GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Phyllobacterium brassicacearum STM 196

Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate WP_106714515.1 CU102_RS28785 sugar ABC transporter ATP-binding protein

Query= TCDB::P0AAG8
         (506 letters)



>NCBI__GCF_003010955.1:WP_106714515.1
          Length = 513

 Score =  488 bits (1256), Expect = e-142
 Identities = 252/494 (51%), Positives = 350/494 (70%), Gaps = 3/494 (0%)

Query: 11  EYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTI 70
           E+LL    I K FPGV ALDNV  +++  ++HALMGENGAGKSTL+K L GIY  D G +
Sbjct: 21  EFLLNAENIRKEFPGVLALDNVQFRLKRGTVHALMGENGAGKSTLMKILAGIYIPDQGEV 80

Query: 71  LFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGM-FVDQDKMYRE 129
             +G  I   S  +ALENGI+M+HQELNL+   +V +N+W+ R P  G  FVD  KMY  
Sbjct: 81  YLKGLPIRLKSPLDALENGIAMIHQELNLMPFMTVAENIWIRREPKNGFGFVDHGKMYDM 140

Query: 130 TKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLF 189
           T  +F  L+I +DP ++V  LSV+  QM+EIAKA SY + ++IMDEPTS+LTE+EV HLF
Sbjct: 141 TADLFKRLNITLDPESQVRDLSVANRQMVEIAKAVSYESDVLIMDEPTSALTEREVEHLF 200

Query: 190 TIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRS 249
            IIR L+E+G GIVYI+HKM E+F++ DE +V RDG++I T     +T D II MMVGR 
Sbjct: 201 QIIRDLREQGIGIVYITHKMNELFEIADEFSVFRDGRYIGTHASTDVTRDDIIKMMVGRE 260

Query: 250 LNQRFPDKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETL 309
           + Q FP +    G+V+L V++L SL+     DVSFD+  GEILG+AGLVG+ R+++ ET+
Sbjct: 261 ITQMFPKEIVPIGDVVLSVKDL-SLKNV-FHDVSFDVRAGEILGVAGLVGSGRSNVAETI 318

Query: 310 FGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRN 369
           FG+   ++GTIT+ G+ I  ++  +AI+HG A +TE+R+ TG    LD+  N  I+ +++
Sbjct: 319 FGVTPATSGTITIKGQPIKMNSPTQAISHGMAFITEDRKETGCLLILDVLENMQIAVLQD 378

Query: 370 YKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILM 429
              K G ++  ++    + + D++RVKTP     + +LSGGNQQKV+IGRWLLT P+IL+
Sbjct: 379 RFVKYGFVEEKQIAKACKAMSDTLRVKTPSLEETVENLSGGNQQKVLIGRWLLTNPKILI 438

Query: 430 LDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVD 489
           LDEPTRGIDVGAK EI++LI++LAK G  +I+ISSEMPE+LG++DRI+VM  G V+G +D
Sbjct: 439 LDEPTRGIDVGAKAEIHRLISQLAKTGVAVIMISSEMPEVLGMSDRIMVMHEGRVTGFLD 498

Query: 490 TKTTTQNEILRLAS 503
               TQ +++ LAS
Sbjct: 499 RAEATQVKVMELAS 512


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: 615
Number of extensions: 23
Number of successful extensions: 6
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: 513
Length adjustment: 34
Effective length of query: 472
Effective length of database: 479
Effective search space:   226088
Effective search space used:   226088
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