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 GFF3463 PS417_17730 ribonucleotide-diphosphate reductase subunit alpha

Query= SwissProt::P23924
         (506 letters)



>FitnessBrowser__WCS417:GFF3463
          Length = 502

 Score =  372 bits (954), Expect = e-107
 Identities = 195/494 (39%), Positives = 311/494 (62%), Gaps = 6/494 (1%)

Query: 13  LLEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGSIVF 72
           LL++  I K +PGV+AL ++NL V    IHAL+GENGAGKSTL+K L G+  +D G I+ 
Sbjct: 4   LLKLENICKRYPGVQALKSINLQVERGEIHALLGENGAGKSTLMKILGGVEHQDEGQILI 63

Query: 73  QGKEVDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGM-FVDQDKMYQDTK 131
            G+   F + ++A+  GI +V QE +L+   + ++N++LG   +     + + +M + ++
Sbjct: 64  DGQAQQFATYRDAIAAGIGIVFQEFSLIPYLTAVENIFLGHELSNRFGLLRKREMVEASE 123

Query: 132 AIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTI 191
           A+F  L + ID +  V  LSV++ Q +EIAKA + +A+++++DEPT++LT  E   LF I
Sbjct: 124 ALFKRLGVTIDLQCAVKHLSVAEQQFVEIAKALALDARLLVLDEPTATLTPSEAELLFEI 183

Query: 192 IRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKIIAMMVGRSLN 251
           +R+LK +G  +++ISH +EEIFQ+CD I++LRDG  +    +   D+D ++ MMVGR L 
Sbjct: 184 MRELKRQGVAVIFISHHLEEIFQVCDRISVLRDGGNVGVTDVADSDIDHLVEMMVGRRLA 243

Query: 252 QRFPDKENKP-GDVILEVRHLTSLRQ-PSIRDVSFDLHKGEILGIAGLVGAKRTDIVETL 309
             FP K  +  G ++LEV+ +  +R  P  R   F LHKGEILG AGLVG+ RT++   +
Sbjct: 244 CSFPPKPTRERGPLLLEVKDIQLVRNGPHNR---FQLHKGEILGFAGLVGSGRTELALGM 300

Query: 310 FGIREKSSGTITLHGKKINNHTANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRN 369
            G     S  + L G+KI      +A+ HG  L+ E R+S G+     I  N  ++N+  
Sbjct: 301 MGALPSVSKDVWLRGEKITLDDPAQALAHGIGLLPESRKSEGLITDFSIRENISLNNLPK 360

Query: 370 YKNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILM 429
           Y+N  GL+D +R  +  + ++  + +K P   +++ +LSGGNQQKV+I RW+    ++L+
Sbjct: 361 YQNASGLIDKNRECASVEGLMKQLSIKAPSSESRVFNLSGGNQQKVVIARWINHHCDVLV 420

Query: 430 LDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVD 489
            DEPTRGIDVGAK +IY L+  L ++G  II+ISSE+PE++G+ DR+ V   G +  +++
Sbjct: 421 FDEPTRGIDVGAKAQIYALMRSLTEQGYAIIMISSELPEIIGMCDRVAVFHKGAIVKLLE 480

Query: 490 TKTTTQNEILRLAS 503
                  E++R A+
Sbjct: 481 ASAVNPQEVMRHAT 494



 Score = 71.2 bits (173), Expect = 8e-17
 Identities = 51/247 (20%), Positives = 109/247 (44%), Gaps = 11/247 (4%)

Query: 10  GEYLLEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGS 69
           G  LLE++ I      V+   +    +    I    G  G+G++ L   + G     S  
Sbjct: 255 GPLLLEVKDIQL----VRNGPHNRFQLHKGEILGFAGLVGSGRTELALGMMGALPSVSKD 310

Query: 70  IVFQGKEVDFHSAKEALENGISMVHQELN---LVLQRSVMDNMWLG---RYPTKGMFVDQ 123
           +  +G+++      +AL +GI ++ +      L+   S+ +N+ L    +Y      +D+
Sbjct: 311 VWLRGEKITLDDPAQALAHGIGLLPESRKSEGLITDFSIRENISLNNLPKYQNASGLIDK 370

Query: 124 DKMYQDTKAIFDELDIDI-DPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTE 182
           ++     + +  +L I      +RV  LS    Q + IA+  +++  +++ DEPT  +  
Sbjct: 371 NRECASVEGLMKQLSIKAPSSESRVFNLSGGNQQKVVIARWINHHCDVLVFDEPTRGIDV 430

Query: 183 KEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKII 242
                ++ ++R L E+G  I+ IS ++ EI  +CD + +   G  +       ++  +++
Sbjct: 431 GAKAQIYALMRSLTEQGYAIIMISSELPEIIGMCDRVAVFHKGAIVKLLEASAVNPQEVM 490

Query: 243 AMMVGRS 249
               G S
Sbjct: 491 RHATGGS 497


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: 595
Number of extensions: 26
Number of successful extensions: 6
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: 502
Length adjustment: 34
Effective length of query: 472
Effective length of database: 468
Effective search space:   220896
Effective search space used:   220896
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