GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__WCS417:GFF3463 PS417_17730
           ribonucleotide-diphosphate reductase subunit alpha
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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