Aligments for a candidate for fruK in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Aligments for a candidate for fruK in Klebsiella michiganensis M5al

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate BWI76_RS07240 BWI76_RS07240 D-ribose transporter ATP-binding protein

Query= SwissProt::Q8G847
         (513 letters)



>FitnessBrowser__Koxy:BWI76_RS07240
          Length = 494

 Score =  356 bits (914), Expect = e-103
 Identities = 197/492 (40%), Positives = 313/492 (63%), Gaps = 14/492 (2%)

Query: 11  KGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKP 70
           +GI+  FPGVKALD V L + PG VHALMGENGAGKST++K L G+Y+ + G+I V G+P
Sbjct: 9   EGISKFFPGVKALDNVSLRVRPGTVHALMGENGAGKSTLMKCLIGIYRPDKGAIRVKGEP 68

Query: 71  QQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAAKKYLAQ 130
            QF  T+DA  +GI+ ++QE+NL  +++V EN+ LG E      +D ++     +  L +
Sbjct: 69  VQFQDTMDALRSGISMIHQELNLVPHMTVAENIWLGREPMKYGFVDHRQLARQTQDLLDK 128

Query: 131 MGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKV 190
           + +  +     +  +SIA QQ+V IA+A+  NA ++I+DEPTS+L  +EV  LF I+R +
Sbjct: 129 LNIR-LSADRLVGELSIASQQMVEIAKAVSWNADIVIMDEPTSALTESEVAHLFTIIRDL 187

Query: 191 RDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSAAELSQ 250
           R  G AI+++SH +D+I+ ITD +++ R+G ++    T +  R  LI  M+G+   EL+Q
Sbjct: 188 RQQGKAIIYISHKMDEIFAITDEISVFRDGTWVGSKQTTEFTRQSLITQMVGR---ELTQ 244

Query: 251 IGAKKARREITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRTELGRLLY 310
           +  K        GE+ ++ V+ L +KG  + ++  + +GE++G AGL+G+GR+E+   L+
Sbjct: 245 LFPKFNN---AIGEE-VLTVRNLSRKGAFHDINFSVRRGEILGVAGLVGAGRSEVMESLF 300

Query: 311 GADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNILIALQAT- 369
           G +K DSG   ++G  VNI  P TA++  +A  TE+R+  G+   L+V +N+ I      
Sbjct: 301 GMEKADSGEVLIDGMPVNIDSPSTAIEKGMALLTEDRKKSGLFLVLSVLENMSIVKMPEY 360

Query: 370 --RGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATHPELL 427
             +  F    K   D +  + ++ LN++    D+ + NLSGGNQQKVLI RWL   P++L
Sbjct: 361 IGKTGFVQHLKMAEDCM--EQIRRLNIKTPTMDQIINNLSGGNQQKVLIARWLLAQPKIL 418

Query: 428 ILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHKIAEI 487
           ILDEPTRGID+GAKAEI  ++ +LA++G+ V+ +SSEL E++ +SD + V+ +  +I  I
Sbjct: 419 ILDEPTRGIDVGAKAEIYHLISELANRGVAVIMVSSELPEILGMSDRVMVMHE-GRITGI 477

Query: 488 ENDDTVSQATIV 499
            + +   Q TI+
Sbjct: 478 LDKEDADQETIL 489



 Score = 87.4 bits (215), Expect = 1e-21
 Identities = 54/224 (24%), Positives = 113/224 (50%), Gaps = 6/224 (2%)

Query: 279 INPVDVDIYKGEVVGFAGLLGSGRTELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKN 338
           ++ V + +  G V    G  G+G++ L + L G  +PD G   + G+ V   D   AL++
Sbjct: 21  LDNVSLRVRPGTVHALMGENGAGKSTLMKCLIGIYRPDKGAIRVKGEPVQFQDTMDALRS 80

Query: 339 KIAYSTENRRDEGIIGDLTVRQNILIALQATRGMFKPIPKKEADAIVDKYMKELNVRPAD 398
            I+      ++  ++  +TV +NI +  +  +  F  +  ++        + +LN+R   
Sbjct: 81  GISMI---HQELNLVPHMTVAENIWLGREPMKYGF--VDHRQLARQTQDLLDKLNIR-LS 134

Query: 399 PDRPVKNLSGGNQQKVLIGRWLATHPELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGV 458
            DR V  LS  +QQ V I + ++ + +++I+DEPT  +     A +  ++ DL  QG  +
Sbjct: 135 ADRLVGELSIASQQMVEIAKAVSWNADIVIMDEPTSALTESEVAHLFTIIRDLRQQGKAI 194

Query: 459 VFISSELEEVVRLSDDIEVLKDRHKIAEIENDDTVSQATIVETI 502
           ++IS +++E+  ++D+I V +D   +   +  +   Q+ I + +
Sbjct: 195 IYISHKMDEIFAITDEISVFRDGTWVGSKQTTEFTRQSLITQMV 238



 Score = 87.4 bits (215), Expect = 1e-21
 Identities = 56/224 (25%), Positives = 120/224 (53%), Gaps = 6/224 (2%)

Query: 22  ALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTLDAQN 81
           A   ++ ++  GE+  + G  GAG+S ++++L G+ K ++G +++DG P   +    A  
Sbjct: 268 AFHDINFSVRRGEILGVAGLVGAGRSEVMESLFGMEKADSGEVLIDGMPVNIDSPSTAIE 327

Query: 82  AGIATVYQE---VNLCTNLSVGENVMLGH--EKRGPFG-IDWKKTHEAAKKYLAQMGLES 135
            G+A + ++     L   LSV EN+ +    E  G  G +   K  E   + + ++ +++
Sbjct: 328 KGMALLTEDRKKSGLFLVLSVLENMSIVKMPEYIGKTGFVQHLKMAEDCMEQIRRLNIKT 387

Query: 136 IDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRDSGV 195
                 ++++S   QQ V IAR ++   K+LILDEPT  +D     +++ ++ ++ + GV
Sbjct: 388 PTMDQIINNLSGGNQQKVLIARWLLAQPKILILDEPTRGIDVGAKAEIYHLISELANRGV 447

Query: 196 AILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGM 239
           A++ VS  L +I  ++DR+ ++  G+    +  +D  ++ ++ +
Sbjct: 448 AVIMVSSELPEILGMSDRVMVMHEGRITGILDKEDADQETILSL 491


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: 639
Number of extensions: 29
Number of successful extensions: 9
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: 494
Length adjustment: 34
Effective length of query: 479
Effective length of database: 460
Effective search space:   220340
Effective search space used:   220340
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