GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pgmA in Pseudomonas putida KT2440

Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate PP_4716 PP_4716 Phosphoglucosamine mutase

Query= SwissProt::Q68BJ6
         (456 letters)



>lcl|FitnessBrowser__Putida:PP_4716 PP_4716 Phosphoglucosamine
           mutase
          Length = 446

 Score =  206 bits (523), Expect = 2e-57
 Identities = 157/460 (34%), Positives = 238/460 (51%), Gaps = 30/460 (6%)

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

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

Query: 122 KEREAIVEELFFSEDFHRAKWNEIGEL-RKEDIIKPYIEAIKNRV----DVEAIKKRRPF 176
            E E ++EEL   +     +  ++G++ R  D    YIE  K+ V      E +K     
Sbjct: 122 DEVELMIEEL-LDQPMTVVESGKLGKVSRINDAAGRYIEFCKSSVPSSTSFEGLK----- 175

Query: 177 VVVDTSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIVKALGA 236
           +VVD ++GA     P + RELG  V  ++A PDG     N      +++     V    A
Sbjct: 176 LVVDCAHGATYKVAPSVFRELGADVTVLHAQPDG--LNINEGCGSTHIESLQAAVLVGHA 233

Query: 237 DFGVAQDGDADRAVFIDENGRFIQGDKTFALVADAVLRENG---GGLLVTTIATSNLLDD 293
           D G+A DGD DR + +D  G  + GD+   ++A   L+E+G   GG++ T +  SNL  +
Sbjct: 234 DLGIAFDGDGDRVLMVDHTGAIVDGDELLFIIA-RDLQEHGKLQGGVVGTLM--SNLGLE 290

Query: 294 IAKRN-GAKVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAKIVEI 352
           +A ++     +R KVGD  V   LLE    +GGE +G V+  +     D  +   +++  
Sbjct: 291 LALKDLDIPFVRAKVGDRYVMAELLEREWLVGGENSGHVVCCNHTTTGDAIIAALQVLMA 350

Query: 353 FAKSGKKFSELIDELPKYYQFKTKRHVEGDRKAIVAKVAELAEKKGYKIDTTDGTKIIFD 412
             + G+  ++    L K  Q      V  + +   +KV  L E    K  +   T+ +  
Sbjct: 351 LKRRGETLAQARQALRKCPQ------VLINVRFGASKVDPL-EHPAVKEASAKVTEALAG 403

Query: 413 DGWVLVRASGTEPIIRIFSEAKSEEKAREYLELGIKLLEE 452
            G VL+R SGTEP++R+  E + E + R + E   KL+ E
Sbjct: 404 RGRVLLRKSGTEPLVRVMVEGEDESQVRAHAEALAKLVGE 443


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: 515
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: 446
Length adjustment: 33
Effective length of query: 423
Effective length of database: 413
Effective search space:   174699
Effective search space used:   174699
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 (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