Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate WP_054655718.1 CES79_RS03450 amino acid ABC transporter ATP-binding protein
Query= SwissProt::Q9F9B0 (260 letters) >NCBI__GCF_002217945.1:WP_054655718.1 Length = 247 Score = 99.0 bits (245), Expect = 8e-26 Identities = 64/212 (30%), Positives = 116/212 (54%), Gaps = 14/212 (6%) Query: 12 LVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQ 71 LVK +G L + +++ E++ VIG +G+GKS+ ++ ++ P G I ++ I Sbjct: 12 LVKNFGDNKVLKGINMEVHDNEVVVVIGPSGSGKSTFLRNLNRLEAPTSGSIVIDDMDIA 71 Query: 72 F-RSPMEARQAGIETVYQNLALSPALSIADNMFLGR-EIRKPGIMGKWFRSLDRAAMEKQ 129 ++ + + I V+Q+ L LS+++N+ L E++K + KQ Sbjct: 72 DPKTDINKVRENIGMVFQHFNLFSNLSVSENVMLAPVELKKK----------TKEEATKQ 121 Query: 130 ARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRR 189 A L+ +GL + N V++LSGGQ+Q VA+ARA A V++ DEPT+AL + Sbjct: 122 AHDLLNMVGLES--KFNATVQSLSGGQQQRVAIARALAMNPNVMLFDEPTSALDPEMVGD 179 Query: 190 VLELILDVRRRGLPIVLISHNMPHVFEVADRI 221 VL ++ + ++G+ +++++H M EVADR+ Sbjct: 180 VLAVMKQLAKQGMTMIVVTHEMGFAKEVADRV 211 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: 116 Number of extensions: 9 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: 247 Length adjustment: 24 Effective length of query: 236 Effective length of database: 223 Effective search space: 52628 Effective search space used: 52628 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 24 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