GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mglA in Pseudomonas fluorescens GW456-L13

Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate PfGW456L13_2121 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)

Query= TCDB::P0AAG8
         (506 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2121 L-arabinose
           transport ATP-binding protein AraG (TC 3.A.1.2.2)
          Length = 514

 Score =  388 bits (996), Expect = e-112
 Identities = 204/492 (41%), Positives = 316/492 (64%), Gaps = 7/492 (1%)

Query: 14  LEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILFQ 73
           L  +GI K+FPGVKALDN++    P  +HALMGENGAGKSTLLK L G Y   SG +   
Sbjct: 16  LRFNGIGKTFPGVKALDNISFVAHPGQVHALMGENGAGKSTLLKILGGAYTPCSGALQIG 75

Query: 74  GKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYRETKAI 133
            + +DF S  +++ +G++++HQEL+LV + +V +N++LG  P     +++  + ++  A 
Sbjct: 76  ERTMDFKSTADSIGSGVAVIHQELHLVPEMTVAENLFLGHLPASFGLINRSTLRQQALAC 135

Query: 134 FDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTIIR 193
              L  +IDP+ +VG LS+ Q Q++EIAKA S  A ++  DEPTSSL+ +E++ L  II 
Sbjct: 136 LKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAIIG 195

Query: 194 KLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIAT-EPLAGLTMDKIIAMMVGRSLNQ 252
           +L++ G  ++Y+SH+MEE+F++C+ VTV +DG+++ T + ++ LT D+++  MVGR +  
Sbjct: 196 RLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFDDMSQLTHDQLVTCMVGRDIQD 255

Query: 253 RFPDKENKPGEVILEVRNL--TSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLF 310
            +  +  + G V L+V  L    LR+P    VSF++HKGEILG+ GLVGA RT+++  L 
Sbjct: 256 IYDYRPRQRGAVALKVDGLLGPGLREP----VSFEVHKGEILGLFGLVGAGRTELLRLLS 311

Query: 311 GIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNY 370
           G+   SAG + L G ++   +  +AI  G  L  E+R+  GI     +  N  IS    +
Sbjct: 312 GLARHSAGQLKLRGHELKLRSPRDAIAAGILLCPEDRKKEGILPLASVAENINISARGAH 371

Query: 371 KNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILML 430
                LL     K + +  I +++VKTP    +I  LSGGNQQK I+GRWL    ++L+L
Sbjct: 372 STFGCLLRGLWEKDNAEQQIKALKVKTPNAAQKIMYLSGGNQQKAILGRWLSMPMKVLLL 431

Query: 431 DEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDT 490
           DEPTRGID+GAK EIYQ+I  LA +G  +I++SS++ E++GI+DRILV+  G + G +  
Sbjct: 432 DEPTRGIDIGAKAEIYQIIHNLAAEGIAVIVVSSDLMEVMGISDRILVLCEGALRGELSR 491

Query: 491 KTTTQNEILRLA 502
           +   ++ +L+LA
Sbjct: 492 EQANESNLLQLA 503


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: 607
Number of extensions: 32
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: 514
Length adjustment: 34
Effective length of query: 472
Effective length of database: 480
Effective search space:   226560
Effective search space used:   226560
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, 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