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_040660822.1 ON16_RS07570 ATP-binding cassette domain-containing protein

Query= TCDB::P0AAG8
         (506 letters)



>NCBI__GCF_000307265.1:WP_040660822.1
          Length = 499

 Score =  607 bits (1565), Expect = e-178
 Identities = 299/497 (60%), Positives = 389/497 (78%), Gaps = 2/497 (0%)

Query: 11  EYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTI 70
           E LL+M+ I+K FPGVKALD+V+L V+P ++HALMGENGAGKSTL+KCLFGIY KD G I
Sbjct: 4   EVLLQMTDISKEFPGVKALDHVSLTVKPGTVHALMGENGAGKSTLMKCLFGIYGKDEGKI 63

Query: 71  LFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPT-KGMFVDQDKMYRE 129
             +GKE+ F S+KEA+E+G++MVHQELN  L+RSVMDN+WLGRYPT  G+ V++ KMY +
Sbjct: 64  FLEGKEVSFKSSKEAMESGVAMVHQELNQALKRSVMDNIWLGRYPTIGGVMVNEKKMYAD 123

Query: 130 TKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLF 189
           TKAIFD+L ID+DP   + T+ VSQ QM+EIAKA SYN+K+V+ DEPTSSLTE+EV HLF
Sbjct: 124 TKAIFDDLGIDVDPHRIMSTIPVSQRQMVEIAKAVSYNSKVVVFDEPTSSLTEQEVEHLF 183

Query: 190 TIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRS 249
            II  L++RG GI+YISHKM EI Q+ DEVT++RDG W+AT+    L    II +MVGR 
Sbjct: 184 RIINMLRDRGVGIIYISHKMAEILQISDEVTIMRDGCWVATKSAGELDTATIIKLMVGRE 243

Query: 250 LNQRFPDKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETL 309
           L  +FP K N PGEV LEV +LT+ +   + DVSF   +GEILG+AGL  + RT+ +E +
Sbjct: 244 LGNQFPIKTNTPGEVYLEVEHLTA-QYSQLEDVSFSARRGEILGLAGLDASGRTETLENI 302

Query: 310 FGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRN 369
           FGI  + +GTI L G+++ N N+ E+I +GFAL+TEERR+TGI+  L I  N++IS+++ 
Sbjct: 303 FGIATRKSGTIRLGGREVKNRNSRESIRNGFALLTEERRATGIFGILSIRENTVISSLKK 362

Query: 370 YKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILM 429
           +     +L++  M+ DTQW ID+MR KTP   T+I SLSGGNQQKVI+GRWLLT PE+L+
Sbjct: 363 HLRAGFILNDKTMRQDTQWSIDAMRTKTPSQHTKIRSLSGGNQQKVILGRWLLTNPEVLL 422

Query: 430 LDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVD 489
           LDEPTRGIDVGAKFEIYQLI +LA KGK ++++SSEMPELLG+ DRILVMS G ++G VD
Sbjct: 423 LDEPTRGIDVGAKFEIYQLIIDLANKGKTVLMVSSEMPELLGVCDRILVMSGGRLAGEVD 482

Query: 490 TKTTTQNEILRLASLHL 506
            K+TTQ EI+ LA+ ++
Sbjct: 483 AKSTTQEEIMTLAAKYV 499


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: 658
Number of extensions: 23
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.

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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