Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate 206505 DVU1070 branched chain amino acid ABC transporter, ATP-binding protein (TIGR)
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__DvH:206505 Length = 524 Score = 246 bits (627), Expect = 2e-69 Identities = 160/495 (32%), Positives = 261/495 (52%), Gaps = 22/495 (4%) Query: 3 DKNPIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAG 62 D P+V ++GI F V+A + L + PG + AL+GENGAGKST++ L+G + G Sbjct: 30 DVTPVVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTG 89 Query: 63 SIMVDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTH- 121 I VDG+ +F DA AGI VYQ L +++V ENV+LG G H Sbjct: 90 IIHVDGEAVRFRSPKDALKAGIGMVYQHFMLVDSMTVAENVLLGQS-----GAWLSPVHM 144 Query: 122 -EAAKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEV 180 + A+ GL+ IDP + +S+ +Q V I + + +++VLILDEPT+ L E Sbjct: 145 SRVVAELAARYGLD-IDPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGET 203 Query: 181 RDLFAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRD-ELIGM 239 LF + ++ ++G AI+F+SH + ++ + D + ILR G+ + E + P + EL Sbjct: 204 EQLFEALHRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPGEAELANR 263 Query: 240 MIGKSAAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLG 299 M+G+ ++ + A + PG++ ++ V GL G + + ++ KGEV AG+ G Sbjct: 264 MVGR------EVILEVAAEPLEPGDR-VLHVDGLAGDG-LKGLSFEVRKGEVFAIAGVAG 315 Query: 300 SGRTELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVR 359 +G+ EL + G +P G L G + +AY E+R+ L + Sbjct: 316 NGQRELVECVTGLRRPAEGEVELLGIPWRQFFTKAPRQGGLAYIPEDRQGLATCLSLDLV 375 Query: 360 QNILIALQA--TRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIG 417 N L+ + TRG F + +K ADA + E NV+P + P ++LSGGN QK+++G Sbjct: 376 DNFLLTARGCFTRGPF--LDRKSADAAARDILAEYNVQPGRAEAPARSLSGGNLQKLVVG 433 Query: 418 RWLATHPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEV 477 R P L++ + PT+G+DI A E+ +L++ S GV+ +S +L EV+ L+D + V Sbjct: 434 REFYRKPSLIVAENPTQGLDIAATEEVWARLLEVRSHA-GVLLVSGDLNEVLALADRVAV 492 Query: 478 LKDRHKIAEIENDDT 492 + I ++ DT Sbjct: 493 MYRGCFIGLLDRSDT 507 Score = 85.9 bits (211), Expect = 3e-21 Identities = 64/247 (25%), Positives = 119/247 (48%), Gaps = 15/247 (6%) Query: 266 PIVDVKGLGKK-GTI---NPVDVDIYKGEVVGFAGLLGSGRTELGRLLYGADKPDSGTYT 321 P+V ++G+GK G + + + +DI G + G G+G++ L +L G D+G Sbjct: 33 PVVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGIIH 92 Query: 322 LNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQATRGMFKPIPKKEA 381 ++G+ V P ALK I ++ ++ +TV +N+L+ P+ Sbjct: 93 VDGEAVRFRSPKDALKAGIGMVYQHFM---LVDSMTVAENVLLGQSGA--WLSPVHMSRV 147 Query: 382 DA-IVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELLILDEPTRGIDIGA 440 A + +Y ++ DP V +LS G +Q+V I + L +LILDEPT + G Sbjct: 148 VAELAARYGLDI-----DPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGE 202 Query: 441 KAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAEIENDDTVSQATIVE 500 ++ + + +A G +VFIS +++EV+ L+D+I +L+ + E + +A + Sbjct: 203 TEQLFEALHRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPGEAELAN 262 Query: 501 TIANTNV 507 + V Sbjct: 263 RMVGREV 269 Score = 84.0 bits (206), Expect = 1e-20 Identities = 60/231 (25%), Positives = 114/231 (49%), Gaps = 8/231 (3%) Query: 23 LDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTLDAQNA 82 L G+ + GEV A+ G G G+ +++ +TG+ + G + + G P + T + Sbjct: 295 LKGLSFEVRKGEVFAIAGVAGNGQRELVECVTGLRRPAEGEVELLGIPWRQFFTKAPRQG 354 Query: 83 GIATVYQE---VNLCTNLSVGENVML---GHEKRGPFGIDWKKTHEAAKKYLAQMGLESI 136 G+A + ++ + C +L + +N +L G RGPF +D K AA+ LA+ ++ Sbjct: 355 GLAYIPEDRQGLATCLSLDLVDNFLLTARGCFTRGPF-LDRKSADAAARDILAEYNVQPG 413 Query: 137 DPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRDSGVA 196 P S+S Q + + R +++ + PT LD +++A + +VR S Sbjct: 414 RAEAPARSLSGGNLQKLVVGREFYRKPSLIVAENPTQGLDIAATEEVWARLLEVR-SHAG 472 Query: 197 ILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSAAE 247 +L VS L+++ + DR+ ++ G FI + DT + + IG+M+ + E Sbjct: 473 VLLVSGDLNEVLALADRVAVMYRGCFIGLLDRSDTNKVDAIGLMMAGVSCE 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: 632 Number of extensions: 37 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: 524 Length adjustment: 35 Effective length of query: 478 Effective length of database: 489 Effective search space: 233742 Effective search space used: 233742 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 Apr 09 2024. 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