Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate AZOBR_RS31245 AZOBR_RS31245 ABC transporter ATP-binding protein
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__azobra:AZOBR_RS31245 Length = 518 Score = 140 bits (354), Expect = 4e-38 Identities = 87/239 (36%), Positives = 138/239 (57%), Gaps = 11/239 (4%) Query: 5 PILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPD--EGE 62 PIL +G+ K + V ALD + + GEI A+IG+NGAGKS+++K +SG +GE Sbjct: 4 PILEMKGITKTFPGVKALDDVNLSVREGEIHALIGENGAGKSTLMKVLSGVYPQGSFDGE 63 Query: 63 IRLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLD 122 IR G+P FR ++ + GI ++Q LAL P LSI +N+FLG E G+ +D Sbjct: 64 IRFRGQPQAFRGIADSERLGIIIIHQELALVPLLSITENLFLGNEQASRGV-------ID 116 Query: 123 RAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAAL 182 A +AR L +GL + + G++Q V +A+A + K++I+DEPTA+L Sbjct: 117 WDAATLRARELLRLVGLHDPPET--LITDIGVGKQQLVEIAKALSKEVKLLILDEPTASL 174 Query: 183 GVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMS 241 +S +LEL+L + RG+ +LISH + + +VADR+ I R G + ++ ++ +S Sbjct: 175 NESDSDALLELLLQFKARGIASILISHKLNEIAKVADRVTILRDGTTVETLDCREAVVS 233 Score = 65.9 bits (159), Expect = 2e-15 Identities = 52/207 (25%), Positives = 94/207 (45%), Gaps = 23/207 (11%) Query: 32 GEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQFRSPMEARQAGIETVYQNLA 91 GE++ + G GAG++ ++ G R G+ I+ ++ ++ R+ + T+ + +A Sbjct: 290 GEVVGIAGLMGAGRTEFAMSLFG---------RSYGRNIRGQAFLDGREIDVSTISRAMA 340 Query: 92 LSPALSIADNMFLG----REIRKP-------GIMGKWFRSLDRAAMEKQARAKLSELGLM 140 A + D LG +IR G+ +W +R E Q + + Sbjct: 341 NGLAYATEDRKHLGLVLDNDIRHNVTLANLRGVAKRWVIDHER---EVQVAEEFRRRLRI 397 Query: 141 TIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVLELILDVRRR 200 ++ Q LSGG +Q V +++ +V+I+DEPT + V + +I + Sbjct: 398 RCADVFQETVNLSGGNQQKVVLSKWLFADPQVLILDEPTRGIDVGAKYEIYTIINQLVAE 457 Query: 201 GLPIVLISHNMPHVFEVADRIHIHRLG 227 G +VLIS MP + VADRI++ G Sbjct: 458 GRGVVLISSEMPELLGVADRIYVMNAG 484 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: 15 Number of successful extensions: 5 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 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:
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