Alignments for a candidate for gguA in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for gguA in Escherichia coli BW25113

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate 18115 b4087 fused D-allose transporter subunits of ABC superfamily: ATP-binding components (NCBI)

Query= TCDB::O05176
         (512 letters)



>FitnessBrowser__Keio:18115
          Length = 510

 Score =  342 bits (876), Expect = 2e-98
 Identities = 200/516 (38%), Positives = 309/516 (59%), Gaps = 28/516 (5%)

Query: 1   MANTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTY 60
           MA   + M  I K+F  V AL++VNL V  GEIHAL+GENGAGKSTLMKVLSG++     
Sbjct: 1   MATPYISMAGIGKSFGPVHALKSVNLTVYPGEIHALLGENGAGKSTLMKVLSGIHEPT-- 58

Query: 61  EGEIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASN----GVIS 116
           +G I       N      +  +GI II+QEL+++  L++ EN+++G  +        +I 
Sbjct: 59  KGTITINNISYNKLDHKLAAQLGIGIIYQELSVIDELTVLENLYIGRHLTKKICGVNIID 118

Query: 117 WQQTFNRTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNE 176
           W++   R   +L +VGLK   +  + ++ +  +Q++EIAK L    K++I+DEPT+SL  
Sbjct: 119 WREMRVRAAMMLLRVGLKVDLDEKVANLSISHKQMLEIAKTLMLDAKVIIMDEPTSSLTN 178

Query: 177 SDSEALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQ--EEISE 234
            + + L  ++ + R +G   + I+HKL E+R++ D+ TV++DG +V    C     ++S 
Sbjct: 179 KEVDYLFLIMNQLRKEGTAIVYISHKLAEIRRICDRYTVMKDGSSV----CSGIVSDVSN 234

Query: 235 DVIIRNMVGRDLEDRYPPRDVPIG----ETILEVKNWNAYHQQHRDRQVLHDINVTVRKG 290
           D I+R MVGR+L++R+      +     ET+ EV+N  +     RDR+ + DI+ +V +G
Sbjct: 235 DDIVRLMVGRELQNRFNAMKENVSNLAHETVFEVRNVTS-----RDRKKVRDISFSVCRG 289

Query: 291 EVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDR 350
           E++G AGL+G+GRTE    +FG     R  G++ ++GK +   +   A+  G+AY+TE R
Sbjct: 290 EILGFAGLVGSGRTELMNCLFGVD--KRAGGEIRLNGKDISPRSPLDAVKKGMAYITESR 347

Query: 351 KHLGLVLNDNILHNTTLANL---AGVSKA-SIIDDIKEMKVASDFRTRLRIRSSGIFQET 406
           +  G   N +I  N  ++      G   A  +  ++ E + A + R  L ++   + Q  
Sbjct: 348 RDNGFFPNFSIAQNMAISRSLKDGGYKGAMGLFHEVDEQRTAENQRELLALKCHSVNQNI 407

Query: 407 VNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISS 466
             LSGGNQQKV++SKWL   P+V+I DEPTRGIDVGAK EIY ++ QLA DGK +LM+SS
Sbjct: 408 TELSGGNQQKVLISKWLCCCPEVIIFDEPTRGIDVGAKAEIYKVMRQLADDGKVILMVSS 467

Query: 467 EMPELLGNCDRIYVMNEGRIVAELP-KGEASQESIM 501
           E+PE++  CDRI V  EGR+   L  + + S+E IM
Sbjct: 468 ELPEIITVCDRIAVFCEGRLTQILTNRDDMSEEEIM 503



 Score = 66.6 bits (161), Expect = 2e-15
 Identities = 58/232 (25%), Positives = 110/232 (47%), Gaps = 16/232 (6%)

Query: 280 LHDINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRIT-GDVLIDGKPVDVSTVRKA 338
           L  +N+TV  GE+  + G  GAG++     + G    H  T G + I+    +    + A
Sbjct: 21  LKSVNLTVYPGEIHALLGENGAGKSTLMKVLSGI---HEPTKGTITINNISYNKLDHKLA 77

Query: 339 IDAGLAYVTEDRKHLG--LVLNDNILHNTTLANLAGVSKASIIDDIKEMKVASDF---RT 393
              G+  + ++   +    VL +  +       + GV+    I D +EM+V +     R 
Sbjct: 78  AQLGIGIIYQELSVIDELTVLENLYIGRHLTKKICGVN----IIDWREMRVRAAMMLLRV 133

Query: 394 RLRIRSSGIFQETVNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQ 453
            L++    + ++  NLS  ++Q + ++K L  +  V+I+DEPT  +       ++ I+NQ
Sbjct: 134 GLKV---DLDEKVANLSISHKQMLEIAKTLMLDAKVIIMDEPTSSLTNKEVDYLFLIMNQ 190

Query: 454 LAADGKGVLMISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQESIMRAIM 505
           L  +G  ++ IS ++ E+   CDR  VM +G  V      + S + I+R ++
Sbjct: 191 LRKEGTAIVYISHKLAEIRRICDRYTVMKDGSSVCSGIVSDVSNDDIVRLMV 242


Lambda     K      H
   0.316    0.135    0.374 

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: 659
Number of extensions: 35
Number of successful extensions: 11
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: 512
Length of database: 510
Length adjustment: 35
Effective length of query: 477
Effective length of database: 475
Effective search space:   226575
Effective search space used:   226575
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