GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mglA in Pseudomonas fluorescens FW300-N2E3

Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate AO353_20820 AO353_20820 sugar ABC transporter ATP-binding protein

Query= TCDB::P0AAG8
         (506 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_20820 AO353_20820 sugar ABC
           transporter ATP-binding protein
          Length = 517

 Score =  335 bits (860), Expect = 2e-96
 Identities = 185/493 (37%), Positives = 298/493 (60%), Gaps = 7/493 (1%)

Query: 13  LLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILF 72
           +L +SGI K++     L  ++L +    + AL GENGAGKSTL K + G+    +G + F
Sbjct: 9   VLSVSGIGKTY-AQPVLTGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQF 67

Query: 73  QGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYRETKA 132
           QG++    S  +A E GI MV QELNL+   SV +N++L   P+ G ++ + ++ +   A
Sbjct: 68  QGRDYRPGSRTQAEELGIRMVMQELNLLPTLSVAENLFLDNLPSNGGWISRKQLRKAAIA 127

Query: 133 IFDELDID-IDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTI 191
              ++ +D IDP   VG L +   QM+EIA+    +  ++I+DEPT+ LT +EV  LF  
Sbjct: 128 AMAQVGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQ 187

Query: 192 IRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSLN 251
           I +L+ RG  I+YISH++EE+ ++   + VLRDG  +  EP+A    ++++ +MVGR L 
Sbjct: 188 ITRLQARGVAIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVNLMVGRELG 247

Query: 252 QRFPDKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLFG 311
           +         G   L V+ L+  R   +RDVSF++  GEI GI+GL+GA RT+++  +FG
Sbjct: 248 EHIDLGPRHIGAPALTVKGLS--RSDKVRDVSFEVRSGEIFGISGLIGAGRTELLRLIFG 305

Query: 312 IREKSAGTITLHG--KQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRN 369
                +GT+ L    + ++  +  +A+ HG AL+TE+R+  G+     I  N  + N+  
Sbjct: 306 ADAADSGTVALGSPAQVVSIRSPADAVGHGIALITEDRKGEGLLLTQSISANIALGNMPV 365

Query: 370 YKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILM 429
             +  G++++    +  Q  ID+MR+++      +  LSGGNQQKV+IGRWL  +  +L+
Sbjct: 366 ISSG-GIVNSGDEMALAQRQIDAMRIRSSSPAQLVSELSGGNQQKVVIGRWLERECSVLL 424

Query: 430 LDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVD 489
            DEPTRGIDVGAKF+IY L+ EL ++GK ++++SS++ EL+ I DRI V+S G +    +
Sbjct: 425 FDEPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRLIDTFE 484

Query: 490 TKTTTQNEILRLA 502
             + TQ+++L  A
Sbjct: 485 RDSWTQDDLLAAA 497


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: 573
Number of extensions: 24
Number of successful extensions: 9
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: 517
Length adjustment: 35
Effective length of query: 471
Effective length of database: 482
Effective search space:   227022
Effective search space used:   227022
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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