GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Cupriavidus basilensis 4G11

Align Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate RR42_RS30800 RR42_RS30800 sugar ABC transporter ATP-binding protein

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__Cup4G11:RR42_RS30800
          Length = 530

 Score =  265 bits (678), Expect = 2e-75
 Identities = 170/491 (34%), Positives = 268/491 (54%), Gaps = 23/491 (4%)

Query: 3   PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62
           PIL +  I KRF  + A   +S+E   GEV A++GENGAGKSTL+ I+ G Y  D G + 
Sbjct: 4   PILRLAGITKRFGPLVANDDISLELQRGEVLALLGENGAGKSTLVSILFGHYVADAGTVE 63

Query: 63  YEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAE 122
            +G+ +    P  A+ AGI  V Q  ++ DNLSV +NI +G +      +D     R   
Sbjct: 64  VDGQPLPPGQPRAALTAGIGMVHQHFTLADNLSVLDNIMLGTQPLWQWRLDGHAA-RGKV 122

Query: 123 KFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFE 182
             + E FG+ + P+ ++G+ S+  +Q VEI +A+Y+ A+VLILDEPT+ LT  E E LF 
Sbjct: 123 LALAERFGLAVRPQARVGELSVGERQRVEIVKALYRGARVLILDEPTAVLTPHEAETLFS 182

Query: 183 VVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKL 242
            +  L  +G+++IFISH+L+E+  + D+++VLR G+ +   +    TK ++ E+MVGR +
Sbjct: 183 TLAQLIAEGLSVIFISHKLDEVLRVSDRIAVLRGGKLVALCAAAQTTKAELAELMVGRVV 242

Query: 243 ---EKFYIKEAHE-------PGEVVLE---VKNLSGER-FENVSFSLRRGEILGFAGLVG 288
              E+   + A +       P  + LE    +  +G      VS  +R GEI+G AG+ G
Sbjct: 243 AMPERVARRSAEDGANGNAAPPVLALEHVGARAANGRALLREVSLQVRAGEIVGIAGVSG 302

Query: 289 AGRTELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIM 348
            G+  L E   G      G I + GK +    P   I  G+  VPEDR  +G++  +++ 
Sbjct: 303 NGQAALAELASGMLEASEGRITLAGKPMSAK-PRAWIGAGVARVPEDRHAIGVVGDLAVW 361

Query: 349 HNVSLPSLD--RIKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLA 406
            N     L   R  +   I     +  A   +  FD+R A  D     +SGGN QK++L 
Sbjct: 362 ENAVSEQLSEPRFSRWGVIRRAAAQRFARDLVARFDVRTAGIDVPARTMSGGNMQKLILG 421

Query: 407 KWLALK-----PKILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMS 461
           + L+++     P++++  +PT G+D+GA A +   +   A+EG  V++IS +L E+  ++
Sbjct: 422 RALSVRGEGSAPRLVVASQPTWGLDIGAVAYVRARLLDAAREGAAVLLISEDLDELHALA 481

Query: 462 DRIAVMSFGKL 472
           DRIAVM  G L
Sbjct: 482 DRIAVMHAGHL 492



 Score =  100 bits (249), Expect = 1e-25
 Identities = 70/229 (30%), Positives = 118/229 (51%), Gaps = 16/229 (6%)

Query: 269 ENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEINHPLDAIEQG 328
           +++S  L+RGE+L   G  GAG++ L+  +FG      G + ++G+ +    P  A+  G
Sbjct: 22  DDISLELQRGEVLALLGENGAGKSTLVSILFGHYVADAGTVEVDGQPLPPGQPRAALTAG 81

Query: 329 IGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKG--PFISFKREKELADWAIKTFDIR-- 384
           IG+V +           ++  N+S+  LD I  G  P   ++ +   A   +     R  
Sbjct: 82  IGMVHQH---------FTLADNLSV--LDNIMLGTQPLWQWRLDGHAARGKVLALAERFG 130

Query: 385 -PAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKAEIYRIMSQLAKE 443
               P  +V  LS G +Q+V + K L    ++LILDEPT  +       ++  ++QL  E
Sbjct: 131 LAVRPQARVGELSVGERQRVEIVKALYRGARVLILDEPTAVLTPHEAETLFSTLAQLIAE 190

Query: 444 GVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAAG 492
           G+ VI IS +L EVL++SDRIAV+  GKL  +  A + ++ ++ +L  G
Sbjct: 191 GLSVIFISHKLDEVLRVSDRIAVLRGGKLVALCAAAQTTKAELAELMVG 239


Lambda     K      H
   0.318    0.138    0.385 

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: 614
Number of extensions: 38
Number of successful extensions: 9
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: 494
Length of database: 530
Length adjustment: 35
Effective length of query: 459
Effective length of database: 495
Effective search space:   227205
Effective search space used:   227205
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 (21.7 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