Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate Ga0059261_3874 Ga0059261_3874 ABC-type antimicrobial peptide transport system, ATPase component
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__Korea:Ga0059261_3874 Length = 243 Score = 85.1 bits (209), Expect = 1e-21 Identities = 68/224 (30%), Positives = 107/224 (47%), Gaps = 23/224 (10%) Query: 7 LTARGLVKRYG----RVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGE 62 + AR + K Y R L + PGE+ V+G +G GKS+++ +SG PD+GE Sbjct: 9 IDAREVSKSYTVGQVRTQILFGVSVSVMPGELTLVVGPSGCGKSTLLAILSGLTLPDQGE 68 Query: 63 IRLEGKPIQFRSPMEARQ----AGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWF 118 + G PI R AR A V+Q L AL+ + + + K Sbjct: 69 VDALGNPI-CRMKAGARDAFRLANTGFVFQGFNLFNALTAEEQVAYVLQCMK-------- 119 Query: 119 RSLDRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEP 178 + A ++ARA L +GL + LSGG++Q VA+ARA A +++ DEP Sbjct: 120 --VKPAEARQRARAALEAVGLGPRMRLRPF--ELSGGEKQRVAIARALAKQPRILFADEP 175 Query: 179 TAALGVKESRRVLELILDV-RRRGLPIVLISHNMPHVFEVADRI 221 T+AL V+ L+ D+ +G ++ ++H+ P + ADRI Sbjct: 176 TSALDSHNGHAVIALLRDIAHNQGAAVLCVTHD-PRLLSFADRI 218 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: 121 Number of extensions: 7 Number of successful extensions: 1 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: 243 Length adjustment: 24 Effective length of query: 236 Effective length of database: 219 Effective search space: 51684 Effective search space used: 51684 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