Alignments for a candidate for mglA in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglA in Pseudomonas fluorescens FW300-N2C3

Align Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized)
to candidate AO356_23205 AO356_23205 D-ribose transporter ATP-binding protein

Query= SwissProt::P23924
         (506 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_23205
          Length = 517

 Score =  461 bits (1186), Expect = e-134
 Identities = 235/493 (47%), Positives = 340/493 (68%), Gaps = 4/493 (0%)

Query: 12  YLLEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGSIV 71
           YLLE+  ++K FPGV AL +V L VRP S+ ALMGENGAGKSTL+K + GIYQ D+G + 
Sbjct: 25  YLLEVVNVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELR 84

Query: 72  FQGKEVDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGM-FVDQDKMYQDT 130
            +GK V F +   AL+ GI+M+HQELNL+   S+ +N+W+GR    G+  VD  +M++ T
Sbjct: 85  LRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGLHMVDHGEMHRCT 144

Query: 131 KAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFT 190
             + + L I +DP  +VG LS+++ QM+EIAKA SY++ I+IMDEPTS++TE EV HLF+
Sbjct: 145 ARLLERLRIKLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITETEVAHLFS 204

Query: 191 IIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKIIAMMVGRSL 250
           II  LK +G GI+YI+HKM E+F + DE+ + RDG +I  Q  + +D D +I+MMVGR L
Sbjct: 205 IIADLKSQGKGIIYITHKMNEVFAIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGREL 264

Query: 251 NQRFPDKENKPGDVILEVRHLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLF 310
           +Q FP +E   G+++L VR L+       + VSFDLH GEILGIAGL+G+ RT++ E +F
Sbjct: 265 SQLFPVREQPIGELVLSVRDLS--LDGIFKGVSFDLHAGEILGIAGLMGSGRTNVAEAIF 322

Query: 311 GIREKSSGTITLHGKKINNHTANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNY 370
           G+   + G I L G+ +     + AI  GFAL+TE+R+ +G++  L +  N  ++ + +Y
Sbjct: 323 GVTPSTGGEIRLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHY 382

Query: 371 KNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILML 430
               G +    +++  + +   +RVKTP     I +LSGGNQQK ++ RWL+T P IL+L
Sbjct: 383 VGN-GFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILIL 441

Query: 431 DEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDT 490
           DEPTRGIDVGAK EIY+LI+ LA +G  +I+ISSE+PE+LG++DR++VM  G + G +D 
Sbjct: 442 DEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDR 501

Query: 491 KTTTQNEILRLAS 503
              TQ  +++LAS
Sbjct: 502 SEATQERVMQLAS 514



 Score = 70.5 bits (171), Expect = 1e-16
 Identities = 53/248 (21%), Positives = 111/248 (44%), Gaps = 10/248 (4%)

Query: 8   PSGEYLLEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKDS 67
           P GE +L +R +  S  G+     V+ ++    I  + G  G+G++ + + +FG+     
Sbjct: 274 PIGELVLSVRDL--SLDGI--FKGVSFDLHAGEILGIAGLMGSGRTNVAEAIFGVTPSTG 329

Query: 68  GSIVFQGKEVDFHSAKEALENGISMVHQELNL---VLQRSVMDNMWLGRYP--TKGMFVD 122
           G I   G+ V       A+E G +++ ++  L       SV++NM +   P      F+ 
Sbjct: 330 GEIRLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYVGNGFIQ 389

Query: 123 QDKMYQDTKAIFDELDIDIDPRAR-VGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLT 181
           Q  +    + +  +L +      + + TLS    Q   +A+    N +I+I+DEPT  + 
Sbjct: 390 QKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGID 449

Query: 182 EKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKI 241
                 ++ +I  L   G  ++ IS ++ E+  + D + ++ +G  + T        +++
Sbjct: 450 VGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERV 509

Query: 242 IAMMVGRS 249
           + +  G S
Sbjct: 510 MQLASGLS 517


Lambda     K      H
   0.319    0.137    0.388 

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: 631
Number of extensions: 26
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: 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 ( 7.4 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