GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Escherichia coli BW25113

Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate 17247 b3176 phosphoglucosamine mutase (NCBI)

Query= SwissProt::Q68BJ6
         (456 letters)



>FitnessBrowser__Keio:17247
          Length = 445

 Score =  203 bits (517), Expect = 8e-57
 Identities = 145/448 (32%), Positives = 220/448 (49%), Gaps = 26/448 (5%)

Query: 3   KLFGTFGVRG-IANEEITPEFALKIGMAFGTLLKREGRERPLVVVGRDTRVSGEMLKDAL 61
           K FGT G+RG + +  ITP+F LK+G A G +L R G  +  +++G+DTR+SG ML+ AL
Sbjct: 5   KYFGTDGIRGRVGDAPITPDFVLKLGWAAGKVLARHGSRK--IIIGKDTRISGYMLESAL 62

Query: 62  ISGLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNGMGLK 121
            +GL + G   +  G  PTPA+ + T  F A+ G VI+ASHNP   NGIK    +G  L 
Sbjct: 63  EAGLAAAGLSALFTGPMPTPAVAYLTRTFRAEAGIVISASHNPFYDNGIKFFSIDGTKLP 122

Query: 122 KEREAIVEELFFSEDFHRAKWNEIGEL-RKEDIIKPYIEAIK----NRVDVEAIKKRRPF 176
              E  + E    ++       E+G+  R  D    YIE  K    N + +  +K     
Sbjct: 123 DAVEEAI-EAEMEKEISCVDSAELGKASRIVDAAGRYIEFCKATFPNELSLSELK----- 176

Query: 177 VVVDTSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIVKALGA 236
           +VVD +NGA     P +LRELG  V+++   P+G     N E    +++     V A  A
Sbjct: 177 IVVDCANGATYHIAPNVLRELGANVIAIGCEPNG--VNINAEVGATDVRALQARVLAEKA 234

Query: 237 DFGVAQDGDADRAVFIDENGRFIQGDKTFALVADAVLRENG-GGLLVTTIATSNLLDDIA 295
           D G+A DGD DR + +D  G  + GD+   ++A   LR+    G  V T+ ++  L+   
Sbjct: 235 DLGIAFDGDGDRVIMVDHEGNKVDGDQIMYIIAREGLRQGQLRGGAVGTLMSNMGLELAL 294

Query: 296 KRNGAKVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAKIVEIFAK 355
           K+ G    R KVGD  V   + E    IG E +G VI  D     DG +   +++   A+
Sbjct: 295 KQLGIPFARAKVGDRYVLEKMQEKGWRIGAENSGHVILLDKTTTGDGIVAGLQVLAAMAR 354

Query: 356 SGKKFSELIDELPKYYQFKTK-RHVEGDRKAIVAKVAELAEKKGYKIDTTDGTKIIFDDG 414
           +     +L   +  + Q     R+  G          +  E +  K  T +    + + G
Sbjct: 355 NHMSLHDLCSGMKMFPQILVNVRYTAGS--------GDPLEHESVKAVTAEVEAALGNRG 406

Query: 415 WVLVRASGTEPIIRIFSEAKSEEKAREY 442
            VL+R SGTEP+IR+  E + E +  E+
Sbjct: 407 RVLLRKSGTEPLIRVMVEGEDEAQVTEF 434


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: 526
Number of extensions: 39
Number of successful extensions: 6
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 (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:

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