Alignments for a candidate for fruK in Burkholderia phytofirmans PsJN

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources