GapMind for catabolism of small carbon sources

 

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

Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate Pf6N2E2_3357 Phosphoglucosamine mutase (EC 5.4.2.10)

Query= SwissProt::Q68BJ6
         (456 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3357 Phosphoglucosamine
           mutase (EC 5.4.2.10)
          Length = 445

 Score =  197 bits (500), Expect = 8e-55
 Identities = 153/458 (33%), Positives = 223/458 (48%), Gaps = 27/458 (5%)

Query: 3   KLFGTFGVRGIANE-EITPEFALKIGMAFGTLLKREGRERPLVVVGRDTRVSGEMLKDAL 61
           K FGT G+RG   E  ITP+F LK+G A G   ++ G  +  V+VG+DTR+SG M + AL
Sbjct: 4   KYFGTDGIRGRVGEYPITPDFMLKLGWAAGMAFRKMGACK--VLVGKDTRISGYMFESAL 61

Query: 62  ISGLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNGMGLK 121
            +GL S G DV+ +G  PTPAI + T  F A  G VI+ASHNP + NGIK     G  L 
Sbjct: 62  EAGLTSAGADVMLLGPMPTPAIAYLTRTFQAQAGIVISASHNPHDDNGIKFFSGQGTKLP 121

Query: 122 KEREAIVEELFFSEDFHRAKWNEIGEL-RKEDIIKPYIEAIKNRV----DVEAIKKRRPF 176
            + E ++EEL         + ++IG++ R  D    YIE  K  V        +K     
Sbjct: 122 DDIELMIEEL-LDTPMTVVESSKIGKVSRINDASGRYIEFCKGSVPTGTSFSGLK----- 175

Query: 177 VVVDTSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIVKALGA 236
           +VVD ++GA     P + RELG +VV ++A P+G     N      + +     V A  A
Sbjct: 176 IVVDCAHGATYKVAPSVFRELGAEVVVLSAQPNG--LNINHNCGSTHTEALQAAVLAEQA 233

Query: 237 DFGVAQDGDADRAVFIDENGRFIQGDKTFALVA-DAVLRENGGGLLVTTIATSNLLDDIA 295
           D G+A DGD DR + +D  G  + GD+   ++A D   R    G +V T+ ++  L+   
Sbjct: 234 DLGIAFDGDGDRVLMVDHTGTVVDGDELLFIIARDLHGRGKLQGGVVGTLMSNLGLELAL 293

Query: 296 KRNGAKVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAKIVEIFAK 355
                  +R  VGD  V   LLE N  IGGE +G ++  D     D  +   +++     
Sbjct: 294 ADLDIPFVRANVGDRYVISELLERNWVIGGENSGHIVCFDHTTTGDAIIAALQVLMALKA 353

Query: 356 SGKKFSELIDELPKYYQFKTKRHVEGDRKAIV-AKVAELAEKKGYKIDTTDGTKIIFDDG 414
             +  ++    L K  Q        G    +  AKV + +E           T+ +   G
Sbjct: 354 RNEGLAQSRQALRKCPQVLINVRFGGGVNPLEHAKVKQASEHV---------TQAMAGRG 404

Query: 415 WVLVRASGTEPIIRIFSEAKSEEKAREYLELGIKLLEE 452
            VL+R SGTEP++R+  E + E + R Y E   KL+ E
Sbjct: 405 RVLLRKSGTEPLVRVMVEGEDEAQVRGYAEELAKLVTE 442


Lambda     K      H
   0.317    0.139    0.396 

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: 498
Number of extensions: 36
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 456
Length of database: 445
Length adjustment: 33
Effective length of query: 423
Effective length of database: 412
Effective search space:   174276
Effective search space used:   174276
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 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, 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