Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate 3609459 Dshi_2843 ABC transporter related (RefSeq)
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__Dino:3609459 Length = 548 Score = 262 bits (669), Expect = 3e-74 Identities = 161/493 (32%), Positives = 274/493 (55%), Gaps = 22/493 (4%) Query: 6 PIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIM 65 P + ++GI+ F V+A + + + PG +H ++GENGAGKST++ L G YK +AG I Sbjct: 24 PAIELRGISKAFGPVQANKDISIRVMPGTIHGIIGENGAGKSTLMSILYGFYKADAGEIF 83 Query: 66 VDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAAK 125 + G+ + + A AGI V+Q L N +V ENV+LG E+ G + + A+ Sbjct: 84 IKGQKTEIPDSQAAIRAGIGMVFQHFKLVENFTVLENVVLGAEE----GALLRPSLAKAR 139 Query: 126 KYLAQMGLE---SIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRD 182 K L ++ E ++ P + +S+ QQ V I +A+ A +LILDEPT L E Sbjct: 140 KLLRELSEEYELNVAPDALIEDLSVGHQQRVEILKALYRKADILILDEPTGVLTPAEADH 199 Query: 183 LFAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIG 242 LF I+ ++ G I+ ++H L +I E TD ++++R G+ V T DT ++L +M+G Sbjct: 200 LFRILEGLKAEGKTIILITHKLREIMETTDTVSVMRRGEMTATVKTADTSPEQLAELMVG 259 Query: 243 KSAA-ELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSG 301 + + + A+ +T + +VD +G+ + + + + + GEV+G AG+ G+G Sbjct: 260 RKVLLRVDKTPAQPGAPILTVDDLRVVDDQGVER---VKGISLQVRAGEVLGIAGVAGNG 316 Query: 302 RTELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNK----IAYSTENRRDEGIIGDLT 357 ++EL +L G +P +G T++G++++++ ++ K + IA+ E+R+ EG+I D Sbjct: 317 QSELLEVL-GGMRPATGRVTVSGQQIDLTGKHSNGKTRRAQGIAHVPEDRQAEGLIMDYH 375 Query: 358 VRQNILIALQA----TRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQK 413 +N+ RG+ ADA + + +VRPAD KN SGGNQQK Sbjct: 376 AWENVAFGYHDDPAYNRGLLMDNRAVRADA--EGKIARFDVRPADCWLAAKNFSGGNQQK 433 Query: 414 VLIGRWLATHPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSD 473 +++ R + +PELL++ +PTRG+DIGA I Q ++ L G ++ +S ELEE++ LSD Sbjct: 434 IVLAREIERNPELLLVGQPTRGVDIGAIEFIHQQIIALRDAGKAILLVSVELEEILSLSD 493 Query: 474 DIEVLKDRHKIAE 486 + V+ D + E Sbjct: 494 RVAVMFDGRIMGE 506 Score = 84.7 bits (208), Expect = 8e-21 Identities = 59/235 (25%), Positives = 122/235 (51%), Gaps = 14/235 (5%) Query: 264 EKPIVDVKGLGKK-GTINP---VDVDIYKGEVVGFAGLLGSGRTELGRLLYGADKPDSGT 319 + P ++++G+ K G + + + + G + G G G+G++ L +LYG K D+G Sbjct: 22 QAPAIELRGISKAFGPVQANKDISIRVMPGTIHGIIGENGAGKSTLMSILYGFYKADAGE 81 Query: 320 YTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQATRGMFKPIPK- 378 + G+K I D A++ I ++ + ++ + TV +N+++ + + + K Sbjct: 82 IFIKGQKTEIPDSQAAIRAGIGMVFQHFK---LVENFTVLENVVLGAEEGALLRPSLAKA 138 Query: 379 -KEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLILDEPTRGID 437 K + ++Y ELNV P D +++LS G+QQ+V I + L ++LILDEPT + Sbjct: 139 RKLLRELSEEY--ELNVAP---DALIEDLSVGHQQRVEILKALYRKADILILDEPTGVLT 193 Query: 438 IGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAEIENDDT 492 + +++ L ++G ++ I+ +L E++ +D + V++ A ++ DT Sbjct: 194 PAEADHLFRILEGLKAEGKTIILITHKLREIMETTDTVSVMRRGEMTATVKTADT 248 Score = 75.1 bits (183), Expect = 6e-18 Identities = 65/251 (25%), Positives = 119/251 (47%), Gaps = 17/251 (6%) Query: 6 PIVVMKGI-TIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSI 64 PI+ + + ++ GV+ + G+ L + GEV + G G G+S +++ L G+ + G + Sbjct: 276 PILTVDDLRVVDDQGVERVKGISLQVRAGEVLGIAGVAGNGQSELLEVLGGM-RPATGRV 334 Query: 65 MVDGKPQQFNG------TLDAQNAGIATV---YQEVNLCTNLSVGENVMLGHEKRGPFG- 114 V G+ G T AQ GIA V Q L + ENV G+ + Sbjct: 335 TVSGQQIDLTGKHSNGKTRRAQ--GIAHVPEDRQAEGLIMDYHAWENVAFGYHDDPAYNR 392 Query: 115 ---IDWKKTHEAAKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEP 171 +D + A+ +A+ + D + S QQ + +AR + N ++L++ +P Sbjct: 393 GLLMDNRAVRADAEGKIARFDVRPADCWLAAKNFSGGNQQKIVLAREIERNPELLLVGQP 452 Query: 172 TSSLDANEVRDLFAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDT 231 T +D + + + +RD+G AIL VS L++I ++DR+ ++ +G+ + E +T Sbjct: 453 TRGVDIGAIEFIHQQIIALRDAGKAILLVSVELEEILSLSDRVAVMFDGRIMGERPAAET 512 Query: 232 PRDELIGMMIG 242 EL +M G Sbjct: 513 NEKELGLLMAG 523 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: 708 Number of extensions: 41 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 513 Length of database: 548 Length adjustment: 35 Effective length of query: 478 Effective length of database: 513 Effective search space: 245214 Effective search space used: 245214 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