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 17809 b3749 fused D-ribose transporter subunits of ABC superfamily: ATP-binding components (NCBI)

Query= TCDB::O05176
         (512 letters)



>FitnessBrowser__Keio:17809
          Length = 501

 Score =  379 bits (973), Expect = e-109
 Identities = 211/501 (42%), Positives = 311/501 (62%), Gaps = 16/501 (3%)

Query: 5   ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64
           +L+++ I K FPGVKAL    L V  G + ALVGENGAGKST+MKVL+G+Y      G +
Sbjct: 4   LLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDA--GTL 61

Query: 65  HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASN-GVISWQQTFNR 123
            + G    F     S++ GI IIHQEL L+P L+IAENIFLG E  +  G I W+  +  
Sbjct: 62  LWLGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAE 121

Query: 124 TRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALL 183
             +LL K+ L+   + L+ D+ +G QQ+VEIAK LS   K++I+DEPT +L ++++E+L 
Sbjct: 122 ADKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLF 181

Query: 184 NLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVG 243
            ++ E ++QG   + I+H++ E+ ++ D +TV RDG  +   +     ++ED +I  MVG
Sbjct: 182 RVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREV--ASLTEDSLIEMMVG 239

Query: 244 RDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGR 303
           R LED+YP  D   G+  L+V N             ++D++ T+RKGE++G++GLMGAGR
Sbjct: 240 RKLEDQYPHLDKAPGDIRLKVDNLCG--------PGVNDVSFTLRKGEILGVSGLMGAGR 291

Query: 304 TEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILH 363
           TE    ++G     R +G V +DG  V   + +  +  G+ Y++EDRK  GLVL  ++  
Sbjct: 292 TELMKVLYGAL--PRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKE 349

Query: 364 NTTLANLAGVSKAS-IIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKW 422
           N +L  L   S+A   +    E +  SDF     +++  + Q    LSGGNQQKV +++ 
Sbjct: 350 NMSLTALRYFSRAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARG 409

Query: 423 LFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMN 482
           L + P VLILDEPTRG+DVGAK EIY +INQ  ADG  ++++SSEMPE+LG  DRI VM+
Sbjct: 410 LMTRPKVLILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMH 469

Query: 483 EGRIVAELPKGEASQESIMRA 503
           EG +  E  + +A+QE +M A
Sbjct: 470 EGHLSGEFTREQATQEVLMAA 490



 Score = 70.5 bits (171), Expect = 1e-16
 Identities = 58/225 (25%), Positives = 106/225 (47%), Gaps = 15/225 (6%)

Query: 285 VTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLA 344
           + V  G V+ + G  GAG++   M V    Y  R  G +L  GK    +  + + +AG+ 
Sbjct: 25  LNVYPGRVMALVGENGAGKSTM-MKVLTGIYT-RDAGTLLWLGKETTFTGPKSSQEAGIG 82

Query: 345 YVTEDRKHLG-LVLNDNILHNTTLANLAGVSKASIIDDIKEMKVASD---FRTRLRIRSS 400
            + ++   +  L + +NI       N  G        D K M   +D    +  LR +S 
Sbjct: 83  IIHQELNLIPQLTIAENIFLGREFVNRFGKI------DWKTMYAEADKLLAKLNLRFKSD 136

Query: 401 GIFQETVNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKG 460
            +  +   LS G+QQ V ++K L     V+I+DEPT  +       ++ +I +L + G+G
Sbjct: 137 KLVGD---LSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRVIRELKSQGRG 193

Query: 461 VLMISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQESIMRAIM 505
           ++ IS  M E+   CD + V  +G+ +AE      +++S++  ++
Sbjct: 194 IVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMV 238


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: 647
Number of extensions: 37
Number of successful extensions: 10
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: 501
Length adjustment: 34
Effective length of query: 478
Effective length of database: 467
Effective search space:   223226
Effective search space used:   223226
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