Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate RR42_RS32900 RR42_RS32900 sugar ABC transporter ATPase
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__Cup4G11:RR42_RS32900 Length = 502 Score = 343 bits (880), Expect = 8e-99 Identities = 187/502 (37%), Positives = 298/502 (59%), Gaps = 20/502 (3%) Query: 1 MTDKNPIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKIN 60 +T+ P+ M+GI FPGVKALD V +YPGEVH L+GENGAGKS+++K L GVY + Sbjct: 4 ITEITPLFEMRGICKNFPGVKALDDVSFAIYPGEVHMLLGENGAGKSSLMKVLCGVYVAD 63 Query: 61 AGSIMVDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRG--PFGIDWK 118 AG DG P D GIA ++QE +L L + +N+ LG E RG P +D Sbjct: 64 AGEFYHDGSPVAITSPADTMGLGIAVIFQEFSLVPYLDIAQNIFLGREPRGRIPGSVDAA 123 Query: 119 KTHEAAKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDAN 178 + H A++ L +G+E + TP+ + +A QQ+V IA+A+ NA++L+LDEPT++L Sbjct: 124 RMHAEARRILDILGME-VSTRTPVHRLGVAQQQMVEIAKALSQNARILVLDEPTAALSDR 182 Query: 179 EVRDLFAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIG 238 E LFA++ +++ GV+++++SH + +++ + DR+TILR+G+ + + D DEL+ Sbjct: 183 ETEKLFAVIARLKADGVSMIYISHRMAEVFALGDRITILRDGRKVGACLPGDATPDELVA 242 Query: 239 MMIGKSAAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLL 298 M+G+ ++S R PGE + DV+ + I +++ + GE+VG AGL+ Sbjct: 243 RMVGRK-VDMSY----SRERSAQPGEVAL-DVRNVSADSGIADINLQVRAGEIVGLAGLV 296 Query: 299 GSGRTELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTV 358 GSGR+E+ R ++GAD G + GK++ P A + A E+R+ EG+ TV Sbjct: 297 GSGRSEVARAVFGADPIRQGEIYIFGKRLT-GGPDRARELGAALIPESRKSEGLALIRTV 355 Query: 359 RQNILIALQATRGMFKPIPKK-----EADAIVDKYMKELNVRPADPDRPVKNLSGGNQQK 413 R N+L+A G+ + P + +A+A+ ++ + L + D ++ + LSGGNQQK Sbjct: 356 RDNLLLA-----GLRRAFPARWYRADKAEALAEREIARLRIATPDGNQLAQFLSGGNQQK 410 Query: 414 VLIGRWLATHPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSD 473 ++IG+WL +L I DEPTRGID+GAKAEI ++ L QG GV+ ISSEL E++ + D Sbjct: 411 IVIGKWLVAEAKLFIFDEPTRGIDVGAKAEIFALIDSLVKQGAGVLLISSELPEIINVCD 470 Query: 474 DIEVLKDRHKIAEIENDDTVSQ 495 V++ E+ + + + Sbjct: 471 RTYVMRGGRIAGEVAHAEMTEE 492 Score = 80.1 bits (196), Expect = 2e-19 Identities = 56/218 (25%), Positives = 107/218 (49%), Gaps = 8/218 (3%) Query: 26 VDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTLDAQNAGIA 85 ++L + GE+ L G G+G+S + +A+ G I G I + GK + G A+ G A Sbjct: 280 INLQVRAGEIVGLAGLVGSGRSEVARAVFGADPIRQGEIYIFGK-RLTGGPDRARELGAA 338 Query: 86 TVYQE---VNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEA---AKKYLAQMGLESIDPH 139 + + L +V +N++L +R F W + +A A++ +A++ + + D + Sbjct: 339 LIPESRKSEGLALIRTVRDNLLLAGLRRA-FPARWYRADKAEALAEREIARLRIATPDGN 397 Query: 140 TPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRDSGVAILF 199 +S QQ + I + +V AK+ I DEPT +D ++FA++ + G +L Sbjct: 398 QLAQFLSGGNQQKIVIGKWLVAEAKLFIFDEPTRGIDVGAKAEIFALIDSLVKQGAGVLL 457 Query: 200 VSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELI 237 +S L +I + DR ++R G+ EV + + ++ Sbjct: 458 ISSELPEIINVCDRTYVMRGGRIAGEVAHAEMTEERIL 495 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: 611 Number of extensions: 32 Number of successful extensions: 9 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: 502 Length adjustment: 34 Effective length of query: 479 Effective length of database: 468 Effective search space: 224172 Effective search space used: 224172 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