Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate BPHYT_RS23875 BPHYT_RS23875 sugar ABC transporter ATP-binding protein
Query= SwissProt::Q8G847 (513 letters) >FitnessBrowser__BFirm:BPHYT_RS23875 Length = 549 Score = 461 bits (1187), Expect = e-134 Identities = 233/501 (46%), Positives = 342/501 (68%), Gaps = 14/501 (2%) Query: 6 PIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIM 65 PI+ G++ FPGVKAL VD L+PGE+H LMG+NGAGKST+I LTGV + G+I Sbjct: 41 PILATAGVSKTFPGVKALQRVDFRLFPGEIHTLMGQNGAGKSTLINVLTGVLAPDEGTIR 100 Query: 66 VDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAAK 125 + G+ F +A+ AG+ T+YQEVNLC NLSV EN+ G + R IDW A+ Sbjct: 101 LGGELVAFASPQEAEGAGVRTLYQEVNLCPNLSVAENIFAGRQPRRFGAIDWPDIKRRAQ 160 Query: 126 KYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFA 185 LA++ + ++D L + IA+QQ+VAIARA+ ++A+VLILDEPTSSLD EV LF Sbjct: 161 AALARLDV-TLDVTRSLDAYPIAVQQMVAIARALSVDARVLILDEPTSSLDDGEVSQLFK 219 Query: 186 IMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIG--- 242 I+R ++ SG+AILFV+HF++Q Y I+DR+T++RNG+ E + +D P D+L+ M+G Sbjct: 220 ILRHLKQSGIAILFVTHFIEQTYAISDRITVMRNGEREGEYLARDLPADQLVSKMVGHER 279 Query: 243 ------KSAAELSQIGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAG 296 ++A E Q A + +P V+++G+G++GT+ P+D+D+ G+++G AG Sbjct: 280 MSARLREAAHEGHQGHEAHAGPQAAQAVQPFVELRGVGRRGTMQPIDLDVQPGQILGLAG 339 Query: 297 LLGSGRTELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDL 356 LLGSGRTE RLL+GAD+ DSGT + G+ V + P A+++ I Y E+R+ EGI+ +L Sbjct: 340 LLGSGRTETARLLFGADRADSGTILVEGRPVRLRSPRDAVRHGIGYCAEDRKKEGIVAEL 399 Query: 357 TVRQNILIALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLI 416 ++R NIL+ALQA RG ++ I ++ A + D +++ L ++ AD ++P+ LSGGNQQK L+ Sbjct: 400 SIRDNILLALQARRGWWRKISRQRARELADLWIERLGIKAADAEQPIGLLSGGNQQKALL 459 Query: 417 GRWLATHPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIE 476 RWLAT P+LLILDEPTRGID+ AK +I +L L + G+ ++FISSE+ EV+R+S + Sbjct: 460 ARWLATDPKLLILDEPTRGIDVAAKFDIMDRLLALCASGLSILFISSEISEVLRVSHRVA 519 Query: 477 VLKDRHKIAEI----ENDDTV 493 VL+DR KIAE+ N+D + Sbjct: 520 VLRDRRKIAEVAGKASNEDNI 540 Score = 104 bits (260), Expect = 7e-27 Identities = 61/222 (27%), Positives = 121/222 (54%), Gaps = 5/222 (2%) Query: 26 VDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTLDAQNAGI- 84 +DL + PG++ L G G+G++ + L G + ++G+I+V+G+P + DA GI Sbjct: 325 IDLDVQPGQILGLAGLLGSGRTETARLLFGADRADSGTILVEGRPVRLRSPRDAVRHGIG 384 Query: 85 --ATVYQEVNLCTNLSVGENVMLGHEKRGPFG--IDWKKTHEAAKKYLAQMGLESIDPHT 140 A ++ + LS+ +N++L + R + I ++ E A ++ ++G+++ D Sbjct: 385 YCAEDRKKEGIVAELSIRDNILLALQARRGWWRKISRQRARELADLWIERLGIKAADAEQ 444 Query: 141 PLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRDSGVAILFV 200 P+ +S QQ +AR + + K+LILDEPT +D D+ + + SG++ILF+ Sbjct: 445 PIGLLSGGNQQKALLARWLATDPKLLILDEPTRGIDVAAKFDIMDRLLALCASGLSILFI 504 Query: 201 SHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIG 242 S + ++ ++ R+ +LR+ + I EV K + D + ++ G Sbjct: 505 SSEISEVLRVSHRVAVLRDRRKIAEVAGKASNEDNIYRLIAG 546 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: 714 Number of extensions: 24 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: 549 Length adjustment: 35 Effective length of query: 478 Effective length of database: 514 Effective search space: 245692 Effective search space used: 245692 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