Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate WP_110804307.1 C8J30_RS03205 sugar ABC transporter ATP-binding protein
Query= SwissProt::Q9F9B0 (260 letters) >NCBI__GCF_003217355.1:WP_110804307.1 Length = 257 Score = 418 bits (1075), Expect = e-122 Identities = 209/250 (83%), Positives = 232/250 (92%) Query: 4 EPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEI 63 +PILTARGL KRYG+VTALD DF+LYPGEILAVIGDNGAGKS++IKA+SGAV PDEGEI Sbjct: 2 DPILTARGLTKRYGKVTALDHCDFELYPGEILAVIGDNGAGKSTLIKALSGAVIPDEGEI 61 Query: 64 RLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDR 123 RLEG+PI F SP++AR GIETVYQ LA+SPALSIADNMF+GRE+R+PG+MGK FR LDR Sbjct: 62 RLEGQPINFASPLDARAKGIETVYQTLAMSPALSIADNMFMGRELRRPGMMGKLFRMLDR 121 Query: 124 AAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALG 183 ME+ AR KLSELGLMTIQ+INQAVE+LSGGQRQGVAVARAAAFGSKV+I+DEPTAALG Sbjct: 122 PQMERIAREKLSELGLMTIQDINQAVESLSGGQRQGVAVARAAAFGSKVIILDEPTAALG 181 Query: 184 VKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDA 243 VKESRRVLELILDV+ RG+PI+LISHNMPHVFEVADRIHIHRLGRRLCVI+PK YTMSDA Sbjct: 182 VKESRRVLELILDVKARGIPIILISHNMPHVFEVADRIHIHRLGRRLCVIDPKQYTMSDA 241 Query: 244 VAFMTGAKEP 253 VAFMTGAK P Sbjct: 242 VAFMTGAKLP 251 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: 271 Number of extensions: 3 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: 257 Length adjustment: 24 Effective length of query: 236 Effective length of database: 233 Effective search space: 54988 Effective search space used: 54988 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 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