Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate N515DRAFT_2413 N515DRAFT_2413 simple sugar transport system ATP-binding protein
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__Dyella79:N515DRAFT_2413 Length = 505 Score = 427 bits (1098), Expect = e-124 Identities = 228/501 (45%), Positives = 331/501 (66%), Gaps = 10/501 (1%) Query: 6 PIVVM-KGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSI 64 P+V+ +G+ F ALDGVDL L GEVHALMG+NGAGKST+IK LTGV + + GS+ Sbjct: 10 PVVLQARGLGKRFGATLALDGVDLALRAGEVHALMGQNGAGKSTLIKLLTGVERPDRGSV 69 Query: 65 MVDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGH--EKRGPFGIDWKKTHE 122 +DG+ + ++AQ GI TVYQEVNLC NLSV EN+ G +R IDW++ + Sbjct: 70 ELDGRVIAPSTPMEAQRDGIGTVYQEVNLCPNLSVAENLYAGRYPRRRRLRMIDWRQVRD 129 Query: 123 AAKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRD 182 A+ L Q+ LE +D PL S +A++Q+VAIARA+ ++A+VLILDEPTSSLD EVR+ Sbjct: 130 GARSLLRQLHLE-LDVDAPLGSYPVAIRQMVAIARALGVSARVLILDEPTSSLDEGEVRE 188 Query: 183 LFAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIG 242 LF ++ ++R+ G+AILFV+HFLDQ+Y ++DR+T+LR+G + E D P L+ M+G Sbjct: 189 LFRVIAQLRERGMAILFVTHFLDQVYAVSDRITVLRDGCRVGEYAVADLPPAALVNAMVG 248 Query: 243 KSAAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGR 302 + +L + A R P P +D +GLG +G ++PVD+ + +GE++G GLLGSGR Sbjct: 249 R---DLPTVAGADAERAPPPDAPPAIDAQGLGCRGKLHPVDLQVRRGEMLGLGGLLGSGR 305 Query: 303 TELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNI 362 TEL RLL+G D+ + G + G++V + P A+ +A E R+ +GI+ +L+VR+NI Sbjct: 306 TELARLLFGLDRAERGELRIGGERVELKHPADAVVRGLALCPEERKTDGIVAELSVRENI 365 Query: 363 LIALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLAT 422 ++ALQA +G ++ + + D + + ++ L ++ AD + PV LSGGNQQKV++ RWL T Sbjct: 366 VLALQARQG-WRGMSRARQDELARQLVQALGIKAADIETPVGLLSGGNQQKVMLARWLVT 424 Query: 423 HPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRH 482 P LLILDEPTRGID+ AK E+ V A GM V+FIS+E E+ R D I V+++R Sbjct: 425 EPRLLILDEPTRGIDVAAKQELMAEVTRRAHAGMAVLFISAETGELTRWCDRIAVMRERR 484 Query: 483 KIAEIENDDTVSQATIVETIA 503 K E+ T +A ++ IA Sbjct: 485 KAGELPGGST--EARVLAMIA 503 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: 660 Number of extensions: 36 Number of successful extensions: 8 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: 505 Length adjustment: 34 Effective length of query: 479 Effective length of database: 471 Effective search space: 225609 Effective search space used: 225609 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