Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate Pf6N2E2_523 Inositol transport system ATP-binding protein
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_523 Length = 517 Score = 331 bits (849), Expect = 3e-95 Identities = 180/479 (37%), Positives = 295/479 (61%), Gaps = 9/479 (1%) Query: 3 DKNPIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAG 62 D+ ++ + ++ FPGV AL V L + PG V ALMGENGAGKST++K + G+Y+ +AG Sbjct: 22 DEPYLLEVVNVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAG 81 Query: 63 SIMVDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEK-RGPFGIDWKKTH 121 + + GKP F+ L A AGIA ++QE+NL ++S+ EN+ +G E+ G +D + H Sbjct: 82 ELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGLHMVDHGEMH 141 Query: 122 EAAKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVR 181 + L ++ ++ +DP + ++SIA +Q+V IA+A+ ++ +LI+DEPTS++ EV Sbjct: 142 RCTARLLERLRIK-LDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITETEVA 200 Query: 182 DLFAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMI 241 LF+I+ ++ G I++++H +++++ I D + + R+G +I D LI MM+ Sbjct: 201 HLFSIIADLKSQGKGIIYITHKMNEVFAIADEVAVFRDGAYIGLQRADSMDGDSLISMMV 260 Query: 242 GKSAAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSG 301 G+ ++L + RE G+ ++ V+ L G V D++ GE++G AGL+GSG Sbjct: 261 GRELSQLFPV------REQPIGDL-VLSVRDLSLDGIFKGVSFDLHAGEILGIAGLMGSG 313 Query: 302 RTELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQN 361 RT + ++G G L+G+ V ISDP+ A++ A TE+R+ G+ L+V +N Sbjct: 314 RTNVAEAIFGVTPSTGGEILLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLEN 373 Query: 362 ILIALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLA 421 + +A+ I +K A+ + K+L V+ ++ + LSGGNQQK L+ RWL Sbjct: 374 MEMAVLPHYVGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLM 433 Query: 422 THPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKD 480 T+P +LILDEPTRGID+GAKAEI +++ LAS+GM V+ ISSEL EV+ +SD + V+ + Sbjct: 434 TNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHE 492 Score = 80.1 bits (196), Expect = 2e-19 Identities = 53/226 (23%), Positives = 112/226 (49%), Gaps = 7/226 (3%) Query: 25 GVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTLDAQNAGI 84 GV L+ GE+ + G G+G++ + +A+ GV G I++DG+P + + A G Sbjct: 293 GVSFDLHAGEILGIAGLMGSGRTNVAEAIFGVTPSTGGEILLDGQPVRISDPHMAIEKGF 352 Query: 85 ATVYQEVNLC---TNLSVGENV---MLGHEKRGPFGIDWKKTHEAAKKYLAQMGLESIDP 138 A + ++ L LSV EN+ +L H F I K + ++ +++ Sbjct: 353 ALLTEDRKLSGLFPCLSVLENMEMAVLPHYVGNGF-IQQKALRALCEDMCKKLRVKTPSL 411 Query: 139 HTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRDSGVAIL 198 + ++S QQ +AR ++ N ++LILDEPT +D +++ ++ + G+A++ Sbjct: 412 EQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVI 471 Query: 199 FVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKS 244 +S L ++ ++DR+ ++ G + + + ++ ++ + G S Sbjct: 472 MISSELPEVLGMSDRVMVMHEGDLMGTLNRGEATQERVMQLASGLS 517 Lambda K H 0.316 0.135 0.376 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: 636 Number of extensions: 29 Number of successful extensions: 8 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: 513 Length of database: 517 Length adjustment: 35 Effective length of query: 478 Effective length of database: 482 Effective search space: 230396 Effective search space used: 230396 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 52 (24.6 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