GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Oscillibacter ruminantium GH1

Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate WP_040658978.1 ON16_RS02070 ABC transporter ATP-binding protein

Query= TCDB::P0AAG8
         (506 letters)



>NCBI__GCF_000307265.1:WP_040658978.1
          Length = 519

 Score =  318 bits (815), Expect = 3e-91
 Identities = 184/498 (36%), Positives = 291/498 (58%), Gaps = 12/498 (2%)

Query: 11  EYLLEMSGINKSFP-GVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGT 69
           EY+++M GI K +P G+ A   V+L VR   IHALMGENGAGKSTL+K LFG+ Q  SG 
Sbjct: 4   EYVVQMKGITKVYPNGIAANQGVDLNVRKGEIHALMGENGAGKSTLMKMLFGLEQPTSGE 63

Query: 70  ILFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTK-GMFVDQDKMYR 128
           I   G++++  S   A+  G+ MVHQ   LV   +V +NM LG  P K G+F+D  K   
Sbjct: 64  IWVNGEKVNLTSPTVAIAKGVGMVHQHFMLVPSLTVAENMVLGMVPKKSGLFIDSGKAIE 123

Query: 129 ETKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHL 188
            TK   ++ ++ +DP ARV  + V   Q +EI KA    AKI+I+DEPT+ LT +E   L
Sbjct: 124 ITKEYAEKFNLHVDPTARVCDIPVGMKQKVEILKALVRGAKILILDEPTAVLTTQETTEL 183

Query: 189 FTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGR 248
           F  +  LKE+G  I++ISHK+ EI Q+ D +T+LR G+ +        + +KI  +MVGR
Sbjct: 184 FKELMSLKEQGYTIIFISHKLAEIMQITDRMTILRGGRSMGVYETKDESPEKISRLMVGR 243

Query: 249 SLNQRFPDKENKPGEVILEVRNLTSLRQ---PSIRDVSFDLHKGEILGIAGLVGAKRTDI 305
            +  +    + +PGE +L VR+L  + +     +  VSFDL +GEILGIAG+ G  + ++
Sbjct: 244 DVVLKVEKGKAQPGESVLRVRDLEYINEWGKKMLDKVSFDLRQGEILGIAGVEGNGQKEL 303

Query: 306 VETLFGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGF--NSL 363
           V+ LF +   +AG++ ++G  +   +  +    G +LV E+R    +Y   D G    +L
Sbjct: 304 VDMLFHLNTPNAGSVEVNGASVLGQSQRKIREMGVSLVPEDRM---LYGIADSGTIEENL 360

Query: 364 ISNIRNYK--NKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWL 421
           IS+    K  NK  L D   + ++   +I+   V       Q+  LSGGN QKV++ R  
Sbjct: 361 ISDRCGTKRLNKGPLFDMKAIHNECDQLIEDYTVLCKSGAQQVKMLSGGNIQKVVVAREF 420

Query: 422 LTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSN 481
              P++++ D+PTRGIDVGA   I + + EL++ G  ++++S+++ E++ ++D ++VM  
Sbjct: 421 SNNPKLIIADQPTRGIDVGATEFIRRKLVELSRSGVAVLLVSADLNEVMELSDSLIVMYG 480

Query: 482 GLVSGIVDTKTTTQNEIL 499
           G +S   +  +   +E++
Sbjct: 481 GRISAYFEDTSDLSDEVM 498



 Score = 84.0 bits (206), Expect = 1e-20
 Identities = 61/243 (25%), Positives = 126/243 (51%), Gaps = 11/243 (4%)

Query: 263 EVILEVRNLTSLRQPSI---RDVSFDLHKGEILGIAGLVGAKRTDIVETLFGIREKSAGT 319
           E +++++ +T +    I   + V  ++ KGEI  + G  GA ++ +++ LFG+ + ++G 
Sbjct: 4   EYVVQMKGITKVYPNGIAANQGVDLNVRKGEIHALMGENGAGKSTLMKMLFGLEQPTSGE 63

Query: 320 ITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNYKNKVGL-LD 378
           I ++G+++N  +   AI  G  +V +      +   L +  N ++  +     K GL +D
Sbjct: 64  IWVNGEKVNLTSPTVAIAKGVGMVHQHFM---LVPSLTVAENMVLGMV---PKKSGLFID 117

Query: 379 NSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLDEPTRGID 438
           + +    T+   +   +       ++  +  G +QKV I + L+   +IL+LDEPT  + 
Sbjct: 118 SGKAIEITKEYAEKFNLHVDP-TARVCDIPVGMKQKVEILKALVRGAKILILDEPTAVLT 176

Query: 439 VGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDTKTTTQNEI 498
                E+++ +  L ++G  II IS ++ E++ ITDR+ ++  G   G+ +TK  +  +I
Sbjct: 177 TQETTELFKELMSLKEQGYTIIFISHKLAEIMQITDRMTILRGGRSMGVYETKDESPEKI 236

Query: 499 LRL 501
            RL
Sbjct: 237 SRL 239


Lambda     K      H
   0.318    0.136    0.384 

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: 28
Number of successful extensions: 7
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: 506
Length of database: 519
Length adjustment: 35
Effective length of query: 471
Effective length of database: 484
Effective search space:   227964
Effective search space used:   227964
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 24 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