +G R+ GP D D Sbjct: 62 AGQDITKMSPEARVGLGISQSPEGRQVFGPMSVEDNLRLG--AYRRHGPDIKADMD---- 115 Query: 127 ITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTAN 186 M EM I + + GTLSGG++Q +AIARA+ +VL+LDEP+ L A Sbjct: 116 -RMYEM--FPILHKKRELPAGTLSGGQQQMLAIARALMANPRVLLLDEPSMGLAPLLVAE 172 Query: 187 VLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQ 231 + TI ++ G+ + + N ALA+ DR VL G + T Q Sbjct: 173 IFRTIQALKDGGMTIFLVEQNAYAALAIADRGYVLETGAVVLTDQ 217 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: 151 Number of extensions: 11 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: 234 Length adjustment: 24 Effective length of query: 237 Effective length of database: 210 Effective search space: 49770 Effective search space used: 49770 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