Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate N515DRAFT_2413 N515DRAFT_2413 simple sugar transport system ATP-binding protein
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__Dyella79:N515DRAFT_2413 Length = 505 Score = 156 bits (394), Expect = 9e-43 Identities = 94/252 (37%), Positives = 146/252 (57%), Gaps = 7/252 (2%) Query: 2 AQEPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEG 61 A+ +L ARGL KR+G ALD D L GE+ A++G NGAGKS++IK ++G PD G Sbjct: 8 ARPVVLQARGLGKRFGATLALDGVDLALRAGEVHALMGQNGAGKSTLIKLLTGVERPDRG 67 Query: 62 EIRLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSL 121 + L+G+ I +PMEA++ GI TVYQ + L P LS+A+N++ GR R+ + R + Sbjct: 68 SVELDGRVIAPSTPMEAQRDGIGTVYQEVNLCPNLSVAENLYAGRYPRR-----RRLRMI 122 Query: 122 DRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAA 181 D + AR+ L +L L +++ + + RQ VA+ARA ++V+I+DEPT++ Sbjct: 123 DWRQVRDGARSLLRQLHLEL--DVDAPLGSYPVAIRQMVAIARALGVSARVLILDEPTSS 180 Query: 182 LGVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMS 241 L E R + +I +R RG+ I+ ++H + V+ V+DRI + R G R+ D + Sbjct: 181 LDEGEVRELFRVIAQLRERGMAILFVTHFLDQVYAVSDRITVLRDGCRVGEYAVADLPPA 240 Query: 242 DAVAFMTGAKEP 253 V M G P Sbjct: 241 ALVNAMVGRDLP 252 Score = 76.6 bits (187), Expect = 9e-19 Identities = 66/238 (27%), Positives = 114/238 (47%), Gaps = 34/238 (14%) Query: 5 PILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIR 64 P + A+GL G L D + GE+L + G G+G++ + + + G + GE+R Sbjct: 269 PAIDAQGL----GCRGKLHPVDLQVRRGEMLGLGGLLGSGRTELARLLFGLDRAERGELR 324 Query: 65 LEGKPIQFRSPMEARQAGIETVYQNLALSPA----------LSIADNMFLGREIRKPGIM 114 + G+ ++ + P +A V + LAL P LS+ +N+ L + R+ Sbjct: 325 IGGERVELKHPADA-------VVRGLALCPEERKTDGIVAELSVRENIVLALQARQG--- 374 Query: 115 GKWFRSLDRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVI 174 +R + RA ++ AR + LG+ +I V LSGG +Q V +AR +++I Sbjct: 375 ---WRGMSRARQDELARQLVQALGIKAA-DIETPVGLLSGGNQQKVMLARWLVTEPRLLI 430 Query: 175 MDEPTAALGVKESRRVLELILDVRRR---GLPIVLISHNMPHVFEVADRIHIHRLGRR 229 +DEPT + V + EL+ +V RR G+ ++ IS + DRI + R R+ Sbjct: 431 LDEPTRGIDVAAKQ---ELMAEVTRRAHAGMAVLFISAETGELTRWCDRIAVMRERRK 485 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: 320 Number of extensions: 20 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: 505 Length adjustment: 29 Effective length of query: 231 Effective length of database: 476 Effective search space: 109956 Effective search space used: 109956 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