Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate AZOBR_RS31245 AZOBR_RS31245 ABC transporter ATP-binding protein
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__azobra:AZOBR_RS31245 Length = 518 Score = 332 bits (850), Expect = 3e-95 Identities = 193/497 (38%), Positives = 307/497 (61%), Gaps = 25/497 (5%) Query: 6 PIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINA--GS 63 PI+ MKGIT FPGVKALD V+L++ GE+HAL+GENGAGKST++K L+GVY + G Sbjct: 4 PILEMKGITKTFPGVKALDDVNLSVREGEIHALIGENGAGKSTLMKVLSGVYPQGSFDGE 63 Query: 64 IMVDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEA 123 I G+PQ F G D++ GI ++QE+ L LS+ EN+ LG+E+ IDW Sbjct: 64 IRFRGQPQAFRGIADSERLGIIIIHQELALVPLLSITENLFLGNEQASRGVIDWDAATLR 123 Query: 124 AKKYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDL 183 A++ L +GL P T ++ I + QQLV IA+A+ K+LILDEPT+SL+ ++ L Sbjct: 124 ARELLRLVGLHD-PPETLITDIGVGKQQLVEIAKALSKEVKLLILDEPTASLNESDSDAL 182 Query: 184 FAIMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDT--PRDELIGMMI 241 ++ + + G+A + +SH L++I ++ DR+TILR+G ++ + ++ +D +I M+ Sbjct: 183 LELLLQFKARGIASILISHKLNEIAKVADRVTILRDGTTVETLDCREAVVSQDRIIRGMV 242 Query: 242 GKSAAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINP-------VDVDIYKGEVVGF 294 G++ ++ + RR PG+ + +VKG +P V++ + +GEVVG Sbjct: 243 GRALSD------RYPRRTTVPGDV-LFEVKGWSADHPAHPGRRVVRDVNLTVRRGEVVGI 295 Query: 295 AGLLGSGRTELGRLLYGAD--KPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGI 352 AGL+G+GRTE L+G + G L+G+++++S A+ N +AY+TE+R+ G+ Sbjct: 296 AGLMGAGRTEFAMSLFGRSYGRNIRGQAFLDGREIDVSTISRAMANGLAYATEDRKHLGL 355 Query: 353 IGDLTVRQNILIALQATRGMFKP--IPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGN 410 + D +R N+ +A RG+ K I + + +++ + L +R AD + NLSGGN Sbjct: 356 VLDNDIRHNVTLA--NLRGVAKRWVIDHEREVQVAEEFRRRLRIRCADVFQETVNLSGGN 413 Query: 411 QQKVLIGRWLATHPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVR 470 QQKV++ +WL P++LILDEPTRGID+GAK EI ++ L ++G GVV ISSE+ E++ Sbjct: 414 QQKVVLSKWLFADPQVLILDEPTRGIDVGAKYEIYTIINQLVAEGRGVVLISSEMPELLG 473 Query: 471 LSDDIEVLKDRHKIAEI 487 ++D I V+ +AE+ Sbjct: 474 VADRIYVMNAGEMVAEM 490 Score = 74.7 bits (182), Expect = 7e-18 Identities = 54/233 (23%), Positives = 117/233 (50%), Gaps = 11/233 (4%) Query: 18 PGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTG-VYKINA-GSIMVDGKPQQFNG 75 PG + + V+LT+ GEV + G GAG++ +L G Y N G +DG+ + Sbjct: 275 PGRRVVRDVNLTVRRGEVVGIAGLMGAGRTEFAMSLFGRSYGRNIRGQAFLDGREIDVST 334 Query: 76 TLDAQNAGIATVYQE---VNLCTNLSVGENVML----GHEKRGPFGIDWKKTHEAAKKYL 128 A G+A ++ + L + + NV L G KR + ID ++ + A+++ Sbjct: 335 ISRAMANGLAYATEDRKHLGLVLDNDIRHNVTLANLRGVAKR--WVIDHEREVQVAEEFR 392 Query: 129 AQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMR 188 ++ + D ++S QQ V +++ + + +VLILDEPT +D +++ I+ Sbjct: 393 RRLRIRCADVFQETVNLSGGNQQKVVLSKWLFADPQVLILDEPTRGIDVGAKYEIYTIIN 452 Query: 189 KVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMI 241 ++ G ++ +S + ++ + DR+ ++ G+ + E+ + +++++G ++ Sbjct: 453 QLVAEGRGVVLISSEMPELLGVADRIYVMNAGEMVAEMPAAEASQEKIMGAIM 505 Score = 63.2 bits (152), Expect = 2e-14 Identities = 56/254 (22%), Positives = 118/254 (46%), Gaps = 39/254 (15%) Query: 266 PIVDVKGLGKK----GTINPVDVDIYKGEVVGFAGLLGSGRTELGRLLYGADKPDSGTYT 321 PI+++KG+ K ++ V++ + +GE+ G G+G++ L ++L SG Y Sbjct: 4 PILEMKGITKTFPGVKALDDVNLSVREGEIHALIGENGAGKSTLMKVL-------SGVY- 55 Query: 322 LNGKKVNISDPYTALKNKIAYSTENRRDEGI-----IGDLTVRQNILIA--LQATRGMFK 374 P + +I + + + GI +G + + Q + + L T +F Sbjct: 56 ----------PQGSFDGEIRFRGQPQAFRGIADSERLGIIIIHQELALVPLLSITENLFL 105 Query: 375 PIPKKEADAIVDKYMKELNVRPA--------DPDRPVKNLSGGNQQKVLIGRWLATHPEL 426 ++ + ++D L R P+ + ++ G QQ V I + L+ +L Sbjct: 106 G-NEQASRGVIDWDAATLRARELLRLVGLHDPPETLITDIGVGKQQLVEIAKALSKEVKL 164 Query: 427 LILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAE 486 LILDEPT ++ + +++L ++G+ + IS +L E+ +++D + +L+D + Sbjct: 165 LILDEPTASLNESDSDALLELLLQFKARGIASILISHKLNEIAKVADRVTILRDGTTVET 224 Query: 487 IE-NDDTVSQATIV 499 ++ + VSQ I+ Sbjct: 225 LDCREAVVSQDRII 238 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: 692 Number of extensions: 44 Number of successful extensions: 10 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: 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