Alignments for a candidate for mglA in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments 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 GFF2162 PS417_11030 L-arabinose transporter ATP-binding protein

Query= TCDB::P0AAG8
         (506 letters)



>FitnessBrowser__WCS417:GFF2162
          Length = 500

 Score =  386 bits (992), Expect = e-112
 Identities = 208/492 (42%), Positives = 316/492 (64%), Gaps = 7/492 (1%)

Query: 14  LEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILFQ 73
           L   GI K+FPGVKALD ++    P  +HALMGENGAGKSTLLK L G Y  +SGT+   
Sbjct: 6   LRFDGIGKTFPGVKALDGISFSAHPGQVHALMGENGAGKSTLLKILGGAYIPNSGTLHIG 65

Query: 74  GKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYRETKAI 133
            + + F SA +++ +G++++HQEL+LV + SV +N++LG  P++   V++  + ++  A 
Sbjct: 66  EQVMAFKSAADSIASGVAVIHQELHLVPEMSVAENLFLGHLPSRFGVVNRGLLRKQALAC 125

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

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

Query: 253 RFPDKENKPGEVILEVRNL--TSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLF 310
            +  +  + GEV L+V  L    LR+P    VSF++ KGEILG+ GLVGA RT++   L 
Sbjct: 246 IYDYRPREHGEVALKVDGLLGPGLREP----VSFNVRKGEILGLFGLVGAGRTELFRLLS 301

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

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

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

Query: 491 KTTTQNEILRLA 502
           +  T++ +L+LA
Sbjct: 482 EHATESNLLQLA 493



 Score = 62.4 bits (150), Expect = 4e-14
 Identities = 52/248 (20%), Positives = 112/248 (45%), Gaps = 11/248 (4%)

Query: 10  GEYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGT 69
           GE  L++ G+    PG++  + V+  VR   I  L G  GAG++ L + L G+ +  +G 
Sbjct: 255 GEVALKVDGLLG--PGLR--EPVSFNVRKGEILGLFGLVGAGRTELFRLLSGLERASAGQ 310

Query: 70  ILFQGKEIDFHSAKEALENGISMVHQELN---LVLQRSVMDNMWL---GRYPTKGMFVDQ 123
           +   G+ +   S ++A+  G+ +  ++     ++   SV +N+ +   G + T G  + +
Sbjct: 311 LELCGEPLHLQSPRDAIAAGVLLCPEDRKKEGIIPLSSVAENINISARGAHSTFGWLLRE 370

Query: 124 DKMYRETKAIFDELDIDIDPRA-RVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTE 182
                      + + +     A ++  LS    Q   + +  S   K++++DEPT  +  
Sbjct: 371 GWEKGNADQQINAMKVKTPNAAQKIMYLSGGNQQKSILGRWLSMPMKVLLLDEPTRGIDI 430

Query: 183 KEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKII 242
                ++ II  L  +G  ++ +S  + E+  + D + VL +G     +     T   ++
Sbjct: 431 GAKAEIYQIIHNLAAQGIAVIVVSSDLMEVMGIADRILVLCEGALRGEQTREHATESNLL 490

Query: 243 AMMVGRSL 250
            + + RS+
Sbjct: 491 QLALPRSV 498


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: 584
Number of extensions: 26
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 506
Length of database: 500
Length adjustment: 34
Effective length of query: 472
Effective length of database: 466
Effective search space:   219952
Effective search space used:   219952
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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources