GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Escherichia coli BW25113

Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate 18115 b4087 fused D-allose transporter subunits of ABC superfamily: ATP-binding components (NCBI)

Query= TCDB::P0AAG8
         (506 letters)



>FitnessBrowser__Keio:18115
          Length = 510

 Score =  372 bits (956), Expect = e-107
 Identities = 202/495 (40%), Positives = 306/495 (61%), Gaps = 11/495 (2%)

Query: 14  LEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILFQ 73
           + M+GI KSF  V AL +VNL V P  IHAL+GENGAGKSTL+K L GI++   GTI   
Sbjct: 6   ISMAGIGKSFGPVHALKSVNLTVYPGEIHALLGENGAGKSTLMKVLSGIHEPTKGTITIN 65

Query: 74  GKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGM----FVDQDKMYRE 129
               +    K A + GI +++QEL+++ + +V++N+++GR+ TK +     +D  +M   
Sbjct: 66  NISYNKLDHKLAAQLGIGIIYQELSVIDELTVLENLYIGRHLTKKICGVNIIDWREMRVR 125

Query: 130 TKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLF 189
              +   + + +D   +V  LS+S  QM+EIAK    +AK++IMDEPTSSLT KEV++LF
Sbjct: 126 AAMMLLRVGLKVDLDEKVANLSISHKQMLEIAKTLMLDAKVIIMDEPTSSLTNKEVDYLF 185

Query: 190 TIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRS 249
            I+ +L++ G  IVYISHK+ EI ++CD  TV++DG  + +  ++ ++ D I+ +MVGR 
Sbjct: 186 LIMNQLRKEGTAIVYISHKLAEIRRICDRYTVMKDGSSVCSGIVSDVSNDDIVRLMVGRE 245

Query: 250 LNQRF----PDKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDI 305
           L  RF     +  N   E + EVRN+TS  +  +RD+SF + +GEILG AGLVG+ RT++
Sbjct: 246 LQNRFNAMKENVSNLAHETVFEVRNVTSRDRKKVRDISFSVCRGEILGFAGLVGSGRTEL 305

Query: 306 VETLFGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLIS 365
           +  LFG+ +++ G I L+GK I+  +  +A+  G A +TE RR  G +    I  N  IS
Sbjct: 306 MNCLFGVDKRAGGEIRLNGKDISPRSPLDAVKKGMAYITESRRDNGFFPNFSIAQNMAIS 365

Query: 366 NI---RNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLL 422
                  YK  +GL      +   +   + + +K       I  LSGGNQQKV+I +WL 
Sbjct: 366 RSLKDGGYKGAMGLFHEVDEQRTAENQRELLALKCHSVNQNITELSGGNQQKVLISKWLC 425

Query: 423 TQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNG 482
             PE+++ DEPTRGIDVGAK EIY+++ +LA  GK I+++SSE+PE++ + DRI V   G
Sbjct: 426 CCPEVIIFDEPTRGIDVGAKAEIYKVMRQLADDGKVILMVSSELPEIITVCDRIAVFCEG 485

Query: 483 LVSGIVDTKTTTQNE 497
            ++ I+  +     E
Sbjct: 486 RLTQILTNRDDMSEE 500


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: 625
Number of extensions: 28
Number of successful extensions: 8
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: 510
Length adjustment: 34
Effective length of query: 472
Effective length of database: 476
Effective search space:   224672
Effective search space used:   224672
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