GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mglA in Pseudomonas fluorescens FW300-N2E2

Align Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized)
to candidate Pf6N2E2_523 Inositol transport system ATP-binding protein

Query= SwissProt::P23924
         (506 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_523 Inositol transport
           system ATP-binding protein
          Length = 517

 Score =  461 bits (1187), Expect = e-134
 Identities = 236/497 (47%), Positives = 341/497 (68%), Gaps = 4/497 (0%)

Query: 8   PSGEYLLEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKDS 67
           P   YLLE+  ++K FPGV AL +V L VRP S+ ALMGENGAGKSTL+K + GIYQ D+
Sbjct: 21  PDEPYLLEVVNVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDA 80

Query: 68  GSIVFQGKEVDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGM-FVDQDKM 126
           G +  +GK V F +   AL+ GI+M+HQELNL+   S+ +N+W+GR    G+  VD  +M
Sbjct: 81  GELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGLHMVDHGEM 140

Query: 127 YQDTKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVN 186
           ++ T  + + L I +DP  +VG LS+++ QM+EIAKA SY++ I+IMDEPTS++TE EV 
Sbjct: 141 HRCTARLLERLRIKLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITETEVA 200

Query: 187 HLFTIIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKIIAMMV 246
           HLF+II  LK +G GI+YI+HKM E+F + DE+ + RDG +I  Q  + +D D +I+MMV
Sbjct: 201 HLFSIIADLKSQGKGIIYITHKMNEVFAIADEVAVFRDGAYIGLQRADSMDGDSLISMMV 260

Query: 247 GRSLNQRFPDKENKPGDVILEVRHLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIV 306
           GR L+Q FP +E   GD++L VR L+       + VSFDLH GEILGIAGL+G+ RT++ 
Sbjct: 261 GRELSQLFPVREQPIGDLVLSVRDLS--LDGIFKGVSFDLHAGEILGIAGLMGSGRTNVA 318

Query: 307 ETLFGIREKSSGTITLHGKKINNHTANEAINHGFALVTEERRSTGIYAYLDIGFNSLISN 366
           E +FG+   + G I L G+ +     + AI  GFAL+TE+R+ +G++  L +  N  ++ 
Sbjct: 319 EAIFGVTPSTGGEILLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAV 378

Query: 367 IRNYKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPE 426
           + +Y    G +    +++  + +   +RVKTP     I +LSGGNQQK ++ RWL+T P 
Sbjct: 379 LPHYVGN-GFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPR 437

Query: 427 ILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSG 486
           IL+LDEPTRGIDVGAK EIY+LI+ LA +G  +I+ISSE+PE+LG++DR++VM  G + G
Sbjct: 438 ILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMG 497

Query: 487 IVDTKTTTQNEILRLAS 503
            ++    TQ  +++LAS
Sbjct: 498 TLNRGEATQERVMQLAS 514



 Score = 69.7 bits (169), Expect = 2e-16
 Identities = 52/248 (20%), Positives = 112/248 (45%), Gaps = 10/248 (4%)

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

Query: 68  GSIVFQGKEVDFHSAKEALENGISMVHQELNL---VLQRSVMDNMWLGRYP--TKGMFVD 122
           G I+  G+ V       A+E G +++ ++  L       SV++NM +   P      F+ 
Sbjct: 330 GEILLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYVGNGFIQ 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 VGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLNRGEATQERV 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: 638
Number of extensions: 28
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:

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