Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate HSERO_RS05175 HSERO_RS05175 sugar ABC transporter ATP-binding protein
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__HerbieS:HSERO_RS05175 Length = 516 Score = 454 bits (1167), Expect = e-132 Identities = 238/508 (46%), Positives = 344/508 (67%), Gaps = 8/508 (1%) Query: 2 TDKNPIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINA 61 T P++ + GI F GVKAL V L L+PGEVH LMG+NGAGKST+IK LTGV++ + Sbjct: 7 TQARPMLELSGIHKAFAGVKALTDVGLRLFPGEVHTLMGQNGAGKSTLIKVLTGVHEPDG 66 Query: 62 GSIMVDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTH 121 G I +DG+ TL+AQ GI+TVYQEVNLC NLSV EN+ +G IDWK H Sbjct: 67 GKIELDGRAIAPASTLEAQALGISTVYQEVNLCPNLSVAENIFVGRYPTRFGRIDWKSVH 126 Query: 122 EAAKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVR 181 +++ L Q+ ++ ID PLSS +A+QQ+VAI+RA+ ++AKVLILDEPTSSLD EV+ Sbjct: 127 TQSRQLLQQLQID-IDVAAPLSSYPLAIQQMVAISRALSVSAKVLILDEPTSSLDEAEVQ 185 Query: 182 DLFAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMI 241 LF ++R++R+ G+AILFV+HFLDQ YEI+DR+T+LRNG E + + R +L+ M+ Sbjct: 186 QLFKVLRRLREQGMAILFVTHFLDQTYEISDRITVLRNGVREGEYLVSELSRLDLVNKMV 245 Query: 242 GKSAAELSQI--GAKKARREITPGEKP----IVDVKGLGKKGTINPVDVDIYKGEVVGFA 295 G +A + ++ GA+ E++ + +G G++G + P D+ + +GEV G Sbjct: 246 GVTAVDHRKVEAGAEALASELSTDAAAAGAVFLQAEGFGRRGVLAPQDLQLRRGEVFGLC 305 Query: 296 GLLGSGRTELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGD 355 GLLGSGRTE+ RLL+GAD+ D G + GK+V ++ P A+ I + +E+R+ EG I + Sbjct: 306 GLLGSGRTEMARLLFGADRADCGQLRIEGKEVRLNVPRDAIAAGIGFCSEDRKKEGAILE 365 Query: 356 LTVRQNILIALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVL 415 L+VR+NI++ALQA +G+F+ +P+K + I Y+K L ++ AD + P+ LSGGNQQK L Sbjct: 366 LSVRENIILALQARQGLFRVLPRKRQNQIAADYVKWLGIKTADLETPIGLLSGGNQQKAL 425 Query: 416 IGRWLATHPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDI 475 + RWLAT P +LILDEPTRGID+ AK EI V+ + +GM ++FISSE+ EV+R SD + Sbjct: 426 LARWLATDPGMLILDEPTRGIDVRAKQEIMDFVIAMCRKGMSILFISSEIPEVLRCSDRM 485 Query: 476 EVLKDRHKIAEIENDDTVSQATIVETIA 503 VL+DR E + + + ++++ IA Sbjct: 486 LVLRDRRACGEYRRGE-LDEQSVLQVIA 512 Score = 97.4 bits (241), Expect = 1e-24 Identities = 63/224 (28%), Positives = 117/224 (52%), Gaps = 5/224 (2%) Query: 27 DLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTLDAQNAGIAT 86 DL L GEV L G G+G++ M + L G + + G + ++GK + N DA AGI Sbjct: 293 DLQLRRGEVFGLCGLLGSGRTEMARLLFGADRADCGQLRIEGKEVRLNVPRDAIAAGIGF 352 Query: 87 VYQE---VNLCTNLSVGENVMLGHEKR-GPFGI-DWKKTHEAAKKYLAQMGLESIDPHTP 141 ++ LSV EN++L + R G F + K+ ++ A Y+ +G+++ D TP Sbjct: 353 CSEDRKKEGAILELSVRENIILALQARQGLFRVLPRKRQNQIAADYVKWLGIKTADLETP 412 Query: 142 LSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRDSGVAILFVS 201 + +S QQ +AR + + +LILDEPT +D +++ + + G++ILF+S Sbjct: 413 IGLLSGGNQQKALLARWLATDPGMLILDEPTRGIDVRAKQEIMDFVIAMCRKGMSILFIS 472 Query: 202 HFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSA 245 + ++ +DR+ +LR+ + E + ++ ++ G++A Sbjct: 473 SEIPEVLRCSDRMLVLRDRRACGEYRRGELDEQSVLQVIAGETA 516 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: 624 Number of extensions: 29 Number of successful extensions: 7 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: 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 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