GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gguA in Pseudomonas simiae WCS417

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate GFF2673 PS417_13635 D-ribose transporter ATP-binding protein

Query= TCDB::O05176
         (512 letters)



>FitnessBrowser__WCS417:GFF2673
          Length = 510

 Score =  341 bits (875), Expect = 3e-98
 Identities = 203/500 (40%), Positives = 311/500 (62%), Gaps = 18/500 (3%)

Query: 5   ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64
           +LEM+ I+KTF G++ L+ V LKV  GEIHAL+GENGAGKSTLMK+LSG Y A    GEI
Sbjct: 6   LLEMQGISKTFNGLRVLKTVGLKVYPGEIHALMGENGAGKSTLMKILSGAYQADP-GGEI 64

Query: 65  HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFNRT 124
              G +        ++ +GI +I+QEL+L P LS+AENI+LG E+     I  +      
Sbjct: 65  RIAGQLIPTFDPATAKALGIAVIYQELSLCPNLSVAENIYLGRELRRGWTIDRKGMEAGC 124

Query: 125 RELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALLN 184
            E+L+++G + +P T ++ + + ++QLVEIA+AL    K+L++DEPT  L+  +++ L  
Sbjct: 125 IEVLQRLGAEFTPATRVSSLSIAERQLVEIARALHAHAKILVMDEPTTPLSSRETDRLFA 184

Query: 185 LLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVGR 244
           L+ + R+QG+  I I+H++ E+  ++D+++VLRDG  +  L   ++ +S + +++ MVGR
Sbjct: 185 LIKQLRSQGLAIIYISHRMAEIYALSDRVSVLRDGHYIGELT--RDALSAEALVKMMVGR 242

Query: 245 DLEDRYPPRDVPI--GETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAG 302
           DL   Y         G  ++ V++         D + +   +  +  GEV+GIAGL+GAG
Sbjct: 243 DLSGFYKKEHAAYNPGNVVMRVRDM-------ADGKRVRHCSFDLHAGEVLGIAGLVGAG 295

Query: 303 RTEFAMSVFGKSYGHRITGDVLIDGKPVD-VSTVRKAIDAGLAYVTEDRKHLGLVLNDNI 361
           RTE A  +F      R +G + + GK V  + T   AI AG+ Y+TEDRK  GL L+ ++
Sbjct: 296 RTELARLIFAAD--PRTSGTLEVVGKAVTPLRTPADAIRAGVVYLTEDRKAQGLFLDMSV 353

Query: 362 LHNTTL-ANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLS 420
             N  + A +       ++D    ++ ++D    L IR +        LSGGNQQKV+L+
Sbjct: 354 ADNINVCACVPDAHAGGVLDRDHALQRSNDAIKSLSIRVASGKVNAGALSGGNQQKVLLA 413

Query: 421 KWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYV 480
           + L   P VLILDEPTRG+D+G+K EIY IINQLA  G G+++ISSE+PE++G CDR+ +
Sbjct: 414 RLLEVKPHVLILDEPTRGVDIGSKSEIYRIINQLAQAGIGIVVISSELPEIIGTCDRVLI 473

Query: 481 MNEGRIVAELPKGEASQESI 500
           M EG++VAE+  G AS ++I
Sbjct: 474 MREGQLVAEV--GGASGQAI 491



 Score = 65.9 bits (159), Expect = 3e-15
 Identities = 54/237 (22%), Positives = 112/237 (47%), Gaps = 25/237 (10%)

Query: 278 QVLHDINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRK 337
           +VL  + + V  GE+  + G  GAG++   M +   +Y     G++ I G+ +       
Sbjct: 20  RVLKTVGLKVYPGEIHALMGENGAGKSTL-MKILSGAYQADPGGEIRIAGQLIPTFDPAT 78

Query: 338 AIDAGLAYVTEDRKHLGLVLNDNILHNTTLA---------NLAGVSKASIIDDIKEMKVA 388
           A   G+A + ++   L L  N ++  N  L          +  G+ +A  I+ ++  ++ 
Sbjct: 79  AKALGIAVIYQE---LSLCPNLSVAENIYLGRELRRGWTIDRKGM-EAGCIEVLQ--RLG 132

Query: 389 SDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIY 448
           ++F    R+ S         LS   +Q V +++ L ++  +L++DEPT  +       ++
Sbjct: 133 AEFTPATRVSS---------LSIAERQLVEIARALHAHAKILVMDEPTTPLSSRETDRLF 183

Query: 449 TIINQLAADGKGVLMISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQESIMRAIM 505
            +I QL + G  ++ IS  M E+    DR+ V+ +G  + EL +   S E++++ ++
Sbjct: 184 ALIKQLRSQGLAIIYISHRMAEIYALSDRVSVLRDGHYIGELTRDALSAEALVKMMV 240


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: 611
Number of extensions: 42
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:

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