Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate WP_012042345.1 BBTA_RS09915 sugar ABC transporter ATP-binding protein
Query= SwissProt::Q8G847 (513 letters) >NCBI__GCF_000015165.1:WP_012042345.1 Length = 516 Score = 454 bits (1167), Expect = e-132 Identities = 241/497 (48%), Positives = 339/497 (68%), Gaps = 5/497 (1%) Query: 7 IVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMV 66 ++ ++G+T F +KAL VD TL GE+HAL+GENGAGKST+IK +TGV+ +AG++ + Sbjct: 14 LLEIRGLTKSFGALKALQDVDFTLGEGEIHALLGENGAGKSTLIKVVTGVFARDAGTVRL 73 Query: 67 DGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAAKK 126 G DA AGIATVYQEVNL NLSV +N+ LG + + + A Sbjct: 74 AGDEIAPRSAKDAVEAGIATVYQEVNLLPNLSVAQNLYLGRQPTRFGVVRQAEMRRRAHA 133 Query: 127 YLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAI 186 L GL+ ID PL+S S+A+Q + AIARA+ ++A+VLILDEPT+SLD +EV LF + Sbjct: 134 LLLDYGLD-IDVGAPLASYSVAVQHITAIARAVDLSARVLILDEPTASLDRHEVEILFRV 192 Query: 187 MRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSAA 246 MRK+ G+ I+FVSHFLDQ+YEI DR+T+LRNG+ I D PR +LI MM+G+ A Sbjct: 193 MRKLAADGIGIVFVSHFLDQVYEICDRVTVLRNGRLIGTRDITDLPRLDLIRMMLGRELA 252 Query: 247 ELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTELG 306 E + ++A + + V KG GK+G + P D+++ +GEVVG AGLLGSGRTE Sbjct: 253 ETTH---ERAASQPDTAREVCVSFKGFGKQGYVAPFDLELRRGEVVGLAGLLGSGRTETA 309 Query: 307 RLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIAL 366 RL++GA++ DSG ++ GK V ++ P A Y E R+ EGI+ DLTVR+NI++AL Sbjct: 310 RLVFGAERADSGEASVAGKAVRLNSPRDAAGLGFGYCPEERKTEGIVADLTVRENIVLAL 369 Query: 367 QATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPEL 426 QA RG+ +P+ ++E D I +Y++ L++RP DP+RP+ LSGGNQQK L+ RWLAT P+L Sbjct: 370 QARRGLHRPLSRREQDEIAMRYIRMLDIRPPDPERPIGLLSGGNQQKALLARWLATSPKL 429 Query: 427 LILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAE 486 L+LDEPTRGID+GA AEI ++V DL QG+ ++ ISSEL+E+V S+ + VL+DR + E Sbjct: 430 LVLDEPTRGIDVGAHAEIIRLVRDLCEQGLALLVISSELDEIVTYSNRVVVLRDRAHVEE 489 Query: 487 IENDDTVSQATIVETIA 503 ++ D V ++I+ IA Sbjct: 490 LKG-DAVEVSSILAAIA 505 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: 679 Number of extensions: 26 Number of successful extensions: 7 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: 513 Length of database: 516 Length adjustment: 35 Effective length of query: 478 Effective length of database: 481 Effective search space: 229918 Effective search space used: 229918 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 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