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) >lcl|FitnessBrowser__HerbieS:HSERO_RS05175 HSERO_RS05175 sugar ABC transporter ATP-binding protein 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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