GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Pseudomonas stutzeri RCH2

Align phosphomannose mutase (EC 5.4.2.8) (characterized)
to candidate GFF945 Psest_0974 phosphoglucosamine mutase

Query= metacyc::MONOMER-13382
         (455 letters)



>FitnessBrowser__psRCH2:GFF945
          Length = 445

 Score =  210 bits (535), Expect = 7e-59
 Identities = 142/449 (31%), Positives = 226/449 (50%), Gaps = 33/449 (7%)

Query: 3   KLFGTFGVRG-IANEKITPEFAMKIGMAFGTLLKREGRKKPLVVVGRDTRVSGEMLKEAL 61
           K FGT G+RG +    ITP+F +K+G A G   +++G+ +  +++G+DTR+SG M + AL
Sbjct: 4   KYFGTDGIRGHVGQAPITPDFMLKLGWAAGMAFRKQGKCR--ILIGKDTRISGYMFESAL 61

Query: 62  ISGLLSVGCDVIDVGIAPTPAVQWATKHFNADGGAVITASHNPPEYNGIKLLEPNGMGLK 121
            +GL + G DV+ +G  PTPAV + T+ F+A+ G VI+ASHNP   NGIK     G  L 
Sbjct: 62  QAGLSAAGADVLLLGPMPTPAVAYLTRTFHAEAGIVISASHNPHHDNGIKFFSGRGTKLP 121

Query: 122 KEREAIVEELFFKEDFDRAKWYEIGEVRR-EDIIKPYIEAIKSKV----DVEAIKKRKPF 176
            E E ++EEL         +  ++G+  R  D    YIE  KS V    D   +K     
Sbjct: 122 DEVELMIEEL-IDAPMTVVESAQLGKASRINDAAGRYIEFCKSSVPTSTDFSGLK----- 175

Query: 177 VVVDTSNGAGSLTLPYLLRELGCKVITVNAQPDGYFPARNPEPNEENLKEFMEIVKALGA 236
           +V+D ++GA     P + RELG +V+ + AQPDG     N +    ++ +  + V   GA
Sbjct: 176 LVIDCAHGATYKVAPSVFRELGAEVVVIGAQPDGL--NINADVGSTHVGQLQKAVVDHGA 233

Query: 237 DFGVAQDGDADRAVFIDENGRFIQGDKTFALVA-DAVLKEKGGGLLVTTVATSNLLDDIA 295
           D G+A DGD DR + +D  G  + GD+   ++A D   +++  G +V T+ ++  L+   
Sbjct: 234 DLGIAFDGDGDRVMMVDHTGAVVDGDELLYIIATDLQERDRLSGGVVGTLMSNLGLELAL 293

Query: 296 KKHGAKVMRTKVGDLIVARALYENNGTIGGEENGGVIFPEHVLGRDGAMTVAKVVEIFAK 355
           K       R KVGD  V   + + +  +GGE +G ++  +H    D  +   +VV    +
Sbjct: 294 KARDIPFTRAKVGDRYVIAEMLDRSWVLGGENSGHIVCAQHTTTGDAIIAALQVVLALRR 353

Query: 356 SGKKFSELIDELPKYYQIKTKRHVEGDR----HAIVNKVAEMARERGYTVDTTDGAKIIF 411
            G+  ++      K  Q+       GDR    H  V    +   ER            + 
Sbjct: 354 RGQTLAQERLAWHKCPQVLINVRFSGDRDPISHPSVQAACDSVTER------------MA 401

Query: 412 EDGWVLVRASGTEPIIRIFSEAKSKEKAQ 440
             G VL+R SGTEP++R+  E   + + +
Sbjct: 402 GRGRVLLRKSGTEPLVRVMVEGDDETQVR 430


Lambda     K      H
   0.317    0.138    0.391 

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: 481
Number of extensions: 38
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: 455
Length of database: 445
Length adjustment: 33
Effective length of query: 422
Effective length of database: 412
Effective search space:   173864
Effective search space used:   173864
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