Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate 6939481 Sama_3573 ABC transporter, ATP-binding protein (RefSeq)
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__SB2B:6939481 Length = 284 Score = 102 bits (254), Expect = 2e-26 Identities = 93/313 (29%), Positives = 146/313 (46%), Gaps = 44/313 (14%) Query: 1 MTDKNPIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKIN 60 + + P++ ++G+ F AL+GVDLTL G V L+GENGAGKST+++ + G+ + Sbjct: 5 LMNDGPLLEIRGLKKRFGDKTALNGVDLTLESGMVVGLLGENGAGKSTLMRCILGLIDAD 64 Query: 61 AGSIMVDGKPQQFNGTLDAQ-NAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKK 119 G I G Q TL A A I V Q+ SV + L F DW Sbjct: 65 EGEICTLG---QAPSTLSASTKARIGYVPQQHYGYEGFSVERALSL----HASFYPDWDP 117 Query: 120 THEAAKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANE 179 E + ++ + GL DP ++ +S+ +Q +AI AM +L+LDEP +SLD + Sbjct: 118 KLE--QSWMKRFGL---DPKAQVNRLSVGQRQSLAIIMAMAYRPSLLVLDEPVASLDPSA 172 Query: 180 VR----DLFAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDE 235 R DLF + +SG A++F SH + + + +L++GQ + Sbjct: 173 RRRFMGDLFEL---ALESGSAVIFSSHITSDLERVASHVALLKDGQLL------------ 217 Query: 236 LIGMMIGKSAAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFA 295 ++G EL + + G + + LG++G N V VD ++GE F Sbjct: 218 IMG--------ELDAVRESVRLLTLAEGSQLPDAYRVLGRQG--NRVLVDGFRGE--SFP 265 Query: 296 GLLGSGRTELGRL 308 GLLG L +L Sbjct: 266 GLLGVDTVNLEQL 278 Score = 68.6 bits (166), Expect = 3e-16 Identities = 65/222 (29%), Positives = 101/222 (45%), Gaps = 25/222 (11%) Query: 266 PIVDVKGL----GKKGTINPVDVDIYKGEVVGFAGLLGSGRTELGRLLYGADKPDSGTYT 321 P+++++GL G K +N VD+ + G VVG G G+G++ L R + G D G Sbjct: 10 PLLEIRGLKKRFGDKTALNGVDLTLESGMVVGLLGENGAGKSTLMRCILGLIDADEGEIC 69 Query: 322 LNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQATRGMFKPI--PKK 379 G+ + T K +I Y + G G R ++L A+ F P PK Sbjct: 70 TLGQAPSTLSAST--KARIGYVPQQHY--GYEGFSVERA---LSLHAS---FYPDWDPKL 119 Query: 380 EADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLILDEPTRGIDIG 439 E +MK + DP V LS G +Q + I +A P LL+LDEP +D Sbjct: 120 E-----QSWMKRFGL---DPKAQVNRLSVGQRQSLAIIMAMAYRPSLLVLDEPVASLDPS 171 Query: 440 AKAEIQQVVLDLA-SQGMGVVFISSELEEVVRLSDDIEVLKD 480 A+ + +LA G V+F S ++ R++ + +LKD Sbjct: 172 ARRRFMGDLFELALESGSAVIFSSHITSDLERVASHVALLKD 213 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: 337 Number of extensions: 17 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: 513 Length of database: 284 Length adjustment: 30 Effective length of query: 483 Effective length of database: 254 Effective search space: 122682 Effective search space used: 122682 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: 50 (23.9 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