Align Inositol transport system ATP-binding protein (characterized)
to candidate Ga0059261_3874 Ga0059261_3874 ABC-type antimicrobial peptide transport system, ATPase component
Query= reanno::Phaeo:GFF717 (261 letters) >FitnessBrowser__Korea:Ga0059261_3874 Length = 243 Score = 79.0 bits (193), Expect = 9e-20 Identities = 68/211 (32%), Positives = 99/211 (46%), Gaps = 17/211 (8%) Query: 23 LAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILFEGQPL--HFADPRDAI 80 L GVSV V PGE ++G +G GKST + +SG+ P +G++ G P+ A RDA Sbjct: 28 LFGVSVSVMPGELTLVVGPSGCGKSTLLAILSGLTLPDQGEVDALGNPICRMKAGARDAF 87 Query: 81 A-AGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANRITMEEMRKMGINL 139 A V Q + N E + + A + + +G+ Sbjct: 88 RLANTGFVFQGFNLF-------NALTAEEQVAYVLQCMKVKPAEARQRARAALEAVGL-- 138 Query: 140 RGPDQAVGT--LSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANVLATI-DKVRK 196 GP + LSGGE+Q VAIARA+ ++L DEPTSAL V+A + D Sbjct: 139 -GPRMRLRPFELSGGEKQRVAIARALAKQPRILFADEPTSALDSHNGHAVIALLRDIAHN 197 Query: 197 QGVAVVFITHNVRHALAVGDRFTVLNRGKTL 227 QG AV+ +TH+ R L+ DR + G+ + Sbjct: 198 QGAAVLCVTHDPR-LLSFADRIIHMEDGRII 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: 154 Number of extensions: 10 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 261 Length of database: 243 Length adjustment: 24 Effective length of query: 237 Effective length of database: 219 Effective search space: 51903 Effective search space used: 51903 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