GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mglA in Pseudomonas simiae WCS417

Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate GFF4164 PS417_21330 L-arabinose transporter ATP-binding protein

Query= TCDB::P0AAG8
         (506 letters)



>lcl|FitnessBrowser__WCS417:GFF4164 PS417_21330 L-arabinose
           transporter ATP-binding protein
          Length = 499

 Score =  389 bits (1000), Expect = e-112
 Identities = 206/492 (41%), Positives = 317/492 (64%), Gaps = 7/492 (1%)

Query: 14  LEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILFQ 73
           L  +GI K FPGVKAL  ++ + RP  +HALMGENGAGKSTLLK L G Y   SGT+   
Sbjct: 6   LRFNGIGKEFPGVKALSQISFEARPREVHALMGENGAGKSTLLKILGGAYLPSSGTLQIG 65

Query: 74  GKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYRETKAI 133
            + +DF SA +++  G++++HQEL+LV + +V +N++LG  PT+   V++ ++ ++  A 
Sbjct: 66  EQTMDFKSAADSIACGVAVIHQELHLVPEMTVAENLFLGHLPTRFGVVNRSQLRKQALAC 125

Query: 134 FDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTIIR 193
              L  +IDP  ++G LS+ Q Q++EIAKA S  A ++  DEPTSSL+ +E++ L  II 
Sbjct: 126 LKGLADEIDPDEKLGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAIIT 185

Query: 194 KLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIAT-EPLAGLTMDKIIAMMVGRSLNQ 252
           +L++ G  ++Y+SH+MEE+F++C+ VTV +DG+++ T + +  L+ D+++  MVGR +  
Sbjct: 186 RLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFDDMNALSHDQLVTCMVGRDIQD 245

Query: 253 RFPDKENKPGEVILEVRNL--TSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLF 310
            +  ++ + GEV L+V  L    LR+P    VS ++HKGEILG+ GLVGA RT++   L 
Sbjct: 246 IYDYRQREQGEVALKVEGLLGPGLREP----VSLNVHKGEILGLFGLVGAGRTELFRLLS 301

Query: 311 GIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNY 370
           G+   +AG++ L G+ +   +  +AI  G  L  E+R+  GI     +  N  IS    +
Sbjct: 302 GLTRSTAGSLALCGQTLQLRSPRDAIAAGVLLCPEDRKKEGIIPLSSVAENINISARGAH 361

Query: 371 KNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILML 430
                LL +    ++    I +M+VKTP    +I  LSGGNQQK I+GRWL    ++L+L
Sbjct: 362 STFGWLLRDGWETTNADRQIKAMKVKTPNAEQKIMYLSGGNQQKAILGRWLSMPMKVLLL 421

Query: 431 DEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDT 490
           DEPTRGID+GAK EIYQ+I  LA  G  +I++SS++ E++GI+DRILVMS G ++G +  
Sbjct: 422 DEPTRGIDIGAKSEIYQIIHNLAASGIAVIVVSSDLMEVMGISDRILVMSEGALTGELTR 481

Query: 491 KTTTQNEILRLA 502
               +  +L+LA
Sbjct: 482 DQADEARLLQLA 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: 578
Number of extensions: 30
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 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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