Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate H281DRAFT_03224 H281DRAFT_03224 mannose ABC transporter ATP-binding protein /fructose ABC transporter ATP-binding protein /ribose ABC transporter ATP-binding protein
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__Burk376:H281DRAFT_03224 Length = 265 Score = 336 bits (862), Expect = 3e-97 Identities = 173/255 (67%), Positives = 208/255 (81%), Gaps = 1/255 (0%) Query: 5 PILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIR 64 P+L ARGLVKRYG VTALD DF++ PGEILAVIGDNGAGKSS+IKA+SGA PDEGEI Sbjct: 12 PVLQARGLVKRYGNVTALDGCDFEVLPGEILAVIGDNGAGKSSLIKALSGATVPDEGEIL 71 Query: 65 LEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRA 124 L+GKP++FRSP++AR GIETVYQ LA++PA+SIA+N+FL RE+ KPG G F+ +D+ Sbjct: 72 LDGKPVKFRSPLDARAQGIETVYQELAVAPAMSIAENLFLARELVKPGWRGSIFKMIDKR 131 Query: 125 AMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGV 184 M ++A A + +L + I+++ QAVETLSGGQRQGVAVAR+AAF VVI+DEPTAALGV Sbjct: 132 RMLEEATAHMKDLQI-GIRSMRQAVETLSGGQRQGVAVARSAAFARHVVILDEPTAALGV 190 Query: 185 KESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAV 244 KE VLELI VR RGLP++LISHNMPHVFEVADRIHI RLGRR ++N KD MS+AV Sbjct: 191 KEGNMVLELIRRVRDRGLPVILISHNMPHVFEVADRIHIQRLGRRAALVNTKDVHMSEAV 250 Query: 245 AFMTGAKEPPREAIA 259 A MTGAKE +AIA Sbjct: 251 AIMTGAKEADVKAIA 265 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: 230 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: 265 Length adjustment: 25 Effective length of query: 235 Effective length of database: 240 Effective search space: 56400 Effective search space used: 56400 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: 47 (22.7 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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