Alignments for a candidate for mglA in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglA in Pseudomonas simiae WCS417

Align Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized)
to candidate GFF2332 PS417_11890 D-ribose transporter ATP-binding protein

Query= SwissProt::P23924
         (506 letters)



>FitnessBrowser__WCS417:GFF2332
          Length = 517

 Score =  468 bits (1204), Expect = e-136
 Identities = 242/493 (49%), Positives = 344/493 (69%), Gaps = 4/493 (0%)

Query: 12  YLLEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGSIV 71
           YLLE+  I+K FPGV AL +V L VRP ++ ALMGENGAGKSTL+K + GIYQ D+G I 
Sbjct: 22  YLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIR 81

Query: 72  FQGKEVDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGM-FVDQDKMYQDT 130
            +GK + F +   A + GI+M+HQELNL+   S+ +N+W+GR     +  V+  +M++ T
Sbjct: 82  LRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCT 141

Query: 131 KAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFT 190
             +   L I++DP  +VG LS+++ QM+EIAKA SY++ I+IMDEPTS++TEKEV HLF+
Sbjct: 142 AELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFS 201

Query: 191 IIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKIIAMMVGRSL 250
           II  LK +G GIVYI+HKM E+F + DE+ + RDG +I  Q  + ++ D +I+MMVGR L
Sbjct: 202 IIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGREL 261

Query: 251 NQRFPDKENKPGDVILEVRHLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLF 310
           +Q FP +E   GD++L VR LT       +DVSFDLH GEILGIAGL+G+ RT++ ET+F
Sbjct: 262 SQLFPLRETPIGDLLLTVRDLT--LDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIF 319

Query: 311 GIREKSSGTITLHGKKINNHTANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNY 370
           GI   SSG ITL GK +     + AI  GFAL+TE+R+ +G++  L +  N  ++ + +Y
Sbjct: 320 GITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHY 379

Query: 371 KNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILML 430
               G +    +++  + +   +RVKTP     I +LSGGNQQK ++ RWL+T P +L+L
Sbjct: 380 TGN-GFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLIL 438

Query: 431 DEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDT 490
           DEPTRGIDVGAK EIY+LIA LA +G  +I+ISSE+PE+LG++DR++VM  G + G +D 
Sbjct: 439 DEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDR 498

Query: 491 KTTTQNEILRLAS 503
              TQ ++++LAS
Sbjct: 499 SEATQEKVMQLAS 511



 Score = 76.3 bits (186), Expect = 3e-18
 Identities = 56/246 (22%), Positives = 114/246 (46%), Gaps = 10/246 (4%)

Query: 8   PSGEYLLEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKDS 67
           P G+ LL +R +  +  GV    +V+ ++    I  + G  G+G++ + + +FGI    S
Sbjct: 271 PIGDLLLTVRDL--TLDGV--FKDVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPSSS 326

Query: 68  GSIVFQGKEVDFHSAKEALENGISMVHQELNL---VLQRSVMDNMWLGRYP--TKGMFVD 122
           G I   GK V       A+E G +++ ++  L       SV++NM +   P  T   F+ 
Sbjct: 327 GQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNGFIQ 386

Query: 123 QDKMYQDTKAIFDELDIDIDPRAR-VGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLT 181
           Q  +    + +  +L +      + + TLS    Q   +A+    N +++I+DEPT  + 
Sbjct: 387 QKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILDEPTRGID 446

Query: 182 EKEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKI 241
                 ++ +I  L   G  ++ IS ++ E+  + D + ++ +G+ + T        +K+
Sbjct: 447 VGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKV 506

Query: 242 IAMMVG 247
           + +  G
Sbjct: 507 MQLASG 512


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: 640
Number of extensions: 32
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