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_040662390.1 ON16_RS11055 sugar ABC transporter ATP-binding protein

Query= TCDB::P0AAG8
         (506 letters)



>NCBI__GCF_000307265.1:WP_040662390.1
          Length = 499

 Score =  439 bits (1129), Expect = e-127
 Identities = 225/493 (45%), Positives = 328/493 (66%), Gaps = 2/493 (0%)

Query: 11  EYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTI 70
           EY++EM  INKSF GV  L NV   ++   + AL+GENGAGKSTL+K L G+Y +DSGT+
Sbjct: 3   EYIVEMENINKSFSGVPVLKNVRFTLKAGEVMALLGENGAGKSTLMKILSGVYVRDSGTM 62

Query: 71  LFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYRET 130
              G+E      K+A E G++++HQELN+    +V +N++LGR   KG+ ++  +M + T
Sbjct: 63  KIFGEEQGDLDTKKAQELGVAIIHQELNMCRHLTVAENIFLGREVRKGVTLNNREMVKRT 122

Query: 131 KAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFT 190
           + + D L ID+ P   VG L VS+ QM+EIAKA S +AKI+IMDEPTS+L+ KE++ LF 
Sbjct: 123 QEVLDSLKIDLSPNTVVGDLPVSKQQMVEIAKALSVHAKILIMDEPTSALSSKEIDELFR 182

Query: 191 IIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSL 250
           ++ +L+  GCGIVYISH+MEE+  + + VTV+RDG++I     A  TMD++IA MVGR +
Sbjct: 183 LVDQLRSEGCGIVYISHRMEELSHVANRVTVMRDGEFIMEGNFADYTMDQLIAKMVGRDI 242

Query: 251 NQRFPDKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLF 310
            ++FP  + + GE ILEV+NL + R   +RDVSFDL+ GEI+GIAGLVGA RT+    +F
Sbjct: 243 KEKFPRVQCQRGEKILEVKNLNAGRM--VRDVSFDLYAGEIVGIAGLVGAGRTETTRAIF 300

Query: 311 GIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNY 370
           GI  K +G I L GK ++     +AI  G  L  E+R+  G+   L +  N  I N+   
Sbjct: 301 GIDPKDSGEIVLDGKSVSIKKPIDAIKAGIVLTPEDRKRDGLCTKLGVRENLSIPNLDWL 360

Query: 371 KNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILML 430
            N +G ++  + +     V++ +++K         SLSGGNQQKV+IG+WL     ++M 
Sbjct: 361 SNGIGKVNQKKEREIADKVVEELQIKLSSVEINAESLSGGNQQKVVIGKWLARNSRVIMF 420

Query: 431 DEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDT 490
           DEPTRG+DVGAK EIY L+  L ++G G++ +SSE+PE+LGI+DRILVM +G ++G +  
Sbjct: 421 DEPTRGVDVGAKVEIYNLMNRLKQQGTGVLFVSSELPEILGISDRILVMCDGHLTGELPV 480

Query: 491 KTTTQNEILRLAS 503
              T+++IL  A+
Sbjct: 481 AEATEDKILSYAT 493


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: 619
Number of extensions: 21
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 506
Length of database: 499
Length adjustment: 34
Effective length of query: 472
Effective length of database: 465
Effective search space:   219480
Effective search space used:   219480
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.

Links

Downloads

Related tools

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