Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate WP_085124759.1 B9O00_RS21320 sugar ABC transporter ATP-binding protein
Query= SwissProt::Q9F9B0 (260 letters) >NCBI__GCF_900177295.1:WP_085124759.1 Length = 518 Score = 161 bits (407), Expect = 3e-44 Identities = 89/245 (36%), Positives = 142/245 (57%), Gaps = 9/245 (3%) Query: 5 PILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIR 64 P+L RG+ +R+ V ALD+ DF L PGE+ + G+NGAGKS+MI I+GA+ P EGE R Sbjct: 22 PLLELRGVSRRFPGVLALDKVDFQLRPGEVHVLFGENGAGKSTMISMIAGALRPSEGEFR 81 Query: 65 LEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRA 124 G+P++ S AR GI V+Q +L P +++ +N+FLG E + G+ LDR Sbjct: 82 FRGEPVELNSVHHARGLGISAVFQEFSLVPQMTVEENLFLGAESTRLGL-------LDRR 134 Query: 125 AMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGV 184 A+ +A A L LG V L+ ++Q V +A+A V+I+DEPTA+L Sbjct: 135 ALHDRADAILKRLGFPL--RPRDRVLHLTRAEQQMVEIAKAFRSELSVLILDEPTASLTE 192 Query: 185 KESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAV 244 +E+ ++ +LI V+ +G+ ++ I+H + + + DRI + R GR + ++ + + V Sbjct: 193 RETAQLFKLIEQVKAQGVGVIYITHRLSEIRRIGDRITVLRDGRYVATVDAQTTPEGELV 252 Query: 245 AFMTG 249 MTG Sbjct: 253 RLMTG 257 Score = 74.3 bits (181), Expect = 5e-18 Identities = 59/207 (28%), Positives = 95/207 (45%), Gaps = 7/207 (3%) Query: 25 ADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQFRSPMEARQAGIE 84 A + GEI+ + G G+GKS + +A G EG +RL+G+ + + P + G Sbjct: 291 ASLSVCAGEIVGLAGLVGSGKSEVARACFGLEKIAEGHVRLKGEEVTGQGPKRMLKRGFF 350 Query: 85 TV---YQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQARAKLSELGLMT 141 V ++ L + +N+ L P G LDR + R +L L Sbjct: 351 YVPPDRRDEGLMMMRPVRENVSLPSLTLAPFGNGAL---LDRRGETDRVRRLAEQLNLQP 407 Query: 142 IQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVLELILDVRRRG 201 I +AVE SGG +Q V +A++ +V DEPT + V + E I D+ G Sbjct: 408 -PRIERAVEAFSGGNQQKVLLAKSRTRPVQVFAFDEPTVGVDVGTRVAIYEFIRDLCEAG 466 Query: 202 LPIVLISHNMPHVFEVADRIHIHRLGR 228 I+LIS ++P V +++R ++ GR Sbjct: 467 AGILLISSDLPEVLNLSNRAYVFYRGR 493 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: 291 Number of extensions: 16 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 260 Length of database: 518 Length adjustment: 30 Effective length of query: 230 Effective length of database: 488 Effective search space: 112240 Effective search space used: 112240 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: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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