Alignments for a candidate for mglA in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglA in Pseudomonas putida KT2440

Align Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate PP_2759 PP_2759 ribose ABC transporter - ATP-binding subunit

Query= TCDB::P0AAG8
         (506 letters)



>FitnessBrowser__Putida:PP_2759
          Length = 512

 Score =  331 bits (848), Expect = 4e-95
 Identities = 174/492 (35%), Positives = 296/492 (60%), Gaps = 4/492 (0%)

Query: 13  LLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILF 72
           +LE+ GI K+F   +ALD  +L+V   S+H L+GENGAGKSTL+K L GI++ D+G++L 
Sbjct: 5   VLELRGIVKTFGATRALDGASLRVAAGSVHGLVGENGAGKSTLIKVLAGIHRPDAGSLLL 64

Query: 73  QGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGMFVDQDKMYRETKA 132
            G+     S ++    GI  +HQE  L  + +V + ++ G     G  +D+    RE   
Sbjct: 65  DGQPHGHFSPRQVERLGIGFIHQERLLPARFTVGEALFFGHERRFGPLLDRRSQQREAAR 124

Query: 133 IFDE-LDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTI 191
           + D+   + +   A +G LS ++ QM++I +A     ++++ DEP+ +L ++EV  L  I
Sbjct: 125 LLDDYFGLRLPANALIGELSSAEQQMVQIVRALLIKPRVLVFDEPSVALVQREVERLLRI 184

Query: 192 IRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSLN 251
           +++L++ G  IVYISH ++EI  LCD VTVLR+G+ +A       ++++I  +MV R + 
Sbjct: 185 VQRLRDDGLAIVYISHYLQEIEALCDRVTVLRNGRDVAEVSPRNTSLEQITRLMVNREVG 244

Query: 252 QRFPDKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLFG 311
           + +P      G ++L+VR L   R  + + +   + +GEI+G+ GLVG+   +++ +LFG
Sbjct: 245 ELYPKVAVPAGALLLDVRGLGRAR--AYQGIDLQVRRGEIVGLTGLVGSGAKELLRSLFG 302

Query: 312 IREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNYK 371
           +    +G + L G+ ++  +  EA+  G AL+ EERR  G+   L +  N+ ++ +  + 
Sbjct: 303 LAPPDSGEVRLDGQPLSLRSPREAVAQGVALMPEERRRQGVALDLSVQENTTLAALSRFV 362

Query: 372 NKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILMLD 431
            ++GLL  +R +  T  +I+ +R+K  G   ++  LSGGNQQKV + +W      + +LD
Sbjct: 363 -RLGLLSPARERHTTLELIERLRIKAHGAHAKVRQLSGGNQQKVALAKWFARCSSLYLLD 421

Query: 432 EPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDTK 491
           EP+ GIDVGAK EIY+LI EL K+G G++I+SS++PEL+G+ DRI VM  G ++      
Sbjct: 422 EPSVGIDVGAKVEIYRLIGELVKEGAGVLILSSDLPELIGLCDRIHVMHRGAIAARFAAG 481

Query: 492 TTTQNEILRLAS 503
               + +L +A+
Sbjct: 482 EANSDRLLAVAT 493



 Score = 92.0 bits (227), Expect = 4e-23
 Identities = 66/256 (25%), Positives = 125/256 (48%), Gaps = 14/256 (5%)

Query: 9   SGEYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSG 68
           +G  LL++ G+ ++    +A   ++L+VR   I  L G  G+G   LL+ LFG+   DSG
Sbjct: 254 AGALLLDVRGLGRA----RAYQGIDLQVRRGEIVGLTGLVGSGAKELLRSLFGLAPPDSG 309

Query: 69  TILFQGKEIDFHSAKEALENGISMVHQELN---LVLQRSVMDNMWLG---RYPTKGMFVD 122
            +   G+ +   S +EA+  G++++ +E     + L  SV +N  L    R+   G+   
Sbjct: 310 EVRLDGQPLSLRSPREAVAQGVALMPEERRRQGVALDLSVQENTTLAALSRFVRLGLLSP 369

Query: 123 QDKMYRETKAIFDELDIDID-PRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLT 181
             + +  T  + + L I      A+V  LS    Q + +AK F+  + + ++DEP+  + 
Sbjct: 370 ARERHT-TLELIERLRIKAHGAHAKVRQLSGGNQQKVALAKWFARCSSLYLLDEPSVGID 428

Query: 182 EKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKI 241
                 ++ +I +L + G G++ +S  + E+  LCD + V+  G   A         D++
Sbjct: 429 VGAKVEIYRLIGELVKEGAGVLILSSDLPELIGLCDRIHVMHRGAIAARFAAGEANSDRL 488

Query: 242 IAMMVG--RSLNQRFP 255
           +A+  G  R+ N+  P
Sbjct: 489 LAVATGAQRAQNEERP 504


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: 521
Number of extensions: 22
Number of successful extensions: 8
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: 512
Length adjustment: 34
Effective length of query: 472
Effective length of database: 478
Effective search space:   225616
Effective search space used:   225616
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