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_21385 AO353_21385 D-ribose transporter ATP-binding protein

Query= TCDB::P0AAG8
         (506 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_21385 AO353_21385 D-ribose
           transporter ATP-binding protein
          Length = 521

 Score =  459 bits (1182), Expect = e-134
 Identities = 235/498 (47%), Positives = 341/498 (68%), Gaps = 4/498 (0%)

Query: 7   PSSGEYLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKD 66
           P    YLLE+  ++K FPGV AL +V L+VRP S+ ALMGENGAGKSTL+K + GIYQ D
Sbjct: 21  PVDEPYLLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPD 80

Query: 67  SGTILFQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGM-FVDQDK 125
           +G +  +GK + F +   AL+ GI+M+HQELNL+   S+ +N+W+GR    G   +D  +
Sbjct: 81  AGELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHMIDHRE 140

Query: 126 MYRETKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEV 185
           M+R T  + + L I++DP  +VG LS+++ QM+EIAKA SY++ I+IMDEPTS++T+KEV
Sbjct: 141 MHRCTAQLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEV 200

Query: 186 NHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMM 245
            HLF+II  LK +G GI+YI+HKM E+F + DEV V RDG +I  +    +  D +I+MM
Sbjct: 201 AHLFSIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMM 260

Query: 246 VGRSLNQRFPDKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDI 305
           VGR L+Q FP +E   G++++ VR+L        + VSFDLH GEILGIAGL+G+ RT++
Sbjct: 261 VGRELSQLFPVREKPIGDLLMSVRDLR--LDGVFKGVSFDLHAGEILGIAGLMGSGRTNV 318

Query: 306 VETLFGIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLIS 365
            E +FGI     G I L G+ +   + + AI  GFAL+TE+R+ +G++  L +  N  ++
Sbjct: 319 AEAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMA 378

Query: 366 NIRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQP 425
            + +Y    G +    +++  + +   +RVKTP     I +LSGGNQQK ++ RWL+T P
Sbjct: 379 VLPHYAGN-GFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNP 437

Query: 426 EILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVS 485
            IL+LDEPTRGIDVGAK EIY+LI+ LA +G  +I+ISSE+PE+LG++DR++VM  G + 
Sbjct: 438 RILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLM 497

Query: 486 GIVDTKTTTQNEILRLAS 503
           G +D    TQ  +++LAS
Sbjct: 498 GTLDRSEATQERVMQLAS 515



 Score = 72.4 bits (176), Expect = 4e-17
 Identities = 50/225 (22%), Positives = 103/225 (45%), Gaps = 6/225 (2%)

Query: 32  VNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILFQGKEIDFHSAKEALENGIS 91
           V+  +    I  + G  G+G++ + + +FGI   D G I   G+ +       A+E G +
Sbjct: 295 VSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFA 354

Query: 92  MVHQELNL---VLQRSVMDNMWLGRYP--TKGMFVDQDKMYRETKAIFDELDIDIDPRAR 146
           ++ ++  L       SV++NM +   P      F+ Q  +    + +  +L +      +
Sbjct: 355 LLTEDRKLSGLFPCLSVLENMEMAVLPHYAGNGFIQQKALRALCEDMCKKLRVKTPSLEQ 414

Query: 147 -VGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTIIRKLKERGCGIVYI 205
            + TLS    Q   +A+    N +I+I+DEPT  +       ++ +I  L   G  ++ I
Sbjct: 415 CIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMI 474

Query: 206 SHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSL 250
           S ++ E+  + D V V+ +G  + T   +  T ++++ +  G S+
Sbjct: 475 SSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASGMSV 519


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: 635
Number of extensions: 27
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: 521
Length adjustment: 35
Effective length of query: 471
Effective length of database: 486
Effective search space:   228906
Effective search space used:   228906
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