Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate H281DRAFT_05270 H281DRAFT_05270 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__Burk376:H281DRAFT_05270 Length = 539 Score = 463 bits (1192), Expect = e-135 Identities = 234/500 (46%), Positives = 346/500 (69%), Gaps = 15/500 (3%) Query: 6 PIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIM 65 PI+ G++ FPGVKAL VD L+PGEVH LMG+NGAGKST+I LTGV + G+I Sbjct: 34 PILATTGVSKTFPGVKALQRVDFRLFPGEVHTLMGQNGAGKSTLINVLTGVIAPDTGTIR 93 Query: 66 VDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAAK 125 + G+ F +A+ AG+ T+YQEVNLC NLSV EN+ G + R IDW A+ Sbjct: 94 LAGEVVAFASPQEAEAAGVRTLYQEVNLCPNLSVAENIFAGRQPRRFGAIDWPDIKRRAQ 153 Query: 126 KYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFA 185 LA++ + S+D L + IA+QQ+VAIARA+ ++A+VLILDEPTSSLD +EV LF Sbjct: 154 AALARLDI-SLDVTRSLDAYPIAVQQMVAIARALSVDARVLILDEPTSSLDDSEVAQLFK 212 Query: 186 IMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSA 245 I+R ++ SG+AILFV+HF++Q Y I+DR+T++RNG+ E + ++ D+L+ M+G Sbjct: 213 ILRHLKQSGIAILFVTHFIEQTYAISDRITVMRNGEREGEYLARNLSADQLVAKMVGHE- 271 Query: 246 AELSQIGAKKARREITPG--------EKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGL 297 +S+ + A PG ++++G+GK+GT+ P+D+++ +G+++G AGL Sbjct: 272 -RMSERLREAAHEASAPGGTERGERAASAFIELRGVGKRGTLQPIDLNVERGQILGLAGL 330 Query: 298 LGSGRTELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLT 357 LGSGRTE RLL+GAD+ DSGT ++GK V + P+ A+++ IAY E+R+ EGI+ DL+ Sbjct: 331 LGSGRTETARLLFGADRADSGTMLVDGKPVRLRSPHDAVRHGIAYCAEDRKKEGIVADLS 390 Query: 358 VRQNILIALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIG 417 +R+NIL+ALQA RG ++ I ++ A + D +++ L ++ +D ++P+ LSGGNQQK L+ Sbjct: 391 IRENILLALQARRGWWRKISRQRARELADLWIERLGIKASDAEQPIGLLSGGNQQKALLA 450 Query: 418 RWLATHPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEV 477 RWLAT P+LLILDEPTRGID+ AK +I +L L + G+ ++FISSE+ EV+R+S + V Sbjct: 451 RWLATDPKLLILDEPTRGIDVAAKFDIMDRLLALCANGLSILFISSEISEVLRVSHRVAV 510 Query: 478 LKDRHKIAEIE----NDDTV 493 L+DR KIAE+E N+D + Sbjct: 511 LRDRRKIAEVEGKASNEDNI 530 Score = 104 bits (259), Expect = 9e-27 Identities = 66/236 (27%), Positives = 126/236 (53%), Gaps = 8/236 (3%) Query: 15 IEFPGVK---ALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQ 71 IE GV L +DL + G++ L G G+G++ + L G + ++G+++VDGKP Sbjct: 301 IELRGVGKRGTLQPIDLNVERGQILGLAGLLGSGRTETARLLFGADRADSGTMLVDGKPV 360 Query: 72 QFNGTLDAQNAGIATVYQE---VNLCTNLSVGENVMLGHEKRGPFG--IDWKKTHEAAKK 126 + DA GIA ++ + +LS+ EN++L + R + I ++ E A Sbjct: 361 RLRSPHDAVRHGIAYCAEDRKKEGIVADLSIRENILLALQARRGWWRKISRQRARELADL 420 Query: 127 YLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAI 186 ++ ++G+++ D P+ +S QQ +AR + + K+LILDEPT +D D+ Sbjct: 421 WIERLGIKASDAEQPIGLLSGGNQQKALLARWLATDPKLLILDEPTRGIDVAAKFDIMDR 480 Query: 187 MRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIG 242 + + +G++ILF+S + ++ ++ R+ +LR+ + I EV K + D + ++ G Sbjct: 481 LLALCANGLSILFISSEISEVLRVSHRVAVLRDRRKIAEVEGKASNEDNIYRLIAG 536 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: 708 Number of extensions: 28 Number of successful extensions: 7 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: 539 Length adjustment: 35 Effective length of query: 478 Effective length of database: 504 Effective search space: 240912 Effective search space used: 240912 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