GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Pseudomonas fluorescens FW300-N1B4

Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate Pf1N1B4_410 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)

Query= TCDB::P0AAG8
         (506 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_410
          Length = 514

 Score =  382 bits (981), Expect = e-110
 Identities = 203/492 (41%), Positives = 311/492 (63%), Gaps = 7/492 (1%)

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

Query: 74  GKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYRETKAI 133
            ++  F S  +++ +G++++HQEL+LV + +V +N++LG  P     +++  + ++  A 
Sbjct: 76  EQKRIFKSTADSIGSGVAVIHQELHLVPEMTVAENLFLGHLPASFGLINRGVLRQQALAC 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 E ++ LT D+++  MVGR +  
Sbjct: 196 RLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRFVRTFEDMSALTHDQLVTCMVGRDIQD 255

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

Query: 311 GIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNY 370
           G+   +AG + L G+++  H+  +AI  G  L  E+R+  GI     +  N  IS    +
Sbjct: 312 GLTRNTAGRLELRGRELKLHSPRDAIAAGILLCPEDRKKEGILPLASVAENINISARGAH 371

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

Query: 431 DEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDT 490
           DEPTRGID+GAK EIYQ+I  LA  G  +I++SS++ E++GI+DRILV+  G + G +  
Sbjct: 432 DEPTRGIDIGAKAEIYQIIHNLAASGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELTR 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: 604
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: 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 (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