GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pgmA in Phaeobacter inhibens BS107

Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate GFF641 PGA1_c06550 phosphoglucosamine mutase GlmM

Query= SwissProt::Q68BJ6
         (456 letters)



>lcl|FitnessBrowser__Phaeo:GFF641 PGA1_c06550 phosphoglucosamine
           mutase GlmM
          Length = 448

 Score =  209 bits (533), Expect = 1e-58
 Identities = 153/474 (32%), Positives = 237/474 (50%), Gaps = 48/474 (10%)

Query: 1   MGKLFGTFGVRGIAN-EEITPEFALKIGMAFGTLLKREGRERPLVVVGRDTRVSGEMLKD 59
           M K FGT GVRG AN   +T + AL+IG A G   +R+      VV+G+DTR+SG M + 
Sbjct: 1   MRKFFGTDGVRGTANIHPMTADMALRIGAAVGRYFRRDASGVHRVVIGKDTRLSGYMFES 60

Query: 60  ALISGLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNGMG 119
           AL +GL STG +V+ +G  PTPA+   T    AD G +I+ASHNP   NGIK   P+G  
Sbjct: 61  ALTAGLTSTGMNVLLLGPVPTPAVGLMTRSMRADLGVMISASHNPAADNGIKFFGPDGFK 120

Query: 120 L----KKEREAIVE---ELFFSEDFHRAKWNEIGELRKEDIIKPYIEAIKNRVDVEAIKK 172
           L    + E EA++E   E   +++  RAK  +    R  + +K    ++   + ++ +K 
Sbjct: 121 LSDTVEMELEALIEAGVEPAQAQNIGRAKRIDDARFRYGERVK---SSLPRDIRLDGLK- 176

Query: 173 RRPFVVVDTSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIVK 232
               VV+D +NGA     P +L ELG +V+ V   PDG     N +    +     E V 
Sbjct: 177 ----VVIDCANGAAHRAAPEILWELGAEVIPVGVSPDG--TNINRDCGSTHPGTAAETVV 230

Query: 233 ALGADFGVAQDGDADRAVFIDENGRFIQGDKTFALVA-----DAVLRENGGGLLVTTIAT 287
           A GA  G+  DGDADR + ID+ G+   GD+  AL+A     D VL    G  LV+T+ +
Sbjct: 231 AHGAHVGICLDGDADRVIIIDDTGKVADGDQLMALLATRWAEDGVL---AGNALVSTVMS 287

Query: 288 SNLLDDIAKRNGAKVMRTKVGDLIVARALLENNGTIGGEENGGVIFPDFVLGRDGAMTTA 347
           +  L+      G  + RT VGD  V   + E    +GGE++G ++  D+    DG M   
Sbjct: 288 NLGLERHLAARGIALERTAVGDRYVVERMREGGFNLGGEQSGHIVMTDYATTGDGLMAGL 347

Query: 348 KIVEIFAKSGKKFSEL------IDELPKYYQFKT-KRHVEGDRKAIVAKVAELAEKKGYK 400
             +    ++ K  S+L      + +L K  +F   +  +E D+     +VAE        
Sbjct: 348 HFLAEMVRADKPASQLAQQFAPVPQLLKNVRFAAGQTPLESDQVQTAIRVAE-------- 399

Query: 401 IDTTDGTKIIFDDGWVLVRASGTEPIIRIFSEAKSEEKAREYLELGIKLLEEAL 454
                  + +   G +L+R SGTEP++R+ +E +  +     ++  +  +E A+
Sbjct: 400 -------ETLAGQGRLLIRKSGTEPLVRVMAECEDAKVLTAAVDSVVAAVEAAV 446


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: 481
Number of extensions: 29
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: 448
Length adjustment: 33
Effective length of query: 423
Effective length of database: 415
Effective search space:   175545
Effective search space used:   175545
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 preprint 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