Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate Echvi_2204 Echvi_2204 ABC-type antimicrobial peptide transport system, ATPase component
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__Cola:Echvi_2204 Length = 240 Score = 82.0 bits (201), Expect = 1e-20 Identities = 61/195 (31%), Positives = 95/195 (48%), Gaps = 15/195 (7%) Query: 18 RVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQFRSP-- 75 +V AL D+ GE +A +G +G+GKS+++ I TP G L K + + Sbjct: 20 KVQALKSVTIDIIKGEYVAFMGPSGSGKSTLMNIIGCLDTPTAGNYILNNKDVSHMTENE 79 Query: 76 -MEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQARAKL 134 E R I V+Q L P + +N+ L P I + +S DR E +A L Sbjct: 80 LAEIRNKEIGFVFQTFNLLPRATCLENVAL------PLIYAGYSKS-DR---EDKAFLAL 129 Query: 135 SELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVLELI 194 +GL I+ LSGGQRQ VA+ARA +++ DEPT L K S ++ L Sbjct: 130 KSVGLE--DRIHHKPNELSGGQRQRVAIARALVNDPSIILADEPTGNLDTKTSYDIMNLF 187 Query: 195 LDVRRRGLPIVLISH 209 ++ ++G I++++H Sbjct: 188 DELHQKGNTIIMVTH 202 Lambda K H 0.321 0.136 0.383 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: 111 Number of extensions: 4 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: 260 Length of database: 240 Length adjustment: 24 Effective length of query: 236 Effective length of database: 216 Effective search space: 50976 Effective search space used: 50976 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 (21.8 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