Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate GFF385 PGA1_c03960 ribose import ATP-binding protein RbsA
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__Phaeo:GFF385 Length = 509 Score = 272 bits (695), Expect = 2e-77 Identities = 168/500 (33%), Positives = 272/500 (54%), Gaps = 24/500 (4%) Query: 6 PIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIM 65 P + +KGI+ F V+A + + + PG +H ++GENGAGKST++ L G YK + G + Sbjct: 4 PAIELKGISKAFGPVQANKDISIRVAPGTIHGIIGENGAGKSTLMSILYGFYKADKGEVW 63 Query: 66 VDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAAK 125 + GK + + A +AGI V+Q L N +V EN++LG E G K ++ K Sbjct: 64 IHGKRTEIPDSQAAISAGIGMVFQHFKLVENFTVLENIILGAEDGGLLKPSLSKARKSLK 123 Query: 126 KYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFA 185 A+ L ++DP + I + MQQ V I +A+ A +LILDEPT L E LF Sbjct: 124 DLAAEYEL-NVDPDARIDEIGVGMQQRVEILKALYRQADILILDEPTGVLTPAEADQLFR 182 Query: 186 IMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSA 245 I+ ++R G I+ ++H L +I E TD ++++R G+ V T +T + L +M+G+ Sbjct: 183 ILDRLRAEGKTIILITHKLREIMEYTDTVSVMRRGEMTATVKTAETSPEHLAELMVGRKV 242 Query: 246 AELSQIGAKKARREITPGEKPIVDVKGLGKK-----GTINPVDVDIYKGEVVGFAGLLGS 300 L ++ A TPG KPI++++ L + +D+ + GE++G AG+ G+ Sbjct: 243 --LLRVDKVPA----TPG-KPILEIENLSVVDEAGVARVKNIDLTVRAGEILGIAGVAGN 295 Query: 301 GRTELGRLLYGADKPDSGTYTLNGKKVNIS----DPYTALKNKIAYSTENRRDEGIIGDL 356 G++EL +L G + G+ LNG + +S D +A+ E+R+ EG+I D Sbjct: 296 GQSELMEVL-GGMREGQGSIRLNGAPLPLSGAGSDARARRAAHVAHVPEDRQREGLIMDF 354 Query: 357 TVRQNILI----ALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQ 412 +N+ A + RG+ AD + M + +VRP DP KN SGGNQQ Sbjct: 355 HAWENVAFGYHHAPEYQRGLLMNNAALRADT--EAKMAKFDVRPPDPWLAAKNFSGGNQQ 412 Query: 413 KVLIGRWLATHPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLS 472 K+++ R + +PELL++ +PTRG+DIGA I + +++L QG ++ +S ELEE++ L+ Sbjct: 413 KIVVAREIERNPELLLIGQPTRGVDIGAIEFIHKQIVELRDQGKAILLVSVELEEILSLA 472 Query: 473 DDIEVLKDRHKIAEIENDDT 492 D + V+ D + E D T Sbjct: 473 DRVAVMFDGMIMGERPADQT 492 Score = 81.3 bits (199), Expect = 8e-20 Identities = 65/253 (25%), Positives = 119/253 (47%), Gaps = 13/253 (5%) Query: 2 TDKNPIVVMKGITI-EFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKIN 60 T PI+ ++ +++ + GV + +DLT+ GE+ + G G G+S +++ L G+ + Sbjct: 252 TPGKPILEIENLSVVDEAGVARVKNIDLTVRAGEILGIAGVAGNGQSELMEVLGGMRE-G 310 Query: 61 AGSIMVDGKPQQFNGT-LDAQNAGIATVY------QEVNLCTNLSVGENVMLGHEKRGPF 113 GSI ++G P +G DA+ A V Q L + ENV G+ + Sbjct: 311 QGSIRLNGAPLPLSGAGSDARARRAAHVAHVPEDRQREGLIMDFHAWENVAFGYHHAPEY 370 Query: 114 GIDWKKTHEAAKK----YLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILD 169 + A + +A+ + DP + S QQ + +AR + N ++L++ Sbjct: 371 QRGLLMNNAALRADTEAKMAKFDVRPPDPWLAAKNFSGGNQQKIVVAREIERNPELLLIG 430 Query: 170 EPTSSLDANEVRDLFAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTK 229 +PT +D + + + ++RD G AIL VS L++I + DR+ ++ +G + E Sbjct: 431 QPTRGVDIGAIEFIHKQIVELRDQGKAILLVSVELEEILSLADRVAVMFDGMIMGERPAD 490 Query: 230 DTPRDELIGMMIG 242 T EL +M G Sbjct: 491 QTDEKELGLLMAG 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: 643 Number of extensions: 39 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: 509 Length adjustment: 35 Effective length of query: 478 Effective length of database: 474 Effective search space: 226572 Effective search space used: 226572 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