GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruK in Burkholderia phytofirmans PsJN

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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