Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate GFF1357 Psest_1392 ABC-type uncharacterized transport systems, ATPase components
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__psRCH2:GFF1357 Length = 518 Score = 235 bits (599), Expect = 3e-66 Identities = 154/482 (31%), Positives = 253/482 (52%), Gaps = 26/482 (5%) Query: 12 GITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQ 71 GIT ++PG A D +DL++ PGE+HAL+GENGAGKST++K + GV + +AG I G+ Sbjct: 13 GITKQYPGCLANDRIDLSIQPGEIHALLGENGAGKSTLMKIIYGVTQPDAGEIHWQGERV 72 Query: 72 QFNGTLDAQNAGIATVYQEVNLCTNLSVGENV--MLGHEKRGPFGIDWKKTHEAAKKYLA 129 A+ GI V+Q +L LSV EN+ LG + P ++ K E +++Y Sbjct: 73 TMRDPAQARERGIGMVFQHFSLFETLSVAENIALALGAKAGTPKQLE-PKIREVSQRY-- 129 Query: 130 QMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRK 189 G+ ++P + S+SI +Q V I R ++ + ++LILDEPTS L E +LF +R+ Sbjct: 130 --GM-PLEPQRLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADELFVTLRR 186 Query: 190 VRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSAAELS 249 + G +ILF+SH L+++ + T+LR G+ E + + EL +M+G + Sbjct: 187 LAAEGCSILFISHKLNEVRALCQSATVLRAGRVSGECIPAECSDLELARLMVGDAE---- 242 Query: 250 QIGAKKARREITPGEKPIVDVKGLGKKG------TINPVDVDIYKGEVVGFAGLLGSGRT 303 +A + G P + V+ L ++ VD+++ GE+VG AG+ G+G+ Sbjct: 243 ---GLEAEYPKSEGRAPFLRVERLSWHNADPFGVSLKEVDLEVRAGEIVGIAGVAGNGQD 299 Query: 304 ELGRLLYGADKPDSG---TYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQ 360 EL LL G + + G V P ++ +A+ R G + +++ Sbjct: 300 ELLALLSGEQRLQAAQAMRIRFLGDDVAHLRPGARRRHGMAFVPAERLGHGAVPSMSLAD 359 Query: 361 NILIALQATRGMFKP--IPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGR 418 N L+ GM + I + A ++ ++ V+ D P +LSGGN QK ++GR Sbjct: 360 NGLLTAYQQTGMVEQGLIRRGRVRAFAEQVIQRFAVKTPDAQTPAASLSGGNLQKFILGR 419 Query: 419 WLATHPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVL 478 + P+LLI PT G+D+GA A I + +++L G ++ IS +LEE+ ++SD I L Sbjct: 420 EILQQPKLLIAAHPTWGVDVGAAAAIHRALIELRDAGAAILVISEDLEELFQISDRIAAL 479 Query: 479 KD 480 D Sbjct: 480 SD 481 Score = 62.8 bits (151), Expect = 3e-14 Identities = 55/248 (22%), Positives = 107/248 (43%), Gaps = 42/248 (16%) Query: 22 ALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIM---------------- 65 +L VDL + GE+ + G G G+ ++ L+G ++ A M Sbjct: 274 SLKEVDLEVRAGEIVGIAGVAGNGQDELLALLSGEQRLQAAQAMRIRFLGDDVAHLRPGA 333 Query: 66 -----VDGKPQQFNG-----TLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGI 115 + P + G ++ + G+ T YQ+ + V G +RG Sbjct: 334 RRRHGMAFVPAERLGHGAVPSMSLADNGLLTAYQQTGM---------VEQGLIRRG---- 380 Query: 116 DWKKTHEAAKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSL 175 + A++ + + +++ D TP +S+S Q + R ++ K+LI PT + Sbjct: 381 ---RVRAFAEQVIQRFAVKTPDAQTPAASLSGGNLQKFILGREILQQPKLLIAAHPTWGV 437 Query: 176 DANEVRDLFAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDE 235 D + + ++RD+G AIL +S L+++++I+DR+ L +G+ + T T E Sbjct: 438 DVGAAAAIHRALIELRDAGAAILVISEDLEELFQISDRIAALSDGRLSPQRATASTCPVE 497 Query: 236 LIGMMIGK 243 + M G+ Sbjct: 498 VGRWMAGQ 505 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: 567 Number of extensions: 24 Number of successful extensions: 8 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: 518 Length adjustment: 35 Effective length of query: 478 Effective length of database: 483 Effective search space: 230874 Effective search space used: 230874 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