GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Marinobacter adhaerens HP15

Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate GFF3130 HP15_3072 phosphoglucosamine mutase

Query= SwissProt::Q68BJ6
         (456 letters)



>FitnessBrowser__Marino:GFF3130
          Length = 447

 Score =  209 bits (531), Expect = 2e-58
 Identities = 158/463 (34%), Positives = 229/463 (49%), Gaps = 34/463 (7%)

Query: 3   KLFGTFGVRGIANE-EITPEFALKIGMAFGTLLKREGRERPLVVVGRDTRVSGEMLKDAL 61
           K FGT G+RG   E  ITPEF LK+G A G   KR+G +R  V++G+DTR+SG M + AL
Sbjct: 5   KYFGTDGIRGHVGEFPITPEFMLKLGWAAGQAFKRDG-QRNSVLIGKDTRLSGYMFESAL 63

Query: 62  ISGLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNGMGLK 121
            +GL + G DV  +G  PTPAI + T  F A  G VI+ASHNP   NGIK     G  L 
Sbjct: 64  EAGLAAAGVDVKLLGPMPTPAIAYLTRTFRASAGIVISASHNPHHDNGIKFFSAAGTKLD 123

Query: 122 KEREAIVEELFFSEDFHRAKWNEIGEL-RKEDIIKPYIEAIKNRVDVEAIKKRRPFVVVD 180
              EA +E  +  +        E+G+  R +D    Y+E  K+ V  E        +V+D
Sbjct: 124 DALEAEIER-WLDKPIEVCGPTELGKASRVDDAPGRYVEFCKSTVPNEFTLDGMN-IVLD 181

Query: 181 TSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIVKALGADFGV 240
            ++GA     P + RELG KV  +   PDG     N      +L+     V    AD G+
Sbjct: 182 CAHGATYHVAPKVFRELGAKVSVIGGDPDG--LNINLNVGSTHLQALKAAVIEKNADLGI 239

Query: 241 AQDGDADRAVFIDENGRFIQGDKTFALVADAVLREN---GG--GLLVTTIATSNLLDDIA 295
           A DGD DR + +D +G  + GD+   ++A     E+   GG  G L+T +     L++I 
Sbjct: 240 AFDGDGDRVLMVDRDGSEVDGDELLYVIASQRFAEDRLKGGVVGTLMTNLGVELALNEI- 298

Query: 296 KRNGAKVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTAKIVEIFAK 355
              G +  R KVGD  V   LL NN  +GGE +G ++  D     DG ++  +++    K
Sbjct: 299 ---GIEFERAKVGDRYVMERLLANNWVLGGEGSGHMVIRDCTSTGDGIVSALQVLLSVWK 355

Query: 356 SGKKFSELIDELPKYYQFK-----TKRHVEGDRKAIVAKVAELAEKKGYKIDTTDGTKII 410
           SGK  ++L   + K  Q        +R     R  IVA V +   + G            
Sbjct: 356 SGKTLADLRKGMSKLPQKMINVRVAQRFDPFSRDDIVAAVRKAETELG------------ 403

Query: 411 FDDGWVLVRASGTEPIIRIFSEAKSEEKAREYLELGIKLLEEA 453
              G +L+RASGTEP+IR+ +E +   +    +E   K++E++
Sbjct: 404 -SSGRILLRASGTEPLIRVMAEGQDASEILRVVEELAKVVEKS 445


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: 534
Number of extensions: 28
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: 447
Length adjustment: 33
Effective length of query: 423
Effective length of database: 414
Effective search space:   175122
Effective search space used:   175122
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